Starting phenix.real_space_refine on Sun Oct 13 05:36:28 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q01_18048/10_2024/8q01_18048.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q01_18048/10_2024/8q01_18048.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.58 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q01_18048/10_2024/8q01_18048.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q01_18048/10_2024/8q01_18048.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q01_18048/10_2024/8q01_18048.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q01_18048/10_2024/8q01_18048.cif" } resolution = 3.58 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= 0.006 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 Zn 6 6.06 5 S 258 5.16 5 C 41850 2.51 5 N 10854 2.21 5 O 12582 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5477/modules/chem_data/mon_lib" Total number of atoms: 65550 Number of models: 1 Model: "" Number of chains: 48 Chain: "A" Number of atoms: 1091 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1091 Classifications: {'peptide': 139} Link IDs: {'PTRANS': 2, 'TRANS': 136} Chain: "M" Number of atoms: 2230 Number of conformers: 1 Conformer: "" Number of residues, atoms: 277, 2230 Classifications: {'peptide': 277} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 271} Chain: "G" Number of atoms: 1102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1102 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 2, 'TRANS': 137} Chain: "r" Number of atoms: 448 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 448 Classifications: {'peptide': 56} Link IDs: {'PTRANS': 2, 'TRANS': 53} Chain breaks: 1 Chain: "S" Number of atoms: 1887 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1887 Classifications: {'peptide': 227} Link IDs: {'PTRANS': 13, 'TRANS': 213} Chain breaks: 1 Chain: "b" Number of atoms: 2083 Number of conformers: 1 Conformer: "" Number of residues, atoms: 259, 2083 Classifications: {'peptide': 259} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 242} Chain breaks: 1 Chain: "c" Number of atoms: 2083 Number of conformers: 1 Conformer: "" Number of residues, atoms: 259, 2083 Classifications: {'peptide': 259} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 242} Chain breaks: 1 Chain: "S" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 1091 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1091 Classifications: {'peptide': 139} Link IDs: {'PTRANS': 2, 'TRANS': 136} Chain: "C" Number of atoms: 2230 Number of conformers: 1 Conformer: "" Number of residues, atoms: 277, 2230 Classifications: {'peptide': 277} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 271} Chain: "D" Number of atoms: 1102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1102 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 2, 'TRANS': 137} Chain: "E" Number of atoms: 448 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 448 Classifications: {'peptide': 56} Link IDs: {'PTRANS': 2, 'TRANS': 53} Chain breaks: 1 Chain: "F" Number of atoms: 1887 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1887 Classifications: {'peptide': 227} Link IDs: {'PTRANS': 13, 'TRANS': 213} Chain breaks: 1 Chain: "H" Number of atoms: 2083 Number of conformers: 1 Conformer: "" Number of residues, atoms: 259, 2083 Classifications: {'peptide': 259} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 242} Chain breaks: 1 Chain: "I" Number of atoms: 2083 Number of conformers: 1 Conformer: "" Number of residues, atoms: 259, 2083 Classifications: {'peptide': 259} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 242} Chain breaks: 1 Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "J" Number of atoms: 1091 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1091 Classifications: {'peptide': 139} Link IDs: {'PTRANS': 2, 'TRANS': 136} Chain: "K" Number of atoms: 2230 Number of conformers: 1 Conformer: "" Number of residues, atoms: 277, 2230 Classifications: {'peptide': 277} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 271} Chain: "L" Number of atoms: 1102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1102 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 2, 'TRANS': 137} Chain: "N" Number of atoms: 448 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 448 Classifications: {'peptide': 56} Link IDs: {'PTRANS': 2, 'TRANS': 53} Chain breaks: 1 Chain: "O" Number of atoms: 1887 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1887 Classifications: {'peptide': 227} Link IDs: {'PTRANS': 13, 'TRANS': 213} Chain breaks: 1 Chain: "P" Number of atoms: 2083 Number of conformers: 1 Conformer: "" Number of residues, atoms: 259, 2083 Classifications: {'peptide': 259} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 242} Chain breaks: 1 Chain: "Q" Number of atoms: 2083 Number of conformers: 1 Conformer: "" Number of residues, atoms: 259, 2083 Classifications: {'peptide': 259} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 242} Chain breaks: 1 Chain: "O" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "R" Number of atoms: 1091 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1091 Classifications: {'peptide': 139} Link IDs: {'PTRANS': 2, 'TRANS': 136} Chain: "T" Number of atoms: 2230 Number of conformers: 1 Conformer: "" Number of residues, atoms: 277, 2230 Classifications: {'peptide': 277} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 271} Chain: "U" Number of atoms: 1102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1102 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 2, 'TRANS': 137} Chain: "V" Number of atoms: 448 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 448 Classifications: {'peptide': 56} Link IDs: {'PTRANS': 2, 'TRANS': 53} Chain breaks: 1 Chain: "W" Number of atoms: 1887 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1887 Classifications: {'peptide': 227} Link IDs: {'PTRANS': 13, 'TRANS': 213} Chain breaks: 1 Chain: "X" Number of atoms: 2083 Number of conformers: 1 Conformer: "" Number of residues, atoms: 259, 2083 Classifications: {'peptide': 259} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 242} Chain breaks: 1 Chain: "Y" Number of atoms: 2083 Number of conformers: 1 Conformer: "" Number of residues, atoms: 259, 2083 Classifications: {'peptide': 259} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 242} Chain breaks: 1 Chain: "W" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "Z" Number of atoms: 1091 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1091 Classifications: {'peptide': 139} Link IDs: {'PTRANS': 2, 'TRANS': 136} Chain: "0" Number of atoms: 2230 Number of conformers: 1 Conformer: "" Number of residues, atoms: 277, 2230 Classifications: {'peptide': 277} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 271} Chain: "1" Number of atoms: 1102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1102 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 2, 'TRANS': 137} Chain: "2" Number of atoms: 448 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 448 Classifications: {'peptide': 56} Link IDs: {'PTRANS': 2, 'TRANS': 53} Chain breaks: 1 Chain: "3" Number of atoms: 1887 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1887 Classifications: {'peptide': 227} Link IDs: {'PTRANS': 13, 'TRANS': 213} Chain breaks: 1 Chain: "4" Number of atoms: 2083 Number of conformers: 1 Conformer: "" Number of residues, atoms: 259, 2083 Classifications: {'peptide': 259} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 242} Chain breaks: 1 Chain: "5" Number of atoms: 2083 Number of conformers: 1 Conformer: "" Number of residues, atoms: 259, 2083 Classifications: {'peptide': 259} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 242} Chain breaks: 1 Chain: "3" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "6" Number of atoms: 1091 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1091 Classifications: {'peptide': 139} Link IDs: {'PTRANS': 2, 'TRANS': 136} Chain: "7" Number of atoms: 2230 Number of conformers: 1 Conformer: "" Number of residues, atoms: 277, 2230 Classifications: {'peptide': 277} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 271} Chain: "8" Number of atoms: 1102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1102 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 2, 'TRANS': 137} Chain: "9" Number of atoms: 448 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 448 Classifications: {'peptide': 56} Link IDs: {'PTRANS': 2, 'TRANS': 53} Chain breaks: 1 Chain: "a" Number of atoms: 1887 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1887 Classifications: {'peptide': 227} Link IDs: {'PTRANS': 13, 'TRANS': 213} Chain breaks: 1 Chain: "d" Number of atoms: 2083 Number of conformers: 1 Conformer: "" Number of residues, atoms: 259, 2083 Classifications: {'peptide': 259} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 242} Chain breaks: 1 Chain: "e" Number of atoms: 2083 Number of conformers: 1 Conformer: "" Number of residues, atoms: 259, 2083 Classifications: {'peptide': 259} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 242} Chain breaks: 1 Chain: "a" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 5195 SG CYS S 66 45.266 54.699 123.225 1.00 70.08 S ATOM 5208 SG CYS S 68 46.628 54.744 126.720 1.00 71.61 S ATOM 5299 SG CYS S 80 46.110 51.356 125.045 1.00 76.12 S ATOM 5323 SG CYS S 83 48.650 53.783 123.630 1.00 74.98 S ATOM 16120 SG CYS F 66 83.554 37.534 123.225 1.00 70.08 S ATOM 16133 SG CYS F 68 84.196 38.736 126.720 1.00 71.61 S ATOM 16224 SG CYS F 80 86.871 36.594 125.045 1.00 76.12 S ATOM 16248 SG CYS F 83 86.039 40.007 123.630 1.00 74.98 S ATOM 27045 SG CYS O 66 117.563 62.110 123.225 1.00 70.08 S ATOM 27058 SG CYS O 68 116.843 63.267 126.720 1.00 71.61 S ATOM 27149 SG CYS O 80 120.036 64.513 125.045 1.00 76.12 S ATOM 27173 SG CYS O 83 116.664 65.499 123.630 1.00 74.98 S ATOM 37970 SG CYS W 66 113.284 103.851 123.225 1.00 70.08 S ATOM 37983 SG CYS W 68 111.922 103.806 126.720 1.00 71.61 S ATOM 38074 SG CYS W 80 112.440 107.194 125.045 1.00 76.12 S ATOM 38098 SG CYS W 83 109.900 104.767 123.630 1.00 74.98 S ATOM 48895 SG CYS 3 66 74.996 121.016 123.225 1.00 70.08 S ATOM 48908 SG CYS 3 68 74.354 119.814 126.720 1.00 71.61 S ATOM 48999 SG CYS 3 80 71.679 121.956 125.045 1.00 76.12 S ATOM 49023 SG CYS 3 83 72.511 118.543 123.630 1.00 74.98 S ATOM 59820 SG CYS a 66 40.987 