Starting phenix.real_space_refine on Mon Sep 30 06:37:41 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iyl_35825/09_2024/8iyl_35825.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iyl_35825/09_2024/8iyl_35825.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iyl_35825/09_2024/8iyl_35825.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iyl_35825/09_2024/8iyl_35825.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iyl_35825/09_2024/8iyl_35825.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iyl_35825/09_2024/8iyl_35825.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.082 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Fe 12 7.16 5 S 276 5.16 5 C 48441 2.51 5 N 13224 2.21 5 O 15417 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 137 residue(s): 0.16s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 77370 Number of models: 1 Model: "" Number of chains: 45 Chain: "M" Number of atoms: 884 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 884 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 6, 'TRANS': 102} Chain: "J" Number of atoms: 6720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 861, 6720 Classifications: {'peptide': 861} Link IDs: {'PTRANS': 40, 'TRANS': 820} Chain: "m" Number of atoms: 884 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 884 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 6, 'TRANS': 102} Chain: "L" Number of atoms: 1801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1801 Classifications: {'peptide': 232} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 222} Chain: "H" Number of atoms: 250 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 250 Classifications: {'peptide': 33} Link IDs: {'PTRANS': 1, 'TRANS': 31} Chain: "I" Number of atoms: 865 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 865 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 3, 'TRANS': 118} Chain: "V" Number of atoms: 1792 Number of conformers: 1 Conformer: "" Number of residues, atoms: 243, 1792 Classifications: {'peptide': 243} Link IDs: {'PTRANS': 11, 'TRANS': 231} Chain: "v" Number of atoms: 1792 Number of conformers: 1 Conformer: "" Number of residues, atoms: 243, 1792 Classifications: {'peptide': 243} Link IDs: {'PTRANS': 11, 'TRANS': 231} Chain: "B" Number of atoms: 1799 Number of conformers: 1 Conformer: "" Number of residues, atoms: 244, 1799 Classifications: {'peptide': 244} Link IDs: {'PTRANS': 12, 'TRANS': 231} Chain: "b" Number of atoms: 1799 Number of conformers: 1 Conformer: "" Number of residues, atoms: 244, 1799 Classifications: {'peptide': 244} Link IDs: {'PTRANS': 12, 'TRANS': 231} Chain: "A" Number of atoms: 1799 Number of conformers: 1 Conformer: "" Number of residues, atoms: 244, 1799 Classifications: {'peptide': 244} Link IDs: {'PTRANS': 12, 'TRANS': 231} Chain: "a" Number of atoms: 1799 Number of conformers: 1 Conformer: "" Number of residues, atoms: 244, 1799 Classifications: {'peptide': 244} Link IDs: {'PTRANS': 12, 'TRANS': 231} Chain: "C" Number of atoms: 1799 Number of conformers: 1 Conformer: "" Number of residues, atoms: 244, 1799 Classifications: {'peptide': 244} Link IDs: {'PTRANS': 12, 'TRANS': 231} Chain: "c" Number of atoms: 1799 Number of conformers: 1 Conformer: "" Number of residues, atoms: 244, 1799 Classifications: {'peptide': 244} Link IDs: {'PTRANS': 12, 'TRANS': 231} Chain: "D" Number of atoms: 884 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 884 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 6, 'TRANS': 102} Chain: "E" Number of atoms: 6720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 861, 6720 Classifications: {'peptide': 861} Link IDs: {'PTRANS': 40, 'TRANS': 820} Chain: "F" Number of atoms: 884 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 884 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 6, 'TRANS': 102} Chain: "G" Number of atoms: 1801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1801 Classifications: {'peptide': 232} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 222} Chain: "K" Number of atoms: 250 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 250 Classifications: {'peptide': 33} Link IDs: {'PTRANS': 1, 'TRANS': 31} Chain: "N" Number of atoms: 865 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 865 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 3, 'TRANS': 118} Chain: "O" Number of atoms: 1792 Number of conformers: 1 Conformer: "" Number of residues, atoms: 243, 1792 Classifications: {'peptide': 243} Link IDs: {'PTRANS': 11, 'TRANS': 231} Chain: "P" Number of atoms: 1792 Number of conformers: 1 Conformer: "" Number of residues, atoms: 243, 1792 Classifications: {'peptide': 243} Link IDs: {'PTRANS': 11, 'TRANS': 231} Chain: "Q" Number of atoms: 1799 Number of conformers: 1 Conformer: "" Number of residues, atoms: 244, 1799 Classifications: {'peptide': 244} Link IDs: {'PTRANS': 12, 'TRANS': 231} Chain: "R" Number of atoms: 1799 Number of conformers: 1 Conformer: "" Number of residues, atoms: 244, 1799 Classifications: {'peptide': 244} Link IDs: {'PTRANS': 12, 'TRANS': 231} Chain: "S" Number of atoms: 1799 Number of conformers: 1 Conformer: "" Number of residues, atoms: 244, 1799 Classifications: {'peptide': 244} Link IDs: {'PTRANS': 12, 'TRANS': 231} Chain: "T" Number of atoms: 1799 Number of conformers: 1 Conformer: "" Number of residues, atoms: 244, 1799 Classifications: {'peptide': 244} Link IDs: {'PTRANS': 12, 'TRANS': 231} Chain: "U" Number of atoms: 1799 Number of conformers: 1 Conformer: "" Number of residues, atoms: 244, 1799 Classifications: {'peptide': 244} Link IDs: {'PTRANS': 12, 'TRANS': 231} Chain: "W" Number of atoms: 1799 Number of conformers: 1 Conformer: "" Number of residues, atoms: 244, 1799 Classifications: {'peptide': 244} Link IDs: {'PTRANS': 12, 'TRANS': 231} Chain: "X" Number of atoms: 884 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 884 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 6, 'TRANS': 102} Chain: "Y" Number of atoms: 6720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 861, 6720 Classifications: {'peptide': 861} Link IDs: {'PTRANS': 40, 'TRANS': 820} Chain: "Z" Number of atoms: 884 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 884 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 6, 'TRANS': 102} Chain: "d" Number of atoms: 1801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1801 Classifications: {'peptide': 232} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 222} Chain: "e" Number of atoms: 250 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 250 Classifications: {'peptide': 33} Link IDs: {'PTRANS': 1, 'TRANS': 31} Chain: "f" Number of atoms: 865 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 865 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 3, 'TRANS': 118} Chain: "g" Number of atoms: 1792 Number of conformers: 1 Conformer: "" Number of residues, atoms: 243, 1792 Classifications: {'peptide': 243} Link IDs: {'PTRANS': 11, 'TRANS': 231} Chain: "h" Number of atoms: 1792 Number of conformers: 1 Conformer: "" Number of residues, atoms: 243, 1792 Classifications: {'peptide': 243} Link IDs: {'PTRANS': 11, 'TRANS': 231} Chain: "i" Number of atoms: 1799 Number of conformers: 1 Conformer: "" Number of residues, atoms: 244, 1799 Classifications: {'peptide': 244} Link IDs: {'PTRANS': 12, 'TRANS': 231} Chain: "j" Number of atoms: 1799 Number of conformers: 1 Conformer: "" Number of residues, atoms: 244, 1799 Classifications: {'peptide': 244} Link IDs: {'PTRANS': 12, 'TRANS': 231} Chain: "k" Number of atoms: 1799 Number of conformers: 1 Conformer: "" Number of residues, atoms: 244, 1799 Classifications: {'peptide': 244} Link IDs: {'PTRANS': 12, 'TRANS': 231} Chain: "l" Number of atoms: 1799 Number of conformers: 1 Conformer: "" Number of residues, atoms: 244, 1799 Classifications: {'peptide': 244} Link IDs: {'PTRANS': 12, 'TRANS': 231} Chain: "n" Number of atoms: 1799 Number of conformers: 1 Conformer: "" Number of residues, atoms: 244, 1799 Classifications: {'peptide': 244} Link IDs: {'PTRANS': 12, 'TRANS': 231} Chain: "o" Number of atoms: 1799 Number of conformers: 1 Conformer: "" Number of residues, atoms: 244, 1799 Classifications: {'peptide': 244} Link IDs: {'PTRANS': 12, 'TRANS': 231} Chain: "L" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Unusual residues: {'SF4': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Unusual residues: {'SF4': 1} Classifications: {'undetermined': 1} Chain: "d" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Unusual residues: {'SF4': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 9915 SG CYS L 182 50.859 85.736 171.143 1.00 66.08 S ATOM 10086 SG CYS L 205 50.801 78.928 170.569 1.00 70.49 S ATOM 9837 SG CYS L 173 56.067 82.302 169.731 1.00 69.69 S ATOM 10131 SG CYS L 212 51.845 81.910 165.676 1.00 77.17 S ATOM 35697 SG CYS G 182 100.103 38.365 171.127 1.00 68.94 S ATOM 35868 SG CYS G 205 105.997 41.855 170.634 1.00 72.28 S ATOM 35619 SG CYS G 173 100.520 44.588 169.736 1.00 68.58 S ATOM 35913 SG CYS G 212 102.977 41.094 165.666 1.00 76.40 S ATOM 61479 SG CYS d 182 116.478 104.764 171.088 1.00 71.35 S ATOM 61650 SG CYS d 205 110.600 108.173 170.607 1.00 71.77 S ATOM 61401 SG CYS d 173 110.940 101.920 169.751 1.00 69.26 S ATOM 61695 SG CYS d 212 112.765 105.785 165.608 1.00 80.26 S Time building chain proxies: 34.15, per 1000 atoms: 0.44 Number of scatterers: 77370 At special positions: 0 Unit cell: (180.466, 166.501, 450.09, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Fe 12 26.01 S 276 16.00 O 15417 8.00 N 13224 7.00 C 48441 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 13.77 Conformation dependent library (CDL) restraints added in 7.5 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" SF4 G 301 " pdb="FE2 SF4 G 301 " - pdb=" SG CYS G 205 " pdb="FE4 SF4 G 301 " - pdb=" SG CYS G 212 " pdb="FE1 SF4 G 301 " - pdb=" SG CYS G 182 " pdb="FE3 SF4 G 301 " - pdb=" SG CYS G 173 " pdb=" SF4 L 301 " pdb="FE2 SF4 L 301 " - pdb=" SG CYS L 205 " pdb="FE4 SF4 L 301 " - pdb=" SG CYS L 212 " pdb="FE1 SF4 L 301 " - pdb=" SG CYS L 182 " pdb="FE3 SF4 L 301 " - pdb=" SG CYS L 173 " pdb=" SF4 d 301 " pdb="FE2 SF4 d 301 " - pdb=" SG CYS d 205 " pdb="FE4 SF4 d 301 " - pdb=" SG CYS d 212 " pdb="FE1 SF4 d 301 " - pdb=" SG CYS d 182 " pdb="FE3 SF4 d 301 " - pdb=" SG CYS d 173 " Number of angles added : 36 20328 Ramachandran restraints generated. 10164 Oldfield, 0 Emsley, 10164 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 18648 Finding SS restraints... Secondary structure from input PDB file: 111 helices and 145 sheets defined 10.4% alpha, 27.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 9.54 Creating SS restraints... Processing helix chain 'M' and resid 53 through 66 removed outlier: 4.160A pdb=" N VAL M 57 " --> pdb=" O GLU M 53 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N HIS M 65 " --> pdb=" O PHE M 61 " (cutoff:3.500A) Processing helix chain 'J' and resid 41 through 43 No H-bonds generated for 'chain 'J' and resid 41 through 43' Processing helix chain 'J' and resid 271 through 281 Processing helix chain 'J' and resid 297 through 309 Processing helix chain 'J' and resid 335 through 346 removed outlier: 3.577A pdb=" N MET J 346 " --> pdb=" O PHE J 342 " (cutoff:3.500A) Processing helix chain 'J' and resid 419 through 424 Processing helix chain 'J' and resid 440 through 458 Processing helix chain 'J' and resid 467 through 473 removed outlier: 3.814A pdb=" N LEU J 471 " --> pdb=" O ALA J 468 " (cutoff:3.500A) Processing helix chain 'J' and resid 592 through 594 No H-bonds generated for 'chain 'J' and resid 592 through 594' Processing helix chain 'J' and resid 595 through 600 removed outlier: 3.654A pdb=" N ASP J 600 " --> pdb=" O GLU J 596 " (cutoff:3.500A) Processing helix chain 'J' and resid 758 through 763 Processing helix chain 'J' and resid 811 through 819 removed outlier: 4.471A pdb=" N ASP J 816 " --> pdb=" O GLY J 813 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N PHE J 817 " --> pdb=" O TYR J 814 " (cutoff:3.500A) Processing helix chain 'J' and resid 828 through 836 Processing helix chain 'J' and resid 836 through 861 removed outlier: 3.798A pdb=" N ASP J 840 " --> pdb=" O GLU J 836 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LYS J 850 " --> pdb=" O GLU J 846 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N GLU J 851 " --> pdb=" O GLU J 847 " (cutoff:3.500A) Processing helix chain 'm' and resid 53 through 66 removed outlier: 4.286A pdb=" N VAL m 57 " --> pdb=" O GLU m 53 " (cutoff:3.500A) Processing helix chain 'L' and resid 5 through 13 removed outlier: 3.512A pdb=" N THR L 13 " --> pdb=" O LEU L 9 " (cutoff:3.500A) Processing helix chain 'L' and resid 86 through 95 Processing helix chain 'L' and resid 96 through 99 Processing helix chain 'L' and resid 111 through 113 No H-bonds generated for 'chain 'L' and resid 111 through 113' Processing helix chain 'L' and resid 114 through 118 Processing helix chain 'L' and resid 199 through 203 removed outlier: 3.721A pdb=" N ASP L 203 " --> pdb=" O ILE L 200 " (cutoff:3.500A) Processing helix chain 'L' and resid 208 through 215 removed outlier: 3.754A pdb=" N ARG L 215 " --> pdb=" O GLY L 211 " (cutoff:3.500A) Processing helix chain 'L' and resid 216 through 221 removed outlier: 5.325A pdb=" N GLY L 219 " --> pdb=" O ASN L 216 " (cutoff:3.500A) Processing helix chain 'L' and resid 226 through 231 removed outlier: 4.058A pdb=" N LEU L 230 " --> pdb=" O SER L 226 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N SER L 231 " --> pdb=" O ILE L 227 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 226 through 231' Processing helix chain 'H' and resid 818 through 842 removed outlier: 3.672A pdb=" N LYS H 824 " --> pdb=" O PRO H 820 " (cutoff:3.500A) Processing helix chain 'I' and resid 123 through 130 Processing helix chain 'I' and resid 142 through 147 removed outlier: 3.706A pdb=" N VAL I 147 " --> pdb=" O GLY I 143 " (cutoff:3.500A) Processing helix chain 'I' and resid 150 through 155 removed outlier: 3.541A pdb=" N LEU I 155 " --> pdb=" O ALA I 152 " (cutoff:3.500A) Processing helix chain 'V' and resid 93 through 103 Processing helix chain 'v' and resid 92 through 103 Processing helix chain 'B' and resid 92 through 102 removed outlier: 3.821A pdb=" N GLU B 102 " --> pdb=" O ALA B 98 " (cutoff:3.500A) Processing helix chain 'b' and resid 92 through 103 Processing helix chain 'b' and resid 151 through 156 removed outlier: 4.005A pdb=" N ARG b 155 " --> pdb=" O MET b 151 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N SER b 156 " --> pdb=" O ALA b 152 " (cutoff:3.500A) No H-bonds generated for 'chain 'b' and resid 151 through 156' Processing helix chain 'A' and resid 93 through 102 removed outlier: 3.500A pdb=" N GLU A 102 " --> pdb=" O ALA A 98 " (cutoff:3.500A) Processing helix chain 'a' and resid 92 through 103 Processing helix chain 'C' and resid 92 through 101 Processing helix chain 'c' and resid 92 through 103 Processing helix chain 'c' and resid 151 through 156 Processing helix chain 'D' and resid 53 through 66 removed outlier: 4.202A pdb=" N VAL D 57 " --> pdb=" O GLU D 53 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N HIS D 65 " --> pdb=" O PHE D 61 " (cutoff:3.500A) Processing helix chain 'E' and resid 271 through 281 Processing helix chain 'E' and resid 297 through 309 removed outlier: 3.519A pdb=" N LEU E 301 " --> pdb=" O ASP E 297 " (cutoff:3.500A) Processing helix chain 'E' and resid 335 through 346 Processing helix chain 'E' and resid 419 through 424 Processing helix chain 'E' and resid 440 through 458 Processing helix chain 'E' and resid 467 through 473 removed outlier: 3.820A pdb=" N LEU E 471 " --> pdb=" O ALA E 468 " (cutoff:3.500A) Processing helix chain 'E' and resid 592 through 594 No H-bonds generated for 'chain 'E' and resid 592 through 594' Processing helix chain 'E' and resid 595 through 600 removed outlier: 3.660A pdb=" N ASP E 600 " --> pdb=" O GLU E 596 " (cutoff:3.500A) Processing helix chain 'E' and resid 758 through 763 Processing helix chain 'E' and resid 812 through 817 removed outlier: 3.918A pdb=" N PHE E 817 " --> pdb=" O GLY E 813 " (cutoff:3.500A) Processing helix chain 'E' and resid 828 through 836 Processing helix chain 'E' and resid 836 through 861 removed outlier: 3.862A pdb=" N ASP E 840 " --> pdb=" O GLU E 836 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LYS E 850 " --> pdb=" O GLU E 846 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N GLU E 851 " --> pdb=" O GLU E 847 " (cutoff:3.500A) Processing helix chain 'F' and resid 54 through 66 Processing helix chain 'G' and resid 5 through 14 removed outlier: 3.610A pdb=" N ARG G 14 " --> pdb=" O ASN G 10 " (cutoff:3.500A) Processing helix chain 'G' and resid 86 through 95 Processing helix chain 'G' and resid 96 through 99 Processing helix chain 'G' and resid 111 through 113 No H-bonds generated for 'chain 'G' and resid 111 through 113' Processing helix chain 'G' and resid 114 through 118 Processing helix chain 'G' and resid 199 through 203 Processing helix chain 'G' and resid 208 through 215 removed outlier: 3.657A pdb=" N ARG G 215 " --> pdb=" O GLY G 211 " (cutoff:3.500A) Processing helix chain 'G' and resid 216 through 221 removed outlier: 5.273A pdb=" N GLY G 219 " --> pdb=" O ASN G 216 " (cutoff:3.500A) Processing helix chain 'G' and resid 226 through 231 removed outlier: 3.963A pdb=" N LEU G 230 " --> pdb=" O SER G 226 " (cutoff:3.500A) Processing helix chain 'K' and resid 818 through 842 removed outlier: 3.698A pdb=" N LYS K 824 " --> pdb=" O PRO K 820 " (cutoff:3.500A) Processing helix chain 'N' and resid 123 through 130 Processing helix chain 'N' and resid 142 through 147 removed outlier: 3.679A pdb=" N VAL N 147 " --> pdb=" O GLY N 143 " (cutoff:3.500A) Processing helix chain 'N' and resid 150 through 155 removed outlier: 3.597A pdb=" N LEU N 155 " --> pdb=" O ALA N 152 " (cutoff:3.500A) Processing helix chain 'O' and resid 93 through 103 Processing helix chain 'P' and resid 92 through 103 Processing helix chain 'Q' and resid 92 through 101 Processing helix chain 'R' and resid 92 through 103 Processing helix chain 'S' and resid 93 through 102 removed outlier: 3.551A pdb=" N GLU S 102 " --> pdb=" O ALA S 98 " (cutoff:3.500A) Processing helix chain 'T' and resid 92 through 103 Processing helix chain 'U' and resid 92 through 101 Processing helix chain 'W' and resid 92 through 103 Processing helix chain 'W' and resid 151 through 156 Processing helix chain 'X' and resid 53 through 66 removed outlier: 4.203A pdb=" N VAL X 57 " --> pdb=" O GLU X 53 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N HIS X 65 " --> pdb=" O PHE X 61 " (cutoff:3.500A) Processing helix chain 'Y' and resid 271 through 281 Processing helix chain 'Y' and resid 297 through 309 Processing helix chain 'Y' and resid 335 through 346 Processing helix chain 'Y' and resid 419 through 424 Processing helix chain 'Y' and resid 440 through 458 Processing helix chain 'Y' and resid 467 through 473 removed outlier: 3.775A pdb=" N LEU Y 471 " --> pdb=" O ALA Y 468 " (cutoff:3.500A) Processing helix chain 'Y' and resid 592 through 594 No H-bonds generated for 'chain 'Y' and resid 592 through 594' Processing helix chain 'Y' and resid 595 through 600 removed outlier: 3.537A pdb=" N VAL Y 599 " --> pdb=" O LYS Y 595 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ASP Y 600 " --> pdb=" O GLU Y 596 " (cutoff:3.500A) No H-bonds generated for 'chain 'Y' and resid 595 through 600' Processing helix chain 'Y' and resid 758 through 763 Processing helix chain 'Y' and resid 815 through 819 removed outlier: 3.638A pdb=" N PHE Y 818 " --> pdb=" O LEU Y 815 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LYS Y 819 " --> pdb=" O ASP Y 816 " (cutoff:3.500A) No H-bonds generated for 'chain 'Y' and resid 815 through 819' Processing helix chain 'Y' and resid 828 through 836 Processing helix chain 'Y' and resid 836 through 861 removed outlier: 3.768A pdb=" N ASP Y 840 " --> pdb=" O GLU Y 836 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LYS Y 850 " --> pdb=" O GLU Y 846 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N GLU Y 851 " --> pdb=" O GLU Y 847 " (cutoff:3.500A) Processing helix chain 'Z' and resid 53 through 66 removed outlier: 4.232A pdb=" N VAL Z 57 " --> pdb=" O GLU Z 53 " (cutoff:3.500A) Processing helix chain 'd' and resid 5 through 14 removed outlier: 3.508A pdb=" N THR d 13 " --> pdb=" O LEU d 9 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ARG d 14 " --> pdb=" O ASN d 10 " (cutoff:3.500A) Processing helix chain 'd' and resid 86 through 95 Processing helix chain 'd' and resid 96 through 99 Processing helix chain 'd' and resid 111 through 113 No H-bonds generated for 'chain 'd' and resid 111 through 113' Processing helix chain 'd' and resid 114 through 118 Processing helix chain 'd' and resid 199 through 203 removed outlier: 3.734A pdb=" N ASP d 203 " --> pdb=" O ILE d 200 " (cutoff:3.500A) Processing helix chain 'd' and resid 208 through 215 removed outlier: 3.682A pdb=" N ARG d 215 " --> pdb=" O GLY d 211 " (cutoff:3.500A) Processing helix chain 'd' and resid 216 through 221 removed outlier: 5.318A pdb=" N GLY d 219 " --> pdb=" O ASN d 216 " (cutoff:3.500A) Processing helix chain 'd' and resid 226 through 231 removed outlier: 3.977A pdb=" N LEU d 230 " --> pdb=" O SER d 226 " (cutoff:3.500A) Processing helix chain 'e' and resid 818 through 842 removed outlier: 3.688A pdb=" N LYS e 824 " --> pdb=" O PRO e 820 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N MET e 842 " --> pdb=" O ILE e 838 " (cutoff:3.500A) Processing helix chain 'f' and resid 123 through 130 Processing helix chain 'f' and resid 142 through 147 removed outlier: 3.607A pdb=" N VAL f 147 " --> pdb=" O GLY f 143 " (cutoff:3.500A) Processing helix chain 'f' and resid 150 through 155 removed outlier: 3.563A pdb=" N LEU f 155 " --> pdb=" O ALA f 152 " (cutoff:3.500A) Processing helix chain 'g' and resid 93 through 103 Processing helix chain 'h' and resid 92 through 103 Processing helix chain 'i' and resid 92 through 102 removed outlier: 3.837A pdb=" N GLU i 102 " --> pdb=" O ALA i 98 " (cutoff:3.500A) Processing helix chain 'j' and resid 92 through 103 Processing helix chain 'j' and resid 151 through 155 Processing helix chain 'k' and resid 93 through 102 Processing helix chain 'l' and resid 92 through 103 Processing helix chain 'n' and resid 92 through 102 removed outlier: 3.895A pdb=" N GLU n 102 " --> pdb=" O ALA n 98 " (cutoff:3.500A) Processing helix chain 'o' and resid 92 through 103 Processing helix chain 'o' and resid 151 through 156 Processing sheet with id=AA1, first strand: chain 'M' and resid 13 through 15 WARNING: can't find start of bonding for strands! previous: chain 'M' and resid 43 through 51 current: chain 'M' and resid 82 through 86 WARNING: can't find start of bonding for strands! previous: chain 'M' and resid 82 through 86 current: chain 'M' and resid 97 through 106 WARNING: can't find start of bonding for strands! previous: chain 'M' and resid 97 through 106 current: chain 'm' and resid 43 through 51 WARNING: can't find start of bonding for strands! previous: chain 'm' and resid 43 through 51 current: chain 'm' and resid 82 through 85 WARNING: can't find start of bonding for strands! previous: chain 'm' and resid 82 through 85 current: chain 'm' and resid 97 through 106 WARNING: can't find start of bonding for strands! previous: chain 'm' and resid 97 through 106 current: chain 'D' and resid 43 through 51 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 43 through 51 current: chain 'D' and resid 82 through 86 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 82 through 86 current: chain 'D' and resid 97 through 106 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 97 through 106 current: chain 'F' and resid 43 through 51 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 43 through 51 current: chain 'F' and resid 82 through 85 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 82 through 85 current: chain 'F' and resid 97 through 106 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 97 through 106 current: chain 'X' and resid 43 through 51 WARNING: can't find start of bonding for strands! previous: chain 'X' and resid 43 through 51 current: chain 'X' and resid 82 through 86 WARNING: can't find start of bonding for strands! previous: chain 'X' and resid 82 through 86 current: chain 'X' and resid 97 through 106 WARNING: can't find start of bonding for strands! previous: chain 'X' and resid 97 through 106 current: chain 'Z' and resid 43 through 51 WARNING: can't find start of bonding for strands! previous: chain 'Z' and resid 43 through 51 current: chain 'Z' and resid 82 through 85 WARNING: can't find start of bonding for strands! previous: chain 'Z' and resid 82 through 85 current: chain 'Z' and resid 97 through 106 Processing sheet with id=AA2, first strand: chain 'M' and resid 21 through 24 Processing sheet with id=AA3, first strand: chain 'J' and resid 222 through 223 Processing sheet with id=AA4, first strand: chain 'J' and resid 29 through 30 Processing sheet with id=AA5, first strand: chain 'J' and resid 35 through 38 WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 35 through 38 current: chain 'J' and resid 235 through 241 Processing sheet with id=AA6, first strand: chain 'J' and resid 85 through 93 WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 85 through 93 current: chain 'J' and resid 163 through 164 No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'J' and resid 180 through 183 Processing sheet with id=AA8, first strand: chain 'J' and resid 243 through 246 Processing sheet with id=AA9, first strand: chain 'J' and resid 249 through 250 Processing sheet with id=AB1, first strand: chain 'J' and resid 311 through 313 Processing sheet with id=AB2, first strand: chain 'J' and resid 327 through 329 removed outlier: 3.759A pdb=" N ALA J 327 " --> pdb=" O TYR I 193 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'J' and resid 333 through 334 Processing sheet with id=AB4, first strand: chain 'J' and resid 350 through 352 Processing sheet with id=AB5, first strand: chain 'J' and resid 369 through 372 WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 369 through 372 current: chain 'J' and resid 460 through 463 WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 460 through 463 current: chain 'J' and resid 570 through 578 removed outlier: 5.497A pdb=" N CYS J 573 " --> pdb=" O VAL J 589 " (cutoff:3.500A) removed outlier: 6.053A pdb=" N VAL J 589 " --> pdb=" O CYS J 573 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N SER J 575 " --> pdb=" O THR J 587 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'J' and resid 411 through 418 removed outlier: 3.702A pdb=" N GLU J 411 " --> pdb=" O ASP J 405 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N ALA J 398 " --> pdb=" O THR J 431 " (cutoff:3.500A) removed outlier: 7.765A pdb=" N MET J 433 " --> pdb=" O ALA J 398 " (cutoff:3.500A) removed outlier: 6.097A pdb=" N GLU J 400 " --> pdb=" O MET J 433 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'J' and resid 492 through 499 removed outlier: 3.649A pdb=" N ALA J 497 " --> pdb=" O THR J 506 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N LYS J 543 " --> pdb=" O VAL J 538 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N VAL J 538 " --> pdb=" O LYS J 543 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N LYS J 545 " --> pdb=" O GLN J 536 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'J' and resid 622 through 629 removed outlier: 5.665A pdb=" N HIS J 623 " --> pdb=" O ASP J 642 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N ASP J 642 " --> pdb=" O HIS J 623 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'J' and resid 646 through 647 WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 646 through 647 current: chain 'Y' and resid 216 through 217 WARNING: can't find start of bonding for strands! previous: chain 'Y' and resid 216 through 217 current: chain 'f' and resid 200 through 209 No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'J' and resid 665 through 673 removed outlier: 5.707A pdb=" N LEU J 667 " --> pdb=" O VAL J 658 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N VAL J 658 " --> pdb=" O LEU J 667 " (cutoff:3.500A) removed outlier: 4.870A pdb=" N ASN J 687 " --> pdb=" O THR J 659 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'J' and resid 719 through 724 Processing sheet with id=AC3, first strand: chain 'J' and resid 764 through 769 removed outlier: 3.560A pdb=" N ARG J 764 " --> pdb=" O PHE J 748 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N PHE J 746 " --> pdb=" O LEU J 766 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N THR J 768 " --> pdb=" O PHE J 744 " (cutoff:3.500A) removed outlier: 5.906A pdb=" N PHE J 744 " --> pdb=" O THR J 768 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'm' and resid 21 through 24 Processing sheet with id=AC5, first strand: chain 'L' and resid 49 through 51 removed outlier: 9.796A pdb=" N GLN L 55 " --> pdb=" O ARG L 35 " (cutoff:3.500A) removed outlier: 5.706A pdb=" N PHE L 37 " --> pdb=" O GLN L 55 " (cutoff:3.500A) removed outlier: 5.428A pdb=" N ILE L 137 " --> pdb=" O SER L 153 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N SER L 153 " --> pdb=" O ILE L 137 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N GLN L 139 " --> pdb=" O VAL L 151 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N SER L 149 " --> pdb=" O SER L 141 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N LEU L 143 " --> pdb=" O SER L 147 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N SER L 147 " --> pdb=" O LEU L 143 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'I' and resid 181 through 182 Processing sheet with id=AC7, first strand: chain 'V' and resid 16 through 20 removed outlier: 4.588A pdb=" N LEU V 17 " --> pdb=" O LEU V 39 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'V' and resid 36 through 39 current: chain 'V' and resid 79 through 85 WARNING: can't find start of bonding for strands! previous: chain 'V' and resid 79 through 85 current: chain 'V' and resid 117 through 130 removed outlier: 5.469A pdb=" N VAL V 124 " --> pdb=" O THR V 144 " (cutoff:3.500A) removed outlier: 6.031A pdb=" N THR V 144 " --> pdb=" O VAL V 124 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N THR V 138 " --> pdb=" O ALA V 130 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'V' and resid 138 through 145 current: chain 'v' and resid 70 through 76 Processing sheet with id=AC8, first strand: chain 'V' and resid 50 through 56 removed outlier: 6.636A pdb=" N THR V 51 " --> pdb=" O LYS V 75 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N LYS V 75 " --> pdb=" O THR V 51 " (cutoff:3.500A) removed outlier: 5.526A pdb=" N GLU V 53 " --> pdb=" O GLY V 73 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'V' and resid 70 through 76 current: chain 'h' and resid 36 through 38 WARNING: can't find start of bonding for strands! previous: chain 'h' and resid 36 through 38 current: chain 'h' and resid 79 through 85 WARNING: can't find start of bonding for strands! previous: chain 'h' and resid 79 through 85 current: chain 'h' and resid 117 through 132 removed outlier: 5.519A pdb=" N VAL h 124 " --> pdb=" O THR h 144 " (cutoff:3.500A) removed outlier: 6.059A pdb=" N THR h 144 " --> pdb=" O VAL h 124 " (cutoff:3.500A) removed outlier: 6.037A pdb=" N THR h 132 " --> pdb=" O VAL h 136 " (cutoff:3.500A) removed outlier: 5.252A pdb=" N VAL h 136 " --> pdb=" O THR h 132 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'V' and resid 165 through 167 removed outlier: 4.324A pdb=" N ILE V 214 " --> pdb=" O LEU V 181 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'V' and resid 172 through 173 removed outlier: 4.191A pdb=" N PHE V 235 " --> pdb=" O SER V 230 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'v' and resid 16 through 20 WARNING: can't find start of bonding for strands! previous: chain 'v' and resid 36 through 38 current: chain 'v' and resid 79 through 85 WARNING: can't find start of bonding for strands! previous: chain 'v' and resid 79 through 85 current: chain 'v' and resid 117 through 132 removed outlier: 5.513A pdb=" N VAL v 124 " --> pdb=" O THR v 144 " (cutoff:3.500A) removed outlier: 6.055A pdb=" N THR v 144 " --> pdb=" O VAL v 124 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N THR v 138 " --> pdb=" O ALA v 130 " (cutoff:3.500A) removed outlier: 6.090A pdb=" N THR v 132 " --> pdb=" O VAL v 136 " (cutoff:3.500A) removed outlier: 5.254A pdb=" N VAL v 136 " --> pdb=" O THR v 132 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'v' and resid 135 through 145 current: chain 'O' and resid 70 through 76 Processing sheet with id=AD3, first strand: chain 'v' and resid 164 through 167 removed outlier: 4.013A pdb=" N THR v 165 " --> pdb=" O ALA v 184 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'v' and resid 195 through 197 removed outlier: 4.063A pdb=" N PHE v 235 " --> pdb=" O SER v 230 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 16 through 20 removed outlier: 4.634A pdb=" N LEU B 17 " --> pdb=" O LEU B 39 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 36 through 39 current: chain 'B' and resid 80 through 85 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 80 through 85 current: chain 'B' and resid 117 through 132 removed outlier: 5.415A pdb=" N VAL B 124 " --> pdb=" O THR B 144 " (cutoff:3.500A) removed outlier: 6.064A pdb=" N THR B 144 " --> pdb=" O VAL B 124 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N THR B 138 " --> pdb=" O ALA B 130 " (cutoff:3.500A) removed outlier: 5.806A pdb=" N THR B 132 " --> pdb=" O VAL B 136 " (cutoff:3.500A) removed outlier: 5.227A pdb=" N VAL B 136 " --> pdb=" O THR B 132 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 135 through 145 current: chain 'b' and resid 70 through 76 Processing sheet with id=AD6, first strand: chain 'B' and resid 55 through 56 Processing sheet with id=AD7, first strand: chain 'B' and resid 165 through 167 removed outlier: 4.069A pdb=" N ILE B 214 " --> pdb=" O LEU B 181 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 172 through 173 Processing sheet with id=AD9, first strand: chain 'b' and resid 16 through 20 WARNING: can't find start of bonding for strands! previous: chain 'b' and resid 36 through 38 current: chain 'b' and resid 79 through 85 WARNING: can't find start of bonding for strands! previous: chain 'b' and resid 79 through 85 current: chain 'b' and resid 117 through 130 removed outlier: 4.993A pdb=" N ASP b 118 " --> pdb=" O SER b 150 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N SER b 150 " --> pdb=" O ASP b 118 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N PHE b 120 " --> pdb=" O ARG b 148 " (cutoff:3.500A) removed outlier: 8.972A pdb=" N ARG b 148 " --> pdb=" O PHE b 120 " (cutoff:3.500A) removed outlier: 5.310A pdb=" N GLY b 122 " --> pdb=" O VAL b 146 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N VAL b 146 " --> pdb=" O GLY b 122 " (cutoff:3.500A) removed outlier: 5.491A pdb=" N VAL b 124 " --> pdb=" O THR b 144 " (cutoff:3.500A) removed outlier: 6.005A pdb=" N THR b 144 " --> pdb=" O VAL b 124 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'b' and resid 164 through 167 Processing sheet with id=AE2, first strand: chain 'b' and resid 172 through 173 removed outlier: 3.941A pdb=" N PHE b 235 " --> pdb=" O SER b 230 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'A' and resid 16 through 20 removed outlier: 4.469A pdb=" N LEU A 17 " --> pdb=" O LEU A 39 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 36 through 39 current: chain 'A' and resid 80 through 85 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 80 through 85 current: chain 'A' and resid 117 through 130 removed outlier: 5.450A pdb=" N VAL A 124 " --> pdb=" O THR A 144 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N THR A 144 " --> pdb=" O VAL A 124 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N THR A 138 " --> pdb=" O ALA A 130 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 138 through 145 current: chain 'a' and resid 70 through 76 Processing sheet with id=AE4, first strand: chain 'A' and resid 50 through 51 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 50 through 51 current: chain 'l' and resid 36 through 38 WARNING: can't find start of bonding for strands! previous: chain 'l' and resid 36 through 38 current: chain 'l' and resid 79 through 85 WARNING: can't find start of bonding for strands! previous: chain 'l' and resid 79 through 85 current: chain 'l' and resid 117 through 127 WARNING: can't find start of bonding for strands! previous: chain 'l' and resid 117 through 127 current: chain 'l' and resid 135 through 145 No H-bonds generated for sheet with id=AE4 Processing sheet with id=AE5, first strand: chain 'A' and resid 54 through 56 Processing sheet with id=AE6, first strand: chain 'A' and resid 165 through 167 removed outlier: 4.037A pdb=" N ILE A 214 " --> pdb=" O LEU A 181 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'A' and resid 172 through 173 Processing sheet with id=AE8, first strand: chain 'a' and resid 16 through 20 WARNING: can't find start of bonding for strands! previous: chain 'a' and resid 36 through 38 current: chain 'a' and resid 79 through 85 WARNING: can't find start of bonding for strands! previous: chain 'a' and resid 79 through 85 current: chain 'a' and resid 117 through 132 removed outlier: 5.535A pdb=" N VAL a 124 " --> pdb=" O THR a 144 " (cutoff:3.500A) removed outlier: 5.978A pdb=" N THR a 144 " --> pdb=" O VAL a 124 " (cutoff:3.500A) removed outlier: 6.088A pdb=" N THR a 132 " --> pdb=" O VAL a 136 " (cutoff:3.500A) removed outlier: 5.238A pdb=" N VAL a 136 " --> pdb=" O THR a 132 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'a' and resid 164 through 167 Processing sheet with id=AF1, first strand: chain 'a' and resid 172 through 173 removed outlier: 3.898A pdb=" N PHE a 235 " --> pdb=" O SER a 230 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 16 through 20 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 36 through 38 current: chain 'C' and resid 80 through 85 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 80 through 85 current: chain 'C' and resid 117 through 130 removed outlier: 5.457A pdb=" N VAL C 124 " --> pdb=" O THR C 144 " (cutoff:3.500A) removed outlier: 5.995A pdb=" N THR C 144 " --> pdb=" O VAL C 124 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 138 through 145 current: chain 'c' and resid 70 through 76 Processing sheet with id=AF3, first strand: chain 'C' and resid 54 through 56 Processing sheet with id=AF4, first strand: chain 'C' and resid 165 through 167 removed outlier: 3.939A pdb=" N ILE C 214 " --> pdb=" O LEU C 181 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'C' and resid 172 through 173 removed outlier: 4.342A pdb=" N PHE C 235 " --> pdb=" O SER C 230 