96.440 123.225 1.00 70.08 S ATOM 59833 SG CYS a 68 41.707 95.283 126.720 1.00 71.61 S ATOM 59924 SG CYS a 80 38.514 94.037 125.045 1.00 76.12 S ATOM 59948 SG CYS a 83 41.886 93.051 123.630 1.00 74.98 S Time building chain proxies: 26.36, per 1000 atoms: 0.40 Number of scatterers: 65550 At special positions: 0 Unit cell: (159.607, 159.607, 254.737, 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) Zn 6 29.99 S 258 16.00 O 12582 8.00 N 10854 7.00 C 41850 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: 13.15 Conformation dependent library (CDL) restraints added in 6.1 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN 3 300 " pdb="ZN ZN 3 300 " - pdb=" SG CYS 3 83 " pdb="ZN ZN 3 300 " - pdb=" SG CYS 3 68 " pdb="ZN ZN 3 300 " - pdb=" SG CYS 3 66 " pdb="ZN ZN 3 300 " - pdb=" SG CYS 3 80 " pdb=" ZN F 300 " pdb="ZN ZN F 300 " - pdb=" SG CYS F 83 " pdb="ZN ZN F 300 " - pdb=" SG CYS F 68 " pdb="ZN ZN F 300 " - pdb=" SG CYS F 66 " pdb="ZN ZN F 300 " - pdb=" SG CYS F 80 " pdb=" ZN O 300 " pdb="ZN ZN O 300 " - pdb=" SG CYS O 83 " pdb="ZN ZN O 300 " - pdb=" SG CYS O 68 " pdb="ZN ZN O 300 " - pdb=" SG CYS O 66 " pdb="ZN ZN O 300 " - pdb=" SG CYS O 80 " pdb=" ZN S 300 " pdb="ZN ZN S 300 " - pdb=" SG CYS S 83 " pdb="ZN ZN S 300 " - pdb=" SG CYS S 68 " pdb="ZN ZN S 300 " - pdb=" SG CYS S 66 " pdb="ZN ZN S 300 " - pdb=" SG CYS S 80 " pdb=" ZN W 300 " pdb="ZN ZN W 300 " - pdb=" SG CYS W 83 " pdb="ZN ZN W 300 " - pdb=" SG CYS W 68 " pdb="ZN ZN W 300 " - pdb=" SG CYS W 66 " pdb="ZN ZN W 300 " - pdb=" SG CYS W 80 " pdb=" ZN a 300 " pdb="ZN ZN a 300 " - pdb=" SG CYS a 83 " pdb="ZN ZN a 300 " - pdb=" SG CYS a 68 " pdb="ZN ZN a 300 " - pdb=" SG CYS a 66 " pdb="ZN ZN a 300 " - pdb=" SG CYS a 80 " Number of angles added : 36 16020 Ramachandran restraints generated. 8010 Oldfield, 0 Emsley, 8010 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 15192 Finding SS restraints... Secondary structure from input PDB file: 198 helices and 126 sheets defined 24.4% alpha, 38.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 8.60 Creating SS restraints... Processing helix chain 'A' and resid 82 through 88 Processing helix chain 'M' and resid 5 through 23 Proline residue: M 16 - end of helix Processing helix chain 'M' and resid 24 through 32 removed outlier: 3.666A pdb=" N ILE M 28 " --> pdb=" O ASN M 24 " (cutoff:3.500A) Processing helix chain 'M' and resid 36 through 48 Processing helix chain 'M' and resid 86 through 88 No H-bonds generated for 'chain 'M' and resid 86 through 88' Processing helix chain 'M' and resid 135 through 139 Processing helix chain 'M' and resid 154 through 158 Processing helix chain 'M' and resid 194 through 213 Processing helix chain 'M' and resid 215 through 221 Processing helix chain 'G' and resid 11 through 13 No H-bonds generated for 'chain 'G' and resid 11 through 13' Processing helix chain 'G' and resid 82 through 88 Processing helix chain 'r' and resid 521 through 536 Processing helix chain 'r' and resid 546 through 548 No H-bonds generated for 'chain 'r' and resid 546 through 548' Processing helix chain 'S' and resid 43 through 55 Processing helix chain 'S' and resid 152 through 159 Processing helix chain 'S' and resid 180 through 182 No H-bonds generated for 'chain 'S' and resid 180 through 182' Processing helix chain 'S' and resid 195 through 198 Processing helix chain 'b' and resid 35 through 39 Processing helix chain 'b' and resid 41 through 46 Processing helix chain 'b' and resid 48 through 56 Processing helix chain 'b' and resid 71 through 90 removed outlier: 3.647A pdb=" N TYR b 75 " --> pdb=" O GLY b 71 " (cutoff:3.500A) Processing helix chain 'b' and resid 107 through 112 Processing helix chain 'b' and resid 142 through 144 No H-bonds generated for 'chain 'b' and resid 142 through 144' Processing helix chain 'b' and resid 220 through 240 removed outlier: 3.792A pdb=" N GLU b 224 " --> pdb=" O PRO b 220 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N GLN b 225 " --> pdb=" O PRO b 221 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N GLU b 234 " --> pdb=" O TYR b 230 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N GLN b 237 " --> pdb=" O LYS b 233 " (cutoff:3.500A) Processing helix chain 'b' and resid 273 through 295 Processing helix chain 'c' and resid 35 through 40 removed outlier: 3.857A pdb=" N ASN c 39 " --> pdb=" O SER c 35 " (cutoff:3.500A) Processing helix chain 'c' and resid 41 through 46 Processing helix chain 'c' and resid 48 through 55 removed outlier: 3.935A pdb=" N TYR c 55 " --> pdb=" O ALA c 51 " (cutoff:3.500A) Processing helix chain 'c' and resid 71 through 90 removed outlier: 3.864A pdb=" N TYR c 75 " --> pdb=" O GLY c 71 " (cutoff:3.500A) Processing helix chain 'c' and resid 107 through 112 Processing helix chain 'c' and resid 142 through 144 No H-bonds generated for 'chain 'c' and resid 142 through 144' Processing helix chain 'c' and resid 220 through 240 removed outlier: 3.786A pdb=" N GLU c 224 " --> pdb=" O PRO c 220 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLN c 225 " --> pdb=" O PRO c 221 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N GLU c 234 " --> pdb=" O TYR c 230 " (cutoff:3.500A) Processing helix chain 'c' and resid 273 through 295 Processing helix chain 'B' and resid 82 through 88 Processing helix chain 'C' and resid 5 through 23 Proline residue: C 16 - end of helix Processing helix chain 'C' and resid 24 through 32 removed outlier: 3.665A pdb=" N ILE C 28 " --> pdb=" O ASN C 24 " (cutoff:3.500A) Processing helix chain 'C' and resid 36 through 48 Processing helix chain 'C' and resid 86 through 88 No H-bonds generated for 'chain 'C' and resid 86 through 88' Processing helix chain 'C' and resid 135 through 139 Processing helix chain 'C' and resid 154 through 158 Processing helix chain 'C' and resid 194 through 213 Processing helix chain 'C' and resid 215 through 221 Processing helix chain 'D' and resid 11 through 13 No H-bonds generated for 'chain 'D' and resid 11 through 13' Processing helix chain 'D' and resid 82 through 88 Processing helix chain 'E' and resid 521 through 536 Processing helix chain 'E' and resid 546 through 548 No H-bonds generated for 'chain 'E' and resid 546 through 548' Processing helix chain 'F' and resid 43 through 55 Processing helix chain 'F' and resid 152 through 159 Processing helix chain 'F' and resid 180 through 182 No H-bonds generated for 'chain 'F' and resid 180 through 182' Processing helix chain 'F' and resid 195 through 198 Processing helix chain 'H' and resid 35 through 39 Processing helix chain 'H' and resid 41 through 46 Processing helix chain 'H' and resid 48 through 56 Processing helix chain 'H' and resid 71 through 90 removed outlier: 3.647A pdb=" N TYR H 75 " --> pdb=" O GLY H 71 " (cutoff:3.500A) Processing helix chain 'H' and resid 107 through 112 Processing helix chain 'H' and resid 142 through 144 No H-bonds generated for 'chain 'H' and resid 142 through 144' Processing helix chain 'H' and resid 220 through 240 removed outlier: 3.792A pdb=" N GLU H 224 " --> pdb=" O PRO H 220 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N GLN H 225 " --> pdb=" O PRO H 221 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N GLU H 234 " --> pdb=" O TYR H 230 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N GLN H 237 " --> pdb=" O LYS H 233 " (cutoff:3.500A) Processing helix chain 'H' and resid 273 through 295 Processing helix chain 'I' and resid 35 through 40 removed outlier: 3.857A pdb=" N ASN I 39 " --> pdb=" O SER I 35 " (cutoff:3.500A) Processing helix chain 'I' and resid 41 through 46 Processing helix chain 'I' and resid 48 through 55 removed outlier: 3.936A pdb=" N TYR I 55 " --> pdb=" O ALA I 51 " (cutoff:3.500A) Processing helix chain 'I' and resid 71 through 90 removed outlier: 3.864A pdb=" N TYR I 75 " --> pdb=" O GLY I 71 " (cutoff:3.500A) Processing helix chain 'I' and resid 107 through 112 Processing helix chain 'I' and resid 142 through 144 No H-bonds generated for 'chain 'I' and resid 142 through 144' Processing helix chain 'I' and resid 220 through 240 removed outlier: 3.786A pdb=" N GLU I 224 " --> pdb=" O PRO I 220 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLN I 225 " --> pdb=" O PRO I 221 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N GLU I 234 " --> pdb=" O TYR I 230 " (cutoff:3.500A) Processing helix chain 'I' and resid 273 through 295 Processing helix chain 'J' and resid 82 through 88 Processing helix chain 'K' and resid 5 through 23 Proline residue: K 16 - end of helix Processing helix chain 'K' and resid 24 through 32 removed outlier: 3.665A pdb=" N ILE K 28 " --> pdb=" O ASN K 24 " (cutoff:3.500A) Processing helix chain 'K' and resid 36 through 48 Processing helix chain 'K' and resid 86 through 88 No H-bonds generated for 'chain 'K' and resid 86 through 88' Processing helix chain 'K' and resid 135 through 139 Processing helix chain 'K' and resid 154 through 158 Processing helix chain 'K' and resid 194 through 213 Processing helix chain 'K' and resid 215 through 221 Processing helix chain 'L' and resid 11 through 13 No H-bonds generated for 'chain 'L' and resid 11 through 13' Processing helix chain 'L' and resid 82 through 88 Processing helix chain 'N' and resid 521 through 536 Processing helix chain 'N' and resid 546 through 548 No H-bonds generated for 'chain 'N' and resid 546 through 548' Processing helix chain 'O' and resid 43 through 55 Processing helix chain 'O' and resid 152 through 159 Processing helix chain 'O' and resid 180 through 182 No H-bonds generated for 'chain 'O' and resid 180 through 182' Processing helix chain 'O' and resid 195 through 198 Processing helix chain 'P' and resid 35 through 39 Processing helix chain 'P' and resid 41 through 46 Processing helix chain 'P' and resid 48 through 56 Processing helix chain 'P' and resid 71 through 90 removed outlier: 3.647A pdb=" N TYR P 75 " --> pdb=" O GLY P 71 " (cutoff:3.500A) Processing helix chain 'P' and resid 107 through 112 Processing helix chain 'P' and resid 142 through 144 No H-bonds generated for 'chain 'P' and resid 142 through 144' Processing helix chain 'P' and resid 220 through 240 removed outlier: 3.792A pdb=" N GLU P 224 " --> pdb=" O PRO P 220 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N GLN P 225 " --> pdb=" O PRO P 221 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N GLU P 234 " --> pdb=" O TYR P 230 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N GLN P 237 " --> pdb=" O LYS P 233 " (cutoff:3.500A) Processing helix chain 'P' and resid 273 through 295 Processing helix chain 'Q' and resid 35 through 40 removed outlier: 3.858A pdb=" N ASN Q 39 " --> pdb=" O SER Q 35 " (cutoff:3.500A) Processing helix chain 'Q' and resid 41 through 46 Processing helix chain 'Q' and resid 48 through 55 removed outlier: 3.935A pdb=" N TYR Q 55 " --> pdb=" O ALA Q 51 " (cutoff:3.500A) Processing helix chain 'Q' and resid 71 through 90 removed outlier: 3.864A pdb=" N TYR Q 75 " --> pdb=" O GLY Q 71 " (cutoff:3.500A) Processing helix chain 'Q' and resid 107 through 112 Processing helix chain 'Q' and resid 142 through 144 No H-bonds generated for 'chain 'Q' and resid 142 through 144' Processing helix chain 'Q' and resid 220 through 240 removed outlier: 3.786A pdb=" N GLU Q 224 " --> pdb=" O PRO Q 220 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLN Q 225 " --> pdb=" O PRO Q 221 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N GLU Q 234 " --> pdb=" O TYR Q 230 " (cutoff:3.500A) Processing helix chain 'Q' and resid 273 through 295 Processing helix chain 'R' and resid 82 through 88 Processing helix chain 'T' and resid 5 through 23 Proline residue: T 16 - end of helix Processing helix chain 'T' and resid 24 through 32 removed outlier: 3.666A pdb=" N ILE T 28 " --> pdb=" O ASN T 24 " (cutoff:3.500A) Processing helix chain 'T' and resid 36 through 48 Processing helix chain 'T' and resid 86 through 88 No H-bonds generated for 'chain 'T' and resid 86 through 88' Processing helix chain 'T' and resid 135 through 139 Processing helix chain 'T' and resid 154 through 158 Processing helix chain 'T' and resid 194 through 213 Processing helix chain 'T' and resid 215 through 221 Processing helix chain 'U' and resid 11 through 13 No H-bonds generated for 'chain 'U' and resid 11 through 13' Processing helix chain 'U' and resid 82 through 88 Processing helix chain 'V' and resid 521 through 536 Processing helix chain 'V' and resid 546 through 548 No H-bonds generated for 'chain 'V' and resid 546 through 548' Processing helix chain 'W' and resid 43 through 55 Processing helix chain 'W' and resid 152 through 159 Processing helix chain 'W' and resid 180 through 182 No H-bonds generated for 'chain 'W' and resid 180 through 182' Processing helix chain 'W' and resid 195 through 198 Processing helix chain 'X' and resid 35 through 39 Processing helix chain 'X' and resid 41 through 46 Processing helix chain 'X' and resid 48 through 56 Processing helix chain 'X' and resid 71 through 90 removed outlier: 3.647A pdb=" N TYR X 75 " --> pdb=" O GLY X 71 " (cutoff:3.500A) Processing helix chain 'X' and resid 107 through 112 Processing helix chain 'X' and resid 142 through 144 No H-bonds generated for 'chain 'X' and resid 142 through 144' Processing helix chain 'X' and resid 220 through 240 removed outlier: 3.792A pdb=" N GLU X 224 " --> pdb=" O PRO X 220 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N GLN X 225 " --> pdb=" O PRO X 221 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N GLU X 234 " --> pdb=" O TYR X 230 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N GLN X 237 " --> pdb=" O LYS X 233 " (cutoff:3.500A) Processing helix chain 'X' and resid 273 through 295 Processing helix chain 'Y' and resid 35 through 40 removed outlier: 3.857A pdb=" N ASN Y 39 " --> pdb=" O SER Y 35 " (cutoff:3.500A) Processing helix chain 'Y' and resid 41 through 46 Processing helix chain 'Y' and resid 48 through 55 removed outlier: 3.935A pdb=" N TYR Y 55 " --> pdb=" O ALA Y 51 " (cutoff:3.500A) Processing helix chain 'Y' and resid 71 through 90 removed outlier: 3.864A pdb=" N TYR Y 75 " --> pdb=" O GLY Y 71 " (cutoff:3.500A) Processing helix chain 'Y' and resid 107 through 112 Processing helix chain 'Y' and resid 142 through 144 No H-bonds generated for 'chain 'Y' and resid 142 through 144' Processing helix chain 'Y' and resid 220 through 240 removed outlier: 3.786A pdb=" N GLU Y 224 " --> pdb=" O PRO Y 220 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLN Y 225 " --> pdb=" O PRO Y 221 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N GLU Y 234 " --> pdb=" O TYR Y 230 " (cutoff:3.500A) Processing helix chain 'Y' and resid 273 through 295 Processing helix chain 'Z' and resid 82 through 88 Processing helix chain '0' and resid 5 through 23 Proline residue: 0 16 - end of helix Processing helix chain '0' and resid 24 through 32 removed outlier: 3.665A pdb=" N ILE 0 28 " --> pdb=" O ASN 0 24 " (cutoff:3.500A) Processing helix chain '0' and resid 36 through 48 Processing helix chain '0' and resid 86 through 88 No H-bonds generated for 'chain '0' and resid 86 through 88' Processing helix chain '0' and resid 135 through 139 Processing helix chain '0' and resid 154 through 158 Processing helix chain '0' and resid 194 through 213 Processing helix chain '0' and resid 215 through 221 Processing helix chain '1' and resid 11 through 13 No H-bonds generated for 'chain '1' and resid 11 through 13' Processing helix chain '1' and resid 82 through 88 Processing helix chain '2' and resid 521 through 536 Processing helix chain '2' and resid 546 through 548 No H-bonds generated for 'chain '2' and resid 546 through 548' Processing helix chain '3' and resid 43 through 55 Processing helix chain '3' and resid 152 through 159 Processing helix chain '3' and resid 180 through 182 No H-bonds generated for 'chain '3' and resid 180 through 182' Processing helix chain '3' and resid 195 through 198 Processing helix chain '4' and resid 35 through 39 Processing helix chain '4' and resid 41 through 46 Processing helix chain '4' and resid 48 through 56 Processing helix chain '4' and resid 71 through 90 removed outlier: 3.647A pdb=" N TYR 4 75 " --> pdb=" O GLY 4 71 " (cutoff:3.500A) Processing helix chain '4' and resid 107 through 112 Processing helix chain '4' and resid 142 through 144 No H-bonds generated for 'chain '4' and resid 142 through 144' Processing helix chain '4' and resid 220 through 240 removed outlier: 3.792A pdb=" N GLU 4 224 " --> pdb=" O PRO 4 220 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N GLN 4 225 " --> pdb=" O PRO 4 221 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N GLU 4 234 " --> pdb=" O TYR 4 230 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N GLN 4 237 " --> pdb=" O LYS 4 233 " (cutoff:3.500A) Processing helix chain '4' and resid 273 through 295 Processing helix chain '5' and resid 35 through 40 removed outlier: 3.857A pdb=" N ASN 5 39 " --> pdb=" O SER 5 35 " (cutoff:3.500A) Processing helix chain '5' and resid 41 through 46 Processing helix chain '5' and resid 48 through 55 removed outlier: 3.936A pdb=" N TYR 5 55 " --> pdb=" O ALA 5 51 " (cutoff:3.500A) Processing helix chain '5' and resid 71 through 90 removed outlier: 3.864A pdb=" N TYR 5 75 " --> pdb=" O GLY 5 71 " (cutoff:3.500A) Processing helix chain '5' and resid 107 through 112 Processing helix chain '5' and resid 142 through 144 No H-bonds generated for 'chain '5' and resid 142 through 144' Processing helix chain '5' and resid 220 through 240 removed outlier: 3.786A pdb=" N GLU 5 224 " --> pdb=" O PRO 5 220 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLN 5 225 " --> pdb=" O PRO 5 221 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N GLU 5 234 " --> pdb=" O TYR 5 230 " (cutoff:3.500A) Processing helix chain '5' and resid 273 through 295 Processing helix chain '6' and resid 82 through 88 Processing helix chain '7' and resid 5 through 23 Proline residue: 7 16 - end of helix Processing helix chain '7' and resid 24 through 32 removed outlier: 3.665A pdb=" N ILE 7 28 " --> pdb=" O ASN 7 24 " (cutoff:3.500A) Processing helix chain '7' and resid 36 through 48 Processing helix chain '7' and resid 86 through 88 No H-bonds generated for 'chain '7' and resid 86 through 88' Processing helix chain '7' and resid 135 through 139 Processing helix chain '7' and resid 154 through 158 Processing helix chain '7' and resid 194 through 213 Processing helix chain '7' and resid 215 through 221 Processing helix chain '8' and resid 11 through 13 No H-bonds generated for 'chain '8' and resid 11 through 13' Processing helix chain '8' and resid 82 through 88 Processing helix chain '9' and resid 521 through 536 Processing helix chain '9' and resid 546 through 548 No H-bonds generated for 'chain '9' and resid 546 through 548' Processing helix chain 'a' and resid 43 through 55 Processing helix chain 'a' and resid 152 through 159 Processing helix chain 'a' and resid 180 through 182 No H-bonds generated for 'chain 'a' and resid 180 through 182' Processing helix chain 'a' and resid 195 through 198 Processing helix chain 'd' and resid 35 through 39 Processing helix chain 'd' and resid 41 through 46 Processing helix chain 'd' and resid 48 through 56 Processing helix chain 'd' and resid 71 through 90 removed outlier: 3.647A pdb=" N TYR d 75 " --> pdb=" O GLY d 71 " (cutoff:3.500A) Processing helix chain 'd' and resid 107 through 112 Processing helix chain 'd' and resid 142 through 144 No H-bonds generated for 'chain 'd' and resid 142 through 144' Processing helix chain 'd' and resid 220 through 240 removed outlier: 3.792A pdb=" N GLU d 224 " --> pdb=" O PRO d 220 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N GLN d 225 " --> pdb=" O PRO d 221 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N GLU d 234 " --> pdb=" O TYR d 230 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N GLN d 237 " --> pdb=" O LYS d 233 " (cutoff:3.500A) Processing helix chain 'd' and resid 273 through 295 Processing helix chain 'e' and resid 35 through 40 removed outlier: 3.858A pdb=" N ASN e 39 " --> pdb=" O SER e 35 " (cutoff:3.500A) Processing helix chain 'e' and resid 41 through 46 Processing helix chain 'e' and resid 48 through 55 removed outlier: 3.935A pdb=" N TYR e 55 " --> pdb=" O ALA e 51 " (cutoff:3.500A) Processing helix chain 'e' and resid 71 through 90 removed outlier: 3.864A pdb=" N TYR e 75 " --> pdb=" O GLY e 71 " (cutoff:3.500A) Processing helix chain 'e' and resid 107 through 112 Processing helix chain 'e' and resid 142 through 144 No H-bonds generated for 'chain 'e' and resid 142 through 144' Processing helix chain 'e' and resid 220 through 240 removed outlier: 3.786A pdb=" N GLU e 224 " --> pdb=" O PRO e 220 