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'c' and resid 36 through 38 removed outlier: 5.341A pdb=" N ALA c 107 " --> pdb=" O TYR c 20 " (cutoff:3.500A) removed outlier: 5.371A pdb=" N VAL c 124 " --> pdb=" O THR c 144 " (cutoff:3.500A) removed outlier: 6.012A pdb=" N THR c 144 " --> pdb=" O VAL c 124 " (cutoff:3.500A) removed outlier: 5.619A pdb=" N THR c 132 " --> pdb=" O VAL c 136 " (cutoff:3.500A) removed outlier: 5.108A pdb=" N VAL c 136 " --> pdb=" O THR c 132 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N ALA c 85 " --> pdb=" O VAL c 42 " (cutoff:3.500A) removed outlier: 7.102A pdb=" N VAL c 42 " --> pdb=" O ALA c 85 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'c' and resid 164 through 167 Processing sheet with id=AF8, first strand: chain 'c' and resid 172 through 173 removed outlier: 3.842A pdb=" N PHE c 235 " --> pdb=" O SER c 230 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'D' and resid 21 through 24 Processing sheet with id=AG1, first strand: chain 'E' and resid 22 through 30 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 216 through 217 current: chain 'N' and resid 200 through 209 Processing sheet with id=AG2, first strand: chain 'E' and resid 35 through 38 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 35 through 38 current: chain 'E' and resid 235 through 241 Processing sheet with id=AG3, first strand: chain 'E' and resid 85 through 92 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 85 through 92 current: chain 'E' and resid 163 through 164 No H-bonds generated for sheet with id=AG3 Processing sheet with id=AG4, first strand: chain 'E' and resid 180 through 183 Processing sheet with id=AG5, first strand: chain 'E' and resid 243 through 246 Processing sheet with id=AG6, first strand: chain 'E' and resid 249 through 250 removed outlier: 3.524A pdb=" N GLN E 255 " --> pdb=" O ASN E 250 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'E' and resid 311 through 313 Processing sheet with id=AG8, first strand: chain 'E' and resid 327 through 329 removed outlier: 3.714A pdb=" N ALA E 327 " --> pdb=" O TYR N 193 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'E' and resid 333 through 334 removed outlier: 3.531A pdb=" N ARG E 333 " --> pdb=" O PHE G 163 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'E' and resid 350 through 352 Processing sheet with id=AH2, first strand: chain 'E' and resid 369 through 372 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 369 through 372 current: chain 'E' and resid 460 through 463 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 460 through 463 current: chain 'E' and resid 570 through 578 removed outlier: 5.539A pdb=" N CYS E 573 " --> pdb=" O VAL E 589 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N VAL E 589 " --> pdb=" O CYS E 573 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N SER E 575 " --> pdb=" O THR E 587 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'E' and resid 411 through 418 removed outlier: 3.692A pdb=" N GLU E 411 " --> pdb=" O ASP E 405 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N ALA E 398 " --> pdb=" O THR E 431 " (cutoff:3.500A) removed outlier: 7.777A pdb=" N MET E 433 " --> pdb=" O ALA E 398 " (cutoff:3.500A) removed outlier: 6.071A pdb=" N GLU E 400 " --> pdb=" O MET E 433 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'E' and resid 492 through 499 removed outlier: 3.664A pdb=" N ALA E 497 " --> pdb=" O THR E 506 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N LYS E 543 " --> pdb=" O VAL E 538 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N VAL E 538 " --> pdb=" O LYS E 543 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N LYS E 545 " --> pdb=" O GLN E 536 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N VAL E 524 " --> pdb=" O VAL E 558 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N VAL E 558 " --> pdb=" O VAL E 524 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'E' and resid 622 through 629 removed outlier: 5.675A pdb=" N HIS E 623 " --> pdb=" O ASP E 642 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N ASP E 642 " --> pdb=" O HIS E 623 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'E' and resid 665 through 673 removed outlier: 5.636A pdb=" N LEU E 667 " --> pdb=" O VAL E 658 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N VAL E 658 " --> pdb=" O LEU E 667 " (cutoff:3.500A) removed outlier: 4.873A pdb=" N ASN E 687 " --> pdb=" O THR E 659 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'E' and resid 719 through 724 Processing sheet with id=AH8, first strand: chain 'E' and resid 764 through 769 removed outlier: 3.625A pdb=" N ARG E 764 " --> pdb=" O PHE E 748 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N PHE E 746 " --> pdb=" O LEU E 766 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N THR E 768 " --> pdb=" O PHE E 744 " (cutoff:3.500A) removed outlier: 5.877A pdb=" N PHE E 744 " --> pdb=" O THR E 768 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'F' and resid 21 through 24 Processing sheet with id=AI1, first strand: chain 'G' and resid 49 through 51 removed outlier: 9.789A pdb=" N GLN G 55 " --> pdb=" O ARG G 35 " (cutoff:3.500A) removed outlier: 5.649A pdb=" N PHE G 37 " --> pdb=" O GLN G 55 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N VAL G 151 " --> pdb=" O GLU G 138 " (cutoff:3.500A) removed outlier: 4.720A pdb=" N CYS G 140 " --> pdb=" O SER G 149 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N SER G 149 " --> pdb=" O CYS G 140 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N GLU G 142 " --> pdb=" O SER G 147 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N SER G 147 " --> pdb=" O GLU G 142 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'O' and resid 16 through 20 removed outlier: 4.678A pdb=" N LEU O 17 " --> pdb=" O LEU O 39 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'O' and resid 36 through 39 current: chain 'O' and resid 79 through 85 WARNING: can't find start of bonding for strands! previous: chain 'O' and resid 79 through 85 current: chain 'O' and resid 117 through 130 removed outlier: 5.472A pdb=" N VAL O 124 " --> pdb=" O THR O 144 " (cutoff:3.500A) removed outlier: 6.007A pdb=" N THR O 144 " --> pdb=" O VAL O 124 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N THR O 138 " --> pdb=" O ALA O 130 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'O' and resid 138 through 145 current: chain 'P' and resid 70 through 75 Processing sheet with id=AI3, first strand: chain 'O' and resid 165 through 167 removed outlier: 4.203A pdb=" N ILE O 214 " --> pdb=" O LEU O 181 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'O' and resid 172 through 173 removed outlier: 4.160A pdb=" N PHE O 235 " --> pdb=" O SER O 230 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'P' and resid 16 through 20 WARNING: can't find start of bonding for strands! previous: chain 'P' and resid 36 through 38 current: chain 'P' and resid 79 through 85 WARNING: can't find start of bonding for strands! previous: chain 'P' and resid 79 through 85 current: chain 'P' and resid 117 through 132 removed outlier: 5.506A pdb=" N VAL P 124 " --> pdb=" O THR P 144 " (cutoff:3.500A) removed outlier: 6.101A pdb=" N THR P 144 " --> pdb=" O VAL P 124 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N THR P 132 " --> pdb=" O VAL P 136 " (cutoff:3.500A) removed outlier: 5.210A pdb=" N VAL P 136 " --> pdb=" O THR P 132 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'P' and resid 135 through 145 current: chain 'g' and resid 70 through 76 Processing sheet with id=AI6, first strand: chain 'P' and resid 164 through 167 removed outlier: 3.871A pdb=" N THR P 165 " --> pdb=" O ALA P 184 " (cutoff:3.500A) Processing sheet with id=AI7, first strand: chain 'P' and resid 195 through 197 Processing sheet with id=AI8, first strand: chain 'Q' and resid 16 through 20 removed outlier: 4.514A pdb=" N LEU Q 17 " --> pdb=" O LEU Q 39 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'Q' and resid 36 through 39 current: chain 'Q' and resid 80 through 85 WARNING: can't find start of bonding for strands! previous: chain 'Q' and resid 80 through 85 current: chain 'Q' and resid 117 through 132 removed outlier: 5.417A pdb=" N VAL Q 124 " --> pdb=" O THR Q 144 " (cutoff:3.500A) removed outlier: 6.006A pdb=" N THR Q 144 " --> pdb=" O VAL Q 124 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N THR Q 138 " --> pdb=" O ALA Q 130 " (cutoff:3.500A) removed outlier: 5.792A pdb=" N THR Q 132 " --> pdb=" O VAL Q 136 " (cutoff:3.500A) removed outlier: 5.200A pdb=" N VAL Q 136 " --> pdb=" O THR Q 132 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'Q' and resid 135 through 145 current: chain 'R' and resid 70 through 76 Processing sheet with id=AI9, first strand: chain 'Q' and resid 54 through 56 Processing sheet with id=AJ1, first strand: chain 'Q' and resid 165 through 167 removed outlier: 3.989A pdb=" N ILE Q 214 " --> pdb=" O LEU Q 181 " (cutoff:3.500A) Processing sheet with id=AJ2, first strand: chain 'Q' and resid 172 through 173 Processing sheet with id=AJ3, first strand: chain 'R' and resid 16 through 20 WARNING: can't find start of bonding for strands! previous: chain 'R' and resid 36 through 38 current: chain 'R' and resid 79 through 85 WARNING: can't find start of bonding for strands! previous: chain 'R' and resid 79 through 85 current: chain 'R' and resid 117 through 130 removed outlier: 4.963A pdb=" N ASP R 118 " --> pdb=" O SER R 150 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N SER R 150 " --> pdb=" O ASP R 118 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N PHE R 120 " --> pdb=" O ARG R 148 " (cutoff:3.500A) removed outlier: 8.942A pdb=" N ARG R 148 " --> pdb=" O PHE R 120 " (cutoff:3.500A) removed outlier: 5.114A pdb=" N GLY R 122 " --> pdb=" O VAL R 146 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N VAL R 146 " --> pdb=" O GLY R 122 " (cutoff:3.500A) removed outlier: 5.451A pdb=" N VAL R 124 " --> pdb=" O THR R 144 " (cutoff:3.500A) removed outlier: 5.905A pdb=" N THR R 144 " --> pdb=" O VAL R 124 " (cutoff:3.500A) Processing sheet with id=AJ4, first strand: chain 'R' and resid 164 through 167 Processing sheet with id=AJ5, first strand: chain 'R' and resid 172 through 173 removed outlier: 3.860A pdb=" N PHE R 235 " --> pdb=" O SER R 230 " (cutoff:3.500A) Processing sheet with id=AJ6, first strand: chain 'S' and resid 16 through 20 removed outlier: 4.474A pdb=" N LEU S 17 " --> pdb=" O LEU S 39 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'S' and resid 36 through 39 current: chain 'S' and resid 80 through 85 WARNING: can't find start of bonding for strands! previous: chain 'S' and resid 80 through 85 current: chain 'S' and resid 117 through 130 removed outlier: 5.404A pdb=" N VAL S 124 " --> pdb=" O THR S 144 " (cutoff:3.500A) removed outlier: 6.048A pdb=" N THR S 144 " --> pdb=" O VAL S 124 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N THR S 138 " --> pdb=" O ALA S 130 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'S' and resid 138 through 145 current: chain 'T' and resid 70 through 76 Processing sheet with id=AJ7, first strand: chain 'S' and resid 54 through 56 Processing sheet with id=AJ8, first strand: chain 'S' and resid 165 through 167 removed outlier: 4.017A pdb=" N ILE S 214 " --> pdb=" O LEU S 181 " (cutoff:3.500A) Processing sheet with id=AJ9, first strand: chain 'S' and resid 172 through 173 Processing sheet with id=AK1, first strand: chain 'T' and resid 16 through 20 WARNING: can't find start of bonding for strands! previous: chain 'T' and resid 36 through 38 current: chain 'T' and resid 79 through 85 WARNING: can't find start of bonding for strands! previous: chain 'T' and resid 79 through 85 current: chain 'T' and resid 117 through 132 removed outlier: 5.538A pdb=" N VAL T 124 " --> pdb=" O THR T 144 " (cutoff:3.500A) removed outlier: 5.986A pdb=" N THR T 144 " --> pdb=" O VAL T 124 " (cutoff:3.500A) removed outlier: 6.052A pdb=" N THR T 132 " --> pdb=" O VAL T 136 " (cutoff:3.500A) removed outlier: 5.174A pdb=" N VAL T 136 " --> pdb=" O THR T 132 " (cutoff:3.500A) Processing sheet with id=AK2, first strand: chain 'T' and resid 164 through 167 Processing sheet with id=AK3, first strand: chain 'T' and resid 172 through 173 removed outlier: 3.883A pdb=" N PHE T 235 " --> pdb=" O SER T 230 " (cutoff:3.500A) Processing sheet with id=AK4, first strand: chain 'U' and resid 16 through 20 WARNING: can't find start of bonding for strands! previous: chain 'U' and resid 36 through 38 current: chain 'U' and resid 80 through 85 WARNING: can't find start of bonding for strands! previous: chain 'U' and resid 80 through 85 current: chain 'U' and resid 117 through 130 removed outlier: 5.430A pdb=" N VAL U 124 " --> pdb=" O THR U 144 " (cutoff:3.500A) removed outlier: 5.994A pdb=" N THR U 144 " --> pdb=" O VAL U 124 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'U' and resid 138 through 145 current: chain 'W' and resid 70 through 76 Processing sheet with id=AK5, first strand: chain 'U' and resid 54 through 56 Processing sheet with id=AK6, first strand: chain 'U' and resid 165 through 167 removed outlier: 4.014A pdb=" N ILE U 214 " --> pdb=" O LEU U 181 " (cutoff:3.500A) Processing sheet with id=AK7, first strand: chain 'U' and resid 172 through 173 Processing sheet with id=AK8, first strand: chain 'W' and resid 16 through 20 WARNING: can't find start of bonding for strands! previous: chain 'W' and resid 36 through 38 current: chain 'W' and resid 79 through 85 WARNING: can't find start of bonding for strands! previous: chain 'W' and resid 79 through 85 current: chain 'W' and resid 117 through 127 WARNING: can't find start of bonding for strands! previous: chain 'W' and resid 117 through 127 current: chain 'W' and resid 135 through 145 Processing sheet with id=AK9, first strand: chain 'W' and resid 164 through 167 Processing sheet with id=AL1, first strand: chain 'W' and resid 172 through 173 removed outlier: 3.847A pdb=" N PHE W 235 " --> pdb=" O SER W 230 " (cutoff:3.500A) Processing sheet with id=AL2, first strand: chain 'X' and resid 21 through 24 Processing sheet with id=AL3, first strand: chain 'Y' and resid 45 through 46 Processing sheet with id=AL4, first strand: chain 'Y' and resid 85 through 92 WARNING: can't find start of bonding for strands! previous: chain 'Y' and resid 85 through 92 current: chain 'Y' and resid 163 through 164 No H-bonds generated for sheet with id=AL4 Processing sheet with id=AL5, first strand: chain 'Y' and resid 180 through 183 Processing sheet with id=AL6, first strand: chain 'Y' and resid 243 through 246 Processing sheet with id=AL7, first strand: chain 'Y' and resid 249 through 250 removed outlier: 3.554A pdb=" N GLN Y 255 " --> pdb=" O ASN Y 250 " (cutoff:3.500A) Processing sheet with id=AL8, first strand: chain 'Y' and resid 311 through 313 Processing sheet with id=AL9, first strand: chain 'Y' and resid 327 through 329 removed outlier: 3.701A pdb=" N ALA Y 327 " --> pdb=" O TYR f 193 " (cutoff:3.500A) Processing sheet with id=AM1, first strand: chain 'Y' and resid 333 through 334 removed outlier: 3.533A pdb=" N ARG Y 333 " --> pdb=" O PHE d 163 " (cutoff:3.500A) Processing sheet with id=AM2, first strand: chain 'Y' and resid 350 through 352 Processing sheet with id=AM3, first strand: chain 'Y' and resid 369 through 372 WARNING: can't find start of bonding for strands! previous: chain 'Y' and resid 369 through 372 current: chain 'Y' and resid 460 through 463 WARNING: can't find start of bonding for strands! previous: chain 'Y' and resid 460 through 463 current: chain 'Y' and resid 570 through 578 removed outlier: 5.513A pdb=" N CYS Y 573 " --> pdb=" O VAL Y 589 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N VAL Y 589 " --> pdb=" O CYS Y 573 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N SER Y 575 " --> pdb=" O THR Y 587 " (cutoff:3.500A) Processing sheet with id=AM4, first strand: chain 'Y' and resid 411 through 418 removed outlier: 3.657A pdb=" N GLU Y 411 " --> pdb=" O ASP Y 405 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N ALA Y 398 " --> pdb=" O THR Y 431 " (cutoff:3.500A) removed outlier: 7.859A pdb=" N MET Y 433 " --> pdb=" O ALA Y 398 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N GLU Y 400 " --> pdb=" O MET Y 433 " (cutoff:3.500A) Processing sheet with id=AM5, first strand: chain 'Y' and resid 492 through 499 removed outlier: 3.649A pdb=" N ALA Y 497 " --> pdb=" O THR Y 506 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N LYS Y 543 " --> pdb=" O VAL Y 538 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N VAL Y 538 " --> pdb=" O LYS Y 543 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N LYS Y 545 " --> pdb=" O GLN Y 536 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N VAL Y 524 " --> pdb=" O VAL Y 558 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N VAL Y 558 " --> pdb=" O VAL Y 524 " (cutoff:3.500A) Processing sheet with id=AM6, first strand: chain 'Y' and resid 622 through 629 removed outlier: 5.698A pdb=" N HIS Y 623 " --> pdb=" O ASP Y 642 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N ASP Y 642 " --> pdb=" O HIS Y 623 " (cutoff:3.500A) Processing sheet with id=AM7, first strand: chain 'Y' and resid 665 through 673 removed outlier: 5.628A pdb=" N LEU Y 667 " --> pdb=" O VAL Y 658 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N VAL Y 658 " --> pdb=" O LEU Y 667 " (cutoff:3.500A) removed outlier: 4.868A pdb=" N ASN Y 687 " --> pdb=" O THR Y 659 " (cutoff:3.500A) Processing sheet with id=AM8, first strand: chain 'Y' and resid 719 through 724 Processing sheet with id=AM9, first strand: chain 'Y' and resid 764 through 769 removed outlier: 3.643A pdb=" N ARG Y 764 " --> pdb=" O PHE Y 748 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N PHE Y 746 " --> pdb=" O LEU Y 766 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N THR Y 768 " --> pdb=" O PHE Y 744 " (cutoff:3.500A) removed outlier: 5.848A pdb=" N PHE Y 744 " --> pdb=" O THR Y 768 " (cutoff:3.500A) Processing sheet with id=AN1, first strand: chain 'Z' and resid 21 through 24 Processing sheet with id=AN2, first strand: chain 'd' and resid 49 through 51 removed outlier: 9.768A pdb=" N GLN d 55 " --> pdb=" O ARG d 35 " (cutoff:3.500A) removed outlier: 5.661A pdb=" N PHE d 37 " --> pdb=" O GLN d 55 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N VAL d 151 " --> pdb=" O GLU d 138 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N CYS d 140 " --> pdb=" O SER d 149 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N SER d 149 " --> pdb=" O CYS d 140 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N GLU d 142 " --> pdb=" O SER d 147 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N SER d 147 " --> pdb=" O GLU d 142 " (cutoff:3.500A) Processing sheet with id=AN3, first strand: chain 'g' and resid 36 through 39 removed outlier: 4.505A pdb=" N LEU g 17 " --> pdb=" O LEU g 39 " (cutoff:3.500A) removed outlier: 5.232A pdb=" N ALA g 107 " --> pdb=" O TYR g 20 " (cutoff:3.500A) removed outlier: 5.497A pdb=" N VAL g 124 " --> pdb=" O THR g 144 " (cutoff:3.500A) removed outlier: 6.068A pdb=" N THR g 144 " --> pdb=" O VAL g 124 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N THR g 138 " --> pdb=" O ALA g 130 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N ALA g 85 " --> pdb=" O VAL g 42 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N VAL g 42 " --> pdb=" O ALA g 85 " (cutoff:3.500A) Processing sheet with id=AN4, first strand: chain 'g' and resid 165 through 167 removed outlier: 4.247A pdb=" N ILE g 214 " --> pdb=" O LEU g 181 " (cutoff:3.500A) Processing sheet with id=AN5, first strand: chain 'g' and resid 172 through 173 removed outlier: 4.200A pdb=" N PHE g 235 " --> pdb=" O SER g 230 " (cutoff:3.500A) Processing sheet with id=AN6, first strand: chain 'h' and resid 52 through 56 removed outlier: 5.543A pdb=" N GLU h 53 " --> pdb=" O GLY h 73 " (cutoff:3.500A) Processing sheet with id=AN7, first strand: chain 'h' and resid 164 through 167 removed outlier: 4.014A pdb=" N THR h 165 " --> pdb=" O ALA h 184 " (cutoff:3.500A) Processing sheet with id=AN8, first strand: chain 'h' and resid 195 through 197 Processing sheet with id=AN9, first strand: chain 'i' and resid 16 through 20 removed outlier: 4.705A pdb=" N LEU i 17 " --> pdb=" O LEU i 39 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'i' and resid 36 through 39 current: chain 'i' and resid 80 through 85 WARNING: can't find start of bonding for strands! previous: chain 'i' and resid 80 through 85 current: chain 'i' and resid 117 through 132 removed outlier: 5.467A pdb=" N VAL i 124 " --> pdb=" O THR i 144 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N THR i 144 " --> pdb=" O VAL i 124 " (cutoff:3.500A) removed outlier: 5.763A pdb=" N THR i 132 " --> pdb=" O VAL i 136 " (cutoff:3.500A) removed outlier: 5.167A pdb=" N VAL i 136 " --> pdb=" O THR i 132 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'i' and resid 135 through 145 current: chain 'j' and resid 70 through 76 Processing sheet with id=AO1, first strand: chain 'i' and resid 54 through 56 Processing sheet with id=AO2, first strand: chain 'i' and resid 165 through 167 removed outlier: 4.006A pdb=" N ILE i 214 " --> pdb=" O LEU i 181 " (cutoff:3.500A) Processing sheet with id=AO3, first strand: chain 'i' and resid 172 through 173 Processing sheet with id=AO4, first strand: chain 'j' and resid 36 through 38 removed outlier: 5.355A pdb=" N ALA j 107 " --> pdb=" O TYR j 20 " (cutoff:3.500A) removed outlier: 5.128A pdb=" N ASP j 118 " --> pdb=" O SER j 150 " (cutoff:3.500A) removed outlier: 7.305A pdb=" N SER j 150 " --> pdb=" O ASP j 118 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N PHE j 120 " --> pdb=" O ARG j 148 " (cutoff:3.500A) removed outlier: 9.063A pdb=" N ARG j 148 " --> pdb=" O PHE j 120 " (cutoff:3.500A) removed outlier: 5.315A pdb=" N GLY j 122 " --> pdb=" O VAL j 146 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N VAL j 146 " --> pdb=" O GLY j 122 " (cutoff:3.500A) removed outlier: 5.464A pdb=" N VAL j 124 " --> pdb=" O THR j 144 " (cutoff:3.500A) removed outlier: 5.983A pdb=" N THR j 144 " --> pdb=" O VAL j 124 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N ALA j 85 " --> pdb=" O VAL j 42 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N VAL j 42 " --> pdb=" O ALA j 85 " (cutoff:3.500A) Processing sheet with id=AO5, first strand: chain 'j' and resid 164 through 167 Processing sheet with id=AO6, first strand: chain 'j' and resid 172 through 173 removed outlier: 3.891A pdb=" N PHE j 235 " --> pdb=" O SER j 230 " (cutoff:3.500A) Processing sheet with id=AO7, first strand: chain 'k' and resid 16 through 20 removed outlier: 4.488A pdb=" N LEU k 17 " --> pdb=" O LEU k 39 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'k' and resid 36 through 39 current: chain 'k' and resid 80 through 85 WARNING: can't find start of bonding for strands! previous: chain 'k' and resid 80 through 85 current: chain 'k' and resid 117 through 130 removed outlier: 5.410A pdb=" N VAL k 124 " --> pdb=" O THR k 144 " (cutoff:3.500A) removed outlier: 6.111A pdb=" N THR k 144 " --> pdb=" O VAL k 124 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N THR k 138 " --> pdb=" O ALA k 130 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'k' and resid 138 through 145 current: chain 'l' and resid 70 through 76 Processing sheet with id=AO8, first strand: chain 'k' and resid 54 through 56 Processing sheet with id=AO9, first strand: chain 'k' and resid 165 through 167 removed outlier: 4.003A pdb=" N ILE k 214 " --> pdb=" O LEU k 181 " (cutoff:3.500A) Processing sheet with id=AP1, first strand: chain 'k' and resid 172 through 173 Processing sheet with id=AP2, first strand: chain 'l' and resid 164 through 167 Processing sheet with id=AP3, first strand: chain 'l' and resid 172 through 173 removed outlier: 3.868A pdb=" N PHE l 235 " --> pdb=" O SER l 230 " (cutoff:3.500A) Processing sheet with id=AP4, first strand: chain 'n' and resid 16 through 20 WARNING: can't find start of bonding for strands! previous: chain 'n' and resid 36 through 38 current: chain 'n' and resid 80 through 85 WARNING: can't find start of bonding for strands! previous: chain 'n' and resid 80 through 85 current: chain 'n' and resid 117 through 130 removed outlier: 5.449A pdb=" N VAL n 124 " --> pdb=" O THR n 144 " (cutoff:3.500A) removed outlier: 6.008A pdb=" N THR n 144 " --> pdb=" O VAL n 124 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'n' and resid 138 through 145 current: chain 'o' and resid 70 through 76 Processing sheet with id=AP5, first strand: chain 'n' and resid 54 through 56 Processing sheet with id=AP6, first strand: chain 'n' and resid 165 through 167 removed outlier: 4.011A pdb=" N ILE n 214 " --> pdb=" O LEU n 181 " (cutoff:3.500A) Processing sheet with id=AP7, first strand: chain 'n' and resid 172 through 173 removed outlier: 4.387A pdb=" N PHE n 235 " --> pdb=" O SER n 230 " (cutoff:3.500A) Processing sheet with id=AP8, first strand: chain 'o' and resid 16 through 20 WARNING: can't find start of bonding for strands! previous: chain 'o' and resid 36 through 38 current: chain 'o' and resid 79 through 85 WARNING: can't find start of bonding for strands! previous: chain 'o' and resid 79 through 85 current: chain 'o' and resid 117 through 127 WARNING: can't find start of bonding for strands! previous: chain 'o' and resid 117 through 127 current: chain 'o' and resid 135 through 145 Processing sheet with id=AP9, first strand: chain 'o' and resid 165 through 167 Processing sheet with id=AQ1, first strand: chain 'o' and resid 172 through 173 removed outlier: 3.852A pdb=" N PHE o 235 " --> pdb=" O SER o 230 " (cutoff:3.500A) 1928 hydrogen bonds defined for protein. 5094 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 39.56 Time building geometry restraints manager: 16.70 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.43: 33958 1.43 - 1.65: 44489 1.65 - 1.86: 471 1.86 - 2.07: 0 2.07 - 2.28: 36 Bond restraints: 78954 Sorted by residual: bond pdb=" C PRO Y 173 " pdb=" N PRO Y 174 " ideal model delta sigma weight residual 1.331 1.364 -0.033 1.21e-02 6.83e+03 7.47e+00 bond pdb=" CB GLU C 49 " pdb=" CG GLU C 49 " ideal model delta sigma weight residual 1.520 1.467 0.053 3.00e-02 1.11e+03 3.12e+00 bond pdb=" CB LYS N 158 " pdb=" CG LYS N 158 " ideal model delta sigma weight residual 1.520 1.562 -0.042 3.00e-02 1.11e+03 2.01e+00 bond pdb=" CB GLU e 837 " pdb=" CG GLU e 837 " ideal model delta sigma weight residual 1.520 1.478 0.042 3.00e-02 1.11e+03 1.95e+00 bond pdb=" CB ASP W 64 " pdb=" CG ASP W 64 " ideal model delta sigma weight residual 1.516 1.550 -0.034 2.50e-02 1.60e+03 1.85e+00 ... (remaining 78949 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.64: 107140 3.64 - 7.29: 381 7.29 - 10.93: 48 10.93 - 14.58: 7 14.58 - 18.22: 4 Bond angle restraints: 107580 Sorted by residual: angle pdb=" C GLU a 63 " pdb=" N ASP a 64 " pdb=" CA ASP a 64 " ideal model delta sigma weight residual 121.54 132.10 -10.56 1.91e+00 2.74e-01 3.06e+01 angle pdb=" CA MET j 212 " pdb=" CB MET j 212 " pdb=" CG MET j 212 " ideal model delta sigma weight residual 114.10 124.47 -10.37 2.00e+00 2.50e-01 2.69e+01 angle pdb=" C GLU U 63 " pdb=" N ASP U 64 " pdb=" CA ASP U 64 " ideal model delta sigma weight residual 121.54 131.40 -9.86 1.91e+00 2.74e-01 2.66e+01 angle pdb=" CA MET R 212 " pdb=" CB MET R 212 " pdb=" CG MET R 212 " ideal model delta sigma weight residual 114.10 124.15 -10.05 2.00e+00 2.50e-01 2.53e+01 angle pdb=" C GLU T 63 " pdb=" N ASP T 64 " pdb=" CA ASP T 64 " ideal model delta sigma weight residual 121.54 130.97 -9.43 1.91e+00 2.74e-01 2.44e+01 ... (remaining 107575 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 39782 17.97 - 35.94: 4979 35.94 - 53.91: 1594 53.91 - 71.88: 309 71.88 - 89.85: 94 Dihedral angle restraints: 46758 sinusoidal: 17643 harmonic: 29115 Sorted by residual: dihedral pdb=" CA LEU f 189 " pdb=" C LEU f 189 " pdb=" N PRO f 190 " pdb=" CA PRO f 190 " ideal model delta harmonic sigma weight residual 180.00 134.65 45.35 0 5.00e+00 4.00e-02 8.23e+01 dihedral pdb=" CA LEU I 189 " pdb=" C LEU I 189 " pdb=" N PRO I 190 " pdb=" CA PRO I 190 " ideal model delta harmonic sigma weight residual 180.00 135.05 44.95 0 5.00e+00 4.00e-02 8.08e+01 dihedral pdb=" CA LEU N 189 " pdb=" C LEU N 189 " pdb=" N PRO N 190 " pdb=" CA PRO N 190 " ideal model delta harmonic sigma weight residual 180.00 135.55 44.45 0 5.00e+00 4.00e-02 7.90e+01 ... (remaining 46755 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.071: 10743 0.071 - 0.141: 1591 0.141 - 0.212: 42 0.212 - 0.283: 7 0.283 - 0.353: 1 Chirality restraints: 12384 Sorted by residual: chirality pdb=" CG LEU e 847 " pdb=" CB LEU e 847 " pdb=" CD1 LEU e 847 " pdb=" CD2 LEU e 847 " both_signs ideal model delta sigma weight residual False -2.59 -2.24 -0.35 2.00e-01 2.50e+01 3.12e+00 chirality pdb=" CB VAL I 188 " pdb=" CA VAL I 188 " pdb=" CG1 VAL I 188 " pdb=" CG2 VAL I 188 " both_signs ideal model delta sigma weight residual False -2.63 -2.35 -0.28 2.00e-01 2.50e+01 1.90e+00 chirality pdb=" CG LEU N 189 " pdb=" CB LEU N 189 " pdb=" CD1 LEU N 189 " pdb=" CD2 LEU N 189 " both_signs ideal model delta sigma weight residual False -2.59 -2.32 -0.27 2.00e-01 2.50e+01 1.88e+00 ... (remaining 12381 not shown) Planarity restraints: 13893 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU f 189 " -0.117 5.00e-02 4.00e+02 1.77e-01 5.00e+01 pdb=" N PRO f 190 " 0.305 5.00e-02 4.00e+02 pdb=" CA PRO f 190 " -0.104 5.00e-02 4.00e+02 pdb=" CD PRO f 190 " -0.084 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU I 189 " 0.117 5.00e-02 4.00e+02 1.76e-01 4.97e+01 pdb=" N PRO I 190 " -0.304 5.00e-02 4.00e+02 pdb=" CA PRO I 190 " 0.106 5.00e-02 4.00e+02 pdb=" CD PRO I 190 " 0.082 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU N 189 " 0.115 5.00e-02 4.00e+02 1.74e-01 4.82e+01 pdb=" N PRO N 190 " -0.300 5.00e-02 4.00e+02 pdb=" CA PRO N 190 " 0.103 5.00e-02 4.00e+02 pdb=" CD PRO N 190 " 0.082 5.00e-02 4.00e+02 ... (remaining 13890 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.61: 1339 2.61 - 3.18: 66870 3.18 - 3.76: 119445 3.76 - 4.33: 168827 4.33 - 4.90: 283519 Nonbonded interactions: 640000 Sorted by model distance: nonbonded pdb=" O SER i 210 " pdb=" OG1 THR i 213 " model vdw 2.040 3.040 nonbonded pdb=" O SER Q 210 " pdb=" OG1 THR Q 213 " model vdw 2.044 3.040 nonbonded pdb=" O SER B 210 " pdb=" OG1 THR B 213 " model vdw 2.047 3.040 nonbonded pdb=" OG SER j 199 " pdb=" OD1 ASP j 201 " model vdw 2.126 3.040 nonbonded pdb=" OE1 GLU D 59 " pdb=" OH TYR F 77 " model vdw 2.131 3.040 ... (remaining 639995 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 4 through 246) selection = (chain 'B' and resid 4 through 246) selection = (chain 'C' and resid 4 through 246) selection = chain 'O' selection = chain 'P' selection = (chain 'Q' and resid 4 through 246) selection = (chain 'R' and resid 4 through 246) selection = (chain 'S' and resid 4 through 246) selection = (chain 'T' and resid 4 through 246) selection = (chain 'U' and resid 4 through 246) selection = chain 'V' selection = (chain 'W' and resid 4 through 246) selection = (chain 'a' and resid 4 through 246) selection = (chain 'b' and resid 4 through 246) selection = (chain 'c' and resid 4 through 246) selection = chain 'g' selection = chain 'h' selection = (chain 'i' and resid 4 through 246) selection = (chain 'j' and resid 4 through 246) selection = (chain 'k' and resid 4 through 246) selection = (chain 'l' and resid 4 through 246) selection = (chain 'n' and resid 4 through 246) selection = (chain 'o' and resid 4 through 246) selection = chain 'v' } ncs_group { reference = chain 'D' selection = chain 'F' selection = chain 'M' selection = chain 'X' selection = chain 'Z' selection = chain 'm' } ncs_group { reference = chain 'E' selection = chain 'J' selection = chain 'Y' } ncs_group { reference = chain 'G' selection = chain 'L' selection = chain 'd' } ncs_group { reference = chain 'H' selection = chain 'K' selection = chain 'e' } ncs_group { reference = chain 'I' selection = chain 'N' selection = chain 'f' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 9.540 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.080 Extract box with map and model: 2.350 Check model and map are aligned: 0.440 Set scattering table: 0.540 Process input model: 161.580 Find NCS groups from input model: 3.160 Set up NCS constraints: 0.530 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:10.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 189.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8271 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 78954 Z= 0.244 Angle : 0.663 18.222 107580 Z= 0.344 Chirality : 0.046 0.353 12384 Planarity : 0.005 0.177 13893 Dihedral : 18.103 89.847 28110 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 11.95 Ramachandran Plot: Outliers : 0.60 % Allowed : 7.13 % Favored : 92.27 % Rotamer: Outliers : 7.11 % Allowed : 30.28 % Favored : 62.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.63 % Cis-general : 0.00 % Twisted Proline : 1.26 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.70 (0.08), residues: 10164 helix: 0.22 (0.17), residues: 912 sheet: -0.64 (0.08), residues: 4200 loop : -1.80 (0.08), residues: 5052 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP m 89 HIS 0.007 0.001 HIS E 826 PHE 0.027 0.001 PHE Y 818 TYR 0.023 0.001 TYR n 55 ARG 0.018 0.000 ARG n 121 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 20328 Ramachandran restraints generated. 10164 Oldfield, 0 Emsley, 10164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 20328 Ramachandran restraints generated. 10164 Oldfield, 0 Emsley, 10164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1311 residues out of total 8352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 594 poor density : 717 time to evaluate : 6.474 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 31 SER cc_start: 0.8470 (m) cc_final: 0.8209 (p) REVERT: m 103 GLU cc_start: 0.7842 (pp20) cc_final: 0.7415 (pp20) REVERT: I 158 LYS cc_start: 0.8468 (tppt) cc_final: 0.8071 (tptm) REVERT: B 57 ASP cc_start: 0.8794 (t0) cc_final: 0.8490 (t0) REVERT: P 8 MET cc_start: 0.8684 (mmp) cc_final: 0.8449 (mmm) REVERT: Y 31 SER cc_start: 0.8560 (m) cc_final: 0.8294 (p) REVERT: f 223 ARG cc_start: 0.5895 (ptm-80) cc_final: 0.5425 (ppt-90) REVERT: i 212 MET cc_start: 0.4000 (tpp) cc_final: 0.3521 (tpp) REVERT: n 91 GLN cc_start: 0.8060 (pp30) cc_final: 0.7845 (pm20) REVERT: o 212 MET cc_start: 0.3057 (tpp) cc_final: 0.2421 (tpt) outliers start: 594 outliers final: 560 residues processed: 1289 average time/residue: 1.2988 time to fit residues: 2340.8964 Evaluate side-chains 1263 residues out of total 8352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 560 poor density : 703 time to evaluate : 6.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 41 LEU Chi-restraints excluded: chain M residue 46 VAL Chi-restraints excluded: chain M residue 47 THR Chi-restraints excluded: chain M residue 50 VAL Chi-restraints excluded: chain M residue 84 VAL Chi-restraints excluded: chain M residue 91 SER Chi-restraints excluded: chain M residue 99 GLU Chi-restraints excluded: chain M residue 108 VAL Chi-restraints excluded: chain J residue 26 VAL Chi-restraints excluded: chain J residue 39 VAL Chi-restraints excluded: chain J residue 47 LEU Chi-restraints excluded: chain J residue 49 SER Chi-restraints excluded: chain J residue 65 THR Chi-restraints excluded: chain J residue 88 THR Chi-restraints excluded: chain J residue 97 ASP Chi-restraints excluded: chain J residue 122 VAL Chi-restraints excluded: chain J residue 138 LEU Chi-restraints excluded: chain J residue 149 THR Chi-restraints excluded: chain J residue 153 ILE Chi-restraints excluded: chain J residue 167 VAL Chi-restraints excluded: chain J residue 168 VAL Chi-restraints excluded: chain J residue 177 PHE Chi-restraints excluded: chain J residue 215 THR Chi-restraints excluded: chain J residue 217 LEU Chi-restraints excluded: chain J residue 223 ASP Chi-restraints excluded: chain J residue 233 SER Chi-restraints excluded: chain J residue 257 SER Chi-restraints excluded: chain J residue 325 CYS Chi-restraints excluded: chain J residue 373 ARG Chi-restraints excluded: chain J residue 374 SER Chi-restraints excluded: chain J residue 380 ASP Chi-restraints excluded: chain J residue 412 THR Chi-restraints excluded: chain J residue 439 THR Chi-restraints excluded: chain J residue 461 THR Chi-restraints excluded: chain J residue 465 SER Chi-restraints excluded: chain J residue 484 ASP Chi-restraints excluded: chain J residue 500 SER Chi-restraints excluded: chain J residue 504 THR Chi-restraints excluded: chain J residue 511 ILE Chi-restraints excluded: chain J residue 535 VAL Chi-restraints excluded: chain J residue 539 THR Chi-restraints excluded: chain J residue 540 ASP Chi-restraints excluded: chain J residue 543 LYS Chi-restraints excluded: chain J residue 544 VAL Chi-restraints excluded: chain J residue 583 THR Chi-restraints excluded: chain J residue 596 GLU Chi-restraints excluded: chain J residue 600 ASP Chi-restraints excluded: chain J residue 613 VAL Chi-restraints excluded: chain J residue 629 THR Chi-restraints excluded: chain J residue 646 VAL Chi-restraints excluded: chain J residue 667 LEU Chi-restraints excluded: chain J residue 695 VAL Chi-restraints excluded: chain J residue 770 LEU Chi-restraints excluded: chain J residue 823 THR Chi-restraints excluded: chain J residue 827 LEU Chi-restraints excluded: chain J residue 831 LEU Chi-restraints excluded: chain m residue 46 VAL Chi-restraints excluded: chain m residue 74 THR Chi-restraints excluded: chain L residue 31 VAL Chi-restraints excluded: chain L residue 99 VAL Chi-restraints excluded: chain L residue 120 ASN Chi-restraints excluded: chain L residue 141 SER Chi-restraints excluded: chain L residue 151 VAL Chi-restraints excluded: chain L residue 154 THR Chi-restraints excluded: chain L residue 159 ASP Chi-restraints excluded: chain L residue 167 ILE Chi-restraints excluded: chain L residue 171 ASN Chi-restraints excluded: chain L residue 218 VAL Chi-restraints excluded: chain I residue 105 ILE Chi-restraints excluded: chain I residue 107 LEU Chi-restraints excluded: chain I residue 118 THR Chi-restraints excluded: chain I residue 161 THR Chi-restraints excluded: chain I residue 207 ILE Chi-restraints excluded: chain V residue 32 SER Chi-restraints excluded: chain V residue 51 THR Chi-restraints excluded: chain V residue 68 THR Chi-restraints excluded: chain V residue 70 THR Chi-restraints excluded: chain V residue 83 THR Chi-restraints excluded: chain V residue 117 VAL Chi-restraints excluded: chain V residue 125 SER Chi-restraints excluded: chain V residue 136 VAL Chi-restraints excluded: chain V residue 146 VAL Chi-restraints excluded: chain V residue 166 VAL Chi-restraints excluded: chain V residue 174 VAL Chi-restraints excluded: chain v residue 10 VAL Chi-restraints excluded: chain v residue 16 THR Chi-restraints excluded: chain v residue 32 SER Chi-restraints excluded: chain v residue 33 ASP Chi-restraints excluded: chain v residue 61 ASP Chi-restraints excluded: chain v residue 70 THR Chi-restraints excluded: chain v residue 79 ASP Chi-restraints excluded: chain v residue 80 THR Chi-restraints excluded: chain v residue 84 LEU Chi-restraints excluded: chain v residue 119 VAL Chi-restraints excluded: chain v residue 127 ILE Chi-restraints excluded: chain v residue 132 THR Chi-restraints excluded: chain v residue 158 VAL Chi-restraints excluded: chain v residue 171 THR Chi-restraints excluded: chain v residue 179 THR Chi-restraints excluded: chain v residue 191 THR Chi-restraints excluded: chain B residue 54 SER Chi-restraints excluded: chain B residue 66 ASP Chi-restraints excluded: chain B residue 76 SER Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 150 SER Chi-restraints excluded: chain B residue 156 SER Chi-restraints excluded: chain B residue 182 THR Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 199 SER Chi-restraints excluded: chain B residue 213 THR Chi-restraints excluded: chain B residue 230 SER Chi-restraints excluded: chain B residue 232 ASN Chi-restraints excluded: chain b residue 3 VAL Chi-restraints excluded: chain b residue 16 THR Chi-restraints excluded: chain b residue 17 LEU Chi-restraints excluded: chain b residue 23 SER Chi-restraints excluded: chain b residue 31 LEU Chi-restraints excluded: chain b residue 51 THR Chi-restraints excluded: chain b residue 70 THR Chi-restraints excluded: chain b residue 81 SER Chi-restraints excluded: chain b residue 84 LEU Chi-restraints excluded: chain b residue 110 ILE Chi-restraints excluded: chain b residue 138 THR Chi-restraints excluded: chain b residue 146 VAL Chi-restraints excluded: chain b residue 180 THR Chi-restraints excluded: chain b residue 182 THR Chi-restraints excluded: chain b residue 243 VAL Chi-restraints excluded: chain A residue 17 LEU Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 66 ASP Chi-restraints excluded: chain A residue 76 SER Chi-restraints excluded: chain A residue 83 THR Chi-restraints excluded: chain A residue 125 SER Chi-restraints excluded: chain A residue 127 ILE Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 140 THR Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 186 GLN Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 191 THR Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 232 ASN Chi-restraints excluded: chain A residue 235 PHE Chi-restraints excluded: chain a residue 33 ASP Chi-restraints excluded: chain a residue 37 SER Chi-restraints excluded: chain a residue 70 THR Chi-restraints excluded: chain a residue 117 VAL Chi-restraints excluded: chain a residue 119 VAL Chi-restraints excluded: chain a residue 126 SER Chi-restraints excluded: chain a residue 132 THR Chi-restraints excluded: chain a residue 138 THR Chi-restraints excluded: chain a residue 174 VAL Chi-restraints excluded: chain a residue 185 PHE Chi-restraints excluded: chain a residue 207 VAL Chi-restraints excluded: chain a residue 212 MET Chi-restraints excluded: chain a residue 215 THR Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 17 LEU Chi-restraints excluded: chain C residue 61 ASP Chi-restraints excluded: chain C residue 66 ASP Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 159 THR Chi-restraints excluded: chain C residue 180 THR Chi-restraints excluded: chain c residue 7 THR Chi-restraints excluded: chain c residue 16 THR Chi-restraints excluded: chain c residue 45 LEU Chi-restraints excluded: chain c residue 66 ASP Chi-restraints excluded: chain c residue 83 THR Chi-restraints excluded: chain c residue 117 VAL Chi-restraints excluded: chain c residue 126 SER Chi-restraints excluded: chain c residue 145 ASN Chi-restraints excluded: chain c residue 146 VAL Chi-restraints excluded: chain c residue 180 THR Chi-restraints excluded: chain c residue 240 GLU Chi-restraints excluded: chain D residue 13 ASP Chi-restraints excluded: chain D residue 43 THR Chi-restraints excluded: chain D residue 46 VAL Chi-restraints excluded: chain D residue 47 THR Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 90 SER Chi-restraints excluded: chain D residue 91 SER Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain E residue 10 THR Chi-restraints excluded: chain E residue 21 THR Chi-restraints excluded: chain E residue 26 VAL Chi-restraints excluded: chain E residue 30 ILE Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 49 SER Chi-restraints excluded: chain E residue 64 VAL Chi-restraints excluded: chain E residue 65 THR Chi-restraints excluded: chain E residue 97 ASP Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 122 VAL Chi-restraints excluded: chain E residue 124 THR Chi-restraints excluded: chain E residue 138 LEU Chi-restraints excluded: chain E residue 139 VAL Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain E residue 153 ILE Chi-restraints excluded: chain E residue 168 VAL Chi-restraints excluded: chain E residue 177 PHE Chi-restraints excluded: chain E residue 204 GLU Chi-restraints excluded: chain E residue 215 THR Chi-restraints excluded: chain E residue 217 LEU Chi-restraints excluded: chain E residue 223 ASP Chi-restraints excluded: chain E residue 233 SER Chi-restraints excluded: chain E residue 241 ARG Chi-restraints excluded: chain E residue 257 SER Chi-restraints excluded: chain E residue 281 THR Chi-restraints excluded: chain E residue 324 THR Chi-restraints excluded: chain E residue 325 CYS Chi-restraints excluded: chain E residue 330 THR Chi-restraints excluded: chain E residue 397 ASN Chi-restraints excluded: chain E residue 412 THR Chi-restraints excluded: chain E residue 439 THR Chi-restraints excluded: chain E residue 465 SER Chi-restraints excluded: chain E residue 502 THR Chi-restraints excluded: chain E residue 504 THR Chi-restraints excluded: chain E residue 511 ILE Chi-restraints excluded: chain E residue 531 VAL Chi-restraints excluded: chain E residue 540 ASP Chi-restraints excluded: chain E residue 544 VAL Chi-restraints excluded: chain E residue 566 LEU Chi-restraints excluded: chain E residue 600 ASP Chi-restraints excluded: chain E residue 613 VAL Chi-restraints excluded: chain E residue 648 LYS Chi-restraints excluded: chain E residue 653 LEU Chi-restraints excluded: chain E residue 656 LEU Chi-restraints excluded: chain E residue 667 LEU Chi-restraints excluded: chain E residue 703 ASP Chi-restraints excluded: chain E residue 823 THR Chi-restraints excluded: chain E residue 827 LEU Chi-restraints excluded: chain E residue 840 ASP Chi-restraints excluded: chain F residue 46 VAL Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain F residue 85 THR Chi-restraints excluded: chain G residue 18 SER Chi-restraints excluded: chain G residue 80 THR Chi-restraints excluded: chain G residue 99 VAL Chi-restraints excluded: chain G residue 111 ARG Chi-restraints excluded: chain G residue 151 VAL Chi-restraints excluded: chain G residue 154 THR Chi-restraints excluded: chain G residue 159 ASP Chi-restraints excluded: chain G residue 167 ILE Chi-restraints excluded: chain G residue 171 ASN Chi-restraints excluded: chain G residue 230 LEU Chi-restraints excluded: chain N residue 105 ILE Chi-restraints excluded: chain N residue 107 LEU Chi-restraints excluded: chain N residue 118 THR Chi-restraints excluded: chain N residue 161 THR Chi-restraints excluded: chain N residue 203 VAL Chi-restraints excluded: chain N residue 204 SER Chi-restraints excluded: chain O residue 17 LEU Chi-restraints excluded: chain O residue 41 LYS Chi-restraints excluded: chain O residue 51 THR Chi-restraints excluded: chain O residue 54 SER Chi-restraints excluded: chain O residue 63 GLU Chi-restraints excluded: chain O residue 68 THR Chi-restraints excluded: chain O residue 70 THR Chi-restraints excluded: chain O residue 83 THR Chi-restraints excluded: chain O residue 117 VAL Chi-restraints excluded: chain O residue 125 SER Chi-restraints excluded: chain O residue 136 VAL Chi-restraints excluded: chain O residue 146 VAL Chi-restraints excluded: chain O residue 166 VAL Chi-restraints excluded: chain O residue 174 VAL Chi-restraints excluded: chain O residue 203 THR Chi-restraints excluded: chain O residue 217 ASN Chi-restraints excluded: chain O residue 232 ASN Chi-restraints excluded: chain P residue 31 LEU Chi-restraints excluded: chain P residue 32 SER Chi-restraints excluded: chain P residue 33 ASP Chi-restraints excluded: chain P residue 61 ASP Chi-restraints excluded: chain P residue 66 ASP Chi-restraints excluded: chain P residue 70 THR Chi-restraints excluded: chain P residue 80 THR Chi-restraints excluded: chain P residue 97 LEU Chi-restraints excluded: chain P residue 117 VAL Chi-restraints excluded: chain P residue 119 VAL Chi-restraints excluded: chain P residue 127 ILE Chi-restraints excluded: chain P residue 132 THR Chi-restraints excluded: chain P residue 158 VAL Chi-restraints excluded: chain P residue 171 THR Chi-restraints excluded: chain P residue 179 THR Chi-restraints excluded: chain P residue 191 THR Chi-restraints excluded: chain P residue 219 VAL Chi-restraints excluded: chain Q residue 66 ASP Chi-restraints excluded: chain Q residue 76 SER Chi-restraints excluded: chain Q residue 116 THR Chi-restraints excluded: chain Q residue 119 VAL Chi-restraints excluded: chain Q residue 126 SER Chi-restraints excluded: chain Q residue 131 VAL Chi-restraints excluded: chain Q residue 132 THR Chi-restraints excluded: chain Q residue 136 VAL Chi-restraints excluded: chain Q residue 150 SER Chi-restraints excluded: chain Q residue 156 SER Chi-restraints excluded: chain Q residue 165 THR Chi-restraints excluded: chain Q residue 166 VAL Chi-restraints excluded: chain Q residue 180 THR Chi-restraints excluded: chain Q residue 181 LEU Chi-restraints excluded: chain Q residue 182 THR Chi-restraints excluded: chain Q residue 191 THR Chi-restraints excluded: chain Q residue 198 VAL Chi-restraints excluded: chain Q residue 199 SER Chi-restraints excluded: chain Q residue 230 SER Chi-restraints excluded: chain R residue 16 THR Chi-restraints excluded: chain R residue 17 LEU Chi-restraints excluded: chain R residue 42 VAL Chi-restraints excluded: chain R residue 51 THR Chi-restraints excluded: chain R residue 64 ASP Chi-restraints excluded: chain R residue 70 THR Chi-restraints excluded: chain R residue 81 SER Chi-restraints excluded: chain R residue 84 LEU Chi-restraints excluded: chain R residue 132 THR Chi-restraints excluded: chain R residue 138 THR Chi-restraints excluded: chain R residue 158 VAL Chi-restraints excluded: chain R residue 180 THR Chi-restraints excluded: chain R residue 199 SER Chi-restraints excluded: chain R residue 213 THR Chi-restraints excluded: chain R residue 243 VAL Chi-restraints excluded: chain S residue 37 SER Chi-restraints excluded: chain S residue 76 SER Chi-restraints excluded: chain S residue 83 THR Chi-restraints excluded: chain S residue 116 THR Chi-restraints excluded: chain S residue 136 VAL Chi-restraints excluded: chain S residue 140 THR Chi-restraints excluded: chain S residue 146 VAL Chi-restraints excluded: chain S residue 148 ARG Chi-restraints excluded: chain S residue 186 GLN Chi-restraints excluded: chain S residue 190 VAL Chi-restraints excluded: chain S residue 191 THR Chi-restraints excluded: chain S residue 198 VAL Chi-restraints excluded: chain S residue 215 THR Chi-restraints excluded: chain S residue 230 SER Chi-restraints excluded: chain S residue 232 ASN Chi-restraints excluded: chain T residue 3 VAL Chi-restraints excluded: chain T residue 33 ASP Chi-restraints excluded: chain T residue 35 ASP Chi-restraints excluded: chain T residue 37 SER Chi-restraints excluded: chain T residue 46 THR Chi-restraints excluded: chain T residue 70 THR Chi-restraints excluded: chain T residue 117 VAL Chi-restraints excluded: chain T residue 119 VAL Chi-restraints excluded: chain T residue 126 SER Chi-restraints excluded: chain T residue 140 THR Chi-restraints excluded: chain T residue 180 THR Chi-restraints excluded: chain T residue 207 VAL Chi-restraints excluded: chain T residue 212 MET Chi-restraints excluded: chain T residue 215 THR Chi-restraints excluded: chain U residue 16 THR Chi-restraints excluded: chain U residue 46 THR Chi-restraints excluded: chain U residue 61 ASP Chi-restraints excluded: chain U residue 83 THR Chi-restraints excluded: chain U residue 116 THR Chi-restraints excluded: chain U residue 132 THR Chi-restraints excluded: chain U residue 141 VAL Chi-restraints excluded: chain U residue 146 VAL Chi-restraints excluded: chain U residue 159 THR Chi-restraints excluded: chain U residue 165 THR Chi-restraints excluded: chain U residue 180 THR Chi-restraints excluded: chain U residue 229 VAL Chi-restraints excluded: chain W residue 16 THR Chi-restraints excluded: chain W residue 51 THR Chi-restraints excluded: chain W residue 66 ASP Chi-restraints excluded: chain W residue 83 THR Chi-restraints excluded: chain W residue 110 ILE Chi-restraints excluded: chain W residue 117 VAL Chi-restraints excluded: chain W residue 126 SER Chi-restraints excluded: chain W residue 132 THR Chi-restraints excluded: chain W residue 145 ASN Chi-restraints excluded: chain W residue 180 THR Chi-restraints excluded: chain X residue 43 THR Chi-restraints excluded: chain X residue 46 VAL Chi-restraints excluded: chain X residue 47 THR Chi-restraints excluded: chain X residue 50 VAL Chi-restraints excluded: chain X residue 53 GLU Chi-restraints excluded: chain X residue 64 GLU Chi-restraints excluded: chain X residue 91 SER Chi-restraints excluded: chain X residue 108 VAL Chi-restraints excluded: chain Y residue 26 VAL Chi-restraints excluded: chain Y residue 30 ILE Chi-restraints excluded: chain Y residue 39 VAL Chi-restraints excluded: chain Y residue 49 SER Chi-restraints excluded: chain Y residue 50 THR Chi-restraints excluded: chain Y residue 88 THR Chi-restraints excluded: chain Y residue 97 ASP Chi-restraints excluded: chain Y residue 109 ILE Chi-restraints excluded: chain Y residue 115 THR Chi-restraints excluded: chain Y residue 122 VAL Chi-restraints excluded: chain Y residue 138 LEU Chi-restraints excluded: chain Y residue 149 THR Chi-restraints excluded: chain Y residue 153 ILE Chi-restraints excluded: chain Y residue 168 VAL Chi-restraints excluded: chain Y residue 177 PHE Chi-restraints excluded: chain Y residue 197 THR Chi-restraints excluded: chain Y residue 215 THR Chi-restraints excluded: chain Y residue 217 LEU Chi-restraints excluded: chain Y residue 223 ASP Chi-restraints excluded: chain Y residue 233 SER Chi-restraints excluded: chain Y residue 241 ARG Chi-restraints excluded: chain Y residue 257 SER Chi-restraints excluded: chain Y residue 281 THR Chi-restraints excluded: chain Y residue 324 THR Chi-restraints excluded: chain Y residue 325 CYS Chi-restraints excluded: chain Y residue 330 THR Chi-restraints excluded: chain Y residue 374 SER Chi-restraints excluded: chain Y residue 381 ASP Chi-restraints excluded: chain Y residue 397 ASN Chi-restraints excluded: chain Y residue 412 THR Chi-restraints excluded: chain Y residue 439 THR Chi-restraints excluded: chain Y residue 461 THR Chi-restraints excluded: chain Y residue 469 GLU Chi-restraints excluded: chain Y residue 504 THR Chi-restraints excluded: chain Y residue 511 ILE Chi-restraints excluded: chain Y residue 521 ILE Chi-restraints excluded: chain Y residue 531 VAL Chi-restraints excluded: chain Y residue 535 VAL Chi-restraints excluded: chain Y residue 536 GLN Chi-restraints excluded: chain Y residue 539 THR Chi-restraints excluded: chain Y residue 544 VAL Chi-restraints excluded: chain Y residue 565 THR Chi-restraints excluded: chain Y residue 574 VAL Chi-restraints excluded: chain Y residue 596 GLU Chi-restraints excluded: chain Y residue 600 ASP Chi-restraints excluded: chain Y residue 613 VAL Chi-restraints excluded: chain Y residue 667 LEU Chi-restraints excluded: chain Y residue 703 ASP Chi-restraints excluded: chain Y residue 823 THR Chi-restraints excluded: chain Y residue 827 LEU Chi-restraints excluded: chain Y residue 838 THR Chi-restraints excluded: chain Y residue 840 ASP Chi-restraints excluded: chain Z residue 46 VAL Chi-restraints excluded: chain Z residue 58 LEU Chi-restraints excluded: chain Z residue 74 THR Chi-restraints excluded: chain Z residue 98 VAL Chi-restraints excluded: chain Z residue 106 GLN Chi-restraints excluded: chain d residue 120 ASN Chi-restraints excluded: chain d residue 159 ASP Chi-restraints excluded: chain d residue 167 ILE Chi-restraints excluded: chain d residue 171 ASN Chi-restraints excluded: chain f residue 118 THR Chi-restraints excluded: chain f residue 161 THR Chi-restraints excluded: chain f residue 188 VAL Chi-restraints excluded: chain f residue 191 VAL Chi-restraints excluded: chain f residue 203 VAL Chi-restraints excluded: chain f residue 204 SER Chi-restraints excluded: chain f residue 217 GLN Chi-restraints excluded: chain g residue 51 THR Chi-restraints excluded: chain g residue 63 GLU Chi-restraints excluded: chain g residue 68 THR Chi-restraints excluded: chain g residue 70 THR Chi-restraints excluded: chain g residue 81 SER Chi-restraints excluded: chain g residue 83 THR Chi-restraints excluded: chain g residue 117 VAL Chi-restraints excluded: chain g residue 125 SER Chi-restraints excluded: chain g residue 136 VAL Chi-restraints excluded: chain g residue 146 VAL Chi-restraints excluded: chain g residue 166 VAL Chi-restraints excluded: chain g residue 174 VAL Chi-restraints excluded: chain g residue 191 THR Chi-restraints excluded: chain g residue 203 THR Chi-restraints excluded: chain h residue 31 LEU Chi-restraints excluded: chain h residue 45 LEU Chi-restraints excluded: chain h residue 61 ASP Chi-restraints excluded: chain h residue 70 THR Chi-restraints excluded: chain h residue 80 THR Chi-restraints excluded: chain h residue 117 VAL Chi-restraints excluded: chain h residue 119 VAL Chi-restraints excluded: chain h residue 132 THR Chi-restraints excluded: chain h residue 158 VAL Chi-restraints excluded: chain h residue 171 THR Chi-restraints excluded: chain h residue 179 THR Chi-restraints excluded: chain h residue 182 THR Chi-restraints excluded: chain h residue 191 THR Chi-restraints excluded: chain i residue 17 LEU Chi-restraints excluded: chain i residue 54 SER Chi-restraints excluded: chain i residue 66 ASP Chi-restraints excluded: chain i residue 76 SER Chi-restraints excluded: chain i residue 116 THR Chi-restraints excluded: chain i residue 131 VAL Chi-restraints excluded: chain i residue 132 THR Chi-restraints excluded: chain i residue 140 THR Chi-restraints excluded: chain i residue 150 SER Chi-restraints excluded: chain i residue 156 SER Chi-restraints excluded: chain i residue 181 LEU Chi-restraints excluded: chain i residue 182 THR Chi-restraints excluded: chain i residue 183 VAL Chi-restraints excluded: chain i residue 199 SER Chi-restraints excluded: chain i residue 230 SER Chi-restraints excluded: chain i residue 232 ASN Chi-restraints excluded: chain j residue 23 SER Chi-restraints excluded: chain j residue 64 ASP Chi-restraints excluded: chain j residue 66 ASP Chi-restraints excluded: chain j residue 81 SER Chi-restraints excluded: chain j residue 84 LEU Chi-restraints excluded: chain j residue 116 THR Chi-restraints excluded: chain j residue 132 THR Chi-restraints excluded: chain j residue 146 VAL Chi-restraints excluded: chain j residue 150 SER Chi-restraints excluded: chain j residue 158 VAL Chi-restraints excluded: chain j residue 180 THR Chi-restraints excluded: chain j residue 182 THR Chi-restraints excluded: chain j residue 230 SER Chi-restraints excluded: chain j residue 243 VAL Chi-restraints excluded: chain k residue 66 ASP Chi-restraints excluded: chain k residue 76 SER Chi-restraints excluded: chain k residue 83 THR Chi-restraints excluded: chain k residue 116 THR Chi-restraints excluded: chain k residue 125 SER Chi-restraints excluded: chain k residue 136 VAL Chi-restraints excluded: chain k residue 146 VAL Chi-restraints excluded: chain k residue 186 GLN Chi-restraints excluded: chain k residue 190 VAL Chi-restraints excluded: chain k residue 191 THR Chi-restraints excluded: chain k residue 198 VAL Chi-restraints excluded: chain k residue 207 VAL Chi-restraints excluded: chain k residue 215 THR Chi-restraints excluded: chain k residue 224 VAL Chi-restraints excluded: chain l residue 3 VAL Chi-restraints excluded: chain l residue 33 ASP Chi-restraints excluded: chain l residue 35 ASP Chi-restraints excluded: chain l residue 37 SER Chi-restraints excluded: chain l residue 54 SER Chi-restraints excluded: chain l residue 66 ASP Chi-restraints excluded: chain l residue 70 THR Chi-restraints excluded: chain l residue 117 VAL Chi-restraints excluded: chain l residue 119 VAL Chi-restraints excluded: chain l residue 138 THR Chi-restraints excluded: chain l residue 140 THR Chi-restraints excluded: chain l residue 164 MET Chi-restraints excluded: chain l residue 174 VAL Chi-restraints excluded: chain l residue 180 THR Chi-restraints excluded: chain l residue 190 VAL Chi-restraints excluded: chain l residue 198 VAL Chi-restraints excluded: chain l residue 207 VAL Chi-restraints excluded: chain l residue 215 THR Chi-restraints excluded: chain n residue 16 THR Chi-restraints excluded: chain n residue 66 ASP Chi-restraints excluded: chain n residue 83 THR Chi-restraints excluded: chain n residue 101 ASN Chi-restraints excluded: chain n residue 116 THR Chi-restraints excluded: chain n residue 132 THR Chi-restraints excluded: chain n residue 141 VAL Chi-restraints excluded: chain n residue 146 VAL Chi-restraints excluded: chain n residue 159 THR Chi-restraints excluded: chain n residue 179 THR Chi-restraints excluded: chain o residue 7 THR Chi-restraints excluded: chain o residue 16 THR Chi-restraints excluded: chain o residue 51 THR Chi-restraints excluded: chain o residue 66 ASP Chi-restraints excluded: chain o residue 83 THR Chi-restraints excluded: chain o residue 84 LEU Chi-restraints excluded: chain o residue 117 VAL Chi-restraints excluded: chain o residue 126 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1008 random chunks: chunk 851 optimal weight: 0.6980 chunk 764 optimal weight: 10.0000 chunk 423 optimal weight: 10.0000 chunk 260 optimal weight: 30.0000 chunk 515 optimal weight: 1.9990 chunk 408 optimal weight: 10.0000 chunk 790 optimal weight: 5.9990 chunk 305 optimal weight: 20.0000 chunk 480 optimal weight: 3.9990 chunk 588 optimal weight: 3.9990 chunk 915 optimal weight: 4.9990 overall best weight: 3.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 75 GLN ** J 178 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 408 ASN L 228 ASN I 181 ASN v 225 ASN A 91 GLN C 94 GLN ** c 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 91 GLN E 75 GLN E 237 HIS E 408 ASN E 826 HIS G 232 GLN N 169 ASN Q 91 GLN S 29 ASN T 225 ASN ** W 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 38 ASN Y 75 GLN ** Y 178 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 235 ASN d 228 ASN f 169 ASN j 74 GLN ** o 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 91 GLN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8319 moved from start: 0.0752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.080 78954 Z= 0.395 Angle : 0.670 20.501 107580 Z= 0.348 Chirality : 0.048 0.262 12384 Planarity : 0.006 0.182 13893 Dihedral : 9.229 74.966 11683 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.64 % Allowed : 7.78 % Favored : 91.58 % Rotamer: Outliers : 8.32 % Allowed : 27.91 % Favored : 63.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.63 % Cis-general : 0.00 % Twisted Proline : 1.26 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.73 (0.08), residues: 10164 helix: 0.18 (0.17), residues: 930 sheet: -0.66 (0.08), residues: 4125 loop : -1.81 (0.08), residues: 5109 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP D 89 HIS 0.008 0.001 HIS m 65 PHE 0.023 0.002 PHE j 120 TYR 0.018 0.002 TYR E 426 ARG 0.011 0.001 ARG n 121 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 20328 Ramachandran restraints generated. 10164 Oldfield, 0 Emsley, 10164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 20328 Ramachandran restraints generated. 10164 Oldfield, 0 Emsley, 10164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1427 residues out of total 8352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 695 poor density : 732 time to evaluate : 6.468 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 7 LYS cc_start: 0.8373 (OUTLIER) cc_final: 0.8153 (mtmm) REVERT: M 13 ASP cc_start: 0.8691 (OUTLIER) cc_final: 0.8167 (t70) REVERT: J 241 ARG cc_start: 0.9012 (OUTLIER) cc_final: 0.8654 (mtp180) REVERT: J 675 GLU cc_start: 0.8407 (OUTLIER) cc_final: 0.8196 (mt-10) REVERT: J 757 ARG cc_start: 0.8195 (mtm110) cc_final: 0.7957 (mtm110) REVERT: J 758 GLN cc_start: 0.7856 (mm-40) cc_final: 0.7561 (tt0) REVERT: J 831 LEU cc_start: 0.8301 (OUTLIER) cc_final: 0.8092 (tm) REVERT: m 103 GLU cc_start: 0.7810 (pp20) cc_final: 0.7333 (pp20) REVERT: H 835 ARG cc_start: 0.8007 (OUTLIER) cc_final: 0.7487 (mpp80) REVERT: I 142 LEU cc_start: 0.8384 (OUTLIER) cc_final: 0.8175 (mt) REVERT: V 90 GLU cc_start: 0.8333 (OUTLIER) cc_final: 0.8096 (pp20) REVERT: B 45 LEU cc_start: 0.9237 (OUTLIER) cc_final: 0.8981 (tp) REVERT: b 87 MET cc_start: 0.8417 (OUTLIER) cc_final: 0.7722 (mpp) REVERT: A 17 LEU cc_start: 0.9131 (OUTLIER) cc_final: 0.8879 (tt) REVERT: A 90 GLU cc_start: 0.8568 (tm-30) cc_final: 0.8242 (tm-30) REVERT: a 64 ASP cc_start: 0.7534 (OUTLIER) cc_final: 0.7314 (p0) REVERT: C 61 ASP cc_start: 0.8263 (OUTLIER) cc_final: 0.7753 (p0) REVERT: C 94 GLN cc_start: 0.8212 (OUTLIER) cc_final: 0.7789 (mp-120) REVERT: c 87 MET cc_start: 0.8560 (mmt) cc_final: 0.7625 (mmt) REVERT: D 41 LEU cc_start: 0.7375 (OUTLIER) cc_final: 0.7029 (mm) REVERT: D 103 GLU cc_start: 0.8267 (OUTLIER) cc_final: 0.8033 (tp30) REVERT: E 380 ASP cc_start: 0.7798 (OUTLIER) cc_final: 0.7546 (m-30) REVERT: E 757 ARG cc_start: 0.8192 (mtm110) cc_final: 0.7950 (mtm110) REVERT: E 758 GLN cc_start: 0.7949 (mm-40) cc_final: 0.7679 (tt0) REVERT: G 111 ARG cc_start: 0.8671 (OUTLIER) cc_final: 0.8165 (ttm-80) REVERT: U 21 LYS cc_start: 0.8976 (OUTLIER) cc_final: 0.8642 (pmtt) REVERT: U 164 MET cc_start: 0.3979 (pmm) cc_final: 0.2249 (tpp) REVERT: W 11 LYS cc_start: 0.8161 (mmmm) cc_final: 0.7804 (mmmm) REVERT: W 139 ARG cc_start: 0.8840 (OUTLIER) cc_final: 0.7434 (ttm170) REVERT: X 7 LYS cc_start: 0.8423 (OUTLIER) cc_final: 0.8120 (mtmm) REVERT: X 13 ASP cc_start: 0.8574 (OUTLIER) cc_final: 0.8300 (t70) REVERT: X 103 GLU cc_start: 0.8401 (OUTLIER) cc_final: 0.8149 (tt0) REVERT: Y 147 TRP cc_start: 0.7768 (OUTLIER) cc_final: 0.7108 (m-90) REVERT: Z 1 MET cc_start: 0.5964 (OUTLIER) cc_final: 0.5732 (ttm) REVERT: g 32 SER cc_start: 0.9023 (OUTLIER) cc_final: 0.8715 (m) REVERT: g 90 GLU cc_start: 0.8484 (OUTLIER) cc_final: 0.8187 (pp20) REVERT: h 84 LEU cc_start: 0.8863 (OUTLIER) cc_final: 0.8596 (pt) REVERT: h 102 GLU cc_start: 0.8350 (OUTLIER) cc_final: 0.8010 (mp0) REVERT: n 45 LEU cc_start: 0.8870 (OUTLIER) cc_final: 0.8635 (tp) REVERT: n 61 ASP cc_start: 0.8217 (OUTLIER) cc_final: 0.7598 (p0) REVERT: n 91 GLN cc_start: 0.8106 (pp30) cc_final: 0.7891 (pm20) REVERT: n 164 MET cc_start: 0.3958 (pmm) cc_final: 0.2182 (tpp) REVERT: o 11 LYS cc_start: 0.8417 (mmmm) cc_final: 0.8105 (mmmm) outliers start: 695 outliers final: 398 residues processed: 1330 average time/residue: 1.4136 time to fit residues: 2572.0180 Evaluate side-chains 1127 residues out of total 8352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 429 poor density : 698 time to evaluate : 6.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 7 LYS Chi-restraints excluded: chain M residue 13 ASP Chi-restraints excluded: chain M residue 41 LEU Chi-restraints excluded: chain M residue 43 THR Chi-restraints excluded: chain M residue 46 VAL Chi-restraints excluded: chain M residue 47 THR Chi-restraints excluded: chain M residue 50 VAL Chi-restraints excluded: chain M residue 84 VAL Chi-restraints excluded: chain M residue 108 VAL Chi-restraints excluded: chain M residue 109 ASN Chi-restraints excluded: chain J residue 26 VAL Chi-restraints excluded: chain J residue 30 ILE Chi-restraints excluded: chain J residue 47 LEU Chi-restraints excluded: chain J residue 65 THR Chi-restraints excluded: chain J residue 88 THR Chi-restraints excluded: chain J residue 122 VAL Chi-restraints excluded: chain J residue 138 LEU Chi-restraints excluded: chain J residue 141 ILE Chi-restraints excluded: chain J residue 149 THR Chi-restraints excluded: chain J residue 153 ILE Chi-restraints excluded: chain J residue 168 VAL Chi-restraints excluded: chain J residue 177 PHE Chi-restraints excluded: chain J residue 215 THR Chi-restraints excluded: chain J residue 217 LEU Chi-restraints excluded: chain J residue 233 SER Chi-restraints excluded: chain J residue 241 ARG Chi-restraints excluded: chain J residue 325 CYS Chi-restraints excluded: chain J residue 373 ARG Chi-restraints excluded: chain J residue 374 SER Chi-restraints excluded: chain J residue 381 ASP Chi-restraints excluded: chain J residue 461 THR Chi-restraints excluded: chain J residue 504 THR Chi-restraints excluded: chain J residue 511 ILE Chi-restraints excluded: chain J residue 535 VAL Chi-restraints excluded: chain J residue 539 THR Chi-restraints excluded: chain J residue 542 VAL Chi-restraints excluded: chain J residue 544 VAL Chi-restraints excluded: chain J residue 596 GLU Chi-restraints excluded: chain J residue 598 ILE Chi-restraints excluded: chain J residue 613 VAL Chi-restraints excluded: chain J residue 638 LEU Chi-restraints excluded: chain J residue 667 LEU Chi-restraints excluded: chain J residue 675 GLU Chi-restraints excluded: chain J residue 695 VAL Chi-restraints excluded: chain J residue 823 THR Chi-restraints excluded: chain J residue 831 LEU Chi-restraints excluded: chain m residue 7 LYS Chi-restraints excluded: chain m residue 46 VAL Chi-restraints excluded: chain m residue 74 THR Chi-restraints excluded: chain L residue 18 SER Chi-restraints excluded: chain L residue 78 THR Chi-restraints excluded: chain L residue 99 VAL Chi-restraints excluded: chain L residue 159 ASP Chi-restraints excluded: chain L residue 167 ILE Chi-restraints excluded: chain L residue 171 ASN Chi-restraints excluded: chain L residue 218 VAL Chi-restraints excluded: chain H residue 835 ARG Chi-restraints excluded: chain H residue 844 ASP Chi-restraints excluded: chain H residue 849 SER Chi-restraints excluded: chain I residue 118 THR Chi-restraints excluded: chain I residue 142 LEU Chi-restraints excluded: chain I residue 161 THR Chi-restraints excluded: chain I residue 166 THR Chi-restraints excluded: chain I residue 167 THR Chi-restraints excluded: chain I residue 207 ILE Chi-restraints excluded: chain V residue 17 LEU Chi-restraints excluded: chain V residue 51 THR Chi-restraints excluded: chain V residue 70 THR Chi-restraints excluded: chain V residue 83 THR Chi-restraints excluded: chain V residue 90 GLU Chi-restraints excluded: chain V residue 125 SER Chi-restraints excluded: chain V residue 136 VAL Chi-restraints excluded: chain V residue 146 VAL Chi-restraints excluded: chain V residue 166 VAL Chi-restraints excluded: chain V residue 174 VAL Chi-restraints excluded: chain v residue 16 THR Chi-restraints excluded: chain v residue 70 THR Chi-restraints excluded: chain v residue 84 LEU Chi-restraints excluded: chain v residue 119 VAL Chi-restraints excluded: chain v residue 127 ILE Chi-restraints excluded: chain v residue 132 THR Chi-restraints excluded: chain v residue 158 VAL Chi-restraints excluded: chain v residue 179 THR Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 182 THR Chi-restraints excluded: chain b residue 3 VAL Chi-restraints excluded: chain b residue 31 LEU Chi-restraints excluded: chain b residue 51 THR Chi-restraints excluded: chain b residue 54 SER Chi-restraints excluded: chain b residue 70 THR Chi-restraints excluded: chain b residue 81 SER Chi-restraints excluded: chain b residue 84 LEU Chi-restraints excluded: chain b residue 87 MET Chi-restraints excluded: chain b residue 110 ILE Chi-restraints excluded: chain b residue 138 THR Chi-restraints excluded: chain b residue 146 VAL Chi-restraints excluded: chain b residue 180 THR Chi-restraints excluded: chain A residue 17 LEU Chi-restraints excluded: chain A residue 83 THR Chi-restraints excluded: chain A residue 125 SER Chi-restraints excluded: chain A residue 127 ILE Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 140 THR Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 148 ARG Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 186 GLN Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 191 THR Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain a residue 37 SER Chi-restraints excluded: chain a residue 64 ASP Chi-restraints excluded: chain a residue 70 THR Chi-restraints excluded: chain a residue 117 VAL Chi-restraints excluded: chain a residue 119 VAL Chi-restraints excluded: chain a residue 126 SER Chi-restraints excluded: chain a residue 132 THR Chi-restraints excluded: chain a residue 138 THR Chi-restraints excluded: chain a residue 185 PHE Chi-restraints excluded: chain a residue 207 VAL Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 21 LYS Chi-restraints excluded: chain C residue 61 ASP Chi-restraints excluded: chain C residue 83 THR Chi-restraints excluded: chain C residue 94 GLN Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain c residue 45 LEU Chi-restraints excluded: chain c residue 83 THR Chi-restraints excluded: chain c residue 117 VAL Chi-restraints excluded: chain c residue 240 GLU Chi-restraints excluded: chain D residue 41 LEU Chi-restraints excluded: chain D residue 43 THR Chi-restraints excluded: chain D residue 46 VAL Chi-restraints excluded: chain D residue 47 THR Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 103 GLU Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain E residue 21 THR Chi-restraints excluded: chain E residue 26 VAL Chi-restraints excluded: chain E residue 30 ILE Chi-restraints excluded: chain E residue 65 THR Chi-restraints excluded: chain E residue 97 ASP Chi-restraints excluded: chain E residue 109 ILE Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 122 VAL Chi-restraints excluded: chain E residue 138 LEU Chi-restraints excluded: chain E residue 139 VAL Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain E residue 153 ILE Chi-restraints excluded: chain E residue 168 VAL Chi-restraints excluded: chain E residue 177 PHE Chi-restraints excluded: chain E residue 215 THR Chi-restraints excluded: chain E residue 217 LEU Chi-restraints excluded: chain E residue 233 SER Chi-restraints excluded: chain E residue 324 THR Chi-restraints excluded: chain E residue 325 CYS Chi-restraints excluded: chain E residue 330 THR Chi-restraints excluded: chain E residue 331 THR Chi-restraints excluded: chain E residue 374 SER Chi-restraints excluded: chain E residue 380 ASP Chi-restraints excluded: chain E residue 431 THR Chi-restraints excluded: chain E residue 465 SER Chi-restraints excluded: chain E residue 504 THR Chi-restraints excluded: chain E residue 511 ILE Chi-restraints excluded: chain E residue 531 VAL Chi-restraints excluded: chain E residue 542 VAL Chi-restraints excluded: chain E residue 544 VAL Chi-restraints excluded: chain E residue 570 LEU Chi-restraints excluded: chain E residue 596 GLU Chi-restraints excluded: chain E residue 598 ILE Chi-restraints excluded: chain E residue 613 VAL Chi-restraints excluded: chain E residue 648 LYS Chi-restraints excluded: chain E residue 667 LEU Chi-restraints excluded: chain E residue 675 GLU Chi-restraints excluded: chain E residue 703 ASP Chi-restraints excluded: chain E residue 823 THR Chi-restraints excluded: chain E residue 826 HIS Chi-restraints excluded: chain E residue 827 LEU Chi-restraints excluded: chain E residue 840 ASP Chi-restraints excluded: chain F residue 46 VAL Chi-restraints excluded: chain F residue 58 LEU Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain F residue 85 THR Chi-restraints excluded: chain G residue 21 VAL Chi-restraints excluded: chain G residue 31 VAL Chi-restraints excluded: chain G residue 99 VAL Chi-restraints excluded: chain G residue 111 ARG Chi-restraints excluded: chain G residue 159 ASP Chi-restraints excluded: chain G residue 167 ILE Chi-restraints excluded: chain G residue 230 LEU Chi-restraints excluded: chain K residue 842 MET Chi-restraints excluded: chain N residue 118 THR Chi-restraints excluded: chain N residue 142 LEU Chi-restraints excluded: chain N residue 161 THR Chi-restraints excluded: chain N residue 166 THR Chi-restraints excluded: chain N residue 167 THR Chi-restraints excluded: chain N residue 171 LYS Chi-restraints excluded: chain N residue 203 VAL Chi-restraints excluded: chain N residue 204 SER Chi-restraints excluded: chain O residue 17 LEU Chi-restraints excluded: chain O residue 51 THR Chi-restraints excluded: chain O residue 54 SER Chi-restraints excluded: chain O residue 70 THR Chi-restraints excluded: chain O residue 83 THR Chi-restraints excluded: chain O residue 90 GLU Chi-restraints excluded: chain O residue 125 SER Chi-restraints excluded: chain O residue 136 VAL Chi-restraints excluded: chain O residue 146 VAL Chi-restraints excluded: chain O residue 166 VAL Chi-restraints excluded: chain O residue 174 VAL Chi-restraints excluded: chain P residue 70 THR Chi-restraints excluded: chain P residue 97 LEU Chi-restraints excluded: chain P residue 117 VAL Chi-restraints excluded: chain P residue 119 VAL Chi-restraints excluded: chain P residue 132 THR Chi-restraints excluded: chain P residue 158 VAL Chi-restraints excluded: chain P residue 179 THR Chi-restraints excluded: chain Q residue 45 LEU Chi-restraints excluded: chain Q residue 119 VAL Chi-restraints excluded: chain Q residue 126 SER Chi-restraints excluded: chain Q residue 131 VAL Chi-restraints excluded: chain Q residue 132 THR Chi-restraints excluded: chain Q residue 136 VAL Chi-restraints excluded: chain Q residue 165 THR Chi-restraints excluded: chain Q residue 180 THR Chi-restraints excluded: chain Q residue 181 LEU Chi-restraints excluded: chain Q residue 182 THR Chi-restraints excluded: chain Q residue 198 VAL Chi-restraints excluded: chain R residue 42 VAL Chi-restraints excluded: chain R residue 51 THR Chi-restraints excluded: chain R residue 64 ASP Chi-restraints excluded: chain R residue 70 THR Chi-restraints excluded: chain R residue 81 SER Chi-restraints excluded: chain R residue 84 LEU Chi-restraints excluded: chain R residue 116 THR Chi-restraints excluded: chain R residue 132 THR Chi-restraints excluded: chain R residue 138 THR Chi-restraints excluded: chain R residue 158 VAL