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLN e 225 " --> pdb=" O PRO e 221 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N GLU e 234 " --> pdb=" O TYR e 230 " (cutoff:3.500A) Processing helix chain 'e' and resid 273 through 295 Processing sheet with id=1, first strand: chain 'A' and resid 22 through 23 removed outlier: 5.681A pdb=" N ILE A 91 " --> pdb=" O GLY A 109 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N GLY A 109 " --> pdb=" O ILE A 91 " (cutoff:3.500A) removed outlier: 5.978A pdb=" N ASP A 97 " --> pdb=" O VAL A 103 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N VAL A 103 " --> pdb=" O ASP A 97 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N GLU A 130 " --> pdb=" O ASN A 113 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N TYR A 115 " --> pdb=" O GLU A 128 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N GLU A 128 " --> pdb=" O TYR A 115 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N GLU A 117 " --> pdb=" O THR A 126 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N THR A 126 " --> pdb=" O GLU A 117 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N LEU A 66 " --> pdb=" O ALA A 27 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N ALA A 27 " --> pdb=" O LEU A 66 " (cutoff:3.500A) Processing sheet with id=2, first strand: chain 'A' and resid 22 through 23 removed outlier: 5.681A pdb=" N ILE A 91 " --> pdb=" O GLY A 109 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N GLY A 109 " --> pdb=" O ILE A 91 " (cutoff:3.500A) removed outlier: 5.978A pdb=" N ASP A 97 " --> pdb=" O VAL A 103 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N VAL A 103 " --> pdb=" O ASP A 97 " (cutoff:3.500A) Processing sheet with id=3, first strand: chain 'A' and resid 39 through 43 removed outlier: 6.434A pdb=" N THR A 39 " --> pdb=" O HIS A 52 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N HIS A 52 " --> pdb=" O THR A 39 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N VAL A 41 " --> pdb=" O GLN A 50 " (cutoff:3.500A) removed outlier: 5.276A pdb=" N GLU A 43 " --> pdb=" O MET A 48 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N MET A 48 " --> pdb=" O GLU A 43 " (cutoff:3.500A) Processing sheet with id=4, first strand: chain 'M' and resid 57 through 60 removed outlier: 6.628A pdb=" N THR M 57 " --> pdb=" O TYR M 73 " (cutoff:3.500A) removed outlier: 7.701A pdb=" N ILE M 75 " --> pdb=" O THR M 57 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N GLY M 59 " --> pdb=" O ILE M 75 " (cutoff:3.500A) removed outlier: 8.425A pdb=" N LEU M 77 " --> pdb=" O GLY M 59 " (cutoff:3.500A) removed outlier: 5.582A pdb=" N TYR M 73 " --> pdb=" O LEU M 191 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N LEU M 191 " --> pdb=" O TYR M 73 " (cutoff:3.500A) removed outlier: 5.582A pdb=" N ILE M 75 " --> pdb=" O VAL M 189 " (cutoff:3.500A) removed outlier: 7.266A pdb=" N VAL M 189 " --> pdb=" O ILE M 75 " (cutoff:3.500A) removed outlier: 5.080A pdb=" N LEU M 77 " --> pdb=" O THR M 187 " (cutoff:3.500A) removed outlier: 5.947A pdb=" N THR M 187 " --> pdb=" O LEU M 77 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N GLN M 79 " --> pdb=" O GLN M 185 " (cutoff:3.500A) removed outlier: 7.144A pdb=" N THR M 181 " --> pdb=" O THR M 83 " (cutoff:3.500A) removed outlier: 7.250A pdb=" N GLY M 175 " --> pdb=" O SER M 93 " (cutoff:3.500A) removed outlier: 5.104A pdb=" N SER M 93 " --> pdb=" O GLY M 175 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N VAL M 177 " --> pdb=" O GLN M 91 " (cutoff:3.500A) Processing sheet with id=5, first strand: chain 'M' and resid 57 through 60 removed outlier: 6.628A pdb=" N THR M 57 " --> pdb=" O TYR M 73 " (cutoff:3.500A) removed outlier: 7.701A pdb=" N ILE M 75 " --> pdb=" O THR M 57 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N GLY M 59 " --> pdb=" O ILE M 75 " (cutoff:3.500A) removed outlier: 8.425A pdb=" N LEU M 77 " --> pdb=" O GLY M 59 " (cutoff:3.500A) removed outlier: 5.582A pdb=" N TYR M 73 " --> pdb=" O LEU M 191 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N LEU M 191 " --> pdb=" O TYR M 73 " (cutoff:3.500A) removed outlier: 5.582A pdb=" N ILE M 75 " --> pdb=" O VAL M 189 " (cutoff:3.500A) removed outlier: 7.266A pdb=" N VAL M 189 " --> pdb=" O ILE M 75 " (cutoff:3.500A) removed outlier: 5.080A pdb=" N LEU M 77 " --> pdb=" O THR M 187 " (cutoff:3.500A) removed outlier: 5.947A pdb=" N THR M 187 " --> pdb=" O LEU M 77 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N GLN M 79 " --> pdb=" O GLN M 185 " (cutoff:3.500A) removed outlier: 7.144A pdb=" N THR M 181 " --> pdb=" O THR M 83 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N LYS M 174 " --> pdb=" O ILE M 262 " (cutoff:3.500A) removed outlier: 4.733A pdb=" N PHE M 229 " --> pdb=" O PRO M 247 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N ILE M 249 " --> pdb=" O LEU M 227 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N LEU M 227 " --> pdb=" O ILE M 249 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N LYS M 251 " --> pdb=" O GLN M 225 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N GLN M 225 " --> pdb=" O LYS M 251 " (cutoff:3.500A) Processing sheet with id=6, first strand: chain 'M' and resid 123 through 129 removed outlier: 6.594A pdb=" N THR M 167 " --> pdb=" O GLY M 124 " (cutoff:3.500A) removed outlier: 5.291A pdb=" N LEU M 126 " --> pdb=" O ILE M 165 " (cutoff:3.500A) removed outlier: 7.741A pdb=" N ILE M 165 " --> pdb=" O LEU M 126 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N LYS M 128 " --> pdb=" O ASN M 163 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N ASN M 163 " --> pdb=" O LYS M 128 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N ALA M 162 " --> pdb=" O SER M 105 " (cutoff:3.500A) removed outlier: 4.751A pdb=" N SER M 105 " --> pdb=" O ALA M 162 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N ILE M 164 " --> pdb=" O VAL M 103 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N VAL M 103 " --> pdb=" O ILE M 164 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N PHE M 166 " --> pdb=" O THR M 101 " (cutoff:3.500A) removed outlier: 4.688A pdb=" N THR M 101 " --> pdb=" O PHE M 166 " (cutoff:3.500A) removed outlier: 5.007A pdb=" N GLU M 168 " --> pdb=" O GLY M 99 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N ALA M 97 " --> pdb=" O LYS M 170 " (cutoff:3.500A) removed outlier: 5.784A pdb=" N THR M 107 " --> pdb=" O THR M 118 " (cutoff:3.500A) removed outlier: 4.728A pdb=" N THR M 118 " --> pdb=" O THR M 107 " (cutoff:3.500A) Processing sheet with id=7, first strand: chain 'M' and resid 132 through 133 Processing sheet with id=8, first strand: chain 'M' and resid 233 through 236 removed outlier: 6.667A pdb=" N ILE M 243 " --> pdb=" O ILE M 235 " (cutoff:3.500A) Processing sheet with id=9, first strand: chain 'G' and resid 22 through 23 removed outlier: 6.888A pdb=" N ILE G 93 " --> pdb=" O HIS G 108 " (cutoff:3.500A) removed outlier: 5.382A pdb=" N HIS G 108 " --> pdb=" O ILE G 93 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N VAL G 95 " --> pdb=" O SER G 106 " (cutoff:3.500A) removed outlier: 5.316A pdb=" N SER G 106 " --> pdb=" O VAL G 95 " (cutoff:3.500A) removed outlier: 7.689A pdb=" N ASP G 97 " --> pdb=" O ILE G 104 " (cutoff:3.500A) removed outlier: 7.250A pdb=" N ILE G 104 " --> pdb=" O ASP G 97 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N GLU G 130 " --> pdb=" O ASN G 113 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N TYR G 115 " --> pdb=" O GLU G 128 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N GLU G 128 " --> pdb=" O TYR G 115 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N GLU G 117 " --> pdb=" O THR G 126 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N THR G 126 " --> pdb=" O GLU G 117 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N LEU G 66 " --> pdb=" O ALA G 27 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N ALA G 27 " --> pdb=" O LEU G 66 " (cutoff:3.500A) Processing sheet with id=10, first strand: chain 'G' and resid 22 through 23 removed outlier: 6.888A pdb=" N ILE G 93 " --> pdb=" O HIS G 108 " (cutoff:3.500A) removed outlier: 5.382A pdb=" N HIS G 108 " --> pdb=" O ILE G 93 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N VAL G 95 " --> pdb=" O SER G 106 " (cutoff:3.500A) removed outlier: 5.316A pdb=" N SER G 106 " --> pdb=" O VAL G 95 " (cutoff:3.500A) removed outlier: 7.689A pdb=" N ASP G 97 " --> pdb=" O ILE G 104 " (cutoff:3.500A) removed outlier: 7.250A pdb=" N ILE G 104 " --> pdb=" O ASP G 97 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N THR G 135 " --> pdb=" O HIS G 108 " (cutoff:3.500A) Processing sheet with id=11, first strand: chain 'G' and resid 39 through 41 removed outlier: 4.095A pdb=" N GLU G 51 " --> pdb=" O VAL G 41 " (cutoff:3.500A) Processing sheet with id=12, first strand: chain 'S' and resid 177 through 178 removed outlier: 5.880A pdb=" N ILE S 169 " --> pdb=" O LEU S 207 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N LEU S 207 " --> pdb=" O ILE S 169 " (cutoff:3.500A) removed outlier: 5.343A pdb=" N VAL S 214 " --> pdb=" O LYS S 245 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N LYS S 245 " --> pdb=" O VAL S 214 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N LYS S 241 " --> pdb=" O LEU S 218 " (cutoff:3.500A) removed outlier: 9.602A pdb=" N LYS S 57 " --> pdb=" O PRO S 139 " (cutoff:3.500A) removed outlier: 11.015A pdb=" N ARG S 135 " --> pdb=" O ASP S 216 " (cutoff:3.500A) removed outlier: 12.601A pdb=" N ASP S 216 " --> pdb=" O ARG S 135 " (cutoff:3.500A) removed outlier: 12.112A pdb=" N THR S 137 " --> pdb=" O VAL S 214 " (cutoff:3.500A) removed outlier: 11.537A pdb=" N VAL S 214 " --> pdb=" O THR S 137 " (cutoff:3.500A) removed outlier: 12.067A pdb=" N TYR S 212 " --> pdb=" O PRO S 139 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N VAL S 141 " --> pdb=" O LEU S 210 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N HIS S 200 " --> pdb=" O VAL S 151 " (cutoff:3.500A) Processing sheet with id=13, first strand: chain 'S' and resid 63 through 65 Processing sheet with id=14, first strand: chain 'S' and resid 107 through 110 Processing sheet with id=15, first strand: chain 'S' and resid 160 through 161 Processing sheet with id=16, first strand: chain 'S' and resid 223 through 226 Processing sheet with id=17, first strand: chain 'b' and resid 