Chi-restraints excluded: chain R residue 180 THR Chi-restraints excluded: chain S residue 7 THR Chi-restraints excluded: chain S residue 34 VAL Chi-restraints excluded: chain S residue 83 THR Chi-restraints excluded: chain S residue 125 SER Chi-restraints excluded: chain S residue 127 ILE Chi-restraints excluded: chain S residue 132 THR Chi-restraints excluded: chain S residue 136 VAL Chi-restraints excluded: chain S residue 140 THR Chi-restraints excluded: chain S residue 146 VAL Chi-restraints excluded: chain S residue 186 GLN Chi-restraints excluded: chain S residue 190 VAL Chi-restraints excluded: chain S residue 191 THR Chi-restraints excluded: chain S residue 198 VAL Chi-restraints excluded: chain S residue 215 THR Chi-restraints excluded: chain S residue 224 VAL Chi-restraints excluded: chain T residue 17 LEU Chi-restraints excluded: chain T residue 37 SER Chi-restraints excluded: chain T residue 70 THR Chi-restraints excluded: chain T residue 117 VAL Chi-restraints excluded: chain T residue 119 VAL Chi-restraints excluded: chain T residue 127 ILE Chi-restraints excluded: chain T residue 138 THR Chi-restraints excluded: chain T residue 140 THR Chi-restraints excluded: chain T residue 207 VAL Chi-restraints excluded: chain U residue 16 THR Chi-restraints excluded: chain U residue 17 LEU Chi-restraints excluded: chain U residue 21 LYS Chi-restraints excluded: chain U residue 61 ASP Chi-restraints excluded: chain U residue 132 THR Chi-restraints excluded: chain U residue 141 VAL Chi-restraints excluded: chain U residue 146 VAL Chi-restraints excluded: chain U residue 165 THR Chi-restraints excluded: chain U residue 179 THR Chi-restraints excluded: chain W residue 45 LEU Chi-restraints excluded: chain W residue 83 THR Chi-restraints excluded: chain W residue 117 VAL Chi-restraints excluded: chain W residue 139 ARG Chi-restraints excluded: chain X residue 7 LYS Chi-restraints excluded: chain X residue 13 ASP Chi-restraints excluded: chain X residue 20 VAL Chi-restraints excluded: chain X residue 43 THR Chi-restraints excluded: chain X residue 46 VAL Chi-restraints excluded: chain X residue 47 THR Chi-restraints excluded: chain X residue 50 VAL Chi-restraints excluded: chain X residue 64 GLU Chi-restraints excluded: chain X residue 90 SER Chi-restraints excluded: chain X residue 103 GLU Chi-restraints excluded: chain X residue 108 VAL Chi-restraints excluded: chain Y residue 5 SER Chi-restraints excluded: chain Y residue 21 THR Chi-restraints excluded: chain Y residue 26 VAL Chi-restraints excluded: chain Y residue 30 ILE Chi-restraints excluded: chain Y residue 31 SER Chi-restraints excluded: chain Y residue 50 THR Chi-restraints excluded: chain Y residue 65 THR Chi-restraints excluded: chain Y residue 88 THR Chi-restraints excluded: chain Y residue 115 THR Chi-restraints excluded: chain Y residue 122 VAL Chi-restraints excluded: chain Y residue 138 LEU Chi-restraints excluded: chain Y residue 147 TRP Chi-restraints excluded: chain Y residue 149 THR Chi-restraints excluded: chain Y residue 153 ILE Chi-restraints excluded: chain Y residue 167 VAL Chi-restraints excluded: chain Y residue 168 VAL Chi-restraints excluded: chain Y residue 177 PHE Chi-restraints excluded: chain Y residue 215 THR Chi-restraints excluded: chain Y residue 217 LEU Chi-restraints excluded: chain Y residue 233 SER Chi-restraints excluded: chain Y residue 324 THR Chi-restraints excluded: chain Y residue 325 CYS Chi-restraints excluded: chain Y residue 330 THR Chi-restraints excluded: chain Y residue 381 ASP Chi-restraints excluded: chain Y residue 397 ASN Chi-restraints excluded: chain Y residue 433 MET Chi-restraints excluded: chain Y residue 461 THR Chi-restraints excluded: chain Y residue 504 THR Chi-restraints excluded: chain Y residue 511 ILE Chi-restraints excluded: chain Y residue 521 ILE Chi-restraints excluded: chain Y residue 531 VAL Chi-restraints excluded: chain Y residue 535 VAL Chi-restraints excluded: chain Y residue 536 GLN Chi-restraints excluded: chain Y residue 539 THR Chi-restraints excluded: chain Y residue 542 VAL Chi-restraints excluded: chain Y residue 544 VAL Chi-restraints excluded: chain Y residue 574 VAL Chi-restraints excluded: chain Y residue 613 VAL Chi-restraints excluded: chain Y residue 638 LEU Chi-restraints excluded: chain Y residue 656 LEU Chi-restraints excluded: chain Y residue 703 ASP Chi-restraints excluded: chain Y residue 778 ASN Chi-restraints excluded: chain Y residue 823 THR Chi-restraints excluded: chain Y residue 827 LEU Chi-restraints excluded: chain Y residue 838 THR Chi-restraints excluded: chain Y residue 840 ASP Chi-restraints excluded: chain Z residue 1 MET Chi-restraints excluded: chain Z residue 46 VAL Chi-restraints excluded: chain Z residue 58 LEU Chi-restraints excluded: chain Z residue 74 THR Chi-restraints excluded: chain Z residue 98 VAL Chi-restraints excluded: chain d residue 31 VAL Chi-restraints excluded: chain d residue 143 LEU Chi-restraints excluded: chain d residue 151 VAL Chi-restraints excluded: chain d residue 159 ASP Chi-restraints excluded: chain e residue 847 LEU Chi-restraints excluded: chain f residue 107 LEU Chi-restraints excluded: chain f residue 118 THR Chi-restraints excluded: chain f residue 161 THR Chi-restraints excluded: chain f residue 166 THR Chi-restraints excluded: chain f residue 167 THR Chi-restraints excluded: chain f residue 182 MET Chi-restraints excluded: chain f residue 188 VAL Chi-restraints excluded: chain f residue 203 VAL Chi-restraints excluded: chain f residue 204 SER Chi-restraints excluded: chain f residue 207 ILE Chi-restraints excluded: chain g residue 32 SER Chi-restraints excluded: chain g residue 51 THR Chi-restraints excluded: chain g residue 63 GLU Chi-restraints excluded: chain g residue 70 THR Chi-restraints excluded: chain g residue 81 SER Chi-restraints excluded: chain g residue 83 THR Chi-restraints excluded: chain g residue 90 GLU Chi-restraints excluded: chain g residue 125 SER Chi-restraints excluded: chain g residue 136 VAL Chi-restraints excluded: chain g residue 146 VAL Chi-restraints excluded: chain g residue 166 VAL Chi-restraints excluded: chain g residue 174 VAL Chi-restraints excluded: chain g residue 191 THR Chi-restraints excluded: chain h residue 70 THR Chi-restraints excluded: chain h residue 84 LEU Chi-restraints excluded: chain h residue 102 GLU Chi-restraints excluded: chain h residue 117 VAL Chi-restraints excluded: chain h residue 119 VAL Chi-restraints excluded: chain h residue 127 ILE Chi-restraints excluded: chain h residue 132 THR Chi-restraints excluded: chain h residue 158 VAL Chi-restraints excluded: chain h residue 179 THR Chi-restraints excluded: chain i residue 17 LEU Chi-restraints excluded: chain i residue 45 LEU Chi-restraints excluded: chain i residue 131 VAL Chi-restraints excluded: chain i residue 140 THR Chi-restraints excluded: chain i residue 181 LEU Chi-restraints excluded: chain i residue 182 THR Chi-restraints excluded: chain i residue 183 VAL Chi-restraints excluded: chain i residue 198 VAL Chi-restraints excluded: chain j residue 64 ASP Chi-restraints excluded: chain j residue 70 THR Chi-restraints excluded: chain j residue 81 SER Chi-restraints excluded: chain j residue 84 LEU Chi-restraints excluded: chain j residue 116 THR Chi-restraints excluded: chain j residue 125 SER Chi-restraints excluded: chain j residue 132 THR Chi-restraints excluded: chain j residue 135 GLU Chi-restraints excluded: chain j residue 138 THR Chi-restraints excluded: chain j residue 146 VAL Chi-restraints excluded: chain j residue 158 VAL Chi-restraints excluded: chain j residue 180 THR Chi-restraints excluded: chain j residue 199 SER Chi-restraints excluded: chain k residue 83 THR Chi-restraints excluded: chain k residue 127 ILE Chi-restraints excluded: chain k residue 136 VAL Chi-restraints excluded: chain k residue 146 VAL Chi-restraints excluded: chain k residue 190 VAL Chi-restraints excluded: chain k residue 191 THR Chi-restraints excluded: chain k residue 198 VAL Chi-restraints excluded: chain k residue 215 THR Chi-restraints excluded: chain k residue 224 VAL Chi-restraints excluded: chain l residue 3 VAL Chi-restraints excluded: chain l residue 37 SER Chi-restraints excluded: chain l residue 117 VAL Chi-restraints excluded: chain l residue 119 VAL Chi-restraints excluded: chain l residue 138 THR Chi-restraints excluded: chain l residue 140 THR Chi-restraints excluded: chain l residue 207 VAL Chi-restraints excluded: chain n residue 16 THR Chi-restraints excluded: chain n residue 17 LEU Chi-restraints excluded: chain n residue 45 LEU Chi-restraints excluded: chain n residue 50 LEU Chi-restraints excluded: chain n residue 61 ASP Chi-restraints excluded: chain n residue 83 THR Chi-restraints excluded: chain n residue 97 LEU Chi-restraints excluded: chain n residue 140 THR Chi-restraints excluded: chain n residue 141 VAL Chi-restraints excluded: chain n residue 146 VAL Chi-restraints excluded: chain o residue 45 LEU Chi-restraints excluded: chain o residue 110 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1008 random chunks: chunk 508 optimal weight: 3.9990 chunk 284 optimal weight: 30.0000 chunk 761 optimal weight: 9.9990 chunk 623 optimal weight: 4.9990 chunk 252 optimal weight: 1.9990 chunk 917 optimal weight: 3.9990 chunk 990 optimal weight: 6.9990 chunk 816 optimal weight: 1.9990 chunk 909 optimal weight: 40.0000 chunk 312 optimal weight: 8.9990 chunk 735 optimal weight: 2.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 178 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 460 GLN I 169 ASN B 101 ASN A 91 GLN a 225 ASN C 94 GLN ** c 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 826 HIS P 225 ASN Q 91 GLN ** W 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 91 GLN ** W 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 178 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 235 ASN ** Z 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 74 GLN ** o 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 91 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8323 moved from start: 0.0952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.075 78954 Z= 0.383 Angle : 0.664 20.534 107580 Z= 0.345 Chirality : 0.048 0.282 12384 Planarity : 0.006 0.181 13893 Dihedral : 8.316 115.722 11322 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.64 % Allowed : 7.59 % Favored : 91.77 % Rotamer: Outliers : 8.07 % Allowed : 28.54 % Favored : 63.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.63 % Cis-general : 0.00 % Twisted Proline : 1.26 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.79 (0.08), residues: 10164 helix: 0.15 (0.17), residues: 930 sheet: -0.71 (0.08), residues: 4125 loop : -1.84 (0.08), residues: 5109 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP D 89 HIS 0.012 0.001 HIS E 826 PHE 0.023 0.002 PHE j 120 TYR 0.020 0.002 TYR E 771 ARG 0.011 0.000 ARG n 121 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 20328 Ramachandran restraints generated. 10164 Oldfield, 0 Emsley, 10164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 20328 Ramachandran restraints generated. 10164 Oldfield, 0 Emsley, 10164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1404 residues out of total 8352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 674 poor density : 730 time to evaluate : 6.362 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 7 LYS cc_start: 0.8349 (OUTLIER) cc_final: 0.8130 (mtmm) REVERT: M 13 ASP cc_start: 0.8547 (OUTLIER) cc_final: 0.8072 (t70) REVERT: J 279 MET cc_start: 0.8929 (tmt) cc_final: 0.8723 (tmt) REVERT: J 380 ASP cc_start: 0.7868 (m-30) cc_final: 0.7618 (m-30) REVERT: J 675 GLU cc_start: 0.8418 (OUTLIER) cc_final: 0.8151 (mt-10) REVERT: m 103 GLU cc_start: 0.7799 (pp20) cc_final: 0.7435 (pp20) REVERT: L 111 ARG cc_start: 0.8846 (OUTLIER) cc_final: 0.8381 (ttm-80) REVERT: H 835 ARG cc_start: 0.8018 (OUTLIER) cc_final: 0.7628 (mpp80) REVERT: B 135 GLU cc_start: 0.8020 (OUTLIER) cc_final: 0.7519 (mt-10) REVERT: b 87 MET cc_start: 0.8463 (OUTLIER) cc_final: 0.7696 (mpp) REVERT: A 17 LEU cc_start: 0.9117 (OUTLIER) cc_final: 0.8898 (tt) REVERT: A 90 GLU cc_start: 0.8572 (tm-30) cc_final: 0.8249 (tm-30) REVERT: a 64 ASP cc_start: 0.7492 (OUTLIER) cc_final: 0.7289 (p0) REVERT: C 21 LYS cc_start: 0.8995 (OUTLIER) cc_final: 0.8586 (pmtt) REVERT: C 61 ASP cc_start: 0.8349 (OUTLIER) cc_final: 0.7839 (p0) REVERT: C 94 GLN cc_start: 0.8026 (mt0) cc_final: 0.7650 (mp-120) REVERT: c 11 LYS cc_start: 0.8227 (mmmm) cc_final: 0.7742 (mmmm) REVERT: c 87 MET cc_start: 0.8572 (mmt) cc_final: 0.7559 (mmt) REVERT: D 103 GLU cc_start: 0.8302 (OUTLIER) cc_final: 0.8086 (tp30) REVERT: E 751 LYS cc_start: 0.9089 (OUTLIER) cc_final: 0.8836 (pmtt) REVERT: E 758 GLN cc_start: 0.7954 (mm-40) cc_final: 0.7698 (tt0) REVERT: F 50 VAL cc_start: 0.8749 (OUTLIER) cc_final: 0.8435 (m) REVERT: N 223 ARG cc_start: 0.5735 (ptm-80) cc_final: 0.5419 (ptm-80) REVERT: Q 5 ASN cc_start: 0.9331 (t0) cc_final: 0.9131 (t160) REVERT: T 64 ASP cc_start: 0.7377 (OUTLIER) cc_final: 0.7107 (p0) REVERT: U 21 LYS cc_start: 0.8940 (OUTLIER) cc_final: 0.8629 (pmtt) REVERT: U 61 ASP cc_start: 0.8107 (OUTLIER) cc_final: 0.7533 (p0) REVERT: U 164 MET cc_start: 0.3977 (pmm) cc_final: 0.2217 (tpp) REVERT: W 11 LYS cc_start: 0.8127 (mmmm) cc_final: 0.7731 (mmmm) REVERT: W 29 ASN cc_start: 0.8048 (t0) cc_final: 0.7805 (t0) REVERT: W 55 TYR cc_start: 0.7976 (t80) cc_final: 0.7625 (t80) REVERT: W 212 MET cc_start: 0.3375 (tpp) cc_final: 0.2869 (tpt) REVERT: X 7 LYS cc_start: 0.8416 (OUTLIER) cc_final: 0.8129 (mtmm) REVERT: X 13 ASP cc_start: 0.8609 (OUTLIER) cc_final: 0.8315 (m-30) REVERT: X 21 ARG cc_start: 0.8303 (ttp80) cc_final: 0.8066 (ttp80) REVERT: X 103 GLU cc_start: 0.8441 (OUTLIER) cc_final: 0.8217 (tp30) REVERT: Y 147 TRP cc_start: 0.7779 (OUTLIER) cc_final: 0.7096 (m-90) REVERT: Y 341 ASP cc_start: 0.8080 (m-30) cc_final: 0.7726 (m-30) REVERT: d 9 LEU cc_start: 0.8313 (OUTLIER) cc_final: 0.8096 (mp) REVERT: d 95 MET cc_start: 0.8686 (mmt) cc_final: 0.8424 (mmt) REVERT: d 105 ARG cc_start: 0.8741 (OUTLIER) cc_final: 0.8339 (ptm160) REVERT: d 111 ARG cc_start: 0.8849 (OUTLIER) cc_final: 0.8504 (ttm-80) REVERT: f 139 LEU cc_start: 0.7475 (OUTLIER) cc_final: 0.7146 (mm) REVERT: g 32 SER cc_start: 0.9064 (OUTLIER) cc_final: 0.8775 (m) REVERT: g 90 GLU cc_start: 0.8491 (OUTLIER) cc_final: 0.8235 (pp20) REVERT: g 241 ILE cc_start: 0.1181 (OUTLIER) cc_final: 0.0711 (mp) REVERT: h 102 GLU cc_start: 0.8353 (OUTLIER) cc_final: 0.7940 (mp0) REVERT: j 87 MET cc_start: 0.8318 (mmt) cc_final: 0.8075 (mpp) REVERT: n 49 GLU cc_start: 0.8859 (pm20) cc_final: 0.8657 (pt0) REVERT: n 61 ASP cc_start: 0.8267 (OUTLIER) cc_final: 0.7742 (p0) REVERT: n 164 MET cc_start: 0.3896 (pmm) cc_final: 0.2251 (tpp) REVERT: o 11 LYS cc_start: 0.8427 (mmmm) cc_final: 0.7955 (mmmm) REVERT: o 102 GLU cc_start: 0.8439 (OUTLIER) cc_final: 0.8073 (pp20) outliers start: 674 outliers final: 406 residues processed: 1305 average time/residue: 1.3981 time to fit residues: 2506.3644 Evaluate side-chains 1140 residues out of total 8352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 437 poor density : 703 time to evaluate : 6.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 7 LYS Chi-restraints excluded: chain M residue 12 MET Chi-restraints excluded: chain M residue 13 ASP Chi-restraints excluded: chain M residue 20 VAL Chi-restraints excluded: chain M residue 41 LEU Chi-restraints excluded: chain M residue 46 VAL Chi-restraints excluded: chain M residue 47 THR Chi-restraints excluded: chain M residue 50 VAL Chi-restraints excluded: chain M residue 84 VAL Chi-restraints excluded: chain M residue 109 ASN Chi-restraints excluded: chain J residue 26 VAL Chi-restraints excluded: chain J residue 39 VAL Chi-restraints excluded: chain J residue 47 LEU Chi-restraints excluded: chain J residue 65 THR Chi-restraints excluded: chain J residue 88 THR Chi-restraints excluded: chain J residue 122 VAL Chi-restraints excluded: chain J residue 138 LEU Chi-restraints excluded: chain J residue 149 THR Chi-restraints excluded: chain J residue 153 ILE Chi-restraints excluded: chain J residue 168 VAL Chi-restraints excluded: chain J residue 177 PHE Chi-restraints excluded: chain J residue 215 THR Chi-restraints excluded: chain J residue 217 LEU Chi-restraints excluded: chain J residue 224 SER Chi-restraints excluded: chain J residue 257 SER Chi-restraints excluded: chain J residue 325 CYS Chi-restraints excluded: chain J residue 373 ARG Chi-restraints excluded: chain J residue 374 SER Chi-restraints excluded: chain J residue 381 ASP Chi-restraints excluded: chain J residue 504 THR Chi-restraints excluded: chain J residue 511 ILE Chi-restraints excluded: chain J residue 539 THR Chi-restraints excluded: chain J residue 542 VAL Chi-restraints excluded: chain J residue 583 THR Chi-restraints excluded: chain J residue 598 ILE Chi-restraints excluded: chain J residue 613 VAL Chi-restraints excluded: chain J residue 667 LEU Chi-restraints excluded: chain J residue 675 GLU Chi-restraints excluded: chain J residue 695 VAL Chi-restraints excluded: chain J residue 703 ASP Chi-restraints excluded: chain J residue 823 THR Chi-restraints excluded: chain J residue 827 LEU Chi-restraints excluded: chain m residue 7 LYS Chi-restraints excluded: chain m residue 46 VAL Chi-restraints excluded: chain m residue 85 THR Chi-restraints excluded: chain L residue 18 SER Chi-restraints excluded: chain L residue 31 VAL Chi-restraints excluded: chain L residue 78 THR Chi-restraints excluded: chain L residue 99 VAL Chi-restraints excluded: chain L residue 111 ARG Chi-restraints excluded: chain L residue 151 VAL Chi-restraints excluded: chain L residue 159 ASP Chi-restraints excluded: chain L residue 167 ILE Chi-restraints excluded: chain L residue 218 VAL Chi-restraints excluded: chain H residue 835 ARG Chi-restraints excluded: chain H residue 844 ASP Chi-restraints excluded: chain I residue 118 THR Chi-restraints excluded: chain I residue 161 THR Chi-restraints excluded: chain I residue 166 THR Chi-restraints excluded: chain I residue 167 THR Chi-restraints excluded: chain V residue 17 LEU Chi-restraints excluded: chain V residue 51 THR Chi-restraints excluded: chain V residue 68 THR Chi-restraints excluded: chain V residue 70 THR Chi-restraints excluded: chain V residue 83 THR Chi-restraints excluded: chain V residue 117 VAL Chi-restraints excluded: chain V residue 125 SER Chi-restraints excluded: chain V residue 136 VAL Chi-restraints excluded: chain V residue 146 VAL Chi-restraints excluded: chain V residue 166 VAL Chi-restraints excluded: chain V residue 174 VAL Chi-restraints excluded: chain V residue 225 ASN Chi-restraints excluded: chain v residue 33 ASP Chi-restraints excluded: chain v residue 70 THR Chi-restraints excluded: chain v residue 84 LEU Chi-restraints excluded: chain v residue 97 LEU Chi-restraints excluded: chain v residue 119 VAL Chi-restraints excluded: chain v residue 127 ILE Chi-restraints excluded: chain v residue 132 THR Chi-restraints excluded: chain v residue 179 THR Chi-restraints excluded: chain B residue 53 GLU Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain B residue 87 MET Chi-restraints excluded: chain B residue 135 GLU Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 182 THR Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain b residue 31 LEU Chi-restraints excluded: chain b residue 51 THR Chi-restraints excluded: chain b residue 70 THR Chi-restraints excluded: chain b residue 81 SER Chi-restraints excluded: chain b residue 84 LEU Chi-restraints excluded: chain b residue 87 MET Chi-restraints excluded: chain b residue 110 ILE Chi-restraints excluded: chain b residue 138 THR Chi-restraints excluded: chain b residue 146 VAL Chi-restraints excluded: chain b residue 180 THR Chi-restraints excluded: chain A residue 17 LEU Chi-restraints excluded: chain A residue 83 THR Chi-restraints excluded: chain A residue 87 MET Chi-restraints excluded: chain A residue 127 ILE Chi-restraints excluded: chain A residue 140 THR Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 148 ARG Chi-restraints excluded: chain A residue 186 GLN Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 191 THR Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain a residue 37 SER Chi-restraints excluded: chain a residue 64 ASP Chi-restraints excluded: chain a residue 70 THR Chi-restraints excluded: chain a residue 117 VAL Chi-restraints excluded: chain a residue 119 VAL Chi-restraints excluded: chain a residue 126 SER Chi-restraints excluded: chain a residue 132 THR Chi-restraints excluded: chain a residue 138 THR Chi-restraints excluded: chain a residue 185 PHE Chi-restraints excluded: chain a residue 198 VAL Chi-restraints excluded: chain a residue 207 VAL Chi-restraints excluded: chain a residue 212 MET Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 17 LEU Chi-restraints excluded: chain C residue 21 LYS Chi-restraints excluded: chain C residue 61 ASP Chi-restraints excluded: chain C residue 83 THR Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain c residue 7 THR Chi-restraints excluded: chain c residue 45 LEU Chi-restraints excluded: chain c residue 83 THR Chi-restraints excluded: chain c residue 117 VAL Chi-restraints excluded: chain c residue 240 GLU Chi-restraints excluded: chain D residue 13 ASP Chi-restraints excluded: chain D residue 43 THR Chi-restraints excluded: chain D residue 46 VAL Chi-restraints excluded: chain D residue 47 THR Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 103 GLU Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain E residue 21 THR Chi-restraints excluded: chain E residue 26 VAL Chi-restraints excluded: chain E residue 30 ILE Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 65 THR Chi-restraints excluded: chain E residue 109 ILE Chi-restraints excluded: chain E residue 110 ASP Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 122 VAL Chi-restraints excluded: chain E residue 138 LEU Chi-restraints excluded: chain E residue 139 VAL Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain E residue 153 ILE Chi-restraints excluded: chain E residue 168 VAL Chi-restraints excluded: chain E residue 177 PHE Chi-restraints excluded: chain E residue 215 THR Chi-restraints excluded: chain E residue 217 LEU Chi-restraints excluded: chain E residue 233 SER Chi-restraints excluded: chain E residue 324 THR Chi-restraints excluded: chain E residue 325 CYS Chi-restraints excluded: chain E residue 329 LEU Chi-restraints excluded: chain E residue 330 THR Chi-restraints excluded: chain E residue 331 THR Chi-restraints excluded: chain E residue 373 ARG Chi-restraints excluded: chain E residue 374 SER Chi-restraints excluded: chain E residue 431 THR Chi-restraints excluded: chain E residue 504 THR Chi-restraints excluded: chain E residue 511 ILE Chi-restraints excluded: chain E residue 531 VAL Chi-restraints excluded: chain E residue 542 VAL Chi-restraints excluded: chain E residue 544 VAL Chi-restraints excluded: chain E residue 570 LEU Chi-restraints excluded: chain E residue 596 GLU Chi-restraints excluded: chain E residue 598 ILE Chi-restraints excluded: chain E residue 613 VAL Chi-restraints excluded: chain E residue 638 LEU Chi-restraints excluded: chain E residue 653 LEU Chi-restraints excluded: chain E residue 667 LEU Chi-restraints excluded: chain E residue 703 ASP Chi-restraints excluded: chain E residue 751 LYS Chi-restraints excluded: chain E residue 778 ASN Chi-restraints excluded: chain E residue 783 HIS Chi-restraints excluded: chain E residue 823 THR Chi-restraints excluded: chain E residue 826 HIS Chi-restraints excluded: chain E residue 827 LEU Chi-restraints excluded: chain F residue 46 VAL Chi-restraints excluded: chain F residue 50 VAL Chi-restraints excluded: chain F residue 58 LEU Chi-restraints excluded: chain F residue 85 THR Chi-restraints excluded: chain F residue 88 LYS Chi-restraints excluded: chain G residue 21 VAL Chi-restraints excluded: chain G residue 99 VAL Chi-restraints excluded: chain G residue 154 THR Chi-restraints excluded: chain G residue 159 ASP Chi-restraints excluded: chain G residue 167 ILE Chi-restraints excluded: chain G residue 230 LEU Chi-restraints excluded: chain K residue 842 MET Chi-restraints excluded: chain K residue 849 SER Chi-restraints excluded: chain N residue 107 LEU Chi-restraints excluded: chain N residue 118 THR Chi-restraints excluded: chain N residue 142 LEU Chi-restraints excluded: chain N residue 161 THR Chi-restraints excluded: chain N residue 167 THR Chi-restraints excluded: chain N residue 171 LYS Chi-restraints excluded: chain N residue 204 SER Chi-restraints excluded: chain N residue 207 ILE Chi-restraints excluded: chain O residue 17 LEU Chi-restraints excluded: chain O residue 51 THR Chi-restraints excluded: chain O residue 54 SER Chi-restraints excluded: chain O residue 63 GLU Chi-restraints excluded: chain O residue 70 THR Chi-restraints excluded: chain O residue 83 THR Chi-restraints excluded: chain O residue 90 GLU Chi-restraints excluded: chain O residue 125 SER Chi-restraints excluded: chain O residue 136 VAL Chi-restraints excluded: chain O residue 146 VAL Chi-restraints excluded: chain O residue 166 VAL Chi-restraints excluded: chain O residue 174 VAL Chi-restraints excluded: chain O residue 217 ASN Chi-restraints excluded: chain P residue 70 THR Chi-restraints excluded: chain P residue 97 LEU Chi-restraints excluded: chain P residue 117 VAL Chi-restraints excluded: chain P residue 119 VAL Chi-restraints excluded: chain P residue 132 THR Chi-restraints excluded: chain P residue 179 THR Chi-restraints excluded: chain P residue 191 THR Chi-restraints excluded: chain P residue 219 VAL Chi-restraints excluded: chain Q residue 87 MET Chi-restraints excluded: chain Q residue 119 VAL Chi-restraints excluded: chain Q residue 126 SER Chi-restraints excluded: chain Q residue 131 VAL Chi-restraints excluded: chain Q residue 146 VAL Chi-restraints excluded: chain Q residue 165 THR Chi-restraints excluded: chain Q residue 180 THR Chi-restraints excluded: chain Q residue 181 LEU Chi-restraints excluded: chain Q residue 182 THR Chi-restraints excluded: chain Q residue 191 THR Chi-restraints excluded: chain Q residue 198 VAL Chi-restraints excluded: chain R residue 17 LEU Chi-restraints excluded: chain R residue 42 VAL Chi-restraints excluded: chain R residue 51 THR Chi-restraints excluded: chain R residue 64 ASP Chi-restraints excluded: chain R residue 84 LEU Chi-restraints excluded: chain R residue 116 THR Chi-restraints excluded: chain R residue 125 SER Chi-restraints excluded: chain R residue 132 THR Chi-restraints excluded: chain R residue 138 THR Chi-restraints excluded: chain R residue 158 VAL Chi-restraints excluded: chain R residue 180 THR Chi-restraints excluded: chain S residue 7 THR Chi-restraints excluded: chain S residue 34 VAL Chi-restraints excluded: chain S residue 83 THR Chi-restraints excluded: chain S residue 125 SER Chi-restraints excluded: chain S residue 132 THR Chi-restraints excluded: chain S residue 140 THR Chi-restraints excluded: chain S residue 146 VAL Chi-restraints excluded: chain S residue 186 GLN Chi-restraints excluded: chain S residue 190 VAL Chi-restraints excluded: chain S residue 191 THR Chi-restraints excluded: chain S residue 198 VAL Chi-restraints excluded: chain S residue 215 THR Chi-restraints excluded: chain S residue 224 VAL Chi-restraints excluded: chain T residue 64 ASP Chi-restraints excluded: chain T residue 70 THR Chi-restraints excluded: chain T residue 117 VAL Chi-restraints excluded: chain T residue 119 VAL Chi-restraints excluded: chain T residue 132 THR Chi-restraints excluded: chain T residue 138 THR Chi-restraints excluded: chain T residue 207 VAL Chi-restraints excluded: chain T residue 212 MET Chi-restraints excluded: chain U residue 17 LEU Chi-restraints excluded: chain U residue 21 LYS Chi-restraints excluded: chain U residue 61 ASP Chi-restraints excluded: chain U residue 83 THR Chi-restraints excluded: chain U residue 132 THR Chi-restraints excluded: chain U residue 141 VAL Chi-restraints excluded: chain U residue 146 VAL Chi-restraints excluded: chain U residue 179 THR Chi-restraints excluded: chain U residue 229 VAL Chi-restraints excluded: chain W residue 7 THR Chi-restraints excluded: chain W residue 45 LEU Chi-restraints excluded: chain W residue 83 THR Chi-restraints excluded: chain W residue 110 ILE Chi-restraints excluded: chain W residue 117 VAL Chi-restraints excluded: chain X residue 7 LYS Chi-restraints excluded: chain X residue 13 ASP Chi-restraints excluded: chain X residue 20 VAL Chi-restraints excluded: chain X residue 43 THR Chi-restraints excluded: chain X residue 46 VAL Chi-restraints excluded: chain X residue 47 THR Chi-restraints excluded: chain X residue 50 VAL Chi-restraints excluded: chain X residue 90 SER Chi-restraints excluded: chain X residue 103 GLU Chi-restraints excluded: chain X residue 108 VAL Chi-restraints excluded: chain Y residue 5 SER Chi-restraints excluded: chain Y residue 21 THR Chi-restraints excluded: chain Y residue 26 VAL Chi-restraints excluded: chain Y residue 47 LEU Chi-restraints excluded: chain Y residue 50 THR Chi-restraints excluded: chain Y residue 65 THR Chi-restraints excluded: chain Y residue 88 THR Chi-restraints excluded: chain Y residue 109 ILE Chi-restraints excluded: chain Y residue 115 THR Chi-restraints excluded: chain Y residue 122 VAL Chi-restraints excluded: chain Y residue 138 LEU Chi-restraints excluded: chain Y residue 147 TRP Chi-restraints excluded: chain Y residue 149 THR Chi-restraints excluded: chain Y residue 153 ILE Chi-restraints excluded: chain Y residue 167 VAL Chi-restraints excluded: chain Y residue 168 VAL Chi-restraints excluded: chain Y residue 177 PHE Chi-restraints excluded: chain Y residue 215 THR Chi-restraints excluded: chain Y residue 217 LEU Chi-restraints excluded: chain Y residue 233 SER Chi-restraints excluded: chain Y residue 324 THR Chi-restraints excluded: chain Y residue 325 CYS Chi-restraints excluded: chain Y residue 330 THR Chi-restraints excluded: chain Y residue 381 ASP Chi-restraints excluded: chain Y residue 397 ASN Chi-restraints excluded: chain Y residue 433 MET Chi-restraints excluded: chain Y residue 504 THR Chi-restraints excluded: chain Y residue 511 ILE Chi-restraints excluded: chain Y residue 531 VAL Chi-restraints excluded: chain Y residue 536 GLN Chi-restraints excluded: chain Y residue 539 THR Chi-restraints excluded: chain Y residue 542 VAL Chi-restraints excluded: chain Y residue 544 VAL Chi-restraints excluded: chain Y residue 566 LEU Chi-restraints excluded: chain Y residue 574 VAL Chi-restraints excluded: chain Y residue 613 VAL Chi-restraints excluded: chain Y residue 621 VAL Chi-restraints excluded: chain Y residue 638 LEU Chi-restraints excluded: chain Y residue 667 LEU Chi-restraints excluded: chain Y residue 703 ASP Chi-restraints excluded: chain Y residue 756 ILE Chi-restraints excluded: chain Y residue 823 THR Chi-restraints excluded: chain Y residue 827 LEU Chi-restraints excluded: chain Y residue 838 THR Chi-restraints excluded: chain Y residue 840 ASP Chi-restraints excluded: chain Z residue 46 VAL Chi-restraints excluded: chain Z residue 58 LEU Chi-restraints excluded: chain Z residue 98 VAL Chi-restraints excluded: chain Z residue 109 ASN Chi-restraints excluded: chain d residue 9 LEU Chi-restraints excluded: chain d residue 21 VAL Chi-restraints excluded: chain d residue 31 VAL Chi-restraints excluded: chain d residue 105 ARG Chi-restraints excluded: chain d residue 111 ARG Chi-restraints excluded: chain d residue 143 LEU Chi-restraints excluded: chain d residue 151 VAL Chi-restraints excluded: chain d residue 159 ASP Chi-restraints excluded: chain d residue 167 ILE Chi-restraints excluded: chain e residue 847 LEU Chi-restraints excluded: chain f residue 118 THR Chi-restraints excluded: chain f residue 139 LEU Chi-restraints excluded: chain f residue 161 THR Chi-restraints excluded: chain f residue 166 THR Chi-restraints excluded: chain f residue 167 THR Chi-restraints excluded: chain f residue 182 MET Chi-restraints excluded: chain f residue 188 VAL Chi-restraints excluded: chain f residue 203 VAL Chi-restraints excluded: chain f residue 204 SER Chi-restraints excluded: chain f residue 207 ILE Chi-restraints excluded: chain g residue 32 SER Chi-restraints excluded: chain g residue 51 THR Chi-restraints excluded: chain g residue 63 GLU Chi-restraints excluded: chain g residue 70 THR Chi-restraints excluded: chain g residue 81 SER Chi-restraints excluded: chain g residue 83 THR Chi-restraints excluded: chain g residue 90 GLU Chi-restraints excluded: chain g residue 136 VAL Chi-restraints excluded: chain g residue 146 VAL Chi-restraints excluded: chain g residue 166 VAL Chi-restraints excluded: chain g residue 174 VAL Chi-restraints excluded: chain g residue 191 THR Chi-restraints excluded: chain g residue 241 ILE Chi-restraints excluded: chain h residue 70 THR Chi-restraints excluded: chain h residue 102 GLU Chi-restraints excluded: chain h residue 117 VAL Chi-restraints excluded: chain h residue 119 VAL Chi-restraints excluded: chain h residue 127 ILE Chi-restraints excluded: chain h residue 132 THR Chi-restraints excluded: chain h residue 179 THR Chi-restraints excluded: chain i residue 45 LEU Chi-restraints excluded: chain i residue 131 VAL Chi-restraints excluded: chain i residue 182 THR Chi-restraints excluded: chain i residue 183 VAL Chi-restraints excluded: chain i residue 198 VAL Chi-restraints excluded: chain j residue 54 SER Chi-restraints excluded: chain j residue 64 ASP Chi-restraints excluded: chain j residue 70 THR Chi-restraints excluded: chain j residue 81 SER Chi-restraints excluded: chain j residue 84 LEU Chi-restraints excluded: chain j residue 116 THR Chi-restraints excluded: chain j residue 125 SER Chi-restraints excluded: chain j residue 132 THR Chi-restraints excluded: chain j residue 135 GLU Chi-restraints excluded: chain j residue 138 THR Chi-restraints excluded: chain j residue 146 VAL Chi-restraints excluded: chain j residue 158 VAL Chi-restraints excluded: chain j residue 180 THR Chi-restraints excluded: chain k residue 83 THR Chi-restraints excluded: chain k residue 87 MET Chi-restraints excluded: chain k residue 127 ILE Chi-restraints excluded: chain k residue 136 VAL Chi-restraints excluded: chain k residue 146 VAL Chi-restraints excluded: chain k residue 190 VAL Chi-restraints excluded: chain k residue 191 THR Chi-restraints excluded: chain k residue 198 VAL Chi-restraints excluded: chain k residue 215 THR Chi-restraints excluded: chain k residue 224 VAL Chi-restraints excluded: chain l residue 3 VAL Chi-restraints excluded: chain l residue 70 THR Chi-restraints excluded: chain l residue 117 VAL Chi-restraints excluded: chain l residue 119 VAL Chi-restraints excluded: chain l residue 138 THR Chi-restraints excluded: chain l residue 180 THR Chi-restraints excluded: chain l residue 198 VAL Chi-restraints excluded: chain l residue 207 VAL Chi-restraints excluded: chain n residue 16 THR Chi-restraints excluded: chain n residue 17 LEU Chi-restraints excluded: chain n residue 50 LEU Chi-restraints excluded: chain n residue 61 ASP Chi-restraints excluded: chain n residue 97 LEU Chi-restraints excluded: chain n residue 141 VAL Chi-restraints excluded: chain n residue 146 VAL Chi-restraints excluded: chain o residue 7 THR Chi-restraints excluded: chain o residue 45 LEU Chi-restraints excluded: chain o residue 83 THR Chi-restraints excluded: chain o residue 84 LEU Chi-restraints excluded: chain o residue 102 GLU Chi-restraints excluded: chain o residue 110 ILE Chi-restraints excluded: chain o residue 117 VAL Chi-restraints excluded: chain o residue 126 SER Chi-restraints excluded: chain o residue 132 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1008 random chunks: chunk 906 optimal weight: 6.9990 chunk 689 optimal weight: 0.0170 chunk 475 optimal weight: 4.9990 chunk 101 optimal weight: 0.7980 chunk 437 optimal weight: 0.7980 chunk 615 optimal weight: 4.9990 chunk 920 optimal weight: 0.5980 chunk 974 optimal weight: 3.9990 chunk 480 optimal weight: 1.9990 chunk 872 optimal weight: 3.9990 chunk 262 optimal weight: 0.0570 overall best weight: 0.4536 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 178 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 145 ASN B 72 GLN A 91 GLN ** c 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 91 GLN E 178 ASN ** E 826 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 232 GLN N 217 GLN Q 91 GLN ** W 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 177 GLN ** Y 178 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 235 ASN ** Z 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 74 GLN k 72 GLN ** o 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 91 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 moved from start: 0.1046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 78954 Z= 0.168 Angle : 0.592 17.581 107580 Z= 0.305 Chirality : 0.045 0.245 12384 Planarity : 0.005 0.177 13893 Dihedral : 7.303 61.218 11257 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.60 % Allowed : 6.55 % Favored : 92.85 % Rotamer: Outliers : 5.83 % Allowed : 30.60 % Favored : 63.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.63 % Cis-general : 0.00 % Twisted Proline : 1.26 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.56 (0.08), residues: 10164 helix: 0.65 (0.18), residues: 891 sheet: -0.59 (0.08), residues: 4092 loop : -1.71 (0.08), residues: 5181 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP D 89 HIS 0.016 0.001 HIS E 826 PHE 0.020 0.001 PHE Y 818 TYR 0.024 0.001 TYR E 771 ARG 0.011 0.000 ARG n 121 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 20328 Ramachandran restraints generated. 10164 Oldfield, 0 Emsley, 10164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 20328 Ramachandran restraints generated. 10164 Oldfield, 0 Emsley, 10164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1266 residues out of total 8352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 487 poor density : 779 time to evaluate : 7.471 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 719 ARG cc_start: 0.7886 (OUTLIER) cc_final: 0.7556 (ttp-110) REVERT: J 758 GLN cc_start: 0.8184 (mm110) cc_final: 0.7814 (tt0) REVERT: m 92 ARG cc_start: 0.8247 (tpp80) cc_final: 0.7838 (ttp80) REVERT: m 103 GLU cc_start: 0.7814 (pp20) cc_final: 0.7407 (pp20) REVERT: H 835 ARG cc_start: 0.7881 (OUTLIER) cc_final: 0.7193 (mpp80) REVERT: I 185 GLN cc_start: 0.8303 (OUTLIER) cc_final: 0.7980 (tt0) REVERT: v 102 GLU cc_start: 0.8366 (OUTLIER) cc_final: 0.8051 (mp0) REVERT: b 43 LYS cc_start: 0.8936 (OUTLIER) cc_final: 0.8513 (mmpt) REVERT: A 17 LEU cc_start: 0.9001 (OUTLIER) cc_final: 0.8752 (tt) REVERT: A 90 GLU cc_start: 0.8568 (tm-30) cc_final: 0.8326 (tm-30) REVERT: C 21 LYS cc_start: 0.8969 (OUTLIER) cc_final: 0.8525 (pmtt) REVERT: C 53 GLU cc_start: 0.9028 (pt0) cc_final: 0.8716 (pm20) REVERT: C 61 ASP cc_start: 0.8254 (OUTLIER) cc_final: 0.7705 (p0) REVERT: c 11 LYS cc_start: 0.8162 (mmmm) cc_final: 0.7634 (mmmm) REVERT: c 87 MET cc_start: 0.8612 (mmt) cc_final: 0.7621 (mmt) REVERT: c 212 MET cc_start: 0.2899 (OUTLIER) cc_final: 0.1620 (tpp) REVERT: D 24 ARG cc_start: 0.7969 (ttp80) cc_final: 0.7364 (ttp80) REVERT: D 103 GLU cc_start: 0.8277 (OUTLIER) cc_final: 0.8005 (tp30) REVERT: E 31 SER cc_start: 0.8502 (m) cc_final: 0.8186 (t) REVERT: Q 5 ASN cc_start: 0.9297 (t0) cc_final: 0.9069 (t160) REVERT: R 62 ASP cc_start: 0.8515 (t0) cc_final: 0.8277 (t0) REVERT: R 64 ASP cc_start: 0.7695 (OUTLIER) cc_final: 0.7331 (p0) REVERT: S 90 GLU cc_start: 0.8589 (tm-30) cc_final: 0.8266 (tm-30) REVERT: S 132 THR cc_start: 0.8934 (OUTLIER) cc_final: 0.8707 (t) REVERT: T 64 ASP cc_start: 0.7312 (OUTLIER) cc_final: 0.7034 (p0) REVERT: U 21 LYS cc_start: 0.8889 (OUTLIER) cc_final: 0.8612 (pmtt) REVERT: U 61 ASP cc_start: 0.8029 (OUTLIER) cc_final: 0.7428 (p0) REVERT: U 164 MET cc_start: 0.3999 (pmm) cc_final: 0.2263 (tpp) REVERT: W 11 LYS cc_start: 0.8066 (mmmm) cc_final: 0.7642 (mmmm) REVERT: W 29 ASN cc_start: 0.7997 (t0) cc_final: 0.7772 (t0) REVERT: W 55 TYR cc_start: 0.7923 (t80) cc_final: 0.7495 (t80) REVERT: W 212 MET cc_start: 0.3846 (tpp) cc_final: 0.3319 (tpt) REVERT: X 21 ARG cc_start: 0.8304 (ttp80) cc_final: 0.8085 (ttp80) REVERT: X 103 GLU cc_start: 0.8390 (OUTLIER) cc_final: 0.8179 (tp30) REVERT: Y 31 SER cc_start: 0.8599 (m) cc_final: 0.8249 (t) REVERT: Y 90 LEU cc_start: 0.7604 (OUTLIER) cc_final: 0.7344 (pp) REVERT: Y 147 TRP cc_start: 0.7751 (OUTLIER) cc_final: 0.7079 (m-90) REVERT: Y 329 LEU cc_start: 0.9051 (OUTLIER) cc_final: 0.8723 (mt) REVERT: Y 341 ASP cc_start: 0.8072 (m-30) cc_final: 0.7741 (m-30) REVERT: Y 818 PHE cc_start: 0.8111 (m-80) cc_final: 0.7908 (m-80) REVERT: Z 1 MET cc_start: 0.5973 (ttm) cc_final: 0.5534 (tmm) REVERT: d 111 ARG cc_start: 0.8668 (OUTLIER) cc_final: 0.8321 (ttm-80) REVERT: h 53 GLU cc_start: 0.8447 (OUTLIER) cc_final: 0.8033 (pm20) REVERT: h 102 GLU cc_start: 0.8274 (OUTLIER) cc_final: 0.7833 (mp0) REVERT: k 90 GLU cc_start: 0.8476 (tm-30) cc_final: 0.8117 (tm-30) REVERT: n 49 GLU cc_start: 0.8844 (pm20) cc_final: 0.8626 (pt0) REVERT: n 61 ASP cc_start: 0.7988 (OUTLIER) cc_final: 0.7589 (p0) REVERT: n 164 MET cc_start: 0.4170 (pmm) cc_final: 0.2908 (tpp) REVERT: o 11 LYS cc_start: 0.8268 (mmmm) cc_final: 0.7765 (mmmm) REVERT: o 102 GLU cc_start: 0.8458 (OUTLIER) cc_final: 0.8083 (pp20) outliers start: 487 outliers final: 251 residues processed: 1183 average time/residue: 1.5475 time to fit residues: 2487.8262 Evaluate side-chains 997 residues out of total 8352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 275 poor density : 722 time to evaluate : 6.558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 46 VAL Chi-restraints excluded: chain M residue 47 THR Chi-restraints excluded: chain M residue 50 VAL Chi-restraints excluded: chain J residue 26 VAL Chi-restraints excluded: chain J residue 47 LEU Chi-restraints excluded: chain J residue 88 THR Chi-restraints excluded: chain J residue 122 VAL Chi-restraints excluded: chain J residue 138 LEU Chi-restraints excluded: chain J residue 149 THR Chi-restraints excluded: chain J residue 153 ILE Chi-restraints excluded: chain J residue 168 VAL Chi-restraints excluded: chain J residue 177 PHE Chi-restraints excluded: chain J residue 215 THR Chi-restraints excluded: chain J residue 257 SER Chi-restraints excluded: chain J residue 325 CYS Chi-restraints excluded: chain J residue 504 THR Chi-restraints excluded: chain J residue 511 ILE Chi-restraints excluded: chain J residue 539 THR Chi-restraints excluded: chain J residue 596 GLU Chi-restraints excluded: chain J residue 613 VAL Chi-restraints excluded: chain J residue 621 VAL Chi-restraints excluded: chain J residue 646 VAL Chi-restraints excluded: chain J residue 695 VAL Chi-restraints excluded: chain J residue 703 ASP Chi-restraints excluded: chain J residue 719 ARG Chi-restraints excluded: chain J residue 823 THR Chi-restraints excluded: chain J residue 827 LEU Chi-restraints excluded: chain m residue 74 THR Chi-restraints excluded: chain L residue 99 VAL Chi-restraints excluded: chain L residue 159 ASP Chi-restraints excluded: chain H residue 835 ARG Chi-restraints excluded: chain H residue 844 ASP Chi-restraints excluded: chain I residue 118 THR Chi-restraints excluded: chain I residue 161 THR Chi-restraints excluded: chain I residue 167 THR Chi-restraints excluded: chain I residue 185 GLN Chi-restraints excluded: chain I residue 207 ILE Chi-restraints excluded: chain V residue 51 THR Chi-restraints excluded: chain V residue 70 THR Chi-restraints excluded: chain V residue 83 THR Chi-restraints excluded: chain V residue 146 VAL Chi-restraints excluded: chain v residue 33 ASP Chi-restraints excluded: chain v residue 70 THR Chi-restraints excluded: chain v residue 97 LEU Chi-restraints excluded: chain v residue 102 GLU Chi-restraints excluded: chain v residue 119 VAL Chi-restraints excluded: chain v residue 132 THR Chi-restraints excluded: chain v residue 179 THR Chi-restraints excluded: chain B residue 53 GLU Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 182 THR Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain b residue 43 LYS Chi-restraints excluded: chain b residue 70 THR Chi-restraints excluded: chain b residue 84 LEU Chi-restraints excluded: chain b residue 97 LEU Chi-restraints excluded: chain b residue 110 ILE Chi-restraints excluded: chain b residue 146 VAL Chi-restraints excluded: chain b residue 180 THR Chi-restraints excluded: chain A residue 17 LEU Chi-restraints excluded: chain A residue 83 THR Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 140 THR Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 191 THR Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain a residue 102 GLU Chi-restraints excluded: chain a residue 119 VAL Chi-restraints excluded: chain a residue 132 THR Chi-restraints excluded: chain a residue 185 PHE Chi-restraints excluded: chain a residue 207 VAL Chi-restraints excluded: chain a residue 212 MET Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 17 LEU Chi-restraints excluded: chain C residue 21 LYS Chi-restraints excluded: chain C residue 61 ASP Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain c residue 7 THR Chi-restraints excluded: chain c residue 45 LEU Chi-restraints excluded: chain c residue 83 THR Chi-restraints excluded: chain c residue 117 VAL Chi-restraints excluded: chain c residue 212 MET Chi-restraints excluded: chain c residue 240 GLU Chi-restraints excluded: chain D residue 13 ASP Chi-restraints excluded: chain D residue 46 VAL Chi-restraints excluded: chain D residue 47 THR Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 103 GLU Chi-restraints excluded: chain E residue 21 THR Chi-restraints excluded: chain E residue 26 VAL Chi-restraints excluded: chain E residue 122 VAL Chi-restraints excluded: chain E residue 138 LEU Chi-restraints excluded: chain E residue 139 VAL Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain E residue 168 VAL Chi-restraints excluded: chain E residue 177 PHE Chi-restraints excluded: chain E residue 215 THR Chi-restraints excluded: chain E residue 324 THR Chi-restraints excluded: chain E residue 325 CYS Chi-restraints excluded: chain E residue 329 LEU Chi-restraints excluded: chain E residue 374 SER Chi-restraints excluded: chain E residue 431 THR Chi-restraints excluded: chain E residue 504 THR Chi-restraints excluded: chain E residue 511 ILE Chi-restraints excluded: chain E residue 531 VAL Chi-restraints excluded: chain E residue 596 GLU Chi-restraints excluded: chain E residue 613 VAL Chi-restraints excluded: chain E residue 653 LEU Chi-restraints excluded: chain E residue 756 ILE Chi-restraints excluded: chain E residue 823 THR Chi-restraints excluded: chain E residue 826 HIS Chi-restraints excluded: chain F residue 95 MET Chi-restraints excluded: chain G residue 99 VAL Chi-restraints excluded: chain G residue 159 ASP Chi-restraints excluded: chain N residue 118 THR Chi-restraints excluded: chain N residue 161 THR Chi-restraints excluded: chain N residue 167 THR Chi-restraints excluded: chain N residue 171 LYS Chi-restraints excluded: chain O residue 51 THR Chi-restraints excluded: chain O residue 54 SER Chi-restraints excluded: chain O residue 63 GLU Chi-restraints excluded: chain O residue 70 THR Chi-restraints excluded: chain O residue 83 THR Chi-restraints excluded: chain O residue 146 VAL Chi-restraints excluded: chain O residue 191 THR Chi-restraints excluded: chain P residue 70 THR Chi-restraints excluded: chain P residue 117 VAL Chi-restraints excluded: chain P residue 119 VAL Chi-restraints excluded: chain P residue 132 THR Chi-restraints excluded: chain P residue 179 THR Chi-restraints excluded: chain Q residue 97 LEU Chi-restraints excluded: chain Q residue 119 VAL Chi-restraints excluded: chain Q residue 126 SER Chi-restraints excluded: chain Q residue 131 VAL Chi-restraints excluded: chain Q residue 165 THR Chi-restraints excluded: chain Q residue 180 THR Chi-restraints excluded: chain Q residue 182 THR Chi-restraints excluded: chain Q residue 191 THR Chi-restraints excluded: chain Q residue 198 VAL Chi-restraints excluded: chain R residue 23 SER Chi-restraints excluded: chain R residue 42 VAL Chi-restraints excluded: chain R residue 64 ASP Chi-restraints excluded: chain R residue 84 LEU Chi-restraints excluded: chain R residue 132 THR Chi-restraints excluded: chain R residue 158 VAL Chi-restraints excluded: chain R residue 180 THR Chi-restraints excluded: chain S residue 83 THR Chi-restraints excluded: chain S residue 127 ILE Chi-restraints excluded: chain S residue 132 THR Chi-restraints excluded: chain S residue 191 THR Chi-restraints excluded: chain S residue 198 VAL Chi-restraints excluded: chain S residue 215 THR Chi-restraints excluded: chain S residue 224 VAL Chi-restraints excluded: chain T residue 3 VAL Chi-restraints excluded: chain T residue 64 ASP Chi-restraints excluded: chain T residue 97 LEU Chi-restraints excluded: chain T residue 119 VAL Chi-restraints excluded: chain T residue 207 VAL Chi-restraints excluded: chain T residue 212 MET Chi-restraints excluded: chain U residue 17 LEU Chi-restraints excluded: chain U residue 21 LYS Chi-restraints excluded: chain U residue 61 ASP Chi-restraints excluded: chain U residue 83 THR Chi-restraints excluded: chain U residue 141 VAL Chi-restraints excluded: chain U residue 146 VAL Chi-restraints excluded: chain W residue 7 THR Chi-restraints excluded: chain W residue 83 THR Chi-restraints excluded: chain W residue 117 VAL Chi-restraints excluded: chain X residue 46 VAL Chi-restraints excluded: chain X residue 47 THR Chi-restraints excluded: chain X residue 50 VAL Chi-restraints excluded: chain X residue 90 SER Chi-restraints excluded: chain X residue 103 GLU Chi-restraints excluded: chain X residue 109 ASN Chi-restraints excluded: chain Y residue 21 THR Chi-restraints excluded: chain Y residue 26 VAL Chi-restraints excluded: chain Y residue 50 THR Chi-restraints excluded: chain Y residue 65 THR Chi-restraints excluded: chain Y residue 88 THR Chi-restraints excluded: chain Y residue 90 LEU Chi-restraints excluded: chain Y residue 102 ARG Chi-restraints excluded: chain Y residue 122 VAL Chi-restraints excluded: chain Y residue 138 LEU Chi-restraints excluded: chain Y residue 147 TRP Chi-restraints excluded: chain Y residue 149 THR Chi-restraints excluded: chain Y residue 153 ILE Chi-restraints excluded: chain Y residue 167 VAL Chi-restraints excluded: chain Y residue 168 VAL Chi-restraints excluded: chain Y residue 177 PHE Chi-restraints excluded: chain Y residue 215 THR Chi-restraints excluded: chain Y residue 217 LEU Chi-restraints excluded: chain Y residue 324 THR Chi-restraints excluded: chain Y residue 325 CYS Chi-restraints excluded: chain Y residue 329 LEU Chi-restraints excluded: chain Y residue 381 ASP Chi-restraints excluded: chain Y residue 433 MET Chi-restraints excluded: chain Y residue 504 THR Chi-restraints excluded: chain Y residue 511 ILE Chi-restraints excluded: chain Y residue 531 VAL Chi-restraints excluded: chain Y residue 536 GLN Chi-restraints excluded: chain Y residue 539 THR Chi-restraints excluded: chain Y residue 544 VAL Chi-restraints excluded: chain Y residue 613 VAL Chi-restraints excluded: chain Y residue 621 VAL Chi-restraints excluded: chain Y residue 638 LEU Chi-restraints excluded: chain Y residue 667 LEU Chi-restraints excluded: chain Y residue 823 THR Chi-restraints excluded: chain Y residue 827 LEU Chi-restraints excluded: chain Z residue 46 VAL Chi-restraints excluded: chain Z residue 58 LEU Chi-restraints excluded: chain Z residue 74 THR Chi-restraints excluded: chain Z residue 98 VAL Chi-restraints excluded: chain d residue 31 VAL Chi-restraints excluded: chain d residue 99 VAL Chi-restraints excluded: chain d residue 111 ARG Chi-restraints excluded: chain d residue 159 ASP Chi-restraints excluded: chain e residue 847 LEU Chi-restraints excluded: chain e residue 849 SER Chi-restraints excluded: chain f residue 118 THR Chi-restraints excluded: chain f residue 161 THR Chi-restraints excluded: chain f residue 167 THR Chi-restraints excluded: chain f residue 188 VAL Chi-restraints excluded: chain f residue 203 VAL Chi-restraints excluded: chain f residue 204 SER Chi-restraints excluded: chain g residue 51 THR Chi-restraints excluded: chain g residue 83 THR Chi-restraints excluded: chain g residue 146 VAL Chi-restraints excluded: chain g residue 191 THR Chi-restraints excluded: chain h residue 31 LEU Chi-restraints excluded: chain h residue 53 GLU Chi-restraints excluded: chain h residue 70 THR Chi-restraints excluded: chain h residue 102 GLU Chi-restraints excluded: chain h residue 119 VAL Chi-restraints excluded: chain h residue 132 THR Chi-restraints excluded: chain h residue 179 THR Chi-restraints excluded: chain i residue 131 VAL Chi-restraints excluded: chain i residue 183 VAL Chi-restraints excluded: chain i residue 198 VAL Chi-restraints excluded: chain i residue 199 SER Chi-restraints excluded: chain j residue 64 ASP Chi-restraints excluded: chain j residue 84 LEU Chi-restraints excluded: chain j residue 125 SER Chi-restraints excluded: chain j residue 132 THR Chi-restraints excluded: chain j residue 135 GLU Chi-restraints excluded: chain j residue 138 THR Chi-restraints excluded: chain j residue 146 VAL Chi-restraints excluded: chain j residue 158 VAL Chi-restraints excluded: chain j residue 180 THR Chi-restraints excluded: chain k residue 83 THR Chi-restraints excluded: chain k residue 136 VAL Chi-restraints excluded: chain k residue 146 VAL Chi-restraints excluded: chain k residue 186 GLN Chi-restraints excluded: chain k residue 190 VAL Chi-restraints excluded: chain k residue 198 VAL Chi-restraints excluded: chain k residue 215 THR Chi-restraints excluded: chain k residue 224 VAL Chi-restraints excluded: chain l residue 3 VAL Chi-restraints excluded: chain l residue 97 LEU Chi-restraints excluded: chain l residue 119 VAL Chi-restraints excluded: chain l residue 198 VAL Chi-restraints excluded: chain l residue 207 VAL Chi-restraints excluded: chain n residue 61 ASP Chi-restraints excluded: chain n residue 83 THR Chi-restraints excluded: chain n residue 97 LEU Chi-restraints excluded: chain n residue 140 THR Chi-restraints excluded: chain n residue 141 VAL Chi-restraints excluded: chain n residue 146 VAL Chi-restraints excluded: chain o residue 83 THR Chi-restraints excluded: chain o residue 102 GLU Chi-restraints excluded: chain o residue 110 ILE Chi-restraints excluded: chain o residue 117 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1008 random chunks: chunk 811 optimal weight: 3.9990 chunk 553 optimal weight: 1.9990 chunk 14 optimal weight: 5.9990 chunk 725 optimal weight: 0.7980 chunk 402 optimal weight: 3.9990 chunk 831 optimal weight: 6.9990 chunk 673 optimal weight: 7.9990 chunk 1 optimal weight: 0.9980 chunk 497 optimal weight: 6.9990 chunk 874 optimal weight: 8.9990 chunk 245 optimal weight: 6.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 178 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 91 GLN ** c 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 826 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 217 GLN O 217 ASN Q 91 GLN ** W 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 91 GLN X 38 ASN Y 178 ASN Y 235 ASN ** Z 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 74 GLN l 225 ASN ** o 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 91 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8306 moved from start: 0.1112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 78954 Z= 0.318 Angle : 0.640 19.267 107580 Z= 0.330 Chirality : 0.047 0.233 12384 Planarity : 0.005 0.180 13893 Dihedral : 6.999 59.852 11140 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.62 % Allowed : 7.49 % Favored : 91.89 % Rotamer: Outliers : 6.62 % Allowed : 30.35 % Favored : 63.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.63 % Cis-general : 0.00 % Twisted Proline : 1.26 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.63 (0.08), residues: 10164 helix: 0.52 (0.18), residues: 891 sheet: -0.63 (0.08), residues: 4086 loop : -1.75 (0.08), residues: 5187 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP D 89 HIS 0.006 0.001 HIS Z 65 PHE 0.019 0.002 PHE j 120 TYR 0.024 0.001 TYR E 771 ARG 0.008 0.000 ARG W 121 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 20328 Ramachandran restraints generated. 10164 Oldfield, 0 Emsley, 10164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 20328 Ramachandran restraints generated. 10164 Oldfield, 0 Emsley, 10164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1279 residues out of total 8352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 553 poor density : 726 time to evaluate : 6.427 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 95 MET cc_start: 0.9330 (OUTLIER) cc_final: 0.8901 (tpt) REVERT: J 719 ARG cc_start: 0.7858 (OUTLIER) cc_final: 0.7537 (ttp-110) REVERT: J 721 GLU cc_start: 0.6179 (OUTLIER) cc_final: 0.5934 (mp0) REVERT: J 757 ARG cc_start: 0.8247 (mtm110) cc_final: 0.8027 (mtm110) REVERT: J 758 GLN cc_start: 0.8149 (mm110) cc_final: 0.7786 (tt0) REVERT: m 92 ARG cc_start: 0.8324 (tpp80) cc_final: 0.7926 (ttp80) REVERT: m 103 GLU cc_start: 0.7839 (pp20) cc_final: 0.7393 (pp20) REVERT: I 185 GLN cc_start: 0.8374 (OUTLIER) cc_final: 0.8079 (tt0) REVERT: V 90 GLU cc_start: 0.8305 (OUTLIER) cc_final: 0.8073 (pp20) REVERT: v 102 GLU cc_start: 0.8338 (OUTLIER) cc_final: 0.7953 (mp0) REVERT: B 57 ASP cc_start: 0.8782 (t0) cc_final: 0.8479 (t0) REVERT: B 135 GLU cc_start: 0.8032 (OUTLIER) cc_final: 0.7592 (mt-10) REVERT: b 87 MET cc_start: 0.8402 (OUTLIER) cc_final: 0.7655 (mpp) REVERT: A 17 LEU cc_start: 0.9086 (OUTLIER) cc_final: 0.8875 (tt) REVERT: A 90 GLU cc_start: 0.8535 (tm-30) cc_final: 0.8271 (tm-30) REVERT: C 21 LYS cc_start: 0.8979 (OUTLIER) cc_final: 0.8547 (pmtt) REVERT: C 61 ASP cc_start: 0.8300 (OUTLIER) cc_final: 0.7993 (p0) REVERT: C 155 ARG cc_start: 0.7486 (mtm110) cc_final: 0.6822 (ptt-90) REVERT: c 11 LYS cc_start: 0.8146 (mmmm) cc_final: 0.7640 (mmmm) REVERT: c 43 LYS cc_start: 0.6629 (mmpt) cc_final: 0.6263 (mmpt) REVERT: c 53 GLU cc_start: 0.8743 (pt0) cc_final: 0.8497 (pt0) REVERT: c 87 MET cc_start: 0.8676 (mmt) cc_final: 0.7625 (mmt) REVERT: c 102 GLU cc_start: 0.8399 (OUTLIER) cc_final: 0.8112 (pp20) REVERT: D 103 GLU cc_start: 0.8313 (OUTLIER) cc_final: 0.8099 (tp30) REVERT: E 147 TRP cc_start: 0.7409 (m100) cc_final: 0.5994 (m100) REVERT: E 751 LYS cc_start: 0.9077 (OUTLIER) cc_final: 0.8845 (pmtt) REVERT: F 50 VAL cc_start: 0.8773 (OUTLIER) cc_final: 0.8502 (m) REVERT: K 842 MET cc_start: 0.8700 (OUTLIER) cc_final: 0.8498 (mmm) REVERT: Q 5 ASN cc_start: 0.9321 (t0) cc_final: 0.9090 (t160) REVERT: Q 135 GLU cc_start: 0.8246 (mt-10) cc_final: 0.8016 (mt-10) REVERT: S 90 GLU cc_start: 0.8611 (tm-30) cc_final: 0.8404 (tp30) REVERT: U 21 LYS cc_start: 0.8906 (OUTLIER) cc_final: 0.8643 (pmtt) REVERT: U 49 GLU cc_start: 0.8659 (pt0) cc_final: 0.8409 (pm20) REVERT: U 61 ASP cc_start: 0.8108 (OUTLIER) cc_final: 0.7567 (p0) REVERT: U 164 MET cc_start: 0.4020 (pmm) cc_final: 0.2329 (tpp) REVERT: W 11 LYS cc_start: 0.8160 (mmmm) cc_final: 0.7679 (mmmm) REVERT: W 29 ASN cc_start: 0.8047 (t0) cc_final: 0.7762 (t0) REVERT: W 55 TYR cc_start: 0.7975 (t80) cc_final: 0.7562 (t80) REVERT: W 142 LYS cc_start: 0.9327 (ttpp) cc_final: 0.9049 (tttp) REVERT: W 212 MET cc_start: 0.3979 (tpp) cc_final: 0.3480 (tpt) REVERT: X 21 ARG cc_start: 0.8289 (ttp80) cc_final: 0.8051 (ttp80) REVERT: X 103 GLU cc_start: 0.8448 (OUTLIER) cc_final: 0.8214 (tp30) REVERT: Y 90 LEU cc_start: 0.7656 (OUTLIER) cc_final: 0.7396 (pp) REVERT: Y 147 TRP cc_start: 0.7821 (OUTLIER) cc_final: 0.7412 (m-90) REVERT: Y 329 LEU cc_start: 0.9116 (OUTLIER) cc_final: 0.8804 (mt) REVERT: Y 341 ASP cc_start: 0.8079 (m-30) cc_final: 0.7755 (m-30) REVERT: Y 503 ARG cc_start: 0.7799 (OUTLIER) cc_final: 0.7576 (pmt-80) REVERT: Y 818 PHE cc_start: 0.8160 (m-80) cc_final: 0.7933 (m-80) REVERT: d 105 ARG cc_start: 0.8730 (OUTLIER) cc_final: 0.8348 (ptm160) REVERT: d 111 ARG cc_start: 0.8777 (OUTLIER) cc_final: 0.8379 (ttm-80) REVERT: f 139 LEU cc_start: 0.7355 (OUTLIER) cc_final: 0.7078 (mm) REVERT: g 32 SER cc_start: 0.8717 (OUTLIER) cc_final: 0.8211 (m) REVERT: g 241 ILE cc_start: 0.1108 (OUTLIER) cc_final: 0.0666 (mp) REVERT: h 53 GLU cc_start: 0.8459 (OUTLIER) cc_final: 0.8043 (pm20) REVERT: h 102 GLU cc_start: 0.8299 (OUTLIER) cc_final: 0.8057 (mp0) REVERT: k 17 LEU cc_start: 0.9034 (OUTLIER) cc_final: 0.8817 (mt) REVERT: l 212 MET cc_start: 0.5440 (OUTLIER) cc_final: 0.4354 (tmm) REVERT: n 61 ASP cc_start: 0.8113 (OUTLIER) cc_final: 0.7651 (p0) REVERT: n 91 GLN cc_start: 0.8107 (pp30) cc_final: 0.7803 (pm20) REVERT: n 164 MET cc_start: 0.3977 (pmm) cc_final: 0.2772 (tpp) REVERT: o 102 GLU cc_start: 0.8451 (OUTLIER) cc_final: 0.8070 (pp20) outliers start: 553 outliers final: 327 residues processed: 1186 average time/residue: 1.4687 time to fit residues: 2370.9712 Evaluate side-chains 1071 residues out of total 8352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 361 poor density : 710 time to evaluate : 6.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 46 VAL Chi-restraints excluded: chain M residue 47 THR Chi-restraints excluded: chain M residue 50 VAL Chi-restraints excluded: chain M residue 95 MET Chi-restraints excluded: chain J residue 26 VAL Chi-restraints excluded: chain J residue 30 ILE Chi-restraints excluded: chain J residue 47 LEU Chi-restraints excluded: chain J residue 88 THR Chi-restraints excluded: chain J residue 122 VAL Chi-restraints excluded: chain J residue 138 LEU Chi-restraints excluded: chain J residue 149 THR Chi-restraints excluded: chain J residue 153 ILE Chi-restraints excluded: chain J residue 167 VAL Chi-restraints excluded: chain J residue 168 VAL Chi-restraints excluded: chain J residue 177 PHE Chi-restraints excluded: chain J residue 215 THR Chi-restraints excluded: chain J residue 241 ARG Chi-restraints excluded: chain J residue 257 SER Chi-restraints excluded: chain J residue 325 CYS Chi-restraints excluded: chain J residue 381 ASP Chi-restraints excluded: chain J residue 504 THR Chi-restraints excluded: chain J residue 511 ILE Chi-restraints excluded: chain J residue 539 THR Chi-restraints excluded: chain J residue 542 VAL Chi-restraints excluded: chain J residue 596 GLU Chi-restraints excluded: chain J residue 598 ILE Chi-restraints excluded: chain J residue 613 VAL Chi-restraints excluded: chain J residue 621 VAL Chi-restraints excluded: chain J residue 638 LEU Chi-restraints excluded: chain J residue 703 ASP Chi-restraints excluded: chain J residue 719 ARG Chi-restraints excluded: chain J residue 721 GLU Chi-restraints excluded: chain J residue 823 THR Chi-restraints excluded: chain J residue 827 LEU Chi-restraints excluded: chain m residue 7 LYS Chi-restraints excluded: chain m residue 46 VAL Chi-restraints excluded: chain m residue 74 THR Chi-restraints excluded: chain L residue 99 VAL Chi-restraints excluded: chain L residue 151 VAL Chi-restraints excluded: chain L residue 159 ASP Chi-restraints excluded: chain H residue 844 ASP Chi-restraints excluded: chain I residue 118 THR Chi-restraints excluded: chain I residue 161 THR Chi-restraints excluded: chain I residue 167 THR Chi-restraints excluded: chain I residue 185 GLN Chi-restraints excluded: chain I residue 207 ILE Chi-restraints excluded: chain V residue 17 LEU Chi-restraints excluded: chain V residue 51 THR Chi-restraints excluded: chain V residue 70 THR Chi-restraints excluded: chain V residue 83 THR Chi-restraints excluded: chain V residue 90 GLU Chi-restraints excluded: chain V residue 146 VAL Chi-restraints excluded: chain V residue 166 VAL Chi-restraints excluded: chain V residue 225 ASN Chi-restraints excluded: chain v residue 33 ASP Chi-restraints excluded: chain v residue 70 THR Chi-restraints excluded: chain v residue 97 LEU Chi-restraints excluded: chain v residue 102 GLU Chi-restraints excluded: chain v residue 119 VAL Chi-restraints excluded: chain v residue 132 THR Chi-restraints excluded: chain v residue 179 THR Chi-restraints excluded: chain v residue 219 VAL Chi-restraints excluded: chain B residue 72 GLN Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain B residue 135 GLU Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 182 THR Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 199 SER Chi-restraints excluded: chain b residue 70 THR Chi-restraints excluded: chain b residue 84 LEU Chi-restraints excluded: chain b residue 87 MET Chi-restraints excluded: chain b residue 146 VAL Chi-restraints excluded: chain b residue 180 THR Chi-restraints excluded: chain A residue 17 LEU Chi-restraints excluded: chain A residue 83 THR Chi-restraints excluded: chain A residue 125 SER Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 140 THR Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 191 THR Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain a residue 102 GLU Chi-restraints excluded: chain a residue 119 VAL Chi-restraints excluded: chain a residue 132 THR Chi-restraints excluded: chain a residue 138 THR Chi-restraints excluded: chain a residue 185 PHE Chi-restraints excluded: chain a residue 207 VAL Chi-restraints excluded: chain a residue 212 MET Chi-restraints excluded: chain a residue 242 THR Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 17 LEU Chi-restraints excluded: chain C residue 21 LYS Chi-restraints excluded: chain C residue 61 ASP Chi-restraints excluded: chain C residue 83 THR Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain c residue 7 THR Chi-restraints excluded: chain c residue 45 LEU Chi-restraints excluded: chain c residue 83 THR Chi-restraints excluded: chain c residue 102 GLU Chi-restraints excluded: chain c residue 117 VAL Chi-restraints excluded: chain c residue 132 THR Chi-restraints excluded: chain c residue 240 GLU Chi-restraints excluded: chain D residue 13 ASP Chi-restraints excluded: chain D residue 46 VAL Chi-restraints excluded: chain D residue 47 THR Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 103 GLU Chi-restraints excluded: chain E residue 5 SER Chi-restraints excluded: chain E residue 21 THR Chi-restraints excluded: chain E residue 26 VAL Chi-restraints excluded: chain E residue 109 ILE Chi-restraints excluded: chain E residue 122 VAL Chi-restraints excluded: chain E residue 138 LEU Chi-restraints excluded: chain E residue 139 VAL Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain E residue 168 VAL Chi-restraints excluded: chain E residue 177 PHE Chi-restraints excluded: chain E residue 215 THR Chi-restraints excluded: chain E residue 217 LEU Chi-restraints excluded: chain E residue 324 THR Chi-restraints excluded: chain E residue 325 CYS Chi-restraints excluded: chain E residue 329 LEU Chi-restraints excluded: chain E residue 330 THR Chi-restraints excluded: chain E residue 373 ARG Chi-restraints excluded: chain E residue 374 SER Chi-restraints excluded: chain E residue 431 THR Chi-restraints excluded: chain E residue 504 THR Chi-restraints excluded: chain E residue 511 ILE Chi-restraints excluded: chain E residue 531 VAL Chi-restraints excluded: chain E residue 542 VAL Chi-restraints excluded: chain E residue 596 GLU Chi-restraints excluded: chain E residue 598 ILE Chi-restraints excluded: chain E residue 613 VAL Chi-restraints excluded: chain E residue 648 LYS Chi-restraints excluded: chain E residue 751 LYS Chi-restraints excluded: chain E residue 756 ILE Chi-restraints excluded: chain E residue 783 HIS Chi-restraints excluded: chain E residue 823 THR Chi-restraints excluded: chain E residue 826 HIS Chi-restraints excluded: chain F residue 12 MET Chi-restraints excluded: chain F residue 46 VAL Chi-restraints excluded: chain F residue 50 VAL Chi-restraints excluded: chain F residue 58 LEU Chi-restraints excluded: chain G residue 31 VAL Chi-restraints excluded: chain G residue 99 VAL Chi-restraints excluded: chain G residue 159 ASP Chi-restraints excluded: chain K residue 842 MET Chi-restraints excluded: chain N residue 107 LEU Chi-restraints excluded: chain N residue 118 THR Chi-restraints excluded: chain N residue 142 LEU Chi-restraints excluded: chain N residue 160 ARG Chi-restraints excluded: chain N residue 161 THR Chi-restraints excluded: chain N residue 167 THR Chi-restraints excluded: chain N residue 171 LYS Chi-restraints excluded: chain O residue 51 THR Chi-restraints excluded: chain O residue 54 SER Chi-restraints excluded: chain O residue 58 SER Chi-restraints excluded: chain O residue 63 GLU Chi-restraints excluded: chain O residue 68 THR Chi-restraints excluded: chain O residue 70 THR Chi-restraints excluded: chain O residue 81 SER Chi-restraints excluded: chain O residue 83 THR Chi-restraints excluded: chain O residue 132 THR Chi-restraints excluded: chain O residue 146 VAL Chi-restraints excluded: chain O residue 217 ASN Chi-restraints excluded: chain O residue 225 ASN Chi-restraints excluded: chain P residue 31 LEU Chi-restraints excluded: chain P residue 70 THR Chi-restraints excluded: chain P residue 97 LEU Chi-restraints excluded: chain P residue 117 VAL Chi-restraints excluded: chain P residue 119 VAL Chi-restraints excluded: chain P residue 132 THR Chi-restraints excluded: chain P residue 179 THR Chi-restraints excluded: chain P residue 219 VAL Chi-restraints excluded: chain Q residue 119 VAL Chi-restraints excluded: chain Q residue 131 VAL Chi-restraints excluded: chain Q residue 132 THR Chi-restraints excluded: chain Q residue 165 THR Chi-restraints excluded: chain Q residue 180 THR Chi-restraints excluded: chain Q residue 182 THR Chi-restraints excluded: chain Q residue 191 THR Chi-restraints excluded: chain Q residue 198 VAL Chi-restraints excluded: chain R residue 17 LEU Chi-restraints excluded: chain R residue 23 SER Chi-restraints excluded: chain R residue 42 VAL Chi-restraints excluded: chain R residue 51 THR Chi-restraints excluded: chain R residue 64 ASP Chi-restraints excluded: chain R residue 70 THR Chi-restraints excluded: chain R residue 84 LEU Chi-restraints excluded: chain R residue 116 THR Chi-restraints excluded: chain R residue 131 VAL Chi-restraints excluded: chain R residue 132 THR Chi-restraints excluded: chain R residue 158 VAL Chi-restraints excluded: chain R residue 180 THR Chi-restraints excluded: chain R residue 240 GLU Chi-restraints excluded: chain S residue 34 VAL Chi-restraints excluded: chain S residue 83 THR Chi-restraints excluded: chain S residue 125 SER Chi-restraints excluded: chain S residue 127 ILE Chi-restraints excluded: chain S residue 132 THR Chi-restraints excluded: chain S residue 190 VAL Chi-restraints excluded: chain S residue 191 THR Chi-restraints excluded: chain S residue 198 VAL Chi-restraints excluded: chain S residue 215 THR Chi-restraints excluded: chain S residue 224 VAL Chi-restraints excluded: chain T residue 17 LEU Chi-restraints excluded: chain T residue 117 VAL Chi-restraints excluded: chain T residue 119 VAL Chi-restraints excluded: chain T residue 138 THR Chi-restraints excluded: chain T residue 207 VAL Chi-restraints excluded: chain T residue 212 MET Chi-restraints excluded: chain U residue 17 LEU Chi-restraints excluded: chain U residue 21 LYS Chi-restraints excluded: chain U residue 61 ASP Chi-restraints excluded: chain U residue 83 THR Chi-restraints excluded: chain U residue 141 VAL Chi-restraints excluded: chain U residue 146 VAL Chi-restraints excluded: chain U residue 165 THR Chi-restraints excluded: chain U residue 179 THR Chi-restraints excluded: chain U residue 212 MET Chi-restraints excluded: chain W residue 7 THR Chi-restraints excluded: chain W residue 83 THR Chi-restraints excluded: chain W residue 110 ILE Chi-restraints excluded: chain W residue 117 VAL Chi-restraints excluded: chain X residue 46 VAL Chi-restraints excluded: chain X residue 47 THR Chi-restraints excluded: chain X residue 50 VAL Chi-restraints excluded: chain X residue 64 GLU Chi-restraints excluded: chain X residue 103 GLU Chi-restraints excluded: chain X residue 109 ASN Chi-restraints excluded: chain Y residue 21 THR Chi-restraints excluded: chain Y residue 26 VAL Chi-restraints excluded: chain Y residue 31 SER Chi-restraints excluded: chain Y residue 39 VAL Chi-restraints excluded: chain Y residue 50 THR Chi-restraints excluded: chain Y residue 65 THR Chi-restraints excluded: chain Y residue 88 THR Chi-restraints excluded: chain Y residue 90 LEU Chi-restraints excluded: chain Y residue 122 VAL Chi-restraints excluded: chain Y residue 138 LEU Chi-restraints excluded: chain Y residue 147 TRP Chi-restraints excluded: chain Y residue 149 THR Chi-restraints excluded: chain Y residue 153 ILE Chi-restraints excluded: chain Y residue 167 VAL Chi-restraints excluded: chain Y residue 168 VAL Chi-restraints excluded: chain Y residue 177 PHE Chi-restraints excluded: chain Y residue 215 THR Chi-restraints excluded: chain Y residue 217 LEU Chi-restraints excluded: chain Y residue 324 THR Chi-restraints excluded: chain Y residue 325 CYS Chi-restraints excluded: chain Y residue 329 LEU Chi-restraints excluded: chain Y residue 330 THR Chi-restraints excluded: chain Y residue 381 ASP Chi-restraints excluded: chain Y residue 397 ASN Chi-restraints excluded: chain Y residue 433 MET Chi-restraints excluded: chain Y residue 503 ARG Chi-restraints excluded: chain Y residue 504 THR Chi-restraints excluded: chain Y residue 511 ILE Chi-restraints excluded: chain Y residue 521 ILE Chi-restraints excluded: chain Y residue 531 VAL Chi-restraints excluded: chain Y residue 536 GLN Chi-restraints excluded: chain Y residue 539 THR Chi-restraints excluded: chain Y residue 542 VAL Chi-restraints excluded: chain Y residue 566 LEU Chi-restraints excluded: chain Y residue 574 VAL Chi-restraints excluded: chain Y residue 596 GLU Chi-restraints excluded: chain Y residue 613 VAL Chi-restraints excluded: chain Y residue 621 VAL Chi-restraints excluded: chain Y residue 638 LEU Chi-restraints excluded: chain Y residue 667 LEU Chi-restraints excluded: chain Y residue 823 THR Chi-restraints excluded: chain Y residue 827 LEU Chi-restraints excluded: chain Z residue 46 VAL Chi-restraints excluded: chain Z residue 58 LEU Chi-restraints excluded: chain Z residue 74 THR Chi-restraints excluded: chain Z residue 98 VAL Chi-restraints excluded: chain Z residue 109 ASN Chi-restraints excluded: chain d residue 31 VAL Chi-restraints excluded: chain d residue 105 ARG Chi-restraints excluded: chain d residue 111 ARG Chi-restraints excluded: chain d residue 159 ASP Chi-restraints excluded: chain e residue 847 LEU Chi-restraints excluded: chain e residue 849 SER Chi-restraints excluded: chain f residue 107 LEU Chi-restraints excluded: chain f residue 118 THR Chi-restraints excluded: chain f residue 139 LEU Chi-restraints excluded: chain f residue 161 THR Chi-restraints excluded: chain f residue 167 THR Chi-restraints excluded: chain f residue 188 VAL Chi-restraints excluded: chain f residue 191 VAL Chi-restraints excluded: chain f residue 203 VAL Chi-restraints excluded: chain f residue 204 SER Chi-restraints excluded: chain f residue 207 ILE Chi-restraints excluded: chain g residue 32 SER Chi-restraints excluded: chain g residue 51 THR Chi-restraints excluded: chain g residue 63 GLU Chi-restraints excluded: chain g residue 70 THR Chi-restraints excluded: chain g residue 83 THR Chi-restraints excluded: chain g residue 117 VAL Chi-restraints excluded: chain g residue 146 VAL Chi-restraints excluded: chain g residue 166 VAL Chi-restraints excluded: chain g residue 191 THR Chi-restraints excluded: chain g residue 225 ASN Chi-restraints excluded: chain g residue 241 ILE Chi-restraints excluded: chain h residue 31 LEU Chi-restraints excluded: chain h residue 53 GLU Chi-restraints excluded: chain h residue 70 THR Chi-restraints excluded: chain h residue 102 GLU Chi-restraints excluded: chain h residue 119 VAL Chi-restraints excluded: chain h residue 132 THR Chi-restraints excluded: chain h residue 158 VAL Chi-restraints excluded: chain h residue 179 THR Chi-restraints excluded: chain i residue 17 LEU Chi-restraints excluded: chain i residue 131 VAL Chi-restraints excluded: chain i residue 183 VAL Chi-restraints excluded: chain i residue 198 VAL Chi-restraints excluded: chain j residue 54 SER Chi-restraints excluded: chain j residue 64 ASP Chi-restraints excluded: chain j residue 70 THR Chi-restraints excluded: chain j residue 84 LEU Chi-restraints excluded: chain j residue 125 SER Chi-restraints excluded: chain j residue 132 THR Chi-restraints excluded: chain j residue 135 GLU Chi-restraints excluded: chain j residue 138 THR Chi-restraints excluded: chain j residue 146 VAL Chi-restraints excluded: chain j residue 158 VAL Chi-restraints excluded: chain j residue 180 THR Chi-restraints excluded: chain k residue 17 LEU Chi-restraints excluded: chain k residue 83 THR Chi-restraints excluded: chain k residue 136 VAL Chi-restraints excluded: chain k residue 146 VAL Chi-restraints excluded: chain k residue 186 GLN Chi-restraints excluded: chain k residue 190 VAL Chi-restraints excluded: chain k residue 198 VAL Chi-restraints excluded: chain k residue 215 THR Chi-restraints excluded: chain k residue 224 VAL Chi-restraints excluded: chain l residue 3 VAL Chi-restraints excluded: chain l residue 70 THR Chi-restraints excluded: chain l residue 140 THR Chi-restraints excluded: chain l residue 198 VAL Chi-restraints excluded: chain l residue 207 VAL Chi-restraints excluded: chain l residue 212 MET Chi-restraints excluded: chain l residue 219 VAL Chi-restraints excluded: chain n residue 61 ASP Chi-restraints excluded: chain n residue 83 THR Chi-restraints excluded: chain n residue 97 LEU Chi-restraints excluded: chain n residue 101 ASN Chi-restraints excluded: chain n residue 141 VAL Chi-restraints excluded: chain n residue 146 VAL Chi-restraints excluded: chain o residue 7 THR Chi-restraints excluded: chain o residue 45 LEU Chi-restraints excluded: chain o residue 83 THR Chi-restraints excluded: chain o residue 102 GLU Chi-restraints excluded: chain o residue 110 ILE Chi-restraints excluded: chain o residue 117 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1008 random chunks: chunk 327 optimal weight: 9.9990 chunk 877 optimal weight: 3.9990 chunk 192 optimal weight: 0.0060 chunk 572 optimal weight: 20.0000 chunk 240 optimal weight: 2.9990 chunk 975 optimal weight: 0.0370 chunk 809 optimal weight: 6.9990 chunk 451 optimal weight: 3.9990 chunk 81 optimal weight: 20.0000 chunk 322 optimal weight: 0.9990 chunk 512 optimal weight: 0.9980 overall best weight: 1.0078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 178 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 72 GLN B 94 GLN A 91 GLN ** c 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 91 GLN ** E 826 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 217 ASN Q 91 GLN ** W 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 235 ASN ** Z 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 217 GLN j 74 GLN ** o 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 91 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8270 moved from start: 0.1207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 78954 Z= 0.195 Angle : 0.605 18.381 107580 Z= 0.310 Chirality : 0.046 0.284 12384 Planarity : 0.005 0.177 13893 Dihedral : 6.678 59.944 11134 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.57 % Allowed : 6.56 % Favored : 92.87 % Rotamer: Outliers : 5.56 % Allowed : 31.27 % Favored : 63.