97 through 106 removed outlier: 6.513A pdb=" N TYR b 105 " --> pdb=" O GLN b 195 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N GLN b 195 " --> pdb=" O TYR b 105 " (cutoff:3.500A) removed outlier: 8.192A pdb=" N PHE b 133 " --> pdb=" O PRO b 194 " (cutoff:3.500A) removed outlier: 8.671A pdb=" N MET b 196 " --> pdb=" O LEU b 131 " (cutoff:3.500A) removed outlier: 4.835A pdb=" N LEU b 131 " --> pdb=" O MET b 196 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N ARG b 198 " --> pdb=" O LEU b 129 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N LEU b 129 " --> pdb=" O ARG b 198 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N GLU b 200 " --> pdb=" O GLU b 127 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLN b 125 " --> pdb=" O VAL b 202 " (cutoff:3.500A) removed outlier: 8.328A pdb=" N LEU b 129 " --> pdb=" O LYS b 140 " (cutoff:3.500A) removed outlier: 5.609A pdb=" N LYS b 140 " --> pdb=" O LEU b 129 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N LEU b 131 " --> pdb=" O ILE b 138 " (cutoff:3.500A) Processing sheet with id=18, first strand: chain 'b' and resid 116 through 117 Processing sheet with id=19, first strand: chain 'b' and resid 250 through 255 removed outlier: 6.782A pdb=" N THR b 259 " --> pdb=" O LEU c 253 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N LEU c 253 " --> pdb=" O THR b 259 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N THR b 261 " --> pdb=" O LYS c 251 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N LYS c 251 " --> pdb=" O THR b 261 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N GLY b 263 " --> pdb=" O ALA c 249 " (cutoff:3.500A) Processing sheet with id=20, first strand: chain 'c' and resid 97 through 106 removed outlier: 6.512A pdb=" N TYR c 105 " --> pdb=" O GLN c 195 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N GLN c 195 " --> pdb=" O TYR c 105 " (cutoff:3.500A) removed outlier: 5.416A pdb=" N MET c 196 " --> pdb=" O GLN c 132 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N VAL c 202 " --> pdb=" O VAL c 126 " (cutoff:3.500A) removed outlier: 5.679A pdb=" N VAL c 126 " --> pdb=" O VAL c 202 " (cutoff:3.500A) removed outlier: 8.436A pdb=" N LEU c 129 " --> pdb=" O LYS c 140 " (cutoff:3.500A) removed outlier: 5.753A pdb=" N LYS c 140 " --> pdb=" O LEU c 129 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N LEU c 131 " --> pdb=" O ILE c 138 " (cutoff:3.500A) Processing sheet with id=21, first strand: chain 'c' and resid 116 through 117 Processing sheet with id=22, first strand: chain 'B' and resid 22 through 23 removed outlier: 5.681A pdb=" N ILE B 91 " --> pdb=" O GLY B 109 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N GLY B 109 " --> pdb=" O ILE B 91 " (cutoff:3.500A) removed outlier: 5.978A pdb=" N ASP B 97 " --> pdb=" O VAL B 103 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N VAL B 103 " --> pdb=" O ASP B 97 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N GLU B 130 " --> pdb=" O ASN B 113 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N TYR B 115 " --> pdb=" O GLU B 128 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N GLU B 128 " --> pdb=" O TYR B 115 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N GLU B 117 " --> pdb=" O THR B 126 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N THR B 126 " --> pdb=" O GLU B 117 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N LEU B 66 " --> pdb=" O ALA B 27 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N ALA B 27 " --> pdb=" O LEU B 66 " (cutoff:3.500A) Processing sheet with id=23, first strand: chain 'B' and resid 22 through 23 removed outlier: 5.681A pdb=" N ILE B 91 " --> pdb=" O GLY B 109 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N GLY B 109 " --> pdb=" O ILE B 91 " (cutoff:3.500A) removed outlier: 5.978A pdb=" N ASP B 97 " --> pdb=" O VAL B 103 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N VAL B 103 " --> pdb=" O ASP B 97 " (cutoff:3.500A) Processing sheet with id=24, first strand: chain 'B' and resid 39 through 43 removed outlier: 6.434A pdb=" N THR B 39 " --> pdb=" O HIS B 52 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N HIS B 52 " --> pdb=" O THR B 39 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N VAL B 41 " --> pdb=" O GLN B 50 " (cutoff:3.500A) removed outlier: 5.276A pdb=" N GLU B 43 " --> pdb=" O MET B 48 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N MET B 48 " --> pdb=" O GLU B 43 " (cutoff:3.500A) Processing sheet with id=25, first strand: chain 'C' and resid 57 through 60 removed outlier: 6.628A pdb=" N THR C 57 " --> pdb=" O TYR C 73 " (cutoff:3.500A) removed outlier: 7.701A pdb=" N ILE C 75 " --> pdb=" O THR C 57 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N GLY C 59 " --> pdb=" O ILE C 75 " (cutoff:3.500A) removed outlier: 8.426A pdb=" N LEU C 77 " --> pdb=" O GLY C 59 " (cutoff:3.500A) removed outlier: 5.582A pdb=" N TYR C 73 " --> pdb=" O LEU C 191 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N LEU C 191 " --> pdb=" O TYR C 73 " (cutoff:3.500A) removed outlier: 5.582A pdb=" N ILE C 75 " --> pdb=" O VAL C 189 " (cutoff:3.500A) removed outlier: 7.267A pdb=" N VAL C 189 " --> pdb=" O ILE C 75 " (cutoff:3.500A) removed outlier: 5.080A pdb=" N LEU C 77 " --> pdb=" O THR C 187 " (cutoff:3.500A) removed outlier: 5.947A pdb=" N THR C 187 " --> pdb=" O LEU C 77 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N GLN C 79 " --> pdb=" O GLN C 185 " (cutoff:3.500A) removed outlier: 7.144A pdb=" N THR C 181 " --> pdb=" O THR C 83 " (cutoff:3.500A) removed outlier: 7.250A pdb=" N GLY C 175 " --> pdb=" O SER C 93 " (cutoff:3.500A) removed outlier: 5.104A pdb=" N SER C 93 " --> pdb=" O GLY C 175 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N VAL C 177 " --> pdb=" O GLN C 91 " (cutoff:3.500A) Processing sheet with id=26, first strand: chain 'C' and resid 57 through 60 removed outlier: 6.628A pdb=" N THR C 57 " --> pdb=" O TYR C 73 " (cutoff:3.500A) removed outlier: 7.701A pdb=" N ILE C 75 " --> pdb=" O THR C 57 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N GLY C 59 " --> pdb=" O ILE C 75 " (cutoff:3.500A) removed outlier: 8.426A pdb=" N LEU C 77 " --> pdb=" O GLY C 59 " (cutoff:3.500A) removed outlier: 5.582A pdb=" N TYR C 73 " --> pdb=" O LEU C 191 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N LEU C 191 " --> pdb=" O TYR C 73 " (cutoff:3.500A) removed outlier: 5.582A pdb=" N ILE C 75 " --> pdb=" O VAL C 189 " (cutoff:3.500A) removed outlier: 7.267A pdb=" N VAL C 189 " --> pdb=" O ILE C 75 " (cutoff:3.500A) removed outlier: 5.080A pdb=" N LEU C 77 " --> pdb=" O THR C 187 " (cutoff:3.500A) removed outlier: 5.947A pdb=" N THR C 187 " --> pdb=" O LEU C 77 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N GLN C 79 " --> pdb=" O GLN C 185 " (cutoff:3.500A) removed outlier: 7.144A pdb=" N THR C 181 " --> pdb=" O THR C 83 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N LYS C 174 " --> pdb=" O ILE C 262 " (cutoff:3.500A) removed outlier: 4.733A pdb=" N PHE C 229 " --> pdb=" O PRO C 247 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N ILE C 249 " --> pdb=" O LEU C 227 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N LEU C 227 " --> pdb=" O ILE C 249 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N LYS C 251 " --> pdb=" O GLN C 225 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N GLN C 225 " --> pdb=" O LYS C 251 " (cutoff:3.500A) Processing sheet with id=27, first strand: chain 'C' and resid 123 through 129 removed outlier: 6.594A pdb=" N THR C 167 " --> pdb=" O GLY C 124 " (cutoff:3.500A) removed outlier: 5.291A pdb=" N LEU C 126 " --> pdb=" O ILE C 165 " (cutoff:3.500A) removed outlier: 7.741A pdb=" N ILE C 165 " --> pdb=" O LEU C 126 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N LYS C 128 " --> pdb=" O ASN C 163 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N ASN C 163 " --> pdb=" O LYS C 128 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N ALA C 162 " --> pdb=" O SER C 105 " (cutoff:3.500A) removed outlier: 4.752A pdb=" N SER C 105 " --> pdb=" O ALA C 162 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N ILE C 164 " --> pdb=" O VAL C 103 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N VAL C 103 " --> pdb=" O ILE C 164 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N PHE C 166 " --> pdb=" O THR C 101 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N THR C 101 " --> pdb=" O PHE C 166 " (cutoff:3.500A) removed outlier: 5.007A pdb=" N GLU C 168 " --> pdb=" O GLY C 99 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N ALA C 97 " --> pdb=" O LYS C 170 " (cutoff:3.500A) removed outlier: 5.784A pdb=" N THR C 107 " --> pdb=" O THR C 118 " (cutoff:3.500A) removed outlier: 4.728A pdb=" N THR C 118 " --> pdb=" O THR C 107 " (cutoff:3.500A) Processing sheet with id=28, first strand: chain 'C' and resid 132 through 133 Processing sheet with id=29, first strand: chain 'C' and resid 233 through 236 removed outlier: 6.667A pdb=" N ILE C 243 " --> pdb=" O ILE C 235 " (cutoff:3.500A) Processing sheet with id=30, first strand: chain 'D' and resid 22 through 23 removed outlier: 6.888A pdb=" N ILE D 93 " --> pdb=" O HIS D 108 " (cutoff:3.500A) removed outlier: 5.381A pdb=" N HIS D 108 " --> pdb=" O ILE D 93 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N VAL D 95 " --> pdb=" O SER D 106 " (cutoff:3.500A) removed outlier: 5.316A pdb=" N SER D 106 " --> pdb=" O VAL D 95 " (cutoff:3.500A) removed outlier: 7.690A pdb=" N ASP D 97 " --> pdb=" O ILE D 104 " (cutoff:3.500A) removed outlier: 7.250A pdb=" N ILE D 104 " --> pdb=" O ASP D 97 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N GLU D 130 " --> pdb=" O ASN D 113 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N TYR D 115 " --> pdb=" O GLU D 128 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N GLU D 128 " --> pdb=" O TYR D 115 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N GLU D 117 " --> pdb=" O THR D 126 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N THR D 126 " --> pdb=" O GLU D 117 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N LEU D 66 " --> pdb=" O ALA D 27 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N ALA D 27 " --> pdb=" O LEU D 66 " (cutoff:3.500A) Processing sheet with id=31, first strand: chain 'D' and resid 22 through 23 removed outlier: 6.888A pdb=" N ILE D 93 " --> pdb=" O HIS D 