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.63 % Cis-general : 0.00 % Twisted Proline : 1.26 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.53 (0.08), residues: 10164 helix: 0.65 (0.18), residues: 891 sheet: -0.57 (0.08), residues: 4077 loop : -1.68 (0.08), residues: 5196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP D 89 HIS 0.006 0.001 HIS E 826 PHE 0.017 0.001 PHE Y 818 TYR 0.023 0.001 TYR E 771 ARG 0.015 0.000 ARG n 121 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 20328 Ramachandran restraints generated. 10164 Oldfield, 0 Emsley, 10164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 20328 Ramachandran restraints generated. 10164 Oldfield, 0 Emsley, 10164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1212 residues out of total 8352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 464 poor density : 748 time to evaluate : 6.377 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 13 ASP cc_start: 0.8406 (m-30) cc_final: 0.8074 (t0) REVERT: J 719 ARG cc_start: 0.7844 (OUTLIER) cc_final: 0.7524 (ttp-110) REVERT: J 721 GLU cc_start: 0.6138 (OUTLIER) cc_final: 0.5901 (mp0) REVERT: J 757 ARG cc_start: 0.8198 (mtm110) cc_final: 0.7970 (mtm110) REVERT: J 758 GLN cc_start: 0.8155 (mm110) cc_final: 0.7804 (tt0) REVERT: J 783 HIS cc_start: 0.8547 (m-70) cc_final: 0.7974 (m-70) REVERT: m 92 ARG cc_start: 0.8286 (tpp80) cc_final: 0.7866 (ttp80) REVERT: m 103 GLU cc_start: 0.7817 (pp20) cc_final: 0.7415 (pp20) REVERT: L 1 MET cc_start: 0.6669 (OUTLIER) cc_final: 0.5820 (mmt) REVERT: I 185 GLN cc_start: 0.8355 (OUTLIER) cc_final: 0.8064 (tt0) REVERT: v 102 GLU cc_start: 0.8345 (OUTLIER) cc_final: 0.8008 (mp0) REVERT: B 57 ASP cc_start: 0.8766 (t0) cc_final: 0.8472 (t0) REVERT: B 135 GLU cc_start: 0.7993 (OUTLIER) cc_final: 0.7569 (mt-10) REVERT: b 29 ASN cc_start: 0.8980 (t0) cc_final: 0.8726 (t0) REVERT: b 43 LYS cc_start: 0.8888 (OUTLIER) cc_final: 0.8413 (mmpt) REVERT: b 87 MET cc_start: 0.8331 (OUTLIER) cc_final: 0.7543 (mpp) REVERT: A 90 GLU cc_start: 0.8593 (tm-30) cc_final: 0.8257 (tm-30) REVERT: C 21 LYS cc_start: 0.8936 (OUTLIER) cc_final: 0.8532 (pmtt) REVERT: C 155 ARG cc_start: 0.7530 (mtm110) cc_final: 0.6946 (ptt-90) REVERT: c 11 LYS cc_start: 0.8171 (mmmm) cc_final: 0.7604 (mmmm) REVERT: c 43 LYS cc_start: 0.6571 (mmpt) cc_final: 0.6338 (mmpt) REVERT: c 53 GLU cc_start: 0.8748 (pt0) cc_final: 0.8506 (pt0) REVERT: c 87 MET cc_start: 0.8693 (mmt) cc_final: 0.7605 (mmt) REVERT: c 90 GLU cc_start: 0.9085 (pt0) cc_final: 0.8568 (pt0) REVERT: c 94 GLN cc_start: 0.7708 (OUTLIER) cc_final: 0.6791 (mp10) REVERT: c 102 GLU cc_start: 0.8406 (OUTLIER) cc_final: 0.8128 (pp20) REVERT: c 212 MET cc_start: 0.3026 (OUTLIER) cc_final: 0.1772 (tpp) REVERT: D 24 ARG cc_start: 0.7998 (ttp80) cc_final: 0.7473 (ttp80) REVERT: D 103 GLU cc_start: 0.8290 (OUTLIER) cc_final: 0.8089 (tp30) REVERT: E 147 TRP cc_start: 0.7404 (m100) cc_final: 0.5918 (m100) REVERT: E 751 LYS cc_start: 0.9087 (OUTLIER) cc_final: 0.8854 (pmtt) REVERT: F 50 VAL cc_start: 0.8747 (OUTLIER) cc_final: 0.8489 (m) REVERT: O 90 GLU cc_start: 0.8214 (OUTLIER) cc_final: 0.7834 (pt0) REVERT: Q 5 ASN cc_start: 0.9304 (t0) cc_final: 0.9083 (t160) REVERT: Q 135 GLU cc_start: 0.8090 (mt-10) cc_final: 0.7775 (mt-10) REVERT: T 64 ASP cc_start: 0.7299 (OUTLIER) cc_final: 0.7039 (p0) REVERT: U 21 LYS cc_start: 0.8895 (OUTLIER) cc_final: 0.8641 (pmtt) REVERT: U 49 GLU cc_start: 0.8680 (pt0) cc_final: 0.8410 (pm20) REVERT: U 61 ASP cc_start: 0.8065 (OUTLIER) cc_final: 0.7477 (p0) REVERT: U 135 GLU cc_start: 0.8853 (mm-30) cc_final: 0.8584 (tp30) REVERT: U 164 MET cc_start: 0.4002 (pmm) cc_final: 0.2381 (tpp) REVERT: W 11 LYS cc_start: 0.8199 (mmmm) cc_final: 0.7732 (mmmm) REVERT: W 29 ASN cc_start: 0.8038 (t0) cc_final: 0.7721 (t0) REVERT: W 142 LYS cc_start: 0.9342 (ttpp) cc_final: 0.9050 (tttp) REVERT: X 21 ARG cc_start: 0.8330 (ttp80) cc_final: 0.8111 (ttp80) REVERT: X 103 GLU cc_start: 0.8417 (OUTLIER) cc_final: 0.8201 (tp30) REVERT: Y 90 LEU cc_start: 0.7605 (OUTLIER) cc_final: 0.7309 (pp) REVERT: Y 147 TRP cc_start: 0.7776 (OUTLIER) cc_final: 0.7356 (m-90) REVERT: Y 329 LEU cc_start: 0.9054 (OUTLIER) cc_final: 0.8734 (mt) REVERT: Y 341 ASP cc_start: 0.8083 (m-30) cc_final: 0.7764 (m-30) REVERT: Y 721 GLU cc_start: 0.6012 (OUTLIER) cc_final: 0.5759 (mp0) REVERT: Y 818 PHE cc_start: 0.8143 (m-80) cc_final: 0.7930 (m-80) REVERT: d 105 ARG cc_start: 0.8743 (OUTLIER) cc_final: 0.8369 (ptm160) REVERT: d 111 ARG cc_start: 0.8662 (OUTLIER) cc_final: 0.8379 (ttm-80) REVERT: f 139 LEU cc_start: 0.7269 (OUTLIER) cc_final: 0.7043 (mm) REVERT: h 53 GLU cc_start: 0.8440 (OUTLIER) cc_final: 0.8043 (pm20) REVERT: h 102 GLU cc_start: 0.8273 (OUTLIER) cc_final: 0.8054 (mp0) REVERT: k 90 GLU cc_start: 0.8598 (tm-30) cc_final: 0.8269 (tm-30) REVERT: l 64 ASP cc_start: 0.7514 (OUTLIER) cc_final: 0.7193 (p0) REVERT: n 61 ASP cc_start: 0.7960 (OUTLIER) cc_final: 0.7630 (p0) REVERT: n 164 MET cc_start: 0.3916 (pmm) cc_final: 0.2681 (tpp) REVERT: o 11 LYS cc_start: 0.8173 (mmmm) cc_final: 0.7612 (mmmm) REVERT: o 16 THR cc_start: 0.8244 (OUTLIER) cc_final: 0.7942 (t) REVERT: o 102 GLU cc_start: 0.8451 (OUTLIER) cc_final: 0.8077 (pp20) outliers start: 464 outliers final: 286 residues processed: 1139 average time/residue: 1.5122 time to fit residues: 2320.5274 Evaluate side-chains 1046 residues out of total 8352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 319 poor density : 727 time to evaluate : 6.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 46 VAL Chi-restraints excluded: chain M residue 47 THR Chi-restraints excluded: chain M residue 50 VAL Chi-restraints excluded: chain M residue 95 MET Chi-restraints excluded: chain M residue 99 GLU Chi-restraints excluded: chain M residue 109 ASN Chi-restraints excluded: chain J residue 26 VAL Chi-restraints excluded: chain J residue 47 LEU Chi-restraints excluded: chain J residue 65 THR Chi-restraints excluded: chain J residue 88 THR Chi-restraints excluded: chain J residue 122 VAL Chi-restraints excluded: chain J residue 138 LEU Chi-restraints excluded: chain J residue 149 THR Chi-restraints excluded: chain J residue 153 ILE Chi-restraints excluded: chain J residue 167 VAL Chi-restraints excluded: chain J residue 168 VAL Chi-restraints excluded: chain J residue 177 PHE Chi-restraints excluded: chain J residue 215 THR Chi-restraints excluded: chain J residue 257 SER Chi-restraints excluded: chain J residue 325 CYS Chi-restraints excluded: chain J residue 381 ASP Chi-restraints excluded: chain J residue 504 THR Chi-restraints excluded: chain J residue 511 ILE Chi-restraints excluded: chain J residue 539 THR Chi-restraints excluded: chain J residue 596 GLU Chi-restraints excluded: chain J residue 598 ILE Chi-restraints excluded: chain J residue 613 VAL Chi-restraints excluded: chain J residue 621 VAL Chi-restraints excluded: chain J residue 667 LEU Chi-restraints excluded: chain J residue 719 ARG Chi-restraints excluded: chain J residue 721 GLU Chi-restraints excluded: chain J residue 823 THR Chi-restraints excluded: chain J residue 827 LEU Chi-restraints excluded: chain m residue 46 VAL Chi-restraints excluded: chain m residue 74 THR Chi-restraints excluded: chain L residue 1 MET Chi-restraints excluded: chain L residue 31 VAL Chi-restraints excluded: chain L residue 99 VAL Chi-restraints excluded: chain L residue 159 ASP Chi-restraints excluded: chain H residue 844 ASP Chi-restraints excluded: chain I residue 105 ILE Chi-restraints excluded: chain I residue 118 THR Chi-restraints excluded: chain I residue 161 THR Chi-restraints excluded: chain I residue 167 THR Chi-restraints excluded: chain I residue 185 GLN Chi-restraints excluded: chain I residue 207 ILE Chi-restraints excluded: chain V residue 51 THR Chi-restraints excluded: chain V residue 70 THR Chi-restraints excluded: chain V residue 83 THR Chi-restraints excluded: chain V residue 146 VAL Chi-restraints excluded: chain v residue 10 VAL Chi-restraints excluded: chain v residue 32 SER Chi-restraints excluded: chain v residue 33 ASP Chi-restraints excluded: chain v residue 70 THR Chi-restraints excluded: chain v residue 84 LEU Chi-restraints excluded: chain v residue 97 LEU Chi-restraints excluded: chain v residue 102 GLU Chi-restraints excluded: chain v residue 119 VAL Chi-restraints excluded: chain v residue 179 THR Chi-restraints excluded: chain B residue 87 MET Chi-restraints excluded: chain B residue 135 GLU Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 182 THR Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 199 SER Chi-restraints excluded: chain b residue 43 LYS Chi-restraints excluded: chain b residue 84 LEU Chi-restraints excluded: chain b residue 87 MET Chi-restraints excluded: chain b residue 97 LEU Chi-restraints excluded: chain b residue 110 ILE Chi-restraints excluded: chain b residue 146 VAL Chi-restraints excluded: chain b residue 180 THR Chi-restraints excluded: chain b residue 243 VAL Chi-restraints excluded: chain A residue 83 THR Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 148 ARG Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain a residue 119 VAL Chi-restraints excluded: chain a residue 185 PHE Chi-restraints excluded: chain a residue 212 MET Chi-restraints excluded: chain a residue 242 THR Chi-restraints excluded: chain C residue 17 LEU Chi-restraints excluded: chain C residue 21 LYS Chi-restraints excluded: chain C residue 83 THR Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 165 THR Chi-restraints excluded: chain c residue 7 THR Chi-restraints excluded: chain c residue 83 THR Chi-restraints excluded: chain c residue 94 GLN Chi-restraints excluded: chain c residue 102 GLU Chi-restraints excluded: chain c residue 117 VAL Chi-restraints excluded: chain c residue 132 THR Chi-restraints excluded: chain c residue 212 MET Chi-restraints excluded: chain D residue 13 ASP Chi-restraints excluded: chain D residue 46 VAL Chi-restraints excluded: chain D residue 47 THR Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 103 GLU Chi-restraints excluded: chain E residue 21 THR Chi-restraints excluded: chain E residue 26 VAL Chi-restraints excluded: chain E residue 65 THR Chi-restraints excluded: chain E residue 122 VAL Chi-restraints excluded: chain E residue 138 LEU Chi-restraints excluded: chain E residue 139 VAL Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain E residue 177 PHE Chi-restraints excluded: chain E residue 215 THR Chi-restraints excluded: chain E residue 324 THR Chi-restraints excluded: chain E residue 325 CYS Chi-restraints excluded: chain E residue 329 LEU Chi-restraints excluded: chain E residue 331 THR Chi-restraints excluded: chain E residue 374 SER Chi-restraints excluded: chain E residue 431 THR Chi-restraints excluded: chain E residue 504 THR Chi-restraints excluded: chain E residue 511 ILE Chi-restraints excluded: chain E residue 531 VAL Chi-restraints excluded: chain E residue 596 GLU Chi-restraints excluded: chain E residue 598 ILE Chi-restraints excluded: chain E residue 613 VAL Chi-restraints excluded: chain E residue 621 VAL Chi-restraints excluded: chain E residue 638 LEU Chi-restraints excluded: chain E residue 648 LYS Chi-restraints excluded: chain E residue 667 LEU Chi-restraints excluded: chain E residue 751 LYS Chi-restraints excluded: chain E residue 756 ILE Chi-restraints excluded: chain E residue 783 HIS Chi-restraints excluded: chain E residue 823 THR Chi-restraints excluded: chain F residue 50 VAL Chi-restraints excluded: chain G residue 99 VAL Chi-restraints excluded: chain G residue 159 ASP Chi-restraints excluded: chain N residue 118 THR Chi-restraints excluded: chain N residue 161 THR Chi-restraints excluded: chain N residue 167 THR Chi-restraints excluded: chain N residue 171 LYS Chi-restraints excluded: chain O residue 51 THR Chi-restraints excluded: chain O residue 54 SER Chi-restraints excluded: chain O residue 63 GLU Chi-restraints excluded: chain O residue 70 THR Chi-restraints excluded: chain O residue 81 SER Chi-restraints excluded: chain O residue 83 THR Chi-restraints excluded: chain O residue 90 GLU Chi-restraints excluded: chain O residue 132 THR Chi-restraints excluded: chain O residue 146 VAL Chi-restraints excluded: chain O residue 166 VAL Chi-restraints excluded: chain O residue 225 ASN Chi-restraints excluded: chain P residue 31 LEU Chi-restraints excluded: chain P residue 70 THR Chi-restraints excluded: chain P residue 84 LEU Chi-restraints excluded: chain P residue 97 LEU Chi-restraints excluded: chain P residue 117 VAL Chi-restraints excluded: chain P residue 119 VAL Chi-restraints excluded: chain P residue 179 THR Chi-restraints excluded: chain P residue 219 VAL Chi-restraints excluded: chain Q residue 16 THR Chi-restraints excluded: chain Q residue 97 LEU Chi-restraints excluded: chain Q residue 119 VAL Chi-restraints excluded: chain Q residue 126 SER Chi-restraints excluded: chain Q residue 131 VAL Chi-restraints excluded: chain Q residue 132 THR Chi-restraints excluded: chain Q residue 165 THR Chi-restraints excluded: chain Q residue 182 THR Chi-restraints excluded: chain Q residue 191 THR Chi-restraints excluded: chain Q residue 198 VAL Chi-restraints excluded: chain R residue 23 SER Chi-restraints excluded: chain R residue 42 VAL Chi-restraints excluded: chain R residue 64 ASP Chi-restraints excluded: chain R residue 84 LEU Chi-restraints excluded: chain R residue 125 SER Chi-restraints excluded: chain R residue 131 VAL Chi-restraints excluded: chain R residue 132 THR Chi-restraints excluded: chain R residue 158 VAL Chi-restraints excluded: chain S residue 34 VAL Chi-restraints excluded: chain S residue 83 THR Chi-restraints excluded: chain S residue 127 ILE Chi-restraints excluded: chain S residue 146 VAL Chi-restraints excluded: chain S residue 190 VAL Chi-restraints excluded: chain S residue 191 THR Chi-restraints excluded: chain S residue 198 VAL Chi-restraints excluded: chain S residue 215 THR Chi-restraints excluded: chain S residue 224 VAL Chi-restraints excluded: chain T residue 3 VAL Chi-restraints excluded: chain T residue 64 ASP Chi-restraints excluded: chain T residue 97 LEU Chi-restraints excluded: chain T residue 117 VAL Chi-restraints excluded: chain T residue 119 VAL Chi-restraints excluded: chain T residue 207 VAL Chi-restraints excluded: chain U residue 17 LEU Chi-restraints excluded: chain U residue 21 LYS Chi-restraints excluded: chain U residue 61 ASP Chi-restraints excluded: chain U residue 83 THR Chi-restraints excluded: chain U residue 141 VAL Chi-restraints excluded: chain U residue 146 VAL Chi-restraints excluded: chain U residue 165 THR Chi-restraints excluded: chain U residue 179 THR Chi-restraints excluded: chain U residue 212 MET Chi-restraints excluded: chain W residue 110 ILE Chi-restraints excluded: chain W residue 117 VAL Chi-restraints excluded: chain X residue 46 VAL Chi-restraints excluded: chain X residue 47 THR Chi-restraints excluded: chain X residue 50 VAL Chi-restraints excluded: chain X residue 64 GLU Chi-restraints excluded: chain X residue 103 GLU Chi-restraints excluded: chain X residue 109 ASN Chi-restraints excluded: chain Y residue 21 THR Chi-restraints excluded: chain Y residue 26 VAL Chi-restraints excluded: chain Y residue 50 THR Chi-restraints excluded: chain Y residue 65 THR Chi-restraints excluded: chain Y residue 88 THR Chi-restraints excluded: chain Y residue 90 LEU Chi-restraints excluded: chain Y residue 122 VAL Chi-restraints excluded: chain Y residue 138 LEU Chi-restraints excluded: chain Y residue 147 TRP Chi-restraints excluded: chain Y residue 149 THR Chi-restraints excluded: chain Y residue 153 ILE Chi-restraints excluded: chain Y residue 167 VAL Chi-restraints excluded: chain Y residue 168 VAL Chi-restraints excluded: chain Y residue 177 PHE Chi-restraints excluded: chain Y residue 215 THR Chi-restraints excluded: chain Y residue 217 LEU Chi-restraints excluded: chain Y residue 324 THR Chi-restraints excluded: chain Y residue 325 CYS Chi-restraints excluded: chain Y residue 329 LEU Chi-restraints excluded: chain Y residue 330 THR Chi-restraints excluded: chain Y residue 381 ASP Chi-restraints excluded: chain Y residue 433 MET Chi-restraints excluded: chain Y residue 469 GLU Chi-restraints excluded: chain Y residue 511 ILE Chi-restraints excluded: chain Y residue 531 VAL Chi-restraints excluded: chain Y residue 539 THR Chi-restraints excluded: chain Y residue 544 VAL Chi-restraints excluded: chain Y residue 574 VAL Chi-restraints excluded: chain Y residue 596 GLU Chi-restraints excluded: chain Y residue 613 VAL Chi-restraints excluded: chain Y residue 621 VAL Chi-restraints excluded: chain Y residue 638 LEU Chi-restraints excluded: chain Y residue 721 GLU Chi-restraints excluded: chain Y residue 823 THR Chi-restraints excluded: chain Y residue 827 LEU Chi-restraints excluded: chain Z residue 58 LEU Chi-restraints excluded: chain Z residue 74 THR Chi-restraints excluded: chain Z residue 98 VAL Chi-restraints excluded: chain d residue 31 VAL Chi-restraints excluded: chain d residue 99 VAL Chi-restraints excluded: chain d residue 105 ARG Chi-restraints excluded: chain d residue 111 ARG Chi-restraints excluded: chain d residue 159 ASP Chi-restraints excluded: chain d residue 167 ILE Chi-restraints excluded: chain e residue 847 LEU Chi-restraints excluded: chain e residue 849 SER Chi-restraints excluded: chain f residue 118 THR Chi-restraints excluded: chain f residue 139 LEU Chi-restraints excluded: chain f residue 161 THR Chi-restraints excluded: chain f residue 167 THR Chi-restraints excluded: chain f residue 188 VAL Chi-restraints excluded: chain f residue 191 VAL Chi-restraints excluded: chain f residue 204 SER Chi-restraints excluded: chain g residue 51 THR Chi-restraints excluded: chain g residue 63 GLU Chi-restraints excluded: chain g residue 70 THR Chi-restraints excluded: chain g residue 83 THR Chi-restraints excluded: chain g residue 146 VAL Chi-restraints excluded: chain g residue 191 THR Chi-restraints excluded: chain g residue 225 ASN Chi-restraints excluded: chain h residue 31 LEU Chi-restraints excluded: chain h residue 53 GLU Chi-restraints excluded: chain h residue 70 THR Chi-restraints excluded: chain h residue 84 LEU Chi-restraints excluded: chain h residue 102 GLU Chi-restraints excluded: chain h residue 119 VAL Chi-restraints excluded: chain h residue 132 THR Chi-restraints excluded: chain h residue 158 VAL Chi-restraints excluded: chain h residue 179 THR Chi-restraints excluded: chain i residue 16 THR Chi-restraints excluded: chain i residue 17 LEU Chi-restraints excluded: chain i residue 131 VAL Chi-restraints excluded: chain i residue 183 VAL Chi-restraints excluded: chain i residue 198 VAL Chi-restraints excluded: chain j residue 64 ASP Chi-restraints excluded: chain j residue 70 THR Chi-restraints excluded: chain j residue 84 LEU Chi-restraints excluded: chain j residue 125 SER Chi-restraints excluded: chain j residue 132 THR Chi-restraints excluded: chain j residue 135 GLU Chi-restraints excluded: chain j residue 138 THR Chi-restraints excluded: chain j residue 146 VAL Chi-restraints excluded: chain j residue 158 VAL Chi-restraints excluded: chain j residue 240 GLU Chi-restraints excluded: chain k residue 83 THR Chi-restraints excluded: chain k residue 132 THR Chi-restraints excluded: chain k residue 146 VAL Chi-restraints excluded: chain k residue 190 VAL Chi-restraints excluded: chain k residue 198 VAL Chi-restraints excluded: chain k residue 215 THR Chi-restraints excluded: chain k residue 224 VAL Chi-restraints excluded: chain l residue 3 VAL Chi-restraints excluded: chain l residue 64 ASP Chi-restraints excluded: chain l residue 97 LEU Chi-restraints excluded: chain l residue 180 THR Chi-restraints excluded: chain l residue 198 VAL Chi-restraints excluded: chain l residue 207 VAL Chi-restraints excluded: chain n residue 61 ASP Chi-restraints excluded: chain n residue 83 THR Chi-restraints excluded: chain n residue 97 LEU Chi-restraints excluded: chain n residue 101 ASN Chi-restraints excluded: chain n residue 140 THR Chi-restraints excluded: chain n residue 141 VAL Chi-restraints excluded: chain n residue 146 VAL Chi-restraints excluded: chain o residue 16 THR Chi-restraints excluded: chain o residue 83 THR Chi-restraints excluded: chain o residue 84 LEU Chi-restraints excluded: chain o residue 102 GLU Chi-restraints excluded: chain o residue 110 ILE Chi-restraints excluded: chain o residue 117 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1008 random chunks: chunk 940 optimal weight: 5.9990 chunk 109 optimal weight: 2.9990 chunk 555 optimal weight: 2.9990 chunk 712 optimal weight: 3.9990 chunk 551 optimal weight: 8.9990 chunk 820 optimal weight: 4.9990 chunk 544 optimal weight: 8.9990 chunk 971 optimal weight: 4.9990 chunk 608 optimal weight: 4.9990 chunk 592 optimal weight: 8.9990 chunk 448 optimal weight: 0.9980 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 178 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 91 GLN ** c 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 177 GLN E 397 ASN ** E 826 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 91 GLN ** W 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 91 GLN W 101 ASN X 38 ASN Y 235 ASN Y 536 GLN ** Z 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 217 GLN j 74 GLN ** o 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 91 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 moved from start: 0.1292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.079 78954 Z= 0.399 Angle : 0.684 20.672 107580 Z= 0.353 Chirality : 0.049 0.280 12384 Planarity : 0.006 0.181 13893 Dihedral : 6.890 59.787 11105 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.61 % Allowed : 7.88 % Favored : 91.51 % Rotamer: Outliers : 6.69 % Allowed : 30.15 % Favored : 63.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.63 % Cis-general : 0.00 % Twisted Proline : 1.26 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.68 (0.08), residues: 10164 helix: 0.36 (0.17), residues: 909 sheet: -0.64 (0.08), residues: 4041 loop : -1.78 (0.08), residues: 5214 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP M 89 HIS 0.007 0.001 HIS m 65 PHE 0.021 0.002 PHE j 120 TYR 0.021 0.002 TYR E 771 ARG 0.011 0.001 ARG n 121 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 20328 Ramachandran restraints generated. 10164 Oldfield, 0 Emsley, 10164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 20328 Ramachandran restraints generated. 10164 Oldfield, 0 Emsley, 10164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1287 residues out of total 8352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 559 poor density : 728 time to evaluate : 6.431 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 7 LYS cc_start: 0.8353 (OUTLIER) cc_final: 0.8130 (mtmm) REVERT: M 13 ASP cc_start: 0.8616 (m-30) cc_final: 0.8260 (t0) REVERT: M 95 MET cc_start: 0.9345 (OUTLIER) cc_final: 0.9063 (tpt) REVERT: J 241 ARG cc_start: 0.9013 (OUTLIER) cc_final: 0.8582 (mtp180) REVERT: J 719 ARG cc_start: 0.7855 (OUTLIER) cc_final: 0.7534 (ttp-110) REVERT: J 721 GLU cc_start: 0.6234 (OUTLIER) cc_final: 0.5977 (mp0) REVERT: J 758 GLN cc_start: 0.8196 (mm110) cc_final: 0.7848 (tt0) REVERT: J 783 HIS cc_start: 0.8509 (m-70) cc_final: 0.7926 (m-70) REVERT: m 103 GLU cc_start: 0.7807 (pp20) cc_final: 0.7350 (pp20) REVERT: B 57 ASP cc_start: 0.8804 (t0) cc_final: 0.8457 (t0) REVERT: B 135 GLU cc_start: 0.8055 (OUTLIER) cc_final: 0.7620 (mt-10) REVERT: b 29 ASN cc_start: 0.9048 (t0) cc_final: 0.8779 (t0) REVERT: b 43 LYS cc_start: 0.8960 (OUTLIER) cc_final: 0.8535 (mmpt) REVERT: b 87 MET cc_start: 0.8452 (OUTLIER) cc_final: 0.7677 (mpp) REVERT: A 90 GLU cc_start: 0.8567 (tm-30) cc_final: 0.8220 (tm-30) REVERT: C 21 LYS cc_start: 0.8999 (OUTLIER) cc_final: 0.8581 (pmtt) REVERT: C 121 ARG cc_start: 0.8137 (ttm-80) cc_final: 0.7922 (ttm110) REVERT: C 155 ARG cc_start: 0.7552 (mtm110) cc_final: 0.6812 (ptt-90) REVERT: C 196 ARG cc_start: 0.2201 (OUTLIER) cc_final: 0.1858 (ptt90) REVERT: c 43 LYS cc_start: 0.6626 (mmpt) cc_final: 0.6278 (mmpt) REVERT: c 53 GLU cc_start: 0.8765 (pt0) cc_final: 0.8547 (pt0) REVERT: c 87 MET cc_start: 0.8720 (mmt) cc_final: 0.7612 (mmt) REVERT: c 94 GLN cc_start: 0.7716 (OUTLIER) cc_final: 0.7346 (mt0) REVERT: c 102 GLU cc_start: 0.8432 (OUTLIER) cc_final: 0.8137 (pp20) REVERT: D 103 GLU cc_start: 0.8338 (OUTLIER) cc_final: 0.8135 (tp30) REVERT: E 147 TRP cc_start: 0.7431 (m100) cc_final: 0.6098 (m100) REVERT: E 231 GLN cc_start: 0.7548 (OUTLIER) cc_final: 0.7174 (mm110) REVERT: E 751 LYS cc_start: 0.9057 (OUTLIER) cc_final: 0.8853 (pmtt) REVERT: F 50 VAL cc_start: 0.8798 (OUTLIER) cc_final: 0.8571 (m) REVERT: O 241 ILE cc_start: 0.1197 (OUTLIER) cc_final: 0.0970 (mt) REVERT: P 8 MET cc_start: 0.8818 (mmp) cc_final: 0.8569 (mmm) REVERT: Q 5 ASN cc_start: 0.9339 (t0) cc_final: 0.9098 (t160) REVERT: Q 80 THR cc_start: 0.9160 (OUTLIER) cc_final: 0.8612 (p) REVERT: Q 135 GLU cc_start: 0.8246 (mt-10) cc_final: 0.7938 (mt-10) REVERT: U 21 LYS cc_start: 0.8885 (OUTLIER) cc_final: 0.8644 (pmtt) REVERT: U 135 GLU cc_start: 0.8935 (mm-30) cc_final: 0.8628 (tp30) REVERT: U 164 MET cc_start: 0.4021 (pmm) cc_final: 0.2358 (tpp) REVERT: W 11 LYS cc_start: 0.8288 (mmmm) cc_final: 0.7781 (mmmm) REVERT: W 29 ASN cc_start: 0.8074 (t0) cc_final: 0.7748 (t0) REVERT: W 142 LYS cc_start: 0.9338 (ttpp) cc_final: 0.9007 (tttp) REVERT: X 21 ARG cc_start: 0.8277 (ttp80) cc_final: 0.8017 (ttp80) REVERT: X 103 GLU cc_start: 0.8473 (OUTLIER) cc_final: 0.8234 (tp30) REVERT: Y 90 LEU cc_start: 0.7570 (OUTLIER) cc_final: 0.7307 (pp) REVERT: Y 147 TRP cc_start: 0.7876 (OUTLIER) cc_final: 0.7244 (m-90) REVERT: Y 329 LEU cc_start: 0.9153 (OUTLIER) cc_final: 0.8823 (mt) REVERT: Y 341 ASP cc_start: 0.8100 (m-30) cc_final: 0.7773 (m-30) REVERT: Y 373 ARG cc_start: 0.8278 (OUTLIER) cc_final: 0.7504 (ptm-80) REVERT: Y 721 GLU cc_start: 0.6008 (OUTLIER) cc_final: 0.5767 (mp0) REVERT: Y 818 PHE cc_start: 0.8201 (m-80) cc_final: 0.7970 (m-80) REVERT: d 105 ARG cc_start: 0.8765 (OUTLIER) cc_final: 0.8398 (ptm160) REVERT: d 111 ARG cc_start: 0.8789 (OUTLIER) cc_final: 0.8408 (ttm-80) REVERT: f 139 LEU cc_start: 0.7402 (OUTLIER) cc_final: 0.7116 (mm) REVERT: f 223 ARG cc_start: 0.5875 (ppt170) cc_final: 0.5668 (ptm-80) REVERT: g 32 SER cc_start: 0.9061 (OUTLIER) cc_final: 0.8561 (m) REVERT: g 241 ILE cc_start: 0.1108 (OUTLIER) cc_final: 0.0655 (mp) REVERT: h 53 GLU cc_start: 0.8420 (OUTLIER) cc_final: 0.7980 (pm20) REVERT: h 102 GLU cc_start: 0.8292 (OUTLIER) cc_final: 0.8074 (mp0) REVERT: i 212 MET cc_start: 0.4369 (tpp) cc_final: 0.3798 (tpp) REVERT: k 17 LEU cc_start: 0.9040 (OUTLIER) cc_final: 0.8825 (mt) REVERT: l 212 MET cc_start: 0.5427 (OUTLIER) cc_final: 0.4427 (tmm) REVERT: n 61 ASP cc_start: 0.8150 (OUTLIER) cc_final: 0.7803 (p0) REVERT: n 164 MET cc_start: 0.3910 (pmm) cc_final: 0.2741 (tpp) REVERT: o 102 GLU cc_start: 0.8456 (OUTLIER) cc_final: 0.8074 (pp20) outliers start: 559 outliers final: 361 residues processed: 1205 average time/residue: 1.4598 time to fit residues: 2414.3177 Evaluate side-chains 1103 residues out of total 8352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 397 poor density : 706 time to evaluate : 6.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 7 LYS Chi-restraints excluded: chain M residue 41 LEU Chi-restraints excluded: chain M residue 46 VAL Chi-restraints excluded: chain M residue 47 THR Chi-restraints excluded: chain M residue 50 VAL Chi-restraints excluded: chain M residue 95 MET Chi-restraints excluded: chain M residue 99 GLU Chi-restraints excluded: chain M residue 109 ASN Chi-restraints excluded: chain J residue 26 VAL Chi-restraints excluded: chain J residue 39 VAL Chi-restraints excluded: chain J residue 47 LEU Chi-restraints excluded: chain J residue 65 THR Chi-restraints excluded: chain J residue 88 THR Chi-restraints excluded: chain J residue 122 VAL Chi-restraints excluded: chain J residue 138 LEU Chi-restraints excluded: chain J residue 149 THR Chi-restraints excluded: chain J residue 153 ILE Chi-restraints excluded: chain J residue 167 VAL Chi-restraints excluded: chain J residue 168 VAL Chi-restraints excluded: chain J residue 177 PHE Chi-restraints excluded: chain J residue 215 THR Chi-restraints excluded: chain J residue 241 ARG Chi-restraints excluded: chain J residue 257 SER Chi-restraints excluded: chain J residue 325 CYS Chi-restraints excluded: chain J residue 504 THR Chi-restraints excluded: chain J residue 511 ILE Chi-restraints excluded: chain J residue 539 THR Chi-restraints excluded: chain J residue 542 VAL Chi-restraints excluded: chain J residue 598 ILE Chi-restraints excluded: chain J residue 613 VAL Chi-restraints excluded: chain J residue 621 VAL Chi-restraints excluded: chain J residue 638 LEU Chi-restraints excluded: chain J residue 667 LEU Chi-restraints excluded: chain J residue 703 ASP Chi-restraints excluded: chain J residue 719 ARG Chi-restraints excluded: chain J residue 721 GLU Chi-restraints excluded: chain J residue 823 THR Chi-restraints excluded: chain J residue 827 LEU Chi-restraints excluded: chain m residue 7 LYS Chi-restraints excluded: chain m residue 46 VAL Chi-restraints excluded: chain m residue 74 THR Chi-restraints excluded: chain m residue 85 THR Chi-restraints excluded: chain L residue 18 SER Chi-restraints excluded: chain L residue 31 VAL Chi-restraints excluded: chain L residue 78 THR Chi-restraints excluded: chain L residue 99 VAL Chi-restraints excluded: chain L residue 159 ASP Chi-restraints excluded: chain L residue 167 ILE Chi-restraints excluded: chain H residue 844 ASP Chi-restraints excluded: chain I residue 118 THR Chi-restraints excluded: chain I residue 161 THR Chi-restraints excluded: chain I residue 167 THR Chi-restraints excluded: chain I residue 207 ILE Chi-restraints excluded: chain V residue 17 LEU Chi-restraints excluded: chain V residue 51 THR Chi-restraints excluded: chain V residue 68 THR Chi-restraints excluded: chain V residue 70 THR Chi-restraints excluded: chain V residue 83 THR Chi-restraints excluded: chain V residue 90 GLU Chi-restraints excluded: chain V residue 117 VAL Chi-restraints excluded: chain V residue 146 VAL Chi-restraints excluded: chain V residue 166 VAL Chi-restraints excluded: chain V residue 225 ASN Chi-restraints excluded: chain v residue 10 VAL Chi-restraints excluded: chain v residue 32 SER Chi-restraints excluded: chain v residue 33 ASP Chi-restraints excluded: chain v residue 70 THR Chi-restraints excluded: chain v residue 84 LEU Chi-restraints excluded: chain v residue 97 LEU Chi-restraints excluded: chain v residue 119 VAL Chi-restraints excluded: chain v residue 132 THR Chi-restraints excluded: chain v residue 179 THR Chi-restraints excluded: chain v residue 219 VAL Chi-restraints excluded: chain B residue 72 GLN Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain B residue 87 MET Chi-restraints excluded: chain B residue 135 GLU Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 182 THR Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 199 SER Chi-restraints excluded: chain b residue 43 LYS Chi-restraints excluded: chain b residue 54 SER Chi-restraints excluded: chain b residue 84 LEU Chi-restraints excluded: chain b residue 87 MET Chi-restraints excluded: chain b residue 146 VAL Chi-restraints excluded: chain b residue 180 THR Chi-restraints excluded: chain b residue 243 VAL Chi-restraints excluded: chain A residue 83 THR Chi-restraints excluded: chain A residue 125 SER Chi-restraints excluded: chain A residue 127 ILE Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 148 ARG Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain a residue 32 SER Chi-restraints excluded: chain a residue 119 VAL Chi-restraints excluded: chain a residue 138 THR Chi-restraints excluded: chain a residue 185 PHE Chi-restraints excluded: chain a residue 207 VAL Chi-restraints excluded: chain a residue 212 MET Chi-restraints excluded: chain a residue 242 THR Chi-restraints excluded: chain C residue 17 LEU Chi-restraints excluded: chain C residue 21 LYS Chi-restraints excluded: chain C residue 83 THR Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 165 THR Chi-restraints excluded: chain C residue 179 THR Chi-restraints excluded: chain C residue 196 ARG Chi-restraints excluded: chain c residue 7 THR Chi-restraints excluded: chain c residue 83 THR Chi-restraints excluded: chain c residue 94 GLN Chi-restraints excluded: chain c residue 102 GLU Chi-restraints excluded: chain c residue 117 VAL Chi-restraints excluded: chain c residue 132 THR Chi-restraints excluded: chain c residue 240 GLU Chi-restraints excluded: chain D residue 13 ASP Chi-restraints excluded: chain D residue 46 VAL Chi-restraints excluded: chain D residue 47 THR Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 103 GLU Chi-restraints excluded: chain E residue 5 SER Chi-restraints excluded: chain E residue 21 THR Chi-restraints excluded: chain E residue 26 VAL Chi-restraints excluded: chain E residue 109 ILE Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 122 VAL Chi-restraints excluded: chain E residue 138 LEU Chi-restraints excluded: chain E residue 139 VAL Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain E residue 215 THR Chi-restraints excluded: chain E residue 217 LEU Chi-restraints excluded: chain E residue 231 GLN Chi-restraints excluded: chain E residue 324 THR Chi-restraints excluded: chain E residue 325 CYS Chi-restraints excluded: chain E residue 329 LEU Chi-restraints excluded: chain E residue 330 THR Chi-restraints excluded: chain E residue 331 THR Chi-restraints excluded: chain E residue 373 ARG Chi-restraints excluded: chain E residue 374 SER Chi-restraints excluded: chain E residue 397 ASN Chi-restraints excluded: chain E residue 431 THR Chi-restraints excluded: chain E residue 504 THR Chi-restraints excluded: chain E residue 511 ILE Chi-restraints excluded: chain E residue 531 VAL Chi-restraints excluded: chain E residue 542 VAL Chi-restraints excluded: chain E residue 596 GLU Chi-restraints excluded: chain E residue 598 ILE Chi-restraints excluded: chain E residue 613 VAL Chi-restraints excluded: chain E residue 621 VAL Chi-restraints excluded: chain E residue 638 LEU Chi-restraints excluded: chain E residue 648 LYS Chi-restraints excluded: chain E residue 667 LEU Chi-restraints excluded: chain E residue 751 LYS Chi-restraints excluded: chain E residue 783 HIS Chi-restraints excluded: chain E residue 823 THR Chi-restraints excluded: chain F residue 46 VAL Chi-restraints excluded: chain F residue 50 VAL Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain F residue 85 THR Chi-restraints excluded: chain G residue 31 VAL Chi-restraints excluded: chain G residue 99 VAL Chi-restraints excluded: chain G residue 159 ASP Chi-restraints excluded: chain N residue 107 LEU Chi-restraints excluded: chain N residue 118 THR Chi-restraints excluded: chain N residue 161 THR Chi-restraints excluded: chain N residue 167 THR Chi-restraints excluded: chain N residue 171 LYS Chi-restraints excluded: chain N residue 203 VAL Chi-restraints excluded: chain N residue 204 SER Chi-restraints excluded: chain N residue 207 ILE Chi-restraints excluded: chain O residue 17 LEU Chi-restraints excluded: chain O residue 51 THR Chi-restraints excluded: chain O residue 54 SER Chi-restraints excluded: chain O residue 58 SER Chi-restraints excluded: chain O residue 70 THR Chi-restraints excluded: chain O residue 81 SER Chi-restraints excluded: chain O residue 83 THR Chi-restraints excluded: chain O residue 90 GLU Chi-restraints excluded: chain O residue 125 SER Chi-restraints excluded: chain O residue 127 ILE Chi-restraints excluded: chain O residue 132 THR Chi-restraints excluded: chain O residue 146 VAL Chi-restraints excluded: chain O residue 166 VAL Chi-restraints excluded: chain O residue 174 VAL Chi-restraints excluded: chain O residue 225 ASN Chi-restraints excluded: chain O residue 241 ILE Chi-restraints excluded: chain P residue 31 LEU Chi-restraints excluded: chain P residue 70 THR Chi-restraints excluded: chain P residue 84 LEU Chi-restraints excluded: chain P residue 97 LEU Chi-restraints excluded: chain P residue 117 VAL Chi-restraints excluded: chain P residue 119 VAL Chi-restraints excluded: chain P residue 132 THR Chi-restraints excluded: chain P residue 158 VAL Chi-restraints excluded: chain P residue 179 THR Chi-restraints excluded: chain P residue 219 VAL Chi-restraints excluded: chain Q residue 53 GLU Chi-restraints excluded: chain Q residue 80 THR Chi-restraints excluded: chain Q residue 119 VAL Chi-restraints excluded: chain Q residue 126 SER Chi-restraints excluded: chain Q residue 131 VAL Chi-restraints excluded: chain Q residue 132 THR Chi-restraints excluded: chain Q residue 136 VAL Chi-restraints excluded: chain Q residue 146 VAL Chi-restraints excluded: chain Q residue 165 THR Chi-restraints excluded: chain Q residue 182 THR Chi-restraints excluded: chain Q residue 191 THR Chi-restraints excluded: chain Q residue 198 VAL Chi-restraints excluded: chain R residue 17 LEU Chi-restraints excluded: chain R residue 23 SER Chi-restraints excluded: chain R residue 42 VAL Chi-restraints excluded: chain R residue 51 THR Chi-restraints excluded: chain R residue 64 ASP Chi-restraints excluded: chain R residue 81 SER Chi-restraints excluded: chain R residue 84 LEU Chi-restraints excluded: chain R residue 97 LEU Chi-restraints excluded: chain R residue 125 SER Chi-restraints excluded: chain R residue 131 VAL Chi-restraints excluded: chain R residue 132 THR Chi-restraints excluded: chain R residue 158 VAL Chi-restraints excluded: chain R residue 180 THR Chi-restraints excluded: chain R residue 199 SER Chi-restraints excluded: chain R residue 240 GLU Chi-restraints excluded: chain S residue 34 VAL Chi-restraints excluded: chain S residue 83 THR Chi-restraints excluded: chain S residue 125 SER Chi-restraints excluded: chain S residue 127 ILE Chi-restraints excluded: chain S residue 146 VAL Chi-restraints excluded: chain S residue 191 THR Chi-restraints excluded: chain S residue 198 VAL Chi-restraints excluded: chain S residue 215 THR Chi-restraints excluded: chain S residue 224 VAL Chi-restraints excluded: chain T residue 117 VAL Chi-restraints excluded: chain T residue 119 VAL Chi-restraints excluded: chain T residue 138 THR Chi-restraints excluded: chain T residue 207 VAL Chi-restraints excluded: chain T residue 219 VAL Chi-restraints excluded: chain U residue 17 LEU Chi-restraints excluded: chain U residue 21 LYS Chi-restraints excluded: chain U residue 61 ASP Chi-restraints excluded: chain U residue 83 THR Chi-restraints excluded: chain U residue 141 VAL Chi-restraints excluded: chain U residue 146 VAL Chi-restraints excluded: chain U residue 165 THR Chi-restraints excluded: chain U residue 179 THR Chi-restraints excluded: chain U residue 232 ASN Chi-restraints excluded: chain W residue 7 THR Chi-restraints excluded: chain W residue 45 LEU Chi-restraints excluded: chain W residue 110 ILE Chi-restraints excluded: chain W residue 117 VAL Chi-restraints excluded: chain W residue 132 THR Chi-restraints excluded: chain X residue 46 VAL Chi-restraints excluded: chain X residue 47 THR Chi-restraints excluded: chain X residue 50 VAL Chi-restraints excluded: chain X residue 60 SER Chi-restraints excluded: chain X residue 64 GLU Chi-restraints excluded: chain X residue 103 GLU Chi-restraints excluded: chain X residue 109 ASN Chi-restraints excluded: chain Y residue 5 SER Chi-restraints excluded: chain Y residue 21 THR Chi-restraints excluded: chain Y residue 26 VAL Chi-restraints excluded: chain Y residue 50 THR Chi-restraints excluded: chain Y residue 65 THR Chi-restraints excluded: chain Y residue 88 THR Chi-restraints excluded: chain Y residue 90 LEU Chi-restraints excluded: chain Y residue 109 ILE Chi-restraints excluded: chain Y residue 115 THR Chi-restraints excluded: chain Y residue 122 VAL Chi-restraints excluded: chain Y residue 138 LEU Chi-restraints excluded: chain Y residue 147 TRP Chi-restraints excluded: chain Y residue 149 THR Chi-restraints excluded: chain Y residue 153 ILE Chi-restraints excluded: chain Y residue 167 VAL Chi-restraints excluded: chain Y residue 168 VAL Chi-restraints excluded: chain Y residue 177 PHE Chi-restraints excluded: chain Y residue 215 THR Chi-restraints excluded: chain Y residue 217 LEU Chi-restraints excluded: chain Y residue 324 THR Chi-restraints excluded: chain Y residue 325 CYS Chi-restraints excluded: chain Y residue 329 LEU Chi-restraints excluded: chain Y residue 330 THR Chi-restraints excluded: chain Y residue 331 THR Chi-restraints excluded: chain Y residue 373 ARG Chi-restraints excluded: chain Y residue 381 ASP Chi-restraints excluded: chain Y residue 397 ASN Chi-restraints excluded: chain Y residue 433 MET Chi-restraints excluded: chain Y residue 469 GLU Chi-restraints excluded: chain Y residue 504 THR Chi-restraints excluded: chain Y residue 511 ILE Chi-restraints excluded: chain Y residue 521 ILE Chi-restraints excluded: chain Y residue 531 VAL Chi-restraints excluded: chain Y residue 536 GLN Chi-restraints excluded: chain Y residue 539 THR Chi-restraints excluded: chain Y residue 542 VAL Chi-restraints excluded: chain Y residue 544 VAL Chi-restraints excluded: chain Y residue 574 VAL Chi-restraints excluded: chain Y residue 613 VAL Chi-restraints excluded: chain Y residue 621 VAL Chi-restraints excluded: chain Y residue 638 LEU Chi-restraints excluded: chain Y residue 667 LEU Chi-restraints excluded: chain Y residue 721 GLU Chi-restraints excluded: chain Y residue 823 THR Chi-restraints excluded: chain Y residue 827 LEU Chi-restraints excluded: chain Z residue 58 LEU Chi-restraints excluded: chain Z residue 74 THR Chi-restraints excluded: chain Z residue 98 VAL Chi-restraints excluded: chain Z residue 109 ASN Chi-restraints excluded: chain d residue 31 VAL Chi-restraints excluded: chain d residue 105 ARG Chi-restraints excluded: chain d residue 111 ARG Chi-restraints excluded: chain d residue 159 ASP Chi-restraints excluded: chain d residue 167 ILE Chi-restraints excluded: chain e residue 847 LEU Chi-restraints excluded: chain e residue 849 SER Chi-restraints excluded: chain f residue 107 LEU Chi-restraints excluded: chain f residue 118 THR Chi-restraints excluded: chain f residue 139 LEU Chi-restraints excluded: chain f residue 161 THR Chi-restraints excluded: chain f residue 167 THR Chi-restraints excluded: chain f residue 182 MET Chi-restraints excluded: chain f residue 188 VAL Chi-restraints excluded: chain f residue 203 VAL Chi-restraints excluded: chain f residue 204 SER Chi-restraints excluded: chain f residue 207 ILE Chi-restraints excluded: chain g residue 32 SER Chi-restraints excluded: chain g residue 51 THR Chi-restraints excluded: chain g residue 63 GLU Chi-restraints excluded: chain g residue 70 THR Chi-restraints excluded: chain g residue 81 SER Chi-restraints excluded: chain g residue 83 THR Chi-restraints excluded: chain g residue 127 ILE Chi-restraints excluded: chain g residue 146 VAL Chi-restraints excluded: chain g residue 166 VAL Chi-restraints excluded: chain g residue 191 THR Chi-restraints excluded: chain g residue 225 ASN Chi-restraints excluded: chain g residue 241 ILE Chi-restraints excluded: chain h residue 53 GLU Chi-restraints excluded: chain h residue 70 THR Chi-restraints excluded: chain h residue 84 LEU Chi-restraints excluded: chain h residue 102 GLU Chi-restraints excluded: chain h residue 119 VAL Chi-restraints excluded: chain h residue 132 THR Chi-restraints excluded: chain h residue 158 VAL Chi-restraints excluded: chain h residue 179 THR Chi-restraints excluded: chain i residue 17 LEU Chi-restraints excluded: chain i residue 131 VAL Chi-restraints excluded: chain i residue 182 THR Chi-restraints excluded: chain i residue 183 VAL Chi-restraints excluded: chain i residue 198 VAL Chi-restraints excluded: chain j residue 54 SER Chi-restraints excluded: chain j residue 64 ASP Chi-restraints excluded: chain j residue 70 THR Chi-restraints excluded: chain j residue 84 LEU Chi-restraints excluded: chain j residue 125 SER Chi-restraints excluded: chain j residue 132 THR Chi-restraints excluded: chain j residue 135 GLU Chi-restraints excluded: chain j residue 138 THR Chi-restraints excluded: chain j residue 146 VAL Chi-restraints excluded: chain j residue 158 VAL Chi-restraints excluded: chain j residue 180 THR Chi-restraints excluded: chain k residue 17 LEU Chi-restraints excluded: chain k residue 83 THR Chi-restraints excluded: chain k residue 125 SER Chi-restraints excluded: chain k residue 132 THR Chi-restraints excluded: chain k residue 146 VAL Chi-restraints excluded: chain k residue 190 VAL Chi-restraints excluded: chain k residue 198 VAL Chi-restraints excluded: chain k residue 215 THR Chi-restraints excluded: chain k residue 224 VAL Chi-restraints excluded: chain l residue 3 VAL Chi-restraints excluded: chain l residue 70 THR Chi-restraints excluded: chain l residue 140 THR Chi-restraints excluded: chain l residue 180 THR Chi-restraints excluded: chain l residue 198 VAL Chi-restraints excluded: chain l residue 207 VAL Chi-restraints excluded: chain l residue 212 MET Chi-restraints excluded: chain l residue 219 VAL Chi-restraints excluded: chain n residue 17 LEU Chi-restraints excluded: chain n residue 61 ASP Chi-restraints excluded: chain n residue 83 THR Chi-restraints excluded: chain n residue 97 LEU Chi-restraints excluded: chain n residue 141 VAL Chi-restraints excluded: chain n residue 146 VAL Chi-restraints excluded: chain n residue 216 VAL Chi-restraints excluded: chain o residue 7 THR Chi-restraints excluded: chain o residue 83 THR Chi-restraints excluded: chain o residue 102 GLU Chi-restraints excluded: chain o residue 110 ILE Chi-restraints excluded: chain o residue 117 VAL Chi-restraints excluded: chain o residue 129 LYS Chi-restraints excluded: chain o residue 132 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1008 random chunks: chunk 601 optimal weight: 1.9990 chunk 387 optimal weight: 0.9980 chunk 580 optimal weight: 1.9990 chunk 292 optimal weight: 10.0000 chunk 190 optimal weight: 20.0000 chunk 188 optimal weight: 8.9990 chunk 617 optimal weight: 20.0000 chunk 661 optimal weight: 0.8980 chunk 480 optimal weight: 0.9990 chunk 90 optimal weight: 9.9990 chunk 763 optimal weight: 10.0000 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 178 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 91 GLN ** c 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 91 GLN E 397 ASN ** E 826 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 91 GLN ** W 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 101 ASN W 177 GLN Y 235 ASN Y 536 GLN ** Z 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 74 GLN ** o 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 91 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 moved from start: 0.1312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 78954 Z= 0.228 Angle : 0.639 19.644 107580 Z= 0.327 Chirality : 0.046 0.253 12384 Planarity : 0.005 0.179 13893 Dihedral : 6.624 59.989 11103 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.59 % Allowed : 6.97 % Favored : 92.44 % Rotamer: Outliers : 5.44 % Allowed : 31.32 % Favored : 63.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.63 % Cis-general : 0.00 % Twisted Proline : 1.26 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.61 (0.08), residues: 10164 helix: 0.53 (0.17), residues: 909 sheet: -0.62 (0.08), residues: 4035 loop : -1.72 (0.08), residues: 5220 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP D 89 HIS 0.005 0.001 HIS E 826 PHE 0.022 0.001 PHE N 116 TYR 0.026 0.001 TYR E 771 ARG 0.012 0.000 ARG n 121 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 20328 Ramachandran restraints generated. 10164 Oldfield, 0 Emsley, 10164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 20328 Ramachandran restraints generated. 10164 Oldfield, 0 Emsley, 10164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1178 residues out of total 8352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 454 poor density : 724 time to evaluate : 6.359 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 13 ASP cc_start: 0.8498 (m-30) cc_final: 0.8151 (t0) REVERT: M 95 MET cc_start: 0.9326 (OUTLIER) cc_final: 0.8875 (tpt) REVERT: J 40 ASP cc_start: 0.7999 (t0) cc_final: 0.7786 (t0) REVERT: J 241 ARG cc_start: 0.8921 (OUTLIER) cc_final: 0.8316 (mtp180) REVERT: J 719 ARG cc_start: 0.7844 (OUTLIER) cc_final: 0.7510 (ttp-110) REVERT: J 783 HIS cc_start: 0.8504 (m-70) cc_final: 0.7924 (m-70) REVERT: m 92 ARG cc_start: 0.8344 (tpp80) cc_final: 0.7902 (ttp80) REVERT: m 103 GLU cc_start: 0.7817 (pp20) cc_final: 0.7403 (pp20) REVERT: I 158 LYS cc_start: 0.8452 (tppt) cc_final: 0.8062 (tptm) REVERT: B 57 ASP cc_start: 0.8775 (t0) cc_final: 0.8462 (t0) REVERT: B 135 GLU cc_start: 0.8011 (OUTLIER) cc_final: 0.7601 (mt-10) REVERT: b 29 ASN cc_start: 0.8992 (t0) cc_final: 0.8735 (t0) REVERT: b 43 LYS cc_start: 0.8906 (OUTLIER) cc_final: 0.8486 (mmpt) REVERT: A 90 GLU cc_start: 0.8603 (tm-30) cc_final: 0.8253 (tm-30) REVERT: C 21 LYS cc_start: 0.8961 (OUTLIER) cc_final: 0.8549 (pmtt) REVERT: C 155 ARG cc_start: 0.7613 (mtm110) cc_final: 0.6999 (ptt-90) REVERT: c 43 LYS cc_start: 0.6521 (mmpt) cc_final: 0.6293 (mmpt) REVERT: c 53 GLU cc_start: 0.8770 (pt0) cc_final: 0.8516 (pt0) REVERT: c 87 MET cc_start: 0.8720 (mmt) cc_final: 0.7617 (mmt) REVERT: c 94 GLN cc_start: 0.7762 (OUTLIER) cc_final: 0.7404 (mt0) REVERT: c 102 GLU cc_start: 0.8459 (OUTLIER) cc_final: 0.8163 (pp20) REVERT: E 147 TRP cc_start: 0.7410 (m100) cc_final: 0.5885 (m100) REVERT: E 217 LEU cc_start: 0.8606 (OUTLIER) cc_final: 0.8406 (mp) REVERT: E 231 GLN cc_start: 0.7592 (OUTLIER) cc_final: 0.7241 (mm110) REVERT: E 751 LYS cc_start: 0.9056 (OUTLIER) cc_final: 0.8847 (pmtt) REVERT: F 59 GLU cc_start: 0.7823 (OUTLIER) cc_final: 0.7608 (mt-10) REVERT: F 92 ARG cc_start: 0.8369 (tpp80) cc_final: 0.8165 (tpp80) REVERT: N 185 GLN cc_start: 0.8266 (OUTLIER) cc_final: 0.7362 (tt0) REVERT: O 90 GLU cc_start: 0.8196 (OUTLIER) cc_final: 0.7823 (pt0) REVERT: P 8 MET cc_start: 0.8791 (mmp) cc_final: 0.8533 (mmm) REVERT: Q 5 ASN cc_start: 0.9318 (t0) cc_final: 0.9069 (t160) REVERT: Q 17 LEU cc_start: 0.9527 (OUTLIER) cc_final: 0.9327 (mt) REVERT: Q 80 THR cc_start: 0.9000 (OUTLIER) cc_final: 0.8534 (p) REVERT: Q 135 GLU cc_start: 0.8091 (mt-10) cc_final: 0.7780 (mt-10) REVERT: U 21 LYS cc_start: 0.8873 (OUTLIER) cc_final: 0.8647 (pmtt) REVERT: U 49 GLU cc_start: 0.8776 (pt0) cc_final: 0.8284 (pm20) REVERT: U 135 GLU cc_start: 0.8920 (mm-30) cc_final: 0.8583 (tp30) REVERT: U 164 MET cc_start: 0.4007 (pmm) cc_final: 0.2422 (tpp) REVERT: W 11 LYS cc_start: 0.8245 (mmmm) cc_final: 0.7750 (mmmm) REVERT: W 29 ASN cc_start: 0.8053 (t0) cc_final: 0.7739 (t0) REVERT: W 44 ASP cc_start: 0.8316 (t0) cc_final: 0.8027 (p0) REVERT: W 142 LYS cc_start: 0.9358 (ttpp) cc_final: 0.9022 (tttp) REVERT: W 164 MET cc_start: 0.1935 (tpp) cc_final: 0.1335 (tpp) REVERT: X 21 ARG cc_start: 0.8296 (ttp80) cc_final: 0.8079 (ttp80) REVERT: X 103 GLU cc_start: 0.8448 (OUTLIER) cc_final: 0.8203 (tp30) REVERT: Y 90 LEU cc_start: 0.7615 (OUTLIER) cc_final: 0.7334 (pp) REVERT: Y 329 LEU cc_start: 0.9091 (OUTLIER) cc_final: 0.8782 (mt) REVERT: Y 341 ASP cc_start: 0.8093 (m-30) cc_final: 0.7774 (m-30) REVERT: Y 373 ARG cc_start: 0.8200 (OUTLIER) cc_final: 0.7965 (ptm-80) REVERT: Y 721 GLU cc_start: 0.6046 (OUTLIER) cc_final: 0.5812 (mp0) REVERT: d 105 ARG cc_start: 0.8728 (OUTLIER) cc_final: 0.8332 (ptm160) REVERT: d 111 ARG cc_start: 0.8721 (OUTLIER) cc_final: 0.8431 (ttm-80) REVERT: f 139 LEU cc_start: 0.7344 (OUTLIER) cc_final: 0.7087 (mm) REVERT: h 53 GLU cc_start: 0.8423 (OUTLIER) cc_final: 0.8003 (pm20) REVERT: h 102 GLU cc_start: 0.8278 (OUTLIER) cc_final: 0.8057 (mp0) REVERT: i 212 MET cc_start: 0.4274 (tpp) cc_final: 0.3744 (tpp) REVERT: l 212 MET cc_start: 0.5298 (OUTLIER) cc_final: 0.4381 (tmm) REVERT: n 91 GLN cc_start: 0.8118 (pp30) cc_final: 0.7827 (pm20) REVERT: n 164 MET cc_start: 0.3820 (pmm) cc_final: 0.2631 (tpp) REVERT: o 11 LYS cc_start: 0.8183 (mmmm) cc_final: 0.7606 (mmmm) REVERT: o 102 GLU cc_start: 0.8489 (OUTLIER) cc_final: 0.8109 (pp20) outliers start: 454 outliers final: 321 residues processed: 1108 average time/residue: 1.5017 time to fit residues: 2241.7349 Evaluate side-chains 1062 residues out of total 8352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 350 poor density : 712 time to evaluate : 6.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 12 MET Chi-restraints excluded: chain M residue 46 VAL Chi-restraints excluded: chain M residue 47 THR Chi-restraints excluded: chain M residue 50 VAL Chi-restraints excluded: chain M residue 95 MET Chi-restraints excluded: chain M residue 99 GLU Chi-restraints excluded: chain M residue 109 ASN Chi-restraints excluded: chain J residue 26 VAL Chi-restraints excluded: chain J residue 30 ILE Chi-restraints excluded: chain J residue 47 LEU Chi-restraints excluded: chain J residue 65 THR Chi-restraints excluded: chain J residue 88 THR Chi-restraints excluded: chain J residue 122 VAL Chi-restraints excluded: chain J residue 138 LEU Chi-restraints excluded: chain J residue 149 THR Chi-restraints excluded: chain J residue 167 VAL Chi-restraints excluded: chain J residue 168 VAL Chi-restraints excluded: chain J residue 177 PHE Chi-restraints excluded: chain J residue 215 THR Chi-restraints excluded: chain J residue 241 ARG Chi-restraints excluded: chain J residue 257 SER Chi-restraints excluded: chain J residue 325 CYS Chi-restraints excluded: chain J residue 504 THR Chi-restraints excluded: chain J residue 511 ILE Chi-restraints excluded: chain J residue 539 THR Chi-restraints excluded: chain J residue 583 THR Chi-restraints excluded: chain J residue 598 ILE Chi-restraints excluded: chain J residue 613 VAL Chi-restraints excluded: chain J residue 621 VAL Chi-restraints excluded: chain J residue 638 LEU Chi-restraints excluded: chain J residue 703 ASP Chi-restraints excluded: chain J residue 719 ARG Chi-restraints excluded: chain J residue 823 THR Chi-restraints excluded: chain J residue 827 LEU Chi-restraints excluded: chain m residue 46 VAL Chi-restraints excluded: chain m residue 74 THR Chi-restraints excluded: chain m residue 85 THR Chi-restraints excluded: chain L residue 31 VAL Chi-restraints excluded: chain L residue 99 VAL Chi-restraints excluded: chain L residue 151 VAL Chi-restraints excluded: chain L residue 159 ASP Chi-restraints excluded: chain L residue 167 ILE Chi-restraints excluded: chain H residue 844 ASP Chi-restraints excluded: chain I residue 118 THR Chi-restraints excluded: chain I residue 161 THR Chi-restraints excluded: chain I residue 167 THR Chi-restraints excluded: chain I residue 203 VAL Chi-restraints excluded: chain I residue 207 ILE Chi-restraints excluded: chain V residue 51 THR Chi-restraints excluded: chain V residue 68 THR Chi-restraints excluded: chain V residue 70 THR Chi-restraints excluded: chain V residue 83 THR Chi-restraints excluded: chain V residue 90 GLU Chi-restraints excluded: chain V residue 117 VAL Chi-restraints excluded: chain V residue 146 VAL Chi-restraints excluded: chain v residue 10 VAL Chi-restraints excluded: chain v residue 32 SER Chi-restraints excluded: chain v residue 33 ASP Chi-restraints excluded: chain v residue 70 THR Chi-restraints excluded: chain v residue 84 LEU Chi-restraints excluded: chain v residue 97 LEU Chi-restraints excluded: chain v residue 119 VAL Chi-restraints excluded: chain v residue 132 THR Chi-restraints excluded: chain v residue 179 THR Chi-restraints excluded: chain v residue 219 VAL Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain B residue 87 MET Chi-restraints excluded: chain B residue 135 GLU Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 182 THR Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 199 SER Chi-restraints excluded: chain b residue 43 LYS Chi-restraints excluded: chain b residue 54 SER Chi-restraints excluded: chain b residue 84 LEU Chi-restraints excluded: chain b residue 97 LEU Chi-restraints excluded: chain b residue 146 VAL Chi-restraints excluded: chain b residue 180 THR Chi-restraints excluded: chain b residue 243 VAL Chi-restraints excluded: chain A residue 83 THR Chi-restraints excluded: chain A residue 125 SER Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 148 ARG Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain a residue 119 VAL Chi-restraints excluded: chain a residue 185 PHE Chi-restraints excluded: chain a residue 212 MET Chi-restraints excluded: chain a residue 242 THR Chi-restraints excluded: chain C residue 17 LEU Chi-restraints excluded: chain C residue 21 LYS Chi-restraints excluded: chain C residue 83 THR Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 165 THR Chi-restraints excluded: chain c residue 7 THR Chi-restraints excluded: chain c residue 94 GLN Chi-restraints excluded: chain c residue 102 GLU Chi-restraints excluded: chain c residue 117 VAL Chi-restraints excluded: chain c residue 132 THR Chi-restraints excluded: chain D residue 13 ASP Chi-restraints excluded: chain D residue 46 VAL Chi-restraints excluded: chain D residue 47 THR Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain E residue 26 VAL Chi-restraints excluded: chain E residue 65 THR Chi-restraints excluded: chain E residue 122 VAL Chi-restraints excluded: chain E residue 138 LEU Chi-restraints excluded: chain E residue 139 VAL Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain E residue 177 PHE Chi-restraints excluded: chain E residue 215 THR Chi-restraints excluded: chain E residue 217 LEU Chi-restraints excluded: chain E residue 231 GLN Chi-restraints excluded: chain E residue 324 THR Chi-restraints excluded: chain E residue 325 CYS Chi-restraints excluded: chain E residue 329 LEU Chi-restraints excluded: chain E residue 330 THR Chi-restraints excluded: chain E residue 331 THR Chi-restraints excluded: chain E residue 374 SER Chi-restraints excluded: chain E residue 397 ASN Chi-restraints excluded: chain E residue 431 THR Chi-restraints excluded: chain E residue 504 THR Chi-restraints excluded: chain E residue 511 ILE Chi-restraints excluded: chain E residue 531 VAL Chi-restraints excluded: chain E residue 542 VAL Chi-restraints excluded: chain E residue 596 GLU Chi-restraints excluded: chain E residue 598 ILE Chi-restraints excluded: chain E residue 613 VAL Chi-restraints excluded: chain E residue 621 VAL Chi-restraints excluded: chain E residue 638 LEU Chi-restraints excluded: chain E residue 648 LYS Chi-restraints excluded: chain E residue 653 LEU Chi-restraints excluded: chain E residue 667 LEU Chi-restraints excluded: chain E residue 751 LYS Chi-restraints excluded: chain E residue 771 TYR Chi-restraints excluded: chain E residue 783 HIS Chi-restraints excluded: chain E residue 822 ILE Chi-restraints excluded: chain E residue 823 THR Chi-restraints excluded: chain F residue 46 VAL Chi-restraints excluded: chain F residue 59 GLU Chi-restraints excluded: chain G residue 99 VAL Chi-restraints excluded: chain G residue 154 THR Chi-restraints excluded: chain G residue 159 ASP Chi-restraints excluded: chain N residue 107 LEU Chi-restraints excluded: chain N residue 161 THR Chi-restraints excluded: chain N residue 167 THR Chi-restraints excluded: chain N residue 171 LYS Chi-restraints excluded: chain N residue 185 GLN Chi-restraints excluded: chain N residue 204 SER Chi-restraints excluded: chain O residue 51 THR Chi-restraints excluded: chain O residue 54 SER Chi-restraints excluded: chain O residue 63 GLU Chi-restraints excluded: chain O residue 68 THR Chi-restraints excluded: chain O residue 70 THR Chi-restraints excluded: chain O residue 81 SER Chi-restraints excluded: chain O residue 83 THR Chi-restraints excluded: chain O residue 90 GLU Chi-restraints excluded: chain O residue 117 VAL Chi-restraints excluded: chain O residue 125 SER Chi-restraints excluded: chain O residue 132 THR Chi-restraints excluded: chain O residue 146 VAL Chi-restraints excluded: chain O residue 166 VAL Chi-restraints excluded: chain O residue 174 VAL Chi-restraints excluded: chain O residue 225 ASN Chi-restraints excluded: chain P residue 31 LEU Chi-restraints excluded: chain P residue 70 THR Chi-restraints excluded: chain P residue 84 LEU Chi-restraints excluded: chain P residue 97 LEU Chi-restraints excluded: chain P residue 117 VAL Chi-restraints excluded: chain P residue 119 VAL Chi-restraints excluded: chain P residue 132 THR Chi-restraints excluded: chain P residue 179 THR Chi-restraints excluded: chain P residue 219 VAL Chi-restraints excluded: chain Q residue 17 LEU Chi-restraints excluded: chain Q residue 53 GLU Chi-restraints excluded: chain Q residue 80 THR Chi-restraints excluded: chain Q residue 119 VAL Chi-restraints excluded: chain Q residue 126 SER Chi-restraints excluded: chain Q residue 131 VAL Chi-restraints excluded: chain Q residue 132 THR Chi-restraints excluded: chain Q residue 165 THR Chi-restraints excluded: chain Q residue 182 THR Chi-restraints excluded: chain Q residue 191 THR Chi-restraints excluded: chain Q residue 198 VAL Chi-restraints excluded: chain R residue 23 SER Chi-restraints excluded: chain R residue 42 VAL Chi-restraints excluded: chain R residue 64 ASP Chi-restraints excluded: chain R residue 70 THR Chi-restraints excluded: chain R residue 81 SER Chi-restraints excluded: chain R residue 84 LEU Chi-restraints excluded: chain R residue 97 LEU Chi-restraints excluded: chain R residue 116 THR Chi-restraints excluded: chain R residue 125 SER Chi-restraints excluded: chain R residue 131 VAL Chi-restraints excluded: chain R residue 132 THR Chi-restraints excluded: chain R residue 158 VAL Chi-restraints excluded: chain R residue 180 THR Chi-restraints excluded: chain S residue 34 VAL Chi-restraints excluded: chain S residue 83 THR Chi-restraints excluded: chain S residue 127 ILE Chi-restraints excluded: chain S residue 140 THR Chi-restraints excluded: chain S residue 146 VAL Chi-restraints excluded: chain S residue 191 THR Chi-restraints excluded: chain S residue 198 VAL Chi-restraints excluded: chain S residue 215 THR Chi-restraints excluded: chain S residue 224 VAL Chi-restraints excluded: chain T residue 3 VAL Chi-restraints excluded: chain T residue 117 VAL Chi-restraints excluded: chain T residue 119 VAL Chi-restraints excluded: chain T residue 207 VAL Chi-restraints excluded: chain T residue 219 VAL Chi-restraints excluded: chain U residue 17 LEU Chi-restraints excluded: chain U residue 21 LYS Chi-restraints excluded: chain U residue 61 ASP Chi-restraints excluded: chain U residue 83 THR Chi-restraints excluded: chain U residue 141 VAL Chi-restraints excluded: chain U residue 146 VAL Chi-restraints excluded: chain U residue 165 THR Chi-restraints excluded: chain U residue 179 THR Chi-restraints excluded: chain U residue 212 MET Chi-restraints excluded: chain W residue 7 THR Chi-restraints excluded: chain W residue 110 ILE Chi-restraints excluded: chain W residue 117 VAL Chi-restraints excluded: chain X residue 46 VAL Chi-restraints excluded: chain X residue 47 THR Chi-restraints excluded: chain X residue 50 VAL Chi-restraints excluded: chain X residue 64 GLU Chi-restraints excluded: chain X residue 103 GLU Chi-restraints excluded: chain Y residue 5 SER Chi-restraints excluded: chain Y residue 21 THR Chi-restraints excluded: chain Y residue 26 VAL Chi-restraints excluded: chain Y residue 50 THR Chi-restraints excluded: chain Y residue 65 THR Chi-restraints excluded: chain Y residue 88 THR Chi-restraints excluded: chain Y residue 90 LEU Chi-restraints excluded: chain Y residue 115 THR Chi-restraints excluded: chain Y residue 122 VAL Chi-restraints excluded: chain Y residue 138 LEU Chi-restraints excluded: chain Y residue 149 THR Chi-restraints excluded: chain Y residue 153 ILE Chi-restraints excluded: chain Y residue 167 VAL Chi-restraints excluded: chain Y residue 168 VAL Chi-restraints excluded: chain Y residue 177 PHE Chi-restraints excluded: chain Y residue 215 THR Chi-restraints excluded: chain Y residue 217 LEU Chi-restraints excluded: chain Y residue 324 THR Chi-restraints excluded: chain Y residue 325 CYS Chi-restraints excluded: chain Y residue 329 LEU Chi-restraints excluded: chain Y residue 330 THR Chi-restraints excluded: chain Y residue 331 THR Chi-restraints excluded: chain Y residue 373 ARG Chi-restraints excluded: chain Y residue 381 ASP Chi-restraints excluded: chain Y residue 397 ASN Chi-restraints excluded: chain Y residue 433 MET Chi-restraints excluded: chain Y residue 469 GLU Chi-restraints excluded: chain Y residue 504 THR Chi-restraints excluded: chain Y residue 511 ILE Chi-restraints excluded: chain Y residue 531 VAL Chi-restraints excluded: chain Y residue 536 GLN Chi-restraints excluded: chain Y residue 542 VAL Chi-restraints excluded: chain Y residue 544 VAL Chi-restraints excluded: chain Y residue 574 VAL Chi-restraints excluded: chain Y residue 613 VAL Chi-restraints excluded: chain Y residue 621 VAL Chi-restraints excluded: chain Y residue 638 LEU Chi-restraints excluded: chain Y residue 721 GLU Chi-restraints excluded: chain Y residue 823 THR Chi-restraints excluded: chain Y residue 827 LEU Chi-restraints excluded: chain Z residue 58 LEU Chi-restraints excluded: chain Z residue 74 THR Chi-restraints excluded: chain Z residue 98 VAL Chi-restraints excluded: chain d residue 31 VAL Chi-restraints excluded: chain d residue 99 VAL Chi-restraints excluded: chain d residue 105 ARG Chi-restraints excluded: chain d residue 111 ARG Chi-restraints excluded: chain d residue 159 ASP Chi-restraints excluded: chain d residue 167 ILE Chi-restraints excluded: chain e residue 842 MET Chi-restraints excluded: chain e residue 847 LEU Chi-restraints excluded: chain e residue 849 SER Chi-restraints excluded: chain f residue 118 THR Chi-restraints excluded: chain f residue 139 LEU Chi-restraints excluded: chain f residue 161 THR Chi-restraints excluded: chain f residue 167 THR Chi-restraints excluded: chain f residue 188 VAL Chi-restraints excluded: chain f residue 203 VAL Chi-restraints excluded: chain f residue 204 SER Chi-restraints excluded: chain f residue 207 ILE Chi-restraints excluded: chain g residue 51 THR Chi-restraints excluded: chain g residue 63 GLU Chi-restraints excluded: chain g residue 70 THR Chi-restraints excluded: chain g residue 81 SER Chi-restraints excluded: chain g residue 83 THR Chi-restraints excluded: chain g residue 146 VAL Chi-restraints excluded: chain g residue 166 VAL Chi-restraints excluded: chain g residue 191 THR Chi-restraints excluded: chain g residue 225 ASN Chi-restraints excluded: chain h residue 31 LEU Chi-restraints excluded: chain h residue 53 GLU Chi-restraints excluded: chain h residue 70 THR Chi-restraints excluded: chain h residue 84 LEU Chi-restraints excluded: chain h residue 102 GLU Chi-restraints excluded: chain h residue 119 VAL Chi-restraints excluded: chain h residue 132 THR Chi-restraints excluded: chain h residue 158 VAL Chi-restraints excluded: chain h residue 179 THR Chi-restraints excluded: chain i residue 17 LEU Chi-restraints excluded: chain i residue 131 VAL Chi-restraints excluded: chain i residue 182 THR Chi-restraints excluded: chain i residue 183 VAL Chi-restraints excluded: chain i residue 198 VAL Chi-restraints excluded: chain j residue 54 SER Chi-restraints excluded: chain j residue 64 ASP Chi-restraints excluded: chain j residue 70 THR Chi-restraints excluded: chain j residue 84 LEU Chi-restraints excluded: chain j residue 125 SER Chi-restraints excluded: chain j residue 132 THR Chi-restraints excluded: chain j residue 135 GLU Chi-restraints excluded: chain j residue 138 THR Chi-restraints excluded: chain j residue 146 VAL Chi-restraints excluded: chain j residue 158 VAL Chi-restraints excluded: chain j residue 180 THR Chi-restraints excluded: chain k residue 83 THR Chi-restraints excluded: chain k residue 132 THR Chi-restraints excluded: chain k residue 146 VAL Chi-restraints excluded: chain k residue 190 VAL Chi-restraints excluded: chain k residue 198 VAL Chi-restraints excluded: chain k residue 215 THR Chi-restraints excluded: chain k residue 224 VAL Chi-restraints excluded: chain l residue 3 VAL Chi-restraints excluded: chain l residue 70 THR Chi-restraints excluded: chain l residue 180 THR Chi-restraints excluded: chain l residue 198 VAL Chi-restraints excluded: chain l residue 207 VAL Chi-restraints excluded: chain l residue 212 MET Chi-restraints excluded: chain l residue 219 VAL Chi-restraints excluded: chain n residue 97 LEU Chi-restraints excluded: chain n residue 141 VAL Chi-restraints excluded: chain n residue 146 VAL Chi-restraints excluded: chain o residue 83 THR Chi-restraints excluded: chain o residue 84 LEU Chi-restraints excluded: chain o residue 102 GLU Chi-restraints excluded: chain o residue 110 ILE Chi-restraints excluded: chain o residue 117 VAL Chi-restraints excluded: chain o residue 132 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1008 random chunks: chunk 883 optimal weight: 0.1980 chunk 930 optimal weight: 20.0000 chunk 849 optimal weight: 3.9990 chunk 905 optimal weight: 0.0980 chunk 544 optimal weight: 8.9990 chunk 394 optimal weight: 2.9990 chunk 710 optimal weight: 0.9990 chunk 277 optimal weight: 1.9990 chunk 818 optimal weight: 2.9990 chunk 856 optimal weight: 0.5980 chunk 902 optimal weight: 5.9990 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 178 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 72 GLN A 91 GLN ** c 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 397 ASN ** E 826 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 217 GLN Q 91 GLN Q 94 GLN ** S 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 91 GLN W 101 ASN Y 235 ASN Y 536 GLN ** Z 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 94 GLN j 74 GLN o 74 GLN o 91 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8267 moved from start: 0.1357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 78954 Z= 0.190 Angle : 0.629 18.577 107580 Z= 0.321 Chirality : 0.046 0.274 12384 Planarity : 0.005 0.178 13893 Dihedral : 6.360 59.217 11097 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.58 % Allowed : 7.00 % Favored : 92.42 % Rotamer: Outliers : 4.84 % Allowed : 31.84 % Favored : 63.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.63 % Cis-general : 0.00 % Twisted Proline : 1.26 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.53 (0.08), residues: 10164 helix: 0.65 (0.18), residues: 891 sheet: -0.59 (0.08), residues: 4047 loop : -1.67 (0.08), residues: 5226 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP X 89 HIS 0.008 0.001 HIS E 396 PHE 0.070 0.001 PHE E 177 TYR 0.027 0.001 TYR E 771 ARG 0.019 0.000 ARG n 121 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 20328 Ramachandran restraints generated. 10164 Oldfield, 0 Emsley, 10164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 20328 Ramachandran restraints generated. 10164 Oldfield, 0 Emsley, 10164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1144 residues out of total 8352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 404 poor density : 740 time to evaluate : 6.388 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 7 LYS cc_start: 0.8257 (OUTLIER) cc_final: 0.8018 (mtmm) REVERT: M 13 ASP cc_start: 0.8405 (m-30) cc_final: 0.8063 (t0) REVERT: J 241 ARG cc_start: 0.8877 (OUTLIER) cc_final: 0.8203 (mtp180) REVERT: J 719 ARG cc_start: 0.7832 (OUTLIER) cc_final: 0.7597 (ttp-170) REVERT: J 758 GLN cc_start: 0.8150 (mm110) cc_final: 0.7827 (tt0) REVERT: J 783 HIS cc_start: 0.8510 (m-70) cc_final: 0.7965 (m-70) REVERT: m 7 LYS cc_start: 0.9036 (mtmt) cc_final: 0.8833 (mtmm) REVERT: m 92 ARG cc_start: 0.8279 (tpp80) cc_final: 0.7834 (ttp80) REVERT: m 103 GLU cc_start: 0.7802 (pp20) cc_final: 0.7394 (pp20) REVERT: L 1 MET cc_start: 0.6474 (tmt) cc_final: 0.5986 (mmt) REVERT: I 158 LYS cc_start: 0.8391 (tppt) cc_final: 0.7981 (tptp) REVERT: I 217 GLN cc_start: 0.7228 (mt0) cc_final: 0.6978 (tt0) REVERT: B 57 ASP cc_start: 0.8763 (t0) cc_final: 0.8472 (t0) REVERT: B 135 GLU cc_start: 0.8039 (OUTLIER) cc_final: 0.7616 (mt-10) REVERT: b 29 ASN cc_start: 0.8985 (t0) cc_final: 0.8727 (t0) REVERT: b 43 LYS cc_start: 0.8853 (OUTLIER) cc_final: 0.8386 (mmpt) REVERT: A 90 GLU cc_start: 0.8615 (tm-30) cc_final: 0.8224 (tm-30) REVERT: C 21 LYS cc_start: 0.8937 (OUTLIER) cc_final: 0.8544 (pmtt) REVERT: C 155 ARG cc_start: 0.7663 (mtm110) cc_final: 0.6947 (ptt-90) REVERT: C 196 ARG cc_start: 0.2187 (OUTLIER) cc_final: 0.1965 (ptt90) REVERT: c 11 LYS cc_start: 0.8132 (mmmm) cc_final: 0.7566 (mmmm) REVERT: c 43 LYS cc_start: 0.6761 (mmpt) cc_final: 0.6531 (mmpt) REVERT: c 53 GLU cc_start: 0.8768 (pt0) cc_final: 0.8514 (pt0) REVERT: c 87 MET cc_start: 0.8716 (mmt) cc_final: 0.7530 (mmt) REVERT: c 90 GLU cc_start: 0.9135 (pt0) cc_final: 0.8314 (pp20) REVERT: c 94 GLN cc_start: 0.7782 (OUTLIER) cc_final: 0.6871 (mp10) REVERT: c 102 GLU cc_start: 0.8412 (OUTLIER) cc_final: 0.8131 (pp20) REVERT: D 24 ARG cc_start: 0.7924 (ttp80) cc_final: 0.7397 (ttp80) REVERT: E 147 TRP cc_start: 0.7412 (m100) cc_final: 0.6047 (m100) REVERT: E 648 LYS cc_start: 0.8998 (OUTLIER) cc_final: 0.8759 (tttt) REVERT: E 751 LYS cc_start: 0.9074 (OUTLIER) cc_final: 0.8847 (pmtt) REVERT: F 92 ARG cc_start: 0.8361 (tpp80) cc_final: 0.8151 (tpp80) REVERT: G 62 GLN cc_start: 0.8393 (tt0) cc_final: 0.8089 (tt0) REVERT: P 8 MET cc_start: 0.8802 (mmp) cc_final: 0.8514 (mmm) REVERT: Q 5 ASN cc_start: 0.9295 (t0) cc_final: 0.9061 (t160) REVERT: Q 80 THR cc_start: 0.8982 (OUTLIER) cc_final: 0.8528 (p) REVERT: Q 94 GLN cc_start: 0.9083 (mt0) cc_final: 0.8851 (mt0) REVERT: Q 135 GLU cc_start: 0.8074 (mt-10) cc_final: 0.7760 (mt-10) REVERT: S 17 LEU cc_start: 0.8905 (OUTLIER) cc_final: 0.8646 (mt) REVERT: T 212 MET cc_start: 0.5033 (tpt) cc_final: 0.4201 (tpt) REVERT: U 21 LYS cc_start: 0.8864 (OUTLIER) cc_final: 0.8646 (pmtt) REVERT: U 49 GLU cc_start: 0.8777 (pt0) cc_final: 0.8277 (pm20) REVERT: U 135 GLU cc_start: 0.8922 (mm-30) cc_final: 0.8593 (tp30) REVERT: U 164 MET cc_start: 0.4036 (pmm) cc_final: 0.2442 (tpp) REVERT: W 11 LYS cc_start: 0.8228 (mmmm) cc_final: 0.7747 (mmmm) REVERT: W 29 ASN cc_start: 0.8058 (t0) cc_final: 0.7696 (t0) REVERT: W 44 ASP cc_start: 0.8288 (t0) cc_final: 0.8007 (p0) REVERT: W 142 LYS cc_start: 0.9360 (ttpp) cc_final: 0.9010 (tttp) REVERT: W 164 MET cc_start: 0.1898 (tpp) cc_final: 0.1256 (tpp) REVERT: X 21 ARG cc_start: 0.8296 (ttp80) cc_final: 0.8065 (ttp80) REVERT: X 103 GLU cc_start: 0.8454 (OUTLIER) cc_final: 0.8183 (tp30) REVERT: Y 90 LEU cc_start: 0.7575 (OUTLIER) cc_final: 0.7334 (pp) REVERT: Y 329 LEU cc_start: 0.9052 (OUTLIER) cc_final: 0.8747 (mt) REVERT: Y 341 ASP cc_start: 0.8097 (m-30) cc_final: 0.7780 (m-30) REVERT: Y 373 ARG cc_start: 0.8153 (OUTLIER) cc_final: 0.7922 (ptm-80) REVERT: d 105 ARG cc_start: 0.8736 (OUTLIER) cc_final: 0.8349 (ptm160) REVERT: d 111 ARG cc_start: 0.8644 (OUTLIER) cc_final: 0.8370 (ttm-80) REVERT: f 223 ARG cc_start: 0.5651 (ppt170) cc_final: 0.5442 (pmt-80) REVERT: h 53 GLU cc_start: 0.8494 (OUTLIER) cc_final: 0.8108 (pm20) REVERT: h 102 GLU cc_start: 0.8271 (OUTLIER) cc_final: 0.8050 (mp0) REVERT: i 135 GLU cc_start: 0.8222 (mt-10) cc_final: 0.7853 (pt0) REVERT: i 212 MET cc_start: 0.4469 (tpp) cc_final: 0.4078 (tpp) REVERT: l 212 MET cc_start: 0.5368 (OUTLIER) cc_final: 0.4475 (tmm) REVERT: n 91 GLN cc_start: 0.8067 (pp30) cc_final: 0.7786 (pm20) REVERT: n 164 MET cc_start: 0.3781 (pmm) cc_final: 0.2632 (tpp) REVERT: o 11 LYS cc_start: 0.8178 (mmmm) cc_final: 0.7604 (mmmm) REVERT: o 16 THR cc_start: 0.8239 (OUTLIER) cc_final: 0.7937 (t) REVERT: o 102 GLU cc_start: 0.8498 (OUTLIER) cc_final: 0.8128 (pp20) outliers start: 404 outliers final: 289 residues processed: 1089 average time/residue: 1.4814 time to fit residues: 2178.1016 Evaluate side-chains 1033 residues out of total 8352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 314 poor density : 719 time to evaluate : 6.