108 " (cutoff:3.500A) removed outlier: 5.381A pdb=" N HIS D 108 " --> pdb=" O ILE D 93 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N VAL D 95 " --> pdb=" O SER D 106 " (cutoff:3.500A) removed outlier: 5.316A pdb=" N SER D 106 " --> pdb=" O VAL D 95 " (cutoff:3.500A) removed outlier: 7.690A pdb=" N ASP D 97 " --> pdb=" O ILE D 104 " (cutoff:3.500A) removed outlier: 7.250A pdb=" N ILE D 104 " --> pdb=" O ASP D 97 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N THR D 135 " --> pdb=" O HIS D 108 " (cutoff:3.500A) Processing sheet with id=32, first strand: chain 'D' and resid 39 through 41 removed outlier: 4.095A pdb=" N GLU D 51 " --> pdb=" O VAL D 41 " (cutoff:3.500A) Processing sheet with id=33, first strand: chain 'F' and resid 177 through 178 removed outlier: 5.880A pdb=" N ILE F 169 " --> pdb=" O LEU F 207 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N LEU F 207 " --> pdb=" O ILE F 169 " (cutoff:3.500A) removed outlier: 5.343A pdb=" N VAL F 214 " --> pdb=" O LYS F 245 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N LYS F 245 " --> pdb=" O VAL F 214 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N LYS F 241 " --> pdb=" O LEU F 218 " (cutoff:3.500A) removed outlier: 9.602A pdb=" N LYS F 57 " --> pdb=" O PRO F 139 " (cutoff:3.500A) removed outlier: 11.015A pdb=" N ARG F 135 " --> pdb=" O ASP F 216 " (cutoff:3.500A) removed outlier: 12.601A pdb=" N ASP F 216 " --> pdb=" O ARG F 135 " (cutoff:3.500A) removed outlier: 12.112A pdb=" N THR F 137 " --> pdb=" O VAL F 214 " (cutoff:3.500A) removed outlier: 11.537A pdb=" N VAL F 214 " --> pdb=" O THR F 137 " (cutoff:3.500A) removed outlier: 12.067A pdb=" N TYR F 212 " --> pdb=" O PRO F 139 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N VAL F 141 " --> pdb=" O LEU F 210 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N HIS F 200 " --> pdb=" O VAL F 151 " (cutoff:3.500A) Processing sheet with id=34, first strand: chain 'F' and resid 63 through 65 Processing sheet with id=35, first strand: chain 'F' and resid 107 through 110 Processing sheet with id=36, first strand: chain 'F' and resid 160 through 161 Processing sheet with id=37, first strand: chain 'F' and resid 223 through 226 Processing sheet with id=38, first strand: chain 'H' and resid 97 through 106 removed outlier: 6.514A pdb=" N TYR H 105 " --> pdb=" O GLN H 195 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N GLN H 195 " --> pdb=" O TYR H 105 " (cutoff:3.500A) removed outlier: 8.192A pdb=" N PHE H 133 " --> pdb=" O PRO H 194 " (cutoff:3.500A) removed outlier: 8.671A pdb=" N MET H 196 " --> pdb=" O LEU H 131 " (cutoff:3.500A) removed outlier: 4.834A pdb=" N LEU H 131 " --> pdb=" O MET H 196 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N ARG H 198 " --> pdb=" O LEU H 129 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N LEU H 129 " --> pdb=" O ARG H 198 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N GLU H 200 " --> pdb=" O GLU H 127 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLN H 125 " --> pdb=" O VAL H 202 " (cutoff:3.500A) removed outlier: 8.328A pdb=" N LEU H 129 " --> pdb=" O LYS H 140 " (cutoff:3.500A) removed outlier: 5.609A pdb=" N LYS H 140 " --> pdb=" O LEU H 129 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N LEU H 131 " --> pdb=" O ILE H 138 " (cutoff:3.500A) Processing sheet with id=39, first strand: chain 'H' and resid 116 through 117 Processing sheet with id=40, first strand: chain 'H' and resid 250 through 255 removed outlier: 6.782A pdb=" N THR H 259 " --> pdb=" O LEU I 253 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N LEU I 253 " --> pdb=" O THR H 259 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N THR H 261 " --> pdb=" O LYS I 251 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N LYS I 251 " --> pdb=" O THR H 261 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N GLY H 263 " --> pdb=" O ALA I 249 " (cutoff:3.500A) Processing sheet with id=41, first strand: chain 'I' and resid 97 through 106 removed outlier: 6.512A pdb=" N TYR I 105 " --> pdb=" O GLN I 195 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N GLN I 195 " --> pdb=" O TYR I 105 " (cutoff:3.500A) removed outlier: 5.416A pdb=" N MET I 196 " --> pdb=" O GLN I 132 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N VAL I 202 " --> pdb=" O VAL I 126 " (cutoff:3.500A) removed outlier: 5.679A pdb=" N VAL I 126 " --> pdb=" O VAL I 202 " (cutoff:3.500A) removed outlier: 8.436A pdb=" N LEU I 129 " --> pdb=" O LYS I 140 " (cutoff:3.500A) removed outlier: 5.752A pdb=" N LYS I 140 " --> pdb=" O LEU I 129 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N LEU I 131 " --> pdb=" O ILE I 138 " (cutoff:3.500A) Processing sheet with id=42, first strand: chain 'I' and resid 116 through 117 Processing sheet with id=43, first strand: chain 'J' and resid 22 through 23 removed outlier: 5.681A pdb=" N ILE J 91 " --> pdb=" O GLY J 109 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N GLY J 109 " --> pdb=" O ILE J 91 " (cutoff:3.500A) removed outlier: 5.978A pdb=" N ASP J 97 " --> pdb=" O VAL J 103 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N VAL J 103 " --> pdb=" O ASP J 97 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N GLU J 130 " --> pdb=" O ASN J 113 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N TYR J 115 " --> pdb=" O GLU J 128 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N GLU J 128 " --> pdb=" O TYR J 115 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N GLU J 117 " --> pdb=" O THR J 126 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N THR J 126 " --> pdb=" O GLU J 117 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N LEU J 66 " --> pdb=" O ALA J 27 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N ALA J 27 " --> pdb=" O LEU J 66 " (cutoff:3.500A) Processing sheet with id=44, first strand: chain 'J' and resid 22 through 23 removed outlier: 5.681A pdb=" N ILE J 91 " --> pdb=" O GLY J 109 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N GLY J 109 " --> pdb=" O ILE J 91 " (cutoff:3.500A) removed outlier: 5.978A pdb=" N ASP J 97 " --> pdb=" O VAL J 103 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N VAL J 103 " --> pdb=" O ASP J 97 " (cutoff:3.500A) Processing sheet with id=45, first strand: chain 'J' and resid 39 through 43 removed outlier: 6.434A pdb=" N THR J 39 " --> pdb=" O HIS J 52 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N HIS J 52 " --> pdb=" O THR J 39 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N VAL J 41 " --> pdb=" O GLN J 50 " (cutoff:3.500A) removed outlier: 5.276A pdb=" N GLU J 43 " --> pdb=" O MET J 48 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N MET J 48 " --> pdb=" O GLU J 43 " (cutoff:3.500A) Processing sheet with id=46, first strand: chain 'K' and resid 57 through 60 removed outlier: 6.627A pdb=" N THR K 57 " --> pdb=" O TYR K 73 " (cutoff:3.500A) removed outlier: 7.701A pdb=" N ILE K 75 " --> pdb=" O THR K 57 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N GLY K 59 " --> pdb=" O ILE K 75 " (cutoff:3.500A) removed outlier: 8.425A pdb=" N LEU K 77 " --> pdb=" O GLY K 59 " (cutoff:3.500A) removed outlier: 5.582A pdb=" N TYR K 73 " --> pdb=" O LEU K 191 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N LEU K 191 " --> pdb=" O TYR K 73 " (cutoff:3.500A) removed outlier: 5.581A pdb=" N ILE K 75 " --> pdb=" O VAL K 189 " (cutoff:3.500A) removed outlier: 7.266A pdb=" N VAL K 189 " --> pdb=" O ILE K 75 " (cutoff:3.500A) removed outlier: 5.080A pdb=" N LEU K 77 " --> pdb=" O THR K 187 " (cutoff:3.500A) removed outlier: 5.946A pdb=" N THR K 187 " --> pdb=" O LEU K 77 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N GLN K 79 " --> pdb=" O GLN K 185 " (cutoff:3.500A) removed outlier: 7.144A pdb=" N THR K 181 " --> pdb=" O THR K 83 " (cutoff:3.500A) removed outlier: 7.250A pdb=" N GLY K 175 " --> pdb=" O SER K 93 " (cutoff:3.500A) removed outlier: 5.103A pdb=" N SER K 93 " --> pdb=" O GLY K 175 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N VAL K 177 " --> pdb=" O GLN K 91 " (cutoff:3.500A) Processing sheet with id=47, first strand: chain 'K' and resid 57 through 60 removed outlier: 6.627A pdb=" N THR K 57 " --> pdb=" O TYR K 73 " (cutoff:3.500A) removed outlier: 7.701A pdb=" N ILE K 75 " --> pdb=" O THR K 57 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N GLY K 59 " --> pdb=" O ILE K 75 " (cutoff:3.500A) removed outlier: 8.425A pdb=" N LEU K 77 " --> pdb=" O GLY K 59 " (cutoff:3.500A) removed outlier: 5.582A pdb=" N TYR K 73 " --> pdb=" O LEU K 191 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N LEU K 191 " --> pdb=" O TYR K 73 " (cutoff:3.500A) removed outlier: 5.581A pdb=" N ILE K 75 " --> pdb=" O VAL K 189 " (cutoff:3.500A) removed outlier: 7.266A pdb=" N VAL K 189 " --> pdb=" O ILE K 75 " (cutoff:3.500A) removed outlier: 5.080A pdb=" N LEU K 77 " --> pdb=" O THR K 187 " (cutoff:3.500A) removed outlier: 5.946A pdb=" N THR K 187 " --> pdb=" O LEU K 77 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N GLN K 79 " --> pdb=" O GLN K 185 " (cutoff:3.500A) removed outlier: 7.144A pdb=" N THR K 181 " --> pdb=" O THR K 83 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N LYS K 174 " --> pdb=" O ILE K 262 " (cutoff:3.500A) removed outlier: 4.733A pdb=" N PHE K 229 " --> pdb=" O PRO K 247 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N ILE K 249 " --> pdb=" O LEU K 227 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N LEU K 227 " --> pdb=" O ILE K 249 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N LYS K 251 " --> pdb=" O GLN K 225 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N GLN K 225 " --> pdb=" O LYS K 251 " (cutoff:3.500A) Processing sheet with id=48, first strand: chain 'K' and resid 123 through 129 removed outlier: 6.594A pdb=" N THR K 167 " --> pdb=" O GLY K 124 " (cutoff:3.500A) removed outlier: 5.291A pdb=" N LEU K 126 " --> pdb=" O ILE K 165 " (cutoff:3.500A) removed outlier: 7.741A pdb=" N ILE K 165 " --> pdb=" O LEU K 126 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N LYS K 128 " --> pdb=" O ASN K 163 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N ASN K 163 " --> pdb=" O LYS K 128 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N ALA K 162 " --> pdb=" O SER K 105 " (cutoff:3.500A) removed outlier: 4.751A pdb=" N SER K 105 " --> pdb=" O ALA K 162 