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 7 LYS Chi-restraints excluded: chain M residue 46 VAL Chi-restraints excluded: chain M residue 47 THR Chi-restraints excluded: chain M residue 50 VAL Chi-restraints excluded: chain M residue 99 GLU Chi-restraints excluded: chain M residue 109 ASN Chi-restraints excluded: chain J residue 26 VAL Chi-restraints excluded: chain J residue 47 LEU Chi-restraints excluded: chain J residue 65 THR Chi-restraints excluded: chain J residue 88 THR Chi-restraints excluded: chain J residue 122 VAL Chi-restraints excluded: chain J residue 138 LEU Chi-restraints excluded: chain J residue 149 THR Chi-restraints excluded: chain J residue 153 ILE Chi-restraints excluded: chain J residue 167 VAL Chi-restraints excluded: chain J residue 168 VAL Chi-restraints excluded: chain J residue 215 THR Chi-restraints excluded: chain J residue 241 ARG Chi-restraints excluded: chain J residue 257 SER Chi-restraints excluded: chain J residue 325 CYS Chi-restraints excluded: chain J residue 504 THR Chi-restraints excluded: chain J residue 511 ILE Chi-restraints excluded: chain J residue 583 THR Chi-restraints excluded: chain J residue 598 ILE Chi-restraints excluded: chain J residue 613 VAL Chi-restraints excluded: chain J residue 621 VAL Chi-restraints excluded: chain J residue 638 LEU Chi-restraints excluded: chain J residue 719 ARG Chi-restraints excluded: chain J residue 823 THR Chi-restraints excluded: chain J residue 827 LEU Chi-restraints excluded: chain m residue 46 VAL Chi-restraints excluded: chain m residue 74 THR Chi-restraints excluded: chain m residue 85 THR Chi-restraints excluded: chain L residue 18 SER Chi-restraints excluded: chain L residue 31 VAL Chi-restraints excluded: chain L residue 99 VAL Chi-restraints excluded: chain L residue 151 VAL Chi-restraints excluded: chain L residue 159 ASP Chi-restraints excluded: chain L residue 167 ILE Chi-restraints excluded: chain H residue 844 ASP Chi-restraints excluded: chain I residue 118 THR Chi-restraints excluded: chain I residue 161 THR Chi-restraints excluded: chain I residue 167 THR Chi-restraints excluded: chain I residue 203 VAL Chi-restraints excluded: chain I residue 207 ILE Chi-restraints excluded: chain V residue 51 THR Chi-restraints excluded: chain V residue 68 THR Chi-restraints excluded: chain V residue 70 THR Chi-restraints excluded: chain V residue 83 THR Chi-restraints excluded: chain V residue 90 GLU Chi-restraints excluded: chain V residue 117 VAL Chi-restraints excluded: chain V residue 146 VAL Chi-restraints excluded: chain V residue 225 ASN Chi-restraints excluded: chain v residue 10 VAL Chi-restraints excluded: chain v residue 32 SER Chi-restraints excluded: chain v residue 33 ASP Chi-restraints excluded: chain v residue 84 LEU Chi-restraints excluded: chain v residue 97 LEU Chi-restraints excluded: chain v residue 119 VAL Chi-restraints excluded: chain v residue 179 THR Chi-restraints excluded: chain v residue 219 VAL Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain B residue 87 MET Chi-restraints excluded: chain B residue 135 GLU Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 182 THR Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 199 SER Chi-restraints excluded: chain b residue 43 LYS Chi-restraints excluded: chain b residue 84 LEU Chi-restraints excluded: chain b residue 116 THR Chi-restraints excluded: chain b residue 146 VAL Chi-restraints excluded: chain A residue 83 THR Chi-restraints excluded: chain A residue 125 SER Chi-restraints excluded: chain A residue 127 ILE Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 148 ARG Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain a residue 32 SER Chi-restraints excluded: chain a residue 119 VAL Chi-restraints excluded: chain a residue 185 PHE Chi-restraints excluded: chain a residue 212 MET Chi-restraints excluded: chain a residue 242 THR Chi-restraints excluded: chain C residue 17 LEU Chi-restraints excluded: chain C residue 21 LYS Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain C residue 83 THR Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 165 THR Chi-restraints excluded: chain C residue 196 ARG Chi-restraints excluded: chain c residue 7 THR Chi-restraints excluded: chain c residue 94 GLN Chi-restraints excluded: chain c residue 102 GLU Chi-restraints excluded: chain c residue 117 VAL Chi-restraints excluded: chain c residue 240 GLU Chi-restraints excluded: chain D residue 13 ASP Chi-restraints excluded: chain D residue 46 VAL Chi-restraints excluded: chain D residue 47 THR Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain E residue 26 VAL Chi-restraints excluded: chain E residue 65 THR Chi-restraints excluded: chain E residue 122 VAL Chi-restraints excluded: chain E residue 124 THR Chi-restraints excluded: chain E residue 138 LEU Chi-restraints excluded: chain E residue 139 VAL Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain E residue 215 THR Chi-restraints excluded: chain E residue 324 THR Chi-restraints excluded: chain E residue 325 CYS Chi-restraints excluded: chain E residue 329 LEU Chi-restraints excluded: chain E residue 330 THR Chi-restraints excluded: chain E residue 331 THR Chi-restraints excluded: chain E residue 374 SER Chi-restraints excluded: chain E residue 397 ASN Chi-restraints excluded: chain E residue 431 THR Chi-restraints excluded: chain E residue 531 VAL Chi-restraints excluded: chain E residue 542 VAL Chi-restraints excluded: chain E residue 596 GLU Chi-restraints excluded: chain E residue 598 ILE Chi-restraints excluded: chain E residue 613 VAL Chi-restraints excluded: chain E residue 621 VAL Chi-restraints excluded: chain E residue 648 LYS Chi-restraints excluded: chain E residue 653 LEU Chi-restraints excluded: chain E residue 667 LEU Chi-restraints excluded: chain E residue 751 LYS Chi-restraints excluded: chain E residue 783 HIS Chi-restraints excluded: chain E residue 822 ILE Chi-restraints excluded: chain E residue 823 THR Chi-restraints excluded: chain F residue 46 VAL Chi-restraints excluded: chain G residue 99 VAL Chi-restraints excluded: chain G residue 159 ASP Chi-restraints excluded: chain N residue 161 THR Chi-restraints excluded: chain N residue 167 THR Chi-restraints excluded: chain N residue 171 LYS Chi-restraints excluded: chain N residue 204 SER Chi-restraints excluded: chain O residue 51 THR Chi-restraints excluded: chain O residue 63 GLU Chi-restraints excluded: chain O residue 70 THR Chi-restraints excluded: chain O residue 81 SER Chi-restraints excluded: chain O residue 83 THR Chi-restraints excluded: chain O residue 117 VAL Chi-restraints excluded: chain O residue 125 SER Chi-restraints excluded: chain O residue 132 THR Chi-restraints excluded: chain O residue 146 VAL Chi-restraints excluded: chain O residue 166 VAL Chi-restraints excluded: chain O residue 174 VAL Chi-restraints excluded: chain O residue 225 ASN Chi-restraints excluded: chain P residue 31 LEU Chi-restraints excluded: chain P residue 84 LEU Chi-restraints excluded: chain P residue 97 LEU Chi-restraints excluded: chain P residue 119 VAL Chi-restraints excluded: chain P residue 132 THR Chi-restraints excluded: chain P residue 179 THR Chi-restraints excluded: chain P residue 219 VAL Chi-restraints excluded: chain Q residue 80 THR Chi-restraints excluded: chain Q residue 119 VAL Chi-restraints excluded: chain Q residue 126 SER Chi-restraints excluded: chain Q residue 131 VAL Chi-restraints excluded: chain Q residue 132 THR Chi-restraints excluded: chain Q residue 136 VAL Chi-restraints excluded: chain Q residue 165 THR Chi-restraints excluded: chain Q residue 191 THR Chi-restraints excluded: chain Q residue 198 VAL Chi-restraints excluded: chain R residue 23 SER Chi-restraints excluded: chain R residue 64 ASP Chi-restraints excluded: chain R residue 84 LEU Chi-restraints excluded: chain R residue 97 LEU Chi-restraints excluded: chain R residue 116 THR Chi-restraints excluded: chain R residue 125 SER Chi-restraints excluded: chain R residue 131 VAL Chi-restraints excluded: chain R residue 132 THR Chi-restraints excluded: chain R residue 158 VAL Chi-restraints excluded: chain R residue 180 THR Chi-restraints excluded: chain R residue 199 SER Chi-restraints excluded: chain S residue 17 LEU Chi-restraints excluded: chain S residue 34 VAL Chi-restraints excluded: chain S residue 83 THR Chi-restraints excluded: chain S residue 127 ILE Chi-restraints excluded: chain S residue 146 VAL Chi-restraints excluded: chain S residue 198 VAL Chi-restraints excluded: chain S residue 215 THR Chi-restraints excluded: chain S residue 224 VAL Chi-restraints excluded: chain T residue 3 VAL Chi-restraints excluded: chain T residue 117 VAL Chi-restraints excluded: chain T residue 119 VAL Chi-restraints excluded: chain T residue 219 VAL Chi-restraints excluded: chain U residue 17 LEU Chi-restraints excluded: chain U residue 21 LYS Chi-restraints excluded: chain U residue 61 ASP Chi-restraints excluded: chain U residue 83 THR Chi-restraints excluded: chain U residue 141 VAL Chi-restraints excluded: chain U residue 146 VAL Chi-restraints excluded: chain U residue 165 THR Chi-restraints excluded: chain U residue 179 THR Chi-restraints excluded: chain U residue 212 MET Chi-restraints excluded: chain W residue 7 THR Chi-restraints excluded: chain W residue 110 ILE Chi-restraints excluded: chain W residue 117 VAL Chi-restraints excluded: chain X residue 46 VAL Chi-restraints excluded: chain X residue 47 THR Chi-restraints excluded: chain X residue 50 VAL Chi-restraints excluded: chain X residue 53 GLU Chi-restraints excluded: chain X residue 64 GLU Chi-restraints excluded: chain X residue 103 GLU Chi-restraints excluded: chain Y residue 5 SER Chi-restraints excluded: chain Y residue 21 THR Chi-restraints excluded: chain Y residue 26 VAL Chi-restraints excluded: chain Y residue 50 THR Chi-restraints excluded: chain Y residue 65 THR Chi-restraints excluded: chain Y residue 88 THR Chi-restraints excluded: chain Y residue 90 LEU Chi-restraints excluded: chain Y residue 110 ASP Chi-restraints excluded: chain Y residue 122 VAL Chi-restraints excluded: chain Y residue 138 LEU Chi-restraints excluded: chain Y residue 149 THR Chi-restraints excluded: chain Y residue 153 ILE Chi-restraints excluded: chain Y residue 167 VAL Chi-restraints excluded: chain Y residue 168 VAL Chi-restraints excluded: chain Y residue 177 PHE Chi-restraints excluded: chain Y residue 215 THR Chi-restraints excluded: chain Y residue 217 LEU Chi-restraints excluded: chain Y residue 324 THR Chi-restraints excluded: chain Y residue 325 CYS Chi-restraints excluded: chain Y residue 329 LEU Chi-restraints excluded: chain Y residue 330 THR Chi-restraints excluded: chain Y residue 331 THR Chi-restraints excluded: chain Y residue 373 ARG Chi-restraints excluded: chain Y residue 381 ASP Chi-restraints excluded: chain Y residue 397 ASN Chi-restraints excluded: chain Y residue 433 MET Chi-restraints excluded: chain Y residue 469 GLU Chi-restraints excluded: chain Y residue 531 VAL Chi-restraints excluded: chain Y residue 544 VAL Chi-restraints excluded: chain Y residue 613 VAL Chi-restraints excluded: chain Y residue 621 VAL Chi-restraints excluded: chain Y residue 638 LEU Chi-restraints excluded: chain Y residue 823 THR Chi-restraints excluded: chain Z residue 58 LEU Chi-restraints excluded: chain Z residue 74 THR Chi-restraints excluded: chain Z residue 98 VAL Chi-restraints excluded: chain d residue 21 VAL Chi-restraints excluded: chain d residue 31 VAL Chi-restraints excluded: chain d residue 105 ARG Chi-restraints excluded: chain d residue 111 ARG Chi-restraints excluded: chain d residue 159 ASP Chi-restraints excluded: chain d residue 167 ILE Chi-restraints excluded: chain e residue 847 LEU Chi-restraints excluded: chain e residue 849 SER Chi-restraints excluded: chain f residue 118 THR Chi-restraints excluded: chain f residue 161 THR Chi-restraints excluded: chain f residue 167 THR Chi-restraints excluded: chain f residue 188 VAL Chi-restraints excluded: chain f residue 191 VAL Chi-restraints excluded: chain f residue 203 VAL Chi-restraints excluded: chain f residue 204 SER Chi-restraints excluded: chain g residue 51 THR Chi-restraints excluded: chain g residue 63 GLU Chi-restraints excluded: chain g residue 70 THR Chi-restraints excluded: chain g residue 83 THR Chi-restraints excluded: chain g residue 146 VAL Chi-restraints excluded: chain g residue 191 THR Chi-restraints excluded: chain g residue 225 ASN Chi-restraints excluded: chain h residue 31 LEU Chi-restraints excluded: chain h residue 53 GLU Chi-restraints excluded: chain h residue 70 THR Chi-restraints excluded: chain h residue 84 LEU Chi-restraints excluded: chain h residue 102 GLU Chi-restraints excluded: chain h residue 119 VAL Chi-restraints excluded: chain h residue 158 VAL Chi-restraints excluded: chain h residue 179 THR Chi-restraints excluded: chain i residue 16 THR Chi-restraints excluded: chain i residue 131 VAL Chi-restraints excluded: chain i residue 182 THR Chi-restraints excluded: chain i residue 183 VAL Chi-restraints excluded: chain i residue 198 VAL Chi-restraints excluded: chain j residue 54 SER Chi-restraints excluded: chain j residue 64 ASP Chi-restraints excluded: chain j residue 70 THR Chi-restraints excluded: chain j residue 84 LEU Chi-restraints excluded: chain j residue 125 SER Chi-restraints excluded: chain j residue 132 THR Chi-restraints excluded: chain j residue 135 GLU Chi-restraints excluded: chain j residue 138 THR Chi-restraints excluded: chain j residue 146 VAL Chi-restraints excluded: chain j residue 158 VAL Chi-restraints excluded: chain k residue 83 THR Chi-restraints excluded: chain k residue 127 ILE Chi-restraints excluded: chain k residue 132 THR Chi-restraints excluded: chain k residue 198 VAL Chi-restraints excluded: chain k residue 215 THR Chi-restraints excluded: chain k residue 224 VAL Chi-restraints excluded: chain l residue 3 VAL Chi-restraints excluded: chain l residue 140 THR Chi-restraints excluded: chain l residue 180 THR Chi-restraints excluded: chain l residue 198 VAL Chi-restraints excluded: chain l residue 207 VAL Chi-restraints excluded: chain l residue 212 MET Chi-restraints excluded: chain l residue 219 VAL Chi-restraints excluded: chain n residue 83 THR Chi-restraints excluded: chain n residue 97 LEU Chi-restraints excluded: chain n residue 101 ASN Chi-restraints excluded: chain n residue 141 VAL Chi-restraints excluded: chain n residue 146 VAL Chi-restraints excluded: chain o residue 16 THR Chi-restraints excluded: chain o residue 83 THR Chi-restraints excluded: chain o residue 102 GLU Chi-restraints excluded: chain o residue 110 ILE Chi-restraints excluded: chain o residue 117 VAL Chi-restraints excluded: chain o residue 132 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1008 random chunks: chunk 594 optimal weight: 6.9990 chunk 957 optimal weight: 50.0000 chunk 584 optimal weight: 0.0770 chunk 454 optimal weight: 2.9990 chunk 665 optimal weight: 20.0000 chunk 1004 optimal weight: 30.0000 chunk 924 optimal weight: 3.9990 chunk 799 optimal weight: 4.9990 chunk 83 optimal weight: 9.9990 chunk 617 optimal weight: 9.9990 chunk 490 optimal weight: 3.9990 overall best weight: 3.2146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 178 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 91 GLN E 397 ASN ** E 826 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 232 GLN Q 91 GLN ** T 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 101 ASN Y 235 ASN Y 536 GLN ** Z 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 74 GLN l 94 GLN ** o 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8324 moved from start: 0.1436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.082 78954 Z= 0.410 Angle : 0.710 20.202 107580 Z= 0.364 Chirality : 0.049 0.452 12384 Planarity : 0.006 0.181 13893 Dihedral : 6.653 59.283 11073 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.62 % Allowed : 7.96 % Favored : 91.42 % Rotamer: Outliers : 4.83 % Allowed : 31.90 % Favored : 63.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.63 % Cis-general : 0.00 % Twisted Proline : 1.26 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.73 (0.08), residues: 10164 helix: 0.21 (0.17), residues: 930 sheet: -0.68 (0.08), residues: 4017 loop : -1.79 (0.08), residues: 5217 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP Z 89 HIS 0.008 0.001 HIS E 396 PHE 0.022 0.002 PHE j 120 TYR 0.025 0.002 TYR n 55 ARG 0.019 0.001 ARG n 121 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 20328 Ramachandran restraints generated. 10164 Oldfield, 0 Emsley, 10164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 20328 Ramachandran restraints generated. 10164 Oldfield, 0 Emsley, 10164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1108 residues out of total 8352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 403 poor density : 705 time to evaluate : 6.317 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 7 LYS cc_start: 0.8321 (OUTLIER) cc_final: 0.8090 (mtmm) REVERT: M 13 ASP cc_start: 0.8609 (m-30) cc_final: 0.8284 (t0) REVERT: M 95 MET cc_start: 0.9340 (OUTLIER) cc_final: 0.9077 (tpt) REVERT: J 241 ARG cc_start: 0.8987 (OUTLIER) cc_final: 0.8633 (mtp180) REVERT: J 758 GLN cc_start: 0.8211 (mm110) cc_final: 0.7910 (tt0) REVERT: m 103 GLU cc_start: 0.7816 (pp20) cc_final: 0.7393 (pp20) REVERT: I 185 GLN cc_start: 0.8528 (OUTLIER) cc_final: 0.8205 (tt0) REVERT: B 57 ASP cc_start: 0.8795 (t0) cc_final: 0.8433 (t0) REVERT: B 135 GLU cc_start: 0.8054 (OUTLIER) cc_final: 0.7631 (mt-10) REVERT: b 29 ASN cc_start: 0.9052 (t0) cc_final: 0.8789 (t0) REVERT: b 43 LYS cc_start: 0.8966 (OUTLIER) cc_final: 0.8565 (mmpt) REVERT: A 90 GLU cc_start: 0.8604 (tm-30) cc_final: 0.8267 (tm-30) REVERT: C 21 LYS cc_start: 0.8957 (OUTLIER) cc_final: 0.8568 (pmtt) REVERT: C 155 ARG cc_start: 0.7567 (mtm110) cc_final: 0.6805 (ptt-90) REVERT: C 196 ARG cc_start: 0.2261 (OUTLIER) cc_final: 0.2036 (ptt90) REVERT: c 43 LYS cc_start: 0.6417 (mmpt) cc_final: 0.6097 (mmpt) REVERT: c 53 GLU cc_start: 0.8772 (pt0) cc_final: 0.8550 (pt0) REVERT: c 87 MET cc_start: 0.8770 (mmt) cc_final: 0.7576 (mmt) REVERT: c 102 GLU cc_start: 0.8426 (OUTLIER) cc_final: 0.8122 (pp20) REVERT: c 148 ARG cc_start: 0.8462 (tpt-90) cc_final: 0.7989 (tpt90) REVERT: E 147 TRP cc_start: 0.7460 (m100) cc_final: 0.6085 (m100) REVERT: E 751 LYS cc_start: 0.9077 (OUTLIER) cc_final: 0.8870 (pmtt) REVERT: N 185 GLN cc_start: 0.8376 (OUTLIER) cc_final: 0.7517 (tt0) REVERT: P 8 MET cc_start: 0.8803 (mmp) cc_final: 0.8571 (mmm) REVERT: Q 5 ASN cc_start: 0.9337 (t0) cc_final: 0.9092 (t160) REVERT: Q 80 THR cc_start: 0.9150 (OUTLIER) cc_final: 0.8615 (p) REVERT: Q 135 GLU cc_start: 0.8158 (mt-10) cc_final: 0.7878 (mt-10) REVERT: S 135 GLU cc_start: 0.8810 (pm20) cc_final: 0.8501 (pm20) REVERT: T 212 MET cc_start: 0.4908 (tpt) cc_final: 0.4084 (tpt) REVERT: U 21 LYS cc_start: 0.8866 (OUTLIER) cc_final: 0.8660 (pmtt) REVERT: U 135 GLU cc_start: 0.8931 (mm-30) cc_final: 0.8595 (tp30) REVERT: W 11 LYS cc_start: 0.8271 (mmmm) cc_final: 0.7760 (mmmm) REVERT: W 29 ASN cc_start: 0.8103 (t0) cc_final: 0.7704 (t0) REVERT: W 44 ASP cc_start: 0.8337 (t0) cc_final: 0.8047 (p0) REVERT: W 142 LYS cc_start: 0.9339 (ttpp) cc_final: 0.8982 (tttp) REVERT: X 21 ARG cc_start: 0.8284 (ttp80) cc_final: 0.8036 (ttp80) REVERT: X 103 GLU cc_start: 0.8484 (OUTLIER) cc_final: 0.8236 (tp30) REVERT: Y 90 LEU cc_start: 0.7556 (OUTLIER) cc_final: 0.7295 (pp) REVERT: Y 329 LEU cc_start: 0.9153 (OUTLIER) cc_final: 0.8821 (mt) REVERT: Y 341 ASP cc_start: 0.8107 (m-30) cc_final: 0.7794 (m-30) REVERT: Y 373 ARG cc_start: 0.8299 (OUTLIER) cc_final: 0.7512 (ptm-80) REVERT: Y 721 GLU cc_start: 0.6304 (OUTLIER) cc_final: 0.6010 (mp0) REVERT: d 105 ARG cc_start: 0.8762 (OUTLIER) cc_final: 0.8358 (ptm160) REVERT: d 111 ARG cc_start: 0.8789 (OUTLIER) cc_final: 0.8388 (ttm-80) REVERT: g 32 SER cc_start: 0.9053 (OUTLIER) cc_final: 0.8625 (m) REVERT: h 53 GLU cc_start: 0.8434 (OUTLIER) cc_final: 0.8000 (pm20) REVERT: h 102 GLU cc_start: 0.8298 (OUTLIER) cc_final: 0.8076 (mp0) REVERT: i 135 GLU cc_start: 0.8251 (mt-10) cc_final: 0.7933 (pt0) REVERT: i 212 MET cc_start: 0.4679 (tpp) cc_final: 0.4202 (tpp) REVERT: k 17 LEU cc_start: 0.9024 (OUTLIER) cc_final: 0.8824 (mt) REVERT: k 135 GLU cc_start: 0.8651 (pm20) cc_final: 0.8362 (pm20) REVERT: l 212 MET cc_start: 0.5297 (OUTLIER) cc_final: 0.4519 (tmm) REVERT: n 164 MET cc_start: 0.3951 (pmm) cc_final: 0.2640 (tpp) REVERT: o 16 THR cc_start: 0.8178 (OUTLIER) cc_final: 0.7857 (t) REVERT: o 102 GLU cc_start: 0.8464 (OUTLIER) cc_final: 0.8082 (pp20) outliers start: 403 outliers final: 312 residues processed: 1056 average time/residue: 1.4878 time to fit residues: 2120.7999 Evaluate side-chains 1028 residues out of total 8352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 339 poor density : 689 time to evaluate : 6.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 7 LYS Chi-restraints excluded: chain M residue 41 LEU Chi-restraints excluded: chain M residue 46 VAL Chi-restraints excluded: chain M residue 47 THR Chi-restraints excluded: chain M residue 50 VAL Chi-restraints excluded: chain M residue 95 MET Chi-restraints excluded: chain M residue 99 GLU Chi-restraints excluded: chain M residue 109 ASN Chi-restraints excluded: chain J residue 26 VAL Chi-restraints excluded: chain J residue 47 LEU Chi-restraints excluded: chain J residue 65 THR Chi-restraints excluded: chain J residue 88 THR Chi-restraints excluded: chain J residue 122 VAL Chi-restraints excluded: chain J residue 138 LEU Chi-restraints excluded: chain J residue 149 THR Chi-restraints excluded: chain J residue 153 ILE Chi-restraints excluded: chain J residue 167 VAL Chi-restraints excluded: chain J residue 168 VAL Chi-restraints excluded: chain J residue 215 THR Chi-restraints excluded: chain J residue 241 ARG Chi-restraints excluded: chain J residue 257 SER Chi-restraints excluded: chain J residue 325 CYS Chi-restraints excluded: chain J residue 504 THR Chi-restraints excluded: chain J residue 511 ILE Chi-restraints excluded: chain J residue 583 THR Chi-restraints excluded: chain J residue 598 ILE Chi-restraints excluded: chain J residue 613 VAL Chi-restraints excluded: chain J residue 621 VAL Chi-restraints excluded: chain J residue 638 LEU Chi-restraints excluded: chain J residue 823 THR Chi-restraints excluded: chain J residue 827 LEU Chi-restraints excluded: chain m residue 46 VAL Chi-restraints excluded: chain m residue 74 THR Chi-restraints excluded: chain m residue 85 THR Chi-restraints excluded: chain L residue 18 SER Chi-restraints excluded: chain L residue 31 VAL Chi-restraints excluded: chain L residue 99 VAL Chi-restraints excluded: chain L residue 151 VAL Chi-restraints excluded: chain L residue 159 ASP Chi-restraints excluded: chain L residue 167 ILE Chi-restraints excluded: chain H residue 844 ASP Chi-restraints excluded: chain I residue 118 THR Chi-restraints excluded: chain I residue 161 THR Chi-restraints excluded: chain I residue 167 THR Chi-restraints excluded: chain I residue 185 GLN Chi-restraints excluded: chain I residue 207 ILE Chi-restraints excluded: chain V residue 51 THR Chi-restraints excluded: chain V residue 68 THR Chi-restraints excluded: chain V residue 70 THR Chi-restraints excluded: chain V residue 83 THR Chi-restraints excluded: chain V residue 90 GLU Chi-restraints excluded: chain V residue 117 VAL Chi-restraints excluded: chain V residue 146 VAL Chi-restraints excluded: chain V residue 166 VAL Chi-restraints excluded: chain V residue 225 ASN Chi-restraints excluded: chain v residue 10 VAL Chi-restraints excluded: chain v residue 32 SER Chi-restraints excluded: chain v residue 33 ASP Chi-restraints excluded: chain v residue 84 LEU Chi-restraints excluded: chain v residue 97 LEU Chi-restraints excluded: chain v residue 119 VAL Chi-restraints excluded: chain v residue 132 THR Chi-restraints excluded: chain v residue 179 THR Chi-restraints excluded: chain v residue 219 VAL Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain B residue 87 MET Chi-restraints excluded: chain B residue 135 GLU Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 182 THR Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 199 SER Chi-restraints excluded: chain b residue 43 LYS Chi-restraints excluded: chain b residue 84 LEU Chi-restraints excluded: chain b residue 116 THR Chi-restraints excluded: chain b residue 146 VAL Chi-restraints excluded: chain b residue 243 VAL Chi-restraints excluded: chain A residue 83 THR Chi-restraints excluded: chain A residue 125 SER Chi-restraints excluded: chain A residue 127 ILE Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 148 ARG Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain a residue 32 SER Chi-restraints excluded: chain a residue 119 VAL Chi-restraints excluded: chain a residue 132 THR Chi-restraints excluded: chain a residue 185 PHE Chi-restraints excluded: chain a residue 207 VAL Chi-restraints excluded: chain a residue 212 MET Chi-restraints excluded: chain a residue 242 THR Chi-restraints excluded: chain C residue 17 LEU Chi-restraints excluded: chain C residue 21 LYS Chi-restraints excluded: chain C residue 83 THR Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 165 THR Chi-restraints excluded: chain C residue 196 ARG Chi-restraints excluded: chain c residue 102 GLU Chi-restraints excluded: chain c residue 117 VAL Chi-restraints excluded: chain c residue 240 GLU Chi-restraints excluded: chain D residue 13 ASP Chi-restraints excluded: chain D residue 46 VAL Chi-restraints excluded: chain D residue 47 THR Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain E residue 5 SER Chi-restraints excluded: chain E residue 26 VAL Chi-restraints excluded: chain E residue 65 THR Chi-restraints excluded: chain E residue 109 ILE Chi-restraints excluded: chain E residue 122 VAL Chi-restraints excluded: chain E residue 124 THR Chi-restraints excluded: chain E residue 138 LEU Chi-restraints excluded: chain E residue 139 VAL Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain E residue 215 THR Chi-restraints excluded: chain E residue 324 THR Chi-restraints excluded: chain E residue 325 CYS Chi-restraints excluded: chain E residue 329 LEU Chi-restraints excluded: chain E residue 330 THR Chi-restraints excluded: chain E residue 331 THR Chi-restraints excluded: chain E residue 374 SER Chi-restraints excluded: chain E residue 397 ASN Chi-restraints excluded: chain E residue 431 THR Chi-restraints excluded: chain E residue 531 VAL Chi-restraints excluded: chain E residue 542 VAL Chi-restraints excluded: chain E residue 596 GLU Chi-restraints excluded: chain E residue 598 ILE Chi-restraints excluded: chain E residue 613 VAL Chi-restraints excluded: chain E residue 621 VAL Chi-restraints excluded: chain E residue 648 LYS Chi-restraints excluded: chain E residue 653 LEU Chi-restraints excluded: chain E residue 667 LEU Chi-restraints excluded: chain E residue 751 LYS Chi-restraints excluded: chain E residue 823 THR Chi-restraints excluded: chain F residue 46 VAL Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain F residue 85 THR Chi-restraints excluded: chain G residue 99 VAL Chi-restraints excluded: chain G residue 159 ASP Chi-restraints excluded: chain N residue 107 LEU Chi-restraints excluded: chain N residue 161 THR Chi-restraints excluded: chain N residue 167 THR Chi-restraints excluded: chain N residue 171 LYS Chi-restraints excluded: chain N residue 185 GLN Chi-restraints excluded: chain N residue 204 SER Chi-restraints excluded: chain O residue 51 THR Chi-restraints excluded: chain O residue 63 GLU Chi-restraints excluded: chain O residue 68 THR Chi-restraints excluded: chain O residue 70 THR Chi-restraints excluded: chain O residue 81 SER Chi-restraints excluded: chain O residue 83 THR Chi-restraints excluded: chain O residue 117 VAL Chi-restraints excluded: chain O residue 125 SER Chi-restraints excluded: chain O residue 127 ILE Chi-restraints excluded: chain O residue 132 THR Chi-restraints excluded: chain O residue 136 VAL Chi-restraints excluded: chain O residue 146 VAL Chi-restraints excluded: chain O residue 166 VAL Chi-restraints excluded: chain O residue 174 VAL Chi-restraints excluded: chain O residue 225 ASN Chi-restraints excluded: chain P residue 31 LEU Chi-restraints excluded: chain P residue 84 LEU Chi-restraints excluded: chain P residue 97 LEU Chi-restraints excluded: chain P residue 119 VAL Chi-restraints excluded: chain P residue 132 THR Chi-restraints excluded: chain P residue 179 THR Chi-restraints excluded: chain P residue 219 VAL Chi-restraints excluded: chain Q residue 80 THR Chi-restraints excluded: chain Q residue 119 VAL Chi-restraints excluded: chain Q residue 126 SER Chi-restraints excluded: chain Q residue 131 VAL Chi-restraints excluded: chain Q residue 132 THR Chi-restraints excluded: chain Q residue 136 VAL Chi-restraints excluded: chain Q residue 165 THR Chi-restraints excluded: chain Q residue 198 VAL Chi-restraints excluded: chain R residue 23 SER Chi-restraints excluded: chain R residue 51 THR Chi-restraints excluded: chain R residue 64 ASP Chi-restraints excluded: chain R residue 70 THR Chi-restraints excluded: chain R residue 81 SER Chi-restraints excluded: chain R residue 84 LEU Chi-restraints excluded: chain R residue 97 LEU Chi-restraints excluded: chain R residue 116 THR Chi-restraints excluded: chain R residue 125 SER Chi-restraints excluded: chain R residue 131 VAL Chi-restraints excluded: chain R residue 132 THR Chi-restraints excluded: chain R residue 158 VAL Chi-restraints excluded: chain R residue 180 THR Chi-restraints excluded: chain R residue 199 SER Chi-restraints excluded: chain S residue 7 THR Chi-restraints excluded: chain S residue 34 VAL Chi-restraints excluded: chain S residue 83 THR Chi-restraints excluded: chain S residue 127 ILE Chi-restraints excluded: chain S residue 140 THR Chi-restraints excluded: chain S residue 146 VAL Chi-restraints excluded: chain S residue 198 VAL Chi-restraints excluded: chain S residue 215 THR Chi-restraints excluded: chain S residue 224 VAL Chi-restraints excluded: chain T residue 3 VAL Chi-restraints excluded: chain T residue 117 VAL Chi-restraints excluded: chain T residue 119 VAL Chi-restraints excluded: chain T residue 138 THR Chi-restraints excluded: chain T residue 219 VAL Chi-restraints excluded: chain U residue 17 LEU Chi-restraints excluded: chain U residue 21 LYS Chi-restraints excluded: chain U residue 61 ASP Chi-restraints excluded: chain U residue 83 THR Chi-restraints excluded: chain U residue 141 VAL Chi-restraints excluded: chain U residue 146 VAL Chi-restraints excluded: chain U residue 165 THR Chi-restraints excluded: chain U residue 179 THR Chi-restraints excluded: chain U residue 212 MET Chi-restraints excluded: chain W residue 7 THR Chi-restraints excluded: chain W residue 110 ILE Chi-restraints excluded: chain W residue 117 VAL Chi-restraints excluded: chain X residue 46 VAL Chi-restraints excluded: chain X residue 47 THR Chi-restraints excluded: chain X residue 50 VAL Chi-restraints excluded: chain X residue 64 GLU Chi-restraints excluded: chain X residue 103 GLU Chi-restraints excluded: chain Y residue 5 SER Chi-restraints excluded: chain Y residue 21 THR Chi-restraints excluded: chain Y residue 26 VAL Chi-restraints excluded: chain Y residue 50 THR Chi-restraints excluded: chain Y residue 65 THR Chi-restraints excluded: chain Y residue 88 THR Chi-restraints excluded: chain Y residue 90 LEU Chi-restraints excluded: chain Y residue 110 ASP Chi-restraints excluded: chain Y residue 115 THR Chi-restraints excluded: chain Y residue 122 VAL Chi-restraints excluded: chain Y residue 138 LEU Chi-restraints excluded: chain Y residue 149 THR Chi-restraints excluded: chain Y residue 153 ILE Chi-restraints excluded: chain Y residue 167 VAL Chi-restraints excluded: chain Y residue 168 VAL Chi-restraints excluded: chain Y residue 177 PHE Chi-restraints excluded: chain Y residue 215 THR Chi-restraints excluded: chain Y residue 217 LEU Chi-restraints excluded: chain Y residue 291 LEU Chi-restraints excluded: chain Y residue 324 THR Chi-restraints excluded: chain Y residue 325 CYS Chi-restraints excluded: chain Y residue 329 LEU Chi-restraints excluded: chain Y residue 330 THR Chi-restraints excluded: chain Y residue 331 THR Chi-restraints excluded: chain Y residue 373 ARG Chi-restraints excluded: chain Y residue 381 ASP Chi-restraints excluded: chain Y residue 397 ASN Chi-restraints excluded: chain Y residue 433 MET Chi-restraints excluded: chain Y residue 469 GLU Chi-restraints excluded: chain Y residue 504 THR Chi-restraints excluded: chain Y residue 521 ILE Chi-restraints excluded: chain Y residue 531 VAL Chi-restraints excluded: chain Y residue 536 GLN Chi-restraints excluded: chain Y residue 539 THR Chi-restraints excluded: chain Y residue 542 VAL Chi-restraints excluded: chain Y residue 544 VAL Chi-restraints excluded: chain Y residue 596 GLU Chi-restraints excluded: chain Y residue 613 VAL Chi-restraints excluded: chain Y residue 621 VAL Chi-restraints excluded: chain Y residue 638 LEU Chi-restraints excluded: chain Y residue 721 GLU Chi-restraints excluded: chain Y residue 823 THR Chi-restraints excluded: chain Z residue 58 LEU Chi-restraints excluded: chain Z residue 74 THR Chi-restraints excluded: chain Z residue 98 VAL Chi-restraints excluded: chain d residue 21 VAL Chi-restraints excluded: chain d residue 31 VAL Chi-restraints excluded: chain d residue 105 ARG Chi-restraints excluded: chain d residue 111 ARG Chi-restraints excluded: chain d residue 159 ASP Chi-restraints excluded: chain d residue 167 ILE Chi-restraints excluded: chain e residue 847 LEU Chi-restraints excluded: chain e residue 849 SER Chi-restraints excluded: chain f residue 107 LEU Chi-restraints excluded: chain f residue 118 THR Chi-restraints excluded: chain f residue 161 THR Chi-restraints excluded: chain f residue 167 THR Chi-restraints excluded: chain f residue 188 VAL Chi-restraints excluded: chain f residue 203 VAL Chi-restraints excluded: chain f residue 207 ILE Chi-restraints excluded: chain g residue 32 SER Chi-restraints excluded: chain g residue 51 THR Chi-restraints excluded: chain g residue 63 GLU Chi-restraints excluded: chain g residue 70 THR Chi-restraints excluded: chain g residue 81 SER Chi-restraints excluded: chain g residue 83 THR Chi-restraints excluded: chain g residue 127 ILE Chi-restraints excluded: chain g residue 146 VAL Chi-restraints excluded: chain g residue 191 THR Chi-restraints excluded: chain g residue 225 ASN Chi-restraints excluded: chain h residue 53 GLU Chi-restraints excluded: chain h residue 70 THR Chi-restraints excluded: chain h residue 84 LEU Chi-restraints excluded: chain h residue 102 GLU Chi-restraints excluded: chain h residue 119 VAL Chi-restraints excluded: chain h residue 132 THR Chi-restraints excluded: chain h residue 158 VAL Chi-restraints excluded: chain h residue 179 THR Chi-restraints excluded: chain i residue 131 VAL Chi-restraints excluded: chain i residue 182 THR Chi-restraints excluded: chain i residue 183 VAL Chi-restraints excluded: chain i residue 198 VAL Chi-restraints excluded: chain j residue 54 SER Chi-restraints excluded: chain j residue 64 ASP Chi-restraints excluded: chain j residue 70 THR Chi-restraints excluded: chain j residue 84 LEU Chi-restraints excluded: chain j residue 125 SER Chi-restraints excluded: chain j residue 132 THR Chi-restraints excluded: chain j residue 135 GLU Chi-restraints excluded: chain j residue 138 THR Chi-restraints excluded: chain j residue 146 VAL Chi-restraints excluded: chain j residue 158 VAL Chi-restraints excluded: chain j residue 180 THR Chi-restraints excluded: chain k residue 17 LEU Chi-restraints excluded: chain k residue 83 THR Chi-restraints excluded: chain k residue 127 ILE Chi-restraints excluded: chain k residue 132 THR Chi-restraints excluded: chain k residue 198 VAL Chi-restraints excluded: chain k residue 215 THR Chi-restraints excluded: chain k residue 224 VAL Chi-restraints excluded: chain l residue 3 VAL Chi-restraints excluded: chain l residue 140 THR Chi-restraints excluded: chain l residue 180 THR Chi-restraints excluded: chain l residue 198 VAL Chi-restraints excluded: chain l residue 207 VAL Chi-restraints excluded: chain l residue 212 MET Chi-restraints excluded: chain l residue 219 VAL Chi-restraints excluded: chain n residue 83 THR Chi-restraints excluded: chain n residue 97 LEU Chi-restraints excluded: chain n residue 141 VAL Chi-restraints excluded: chain n residue 146 VAL Chi-restraints excluded: chain o residue 16 THR Chi-restraints excluded: chain o residue 83 THR Chi-restraints excluded: chain o residue 102 GLU Chi-restraints excluded: chain o residue 110 ILE Chi-restraints excluded: chain o residue 117 VAL Chi-restraints excluded: chain o residue 132 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1008 random chunks: chunk 635 optimal weight: 6.9990 chunk 851 optimal weight: 0.6980 chunk 244 optimal weight: 0.8980 chunk 737 optimal weight: 5.9990 chunk 118 optimal weight: 0.3980 chunk 222 optimal weight: 3.9990 chunk 800 optimal weight: 0.6980 chunk 335 optimal weight: 6.9990 chunk 822 optimal weight: 1.9990 chunk 101 optimal weight: 0.8980 chunk 147 optimal weight: 3.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 178 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 91 GLN ** c 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 397 ASN E 826 HIS Q 91 GLN ** T 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 235 ASN ** Z 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 74 GLN ** o 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.131846 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.083183 restraints weight = 141650.939| |-----------------------------------------------------------------------------| r_work (start): 0.3097 rms_B_bonded: 2.47 r_work: 0.2982 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2860 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.2860 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8403 moved from start: 0.1436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.208 78954 Z= 0.362 Angle : 0.762 59.199 107580 Z= 0.398 Chirality : 0.048 0.728 12384 Planarity : 0.006 0.182 13893 Dihedral : 6.646 59.432 11072 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 10.12 Ramachandran Plot: Outliers : 0.63 % Allowed : 8.03 % Favored : 91.34 % Rotamer: Outliers : 4.57 % Allowed : 32.22 % Favored : 63.21 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.63 % Cis-general : 0.00 % Twisted Proline : 1.26 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.71 (0.08), residues: 10164 helix: 0.35 (0.17), residues: 909 sheet: -0.69 (0.08), residues: 4020 loop : -1.77 (0.08), residues: 5235 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP Z 89 HIS 0.007 0.001 HIS m 65 PHE 0.022 0.002 PHE j 120 TYR 0.021 0.002 TYR n 55 ARG 0.019 0.000 ARG I 223 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 34093.11 seconds wall clock time: 582 minutes 24.95 seconds (34944.95 seconds total)