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N ILE K 164 " --> pdb=" O VAL K 103 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N VAL K 103 " --> pdb=" O ILE K 164 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N PHE K 166 " --> pdb=" O THR K 101 " (cutoff:3.500A) removed outlier: 4.688A pdb=" N THR K 101 " --> pdb=" O PHE K 166 " (cutoff:3.500A) removed outlier: 5.007A pdb=" N GLU K 168 " --> pdb=" O GLY K 99 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N ALA K 97 " --> pdb=" O LYS K 170 " (cutoff:3.500A) removed outlier: 5.785A pdb=" N THR K 107 " --> pdb=" O THR K 118 " (cutoff:3.500A) removed outlier: 4.728A pdb=" N THR K 118 " --> pdb=" O THR K 107 " (cutoff:3.500A) Processing sheet with id=49, first strand: chain 'K' and resid 132 through 133 Processing sheet with id=50, first strand: chain 'K' and resid 233 through 236 removed outlier: 6.667A pdb=" N ILE K 243 " --> pdb=" O ILE K 235 " (cutoff:3.500A) Processing sheet with id=51, first strand: chain 'L' and resid 22 through 23 removed outlier: 6.888A pdb=" N ILE L 93 " --> pdb=" O HIS L 108 " (cutoff:3.500A) removed outlier: 5.382A pdb=" N HIS L 108 " --> pdb=" O ILE L 93 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N VAL L 95 " --> pdb=" O SER L 106 " (cutoff:3.500A) removed outlier: 5.316A pdb=" N SER L 106 " --> pdb=" O VAL L 95 " (cutoff:3.500A) removed outlier: 7.690A pdb=" N ASP L 97 " --> pdb=" O ILE L 104 " (cutoff:3.500A) removed outlier: 7.250A pdb=" N ILE L 104 " --> pdb=" O ASP L 97 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N GLU L 130 " --> pdb=" O ASN L 113 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N TYR L 115 " --> pdb=" O GLU L 128 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N GLU L 128 " --> pdb=" O TYR L 115 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N GLU L 117 " --> pdb=" O THR L 126 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N THR L 126 " --> pdb=" O GLU L 117 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N LEU L 66 " --> pdb=" O ALA L 27 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N ALA L 27 " --> pdb=" O LEU L 66 " (cutoff:3.500A) Processing sheet with id=52, first strand: chain 'L' and resid 22 through 23 removed outlier: 6.888A pdb=" N ILE L 93 " --> pdb=" O HIS L 108 " (cutoff:3.500A) removed outlier: 5.382A pdb=" N HIS L 108 " --> pdb=" O ILE L 93 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N VAL L 95 " --> pdb=" O SER L 106 " (cutoff:3.500A) removed outlier: 5.316A pdb=" N SER L 106 " --> pdb=" O VAL L 95 " (cutoff:3.500A) removed outlier: 7.690A pdb=" N ASP L 97 " --> pdb=" O ILE L 104 " (cutoff:3.500A) removed outlier: 7.250A pdb=" N ILE L 104 " --> pdb=" O ASP L 97 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N THR L 135 " --> pdb=" O HIS L 108 " (cutoff:3.500A) Processing sheet with id=53, first strand: chain 'L' and resid 39 through 41 removed outlier: 4.095A pdb=" N GLU L 51 " --> pdb=" O VAL L 41 " (cutoff:3.500A) Processing sheet with id=54, first strand: chain 'O' and resid 177 through 178 removed outlier: 5.880A pdb=" N ILE O 169 " --> pdb=" O LEU O 207 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N LEU O 207 " --> pdb=" O ILE O 169 " (cutoff:3.500A) removed outlier: 5.343A pdb=" N VAL O 214 " --> pdb=" O LYS O 245 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N LYS O 245 " --> pdb=" O VAL O 214 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N LYS O 241 " --> pdb=" O LEU O 218 " (cutoff:3.500A) removed outlier: 9.602A pdb=" N LYS O 57 " --> pdb=" O PRO O 139 " (cutoff:3.500A) removed outlier: 11.015A pdb=" N ARG O 135 " --> pdb=" O ASP O 216 " (cutoff:3.500A) removed outlier: 12.602A pdb=" N ASP O 216 " --> pdb=" O ARG O 135 " (cutoff:3.500A) removed outlier: 12.112A pdb=" N THR O 137 " --> pdb=" O VAL O 214 " (cutoff:3.500A) removed outlier: 11.538A pdb=" N VAL O 214 " --> pdb=" O THR O 137 " (cutoff:3.500A) removed outlier: 12.067A pdb=" N TYR O 212 " --> pdb=" O PRO O 139 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N VAL O 141 " --> pdb=" O LEU O 210 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N HIS O 200 " --> pdb=" O VAL O 151 " (cutoff:3.500A) Processing sheet with id=55, first strand: chain 'O' and resid 63 through 65 Processing sheet with id=56, first strand: chain 'O' and resid 107 through 110 Processing sheet with id=57, first strand: chain 'O' and resid 160 through 161 Processing sheet with id=58, first strand: chain 'O' and resid 223 through 226 Processing sheet with id=59, first strand: chain 'P' and resid 97 through 106 removed outlier: 6.514A pdb=" N TYR P 105 " --> pdb=" O GLN P 195 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N GLN P 195 " --> pdb=" O TYR P 105 " (cutoff:3.500A) removed outlier: 8.192A pdb=" N PHE P 133 " --> pdb=" O PRO P 194 " (cutoff:3.500A) removed outlier: 8.671A pdb=" N MET P 196 " --> pdb=" O LEU P 131 " (cutoff:3.500A) removed outlier: 4.834A pdb=" N LEU P 131 " --> pdb=" O MET P 196 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N ARG P 198 " --> pdb=" O LEU P 129 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N LEU P 129 " --> pdb=" O ARG P 198 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N GLU P 200 " --> pdb=" O GLU P 127 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLN P 125 " --> pdb=" O VAL P 202 " (cutoff:3.500A) removed outlier: 8.328A pdb=" N LEU P 129 " --> pdb=" O LYS P 140 " (cutoff:3.500A) removed outlier: 5.609A pdb=" N LYS P 140 " --> pdb=" O LEU P 129 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N LEU P 131 " --> pdb=" O ILE P 138 " (cutoff:3.500A) Processing sheet with id=60, first strand: chain 'P' and resid 116 through 117 Processing sheet with id=61, first strand: chain 'P' and resid 250 through 255 removed outlier: 6.782A pdb=" N THR P 259 " --> pdb=" O LEU Q 253 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N LEU Q 253 " --> pdb=" O THR P 259 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N THR P 261 " --> pdb=" O LYS Q 251 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N LYS Q 251 " --> pdb=" O THR P 261 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N GLY P 263 " --> pdb=" O ALA Q 249 " (cutoff:3.500A) Processing sheet with id=62, first strand: chain 'Q' and resid 97 through 106 removed outlier: 6.512A pdb=" N TYR Q 105 " --> pdb=" O GLN Q 195 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N GLN Q 195 " --> pdb=" O TYR Q 105 " (cutoff:3.500A) removed outlier: 5.416A pdb=" N MET Q 196 " --> pdb=" O GLN Q 132 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N VAL Q 202 " --> pdb=" O VAL Q 126 " (cutoff:3.500A) removed outlier: 5.679A pdb=" N VAL Q 126 " --> pdb=" O VAL Q 202 " (cutoff:3.500A) removed outlier: 8.436A pdb=" N LEU Q 129 " --> pdb=" O LYS Q 140 " (cutoff:3.500A) removed outlier: 5.752A pdb=" N LYS Q 140 " --> pdb=" O LEU Q 129 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N LEU Q 131 " --> pdb=" O ILE Q 138 " (cutoff:3.500A) Processing sheet with id=63, first strand: chain 'Q' and resid 116 through 117 Processing sheet with id=64, first strand: chain 'R' and resid 22 through 23 removed outlier: 5.681A pdb=" N ILE R 91 " --> pdb=" O GLY R 109 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N GLY R 109 " --> pdb=" O ILE R 91 " (cutoff:3.500A) removed outlier: 5.978A pdb=" N ASP R 97 " --> pdb=" O VAL R 103 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N VAL R 103 " --> pdb=" O ASP R 97 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N GLU R 130 " --> pdb=" O ASN R 113 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N TYR R 115 " --> pdb=" O GLU R 128 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N GLU R 128 " --> pdb=" O TYR R 115 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N GLU R 117 " --> pdb=" O THR R 126 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N THR R 126 " --> pdb=" O GLU R 117 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N LEU R 66 " --> pdb=" O ALA R 27 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N ALA R 27 " --> pdb=" O LEU R 66 " (cutoff:3.500A) Processing sheet with id=65, first strand: chain 'R' and resid 22 through 23 removed outlier: 5.681A pdb=" N ILE R 91 " --> pdb=" O GLY R 109 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N GLY R 109 " --> pdb=" O ILE R 91 " (cutoff:3.500A) removed outlier: 5.978A pdb=" N ASP R 97 " --> pdb=" O VAL R 103 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N VAL R 103 " --> pdb=" O ASP R 97 " (cutoff:3.500A) Processing sheet with id=66, first strand: chain 'R' and resid 39 through 43 removed outlier: 6.434A pdb=" N THR R 39 " --> pdb=" O HIS R 52 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N HIS R 52 " --> pdb=" O THR R 39 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N VAL R 41 " --> pdb=" O GLN R 50 " (cutoff:3.500A) removed outlier: 5.276A pdb=" N GLU R 43 " --> pdb=" O MET R 48 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N MET R 48 " --> pdb=" O GLU R 43 " (cutoff:3.500A) Processing sheet with id=67, first strand: chain 'T' and resid 57 through 60 removed outlier: 6.628A pdb=" N THR T 57 " --> pdb=" O TYR T 73 " (cutoff:3.500A) removed outlier: 7.701A pdb=" N ILE T 75 " --> pdb=" O THR T 57 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N GLY T 59 " --> pdb=" O ILE T 75 " (cutoff:3.500A) removed outlier: 8.425A pdb=" N LEU T 77 " --> pdb=" O GLY T 59 " (cutoff:3.500A) removed outlier: 5.582A pdb=" N TYR T 73 " --> pdb=" O LEU T 191 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N LEU T 191 " --> pdb=" O TYR T 73 " (cutoff:3.500A) removed outlier: 5.582A pdb=" N ILE T 75 " --> pdb=" O VAL T 189 " (cutoff:3.500A) removed outlier: 7.266A pdb=" N VAL T 189 " --> pdb=" O ILE T 75 " (cutoff:3.500A) removed outlier: 5.080A pdb=" N LEU T 77 " --> pdb=" O THR T 187 " (cutoff:3.500A) removed outlier: 5.947A pdb=" N THR T 187 " --> pdb=" O LEU T 77 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N GLN T 79 " --> pdb=" O GLN T 185 " (cutoff:3.500A) removed outlier: 7.144A pdb=" N THR T 181 " --> pdb=" O THR T 83 " (cutoff:3.500A) removed outlier: 7.250A pdb=" N GLY T 175 " --> pdb=" O SER T 93 " (cutoff:3.500A) removed outlier: 5.104A pdb=" N SER T 93 " --> pdb=" O GLY T 175 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N VAL T 177 " --> pdb=" O GLN T 91 " (cutoff:3.500A) Processing sheet with id=68, first strand: chain 'T' and resid 57 through 60 removed outlier: 6.628A pdb=" N THR T 57 " --> pdb=" O TYR T 73 " (cutoff:3.500A) removed outlier: 7.701A pdb=" N ILE T 75 " --> pdb=" O THR T 57 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N GLY T 59 " --> pdb=" O ILE T 75 " (cutoff:3.500A) removed outlier: 8.425A pdb=" N LEU T 77 " --> pdb=" O GLY T 59 " (cutoff:3.500A) removed outlier: 5.582A pdb=" N TYR T 73 " --> pdb=" O LEU T 191 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N LEU T 191 " --> pdb=" O TYR T 73 " (cutoff:3.500A) removed outlier: 5.582A pdb=" N ILE T 75 " --> pdb=" O VAL T 189 " (cutoff:3.500A) removed outlier: 7.266A pdb=" N VAL T 189 " --> pdb=" O ILE T 75 " (cutoff:3.500A) removed outlier: 5.080A pdb=" N LEU T 77 " --> pdb=" O THR T 187 " (cutoff:3.500A) removed outlier: 5.947A pdb=" N THR T 187 " --> pdb=" O LEU T 77 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N GLN T 79 " --> pdb=" O GLN T 185 " (cutoff:3.500A) removed outlier: 7.144A pdb=" N THR T 181 " --> pdb=" O THR T 83 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N LYS T 174 " --> pdb=" O ILE T 262 " (cutoff:3.500A) removed outlier: 4.733A pdb=" N PHE T 229 " --> pdb=" O PRO T 247 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N ILE T 249 " --> pdb=" O LEU T 227 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N LEU T 227 " --> pdb=" O ILE T 249 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N LYS T 251 " --> pdb=" O GLN T 225 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N GLN T 225 " --> pdb=" O LYS T 251 " (cutoff:3.500A) Processing sheet with id=69, first strand: chain 'T' and resid 123 through 129 removed outlier: 6.594A pdb=" N THR T 167 " --> pdb=" O GLY T 124 " (cutoff:3.500A) removed outlier: 5.291A pdb=" N LEU T 126 " --> pdb=" O ILE T 165 " (cutoff:3.500A) removed outlier: 7.741A pdb=" N ILE T 165 " --> pdb=" O LEU T 126 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N LYS T 128 " --> pdb=" O ASN T 163 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N ASN T 163 " --> pdb=" O LYS T 128 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N ALA T 162 " --> pdb=" O SER T 105 " (cutoff:3.500A) removed outlier: 4.751A pdb=" N SER T 105 " --> pdb=" O ALA T 162 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N ILE T 164 " --> pdb=" O VAL T 103 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N VAL T 103 " --> pdb=" O ILE T 164 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N PHE T 166 " --> pdb=" O THR T 101 " (cutoff:3.500A) removed outlier: 4.688A pdb=" N THR T 101 " --> pdb=" O PHE T 166 " (cutoff:3.500A) removed outlier: 5.007A pdb=" N GLU T 168 " --> pdb=" O GLY T 99 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N ALA T 97 " --> pdb=" O LYS T 170 " (cutoff:3.500A) removed outlier: 5.784A pdb=" N THR T 107 " --> pdb=" O THR T 118 " (cutoff:3.500A) removed outlier: 4.728A pdb=" N THR T 118 " --> pdb=" O THR T 107 " (cutoff:3.500A) Processing sheet with id=70, first strand: chain 'T' and resid 132 through 133 Processing sheet with id=71, first strand: chain 'T' and resid 233 through 236 removed outlier: 6.667A pdb=" N ILE T 243 " --> pdb=" O ILE T 235 " (cutoff:3.500A) Processing sheet with id=72, first strand: chain 'U' and resid 22 through 23 removed outlier: 6.888A pdb=" N ILE U 93 " --> pdb=" O HIS U 108 " (cutoff:3.500A) removed outlier: 5.382A pdb=" N HIS U 108 " --> pdb=" O ILE U 93 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N VAL U 95 " --> pdb=" O SER U 106 " (cutoff:3.500A) removed outlier: 5.316A pdb=" N SER U 106 " --> pdb=" O VAL U 95 " (cutoff:3.500A) removed outlier: 7.689A pdb=" N ASP U 97 " --> pdb=" O ILE U 104 " (cutoff:3.500A) removed outlier: 7.250A pdb=" N ILE U 104 " --> pdb=" O ASP U 97 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N GLU U 130 " --> pdb=" O ASN U 113 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N TYR U 115 " --> pdb=" O GLU U 128 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N GLU U 128 " --> pdb=" O TYR U 115 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N GLU U 117 " --> pdb=" O THR U 126 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N THR U 126 " --> pdb=" O GLU U 117 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N LEU U 66 " --> pdb=" O ALA U 27 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N ALA U 27 " --> pdb=" O LEU U 66 " (cutoff:3.500A) Processing sheet with id=73, first strand: chain 'U' and resid 22 through 23 removed outlier: 6.888A pdb=" N ILE U 93 " --> pdb=" O HIS U 108 " (cutoff:3.500A) removed outlier: 5.382A pdb=" N HIS U 108 " --> pdb=" O ILE U 93 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N VAL U 95 " --> pdb=" O SER U 106 " (cutoff:3.500A) removed outlier: 5.316A pdb=" N SER U 106 " --> pdb=" O VAL U 95 " (cutoff:3.500A) removed outlier: 7.689A pdb=" N ASP U 97 " --> pdb=" O ILE U 104 " (cutoff:3.500A) removed outlier: 7.250A pdb=" N ILE U 104 " --> pdb=" O ASP U 97 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N THR U 135 " --> pdb=" O HIS U 108 " (cutoff:3.500A) Processing sheet with id=74, first strand: chain 'U' and resid 39 through 41 removed outlier: 4.095A pdb=" N GLU U 51 " --> pdb=" O VAL U 41 " (cutoff:3.500A) Processing sheet with id=75, first strand: chain 'W' and resid 177 through 178 removed outlier: 5.880A pdb=" N ILE W 169 " --> pdb=" O LEU W 207 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N LEU W 207 " --> pdb=" O ILE W 169 " (cutoff:3.500A) removed outlier: 5.343A pdb=" N VAL W 214 " --> pdb=" O LYS W 245 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N LYS W 245 " --> pdb=" O VAL W 214 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N LYS W 241 " --> pdb=" O LEU W 218 " (cutoff:3.500A) removed outlier: 9.602A pdb=" N LYS W 57 " --> pdb=" O PRO W 139 " (cutoff:3.500A) removed outlier: 11.015A pdb=" N ARG W 135 " --> pdb=" O ASP W 216 " (cutoff:3.500A) removed outlier: 12.601A pdb=" N ASP W 216 " --> pdb=" O ARG W 135 " (cutoff:3.500A) removed outlier: 12.112A pdb=" N THR W 137 " --> pdb=" O VAL W 214 " (cutoff:3.500A) removed outlier: 11.537A pdb=" N VAL W 214 " --> pdb=" O THR W 137 " (cutoff:3.500A) removed outlier: 12.067A pdb=" N TYR W 212 " --> pdb=" O PRO W 139 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N VAL W 141 " --> pdb=" O LEU W 210 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N HIS W 200 " --> pdb=" O VAL W 151 " (cutoff:3.500A) Processing sheet with id=76, first strand: chain 'W' and resid 63 through 65 Processing sheet with id=77, first strand: chain 'W' and resid 107 through 110 Processing sheet with id=78, first strand: chain 'W' and resid 160 through 161 Processing sheet with id=79, first strand: chain 'W' and resid 223 through 226 Processing sheet with id=80, first strand: chain 'X' and resid 97 through 106 removed outlier: 6.513A pdb=" N TYR X 105 " --> pdb=" O GLN X 195 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N GLN X 195 " --> pdb=" O TYR X 105 " (cutoff:3.500A) removed outlier: 8.192A pdb=" N PHE X 133 " --> pdb=" O PRO X 194 " (cutoff:3.500A) removed outlier: 8.671A pdb=" N MET X 196 " --> pdb=" O LEU X 131 " (cutoff:3.500A) removed outlier: 4.835A pdb=" N LEU X 131 " --> pdb=" O MET X 196 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N ARG X 198 " --> pdb=" O LEU X 129 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N LEU X 129 " --> pdb=" O ARG X 198 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N GLU X 200 " --> pdb=" O GLU X 127 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLN X 125 " --> pdb=" O VAL X 202 " (cutoff:3.500A) removed outlier: 8.328A pdb=" N LEU X 129 " --> pdb=" O LYS X 140 " (cutoff:3.500A) removed outlier: 5.609A pdb=" N LYS X 140 " --> pdb=" O LEU X 129 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N LEU X 131 " --> pdb=" O ILE X 138 " (cutoff:3.500A) Processing sheet with id=81, first strand: chain 'X' and resid 116 through 117 Processing sheet with id=82, first strand: chain 'X' and resid 250 through 255 removed outlier: 6.782A pdb=" N THR X 259 " --> pdb=" O LEU Y 253 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N LEU Y 253 " --> pdb=" O THR X 259 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N THR X 261 " --> pdb=" O LYS Y 251 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N LYS Y 251 " --> pdb=" O THR X 261 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N GLY X 263 " --> pdb=" O ALA Y 249 " (cutoff:3.500A) Processing sheet with id=83, first strand: chain 'Y' and resid 97 through 106 removed outlier: 6.512A pdb=" N TYR Y 105 " --> pdb=" O GLN Y 195 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N GLN Y 195 " --> pdb=" O TYR Y 105 " (cutoff:3.500A) removed outlier: 5.416A pdb=" N MET Y 196 " --> pdb=" O GLN Y 132 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N VAL Y 202 " --> pdb=" O VAL Y 126 " (cutoff:3.500A) removed outlier: 5.679A pdb=" N VAL Y 126 " --> pdb=" O VAL Y 202 " (cutoff:3.500A) removed outlier: 8.436A pdb=" N LEU Y 129 " --> pdb=" O LYS Y 140 " (cutoff:3.500A) removed outlier: 5.753A pdb=" N LYS Y 140 " --> pdb=" O LEU Y 129 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N LEU Y 131 " --> pdb=" O ILE Y 138 " (cutoff:3.500A) Processing sheet with id=84, first strand: chain 'Y' and resid 116 through 117 Processing sheet with id=85, first strand: chain 'Z' and resid 22 through 23 removed outlier: 5.681A pdb=" N ILE Z 91 " --> pdb=" O GLY Z 109 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N GLY Z 109 " --> pdb=" O ILE Z 91 " (cutoff:3.500A) removed outlier: 5.978A pdb=" N ASP Z 97 " --> pdb=" O VAL Z 103 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N VAL Z 103 " --> pdb=" O ASP Z 97 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N GLU Z 130 " --> pdb=" O ASN Z 113 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N TYR Z 115 " --> pdb=" O GLU Z 128 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N GLU Z 128 " --> pdb=" O TYR Z 115 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N GLU Z 117 " --> pdb=" O THR Z 126 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N THR Z 126 " --> pdb=" O GLU Z 117 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N LEU Z 66 " --> pdb=" O ALA Z 27 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N ALA Z 27 " --> pdb=" O LEU Z 66 " (cutoff:3.500A) Processing sheet with id=86, first strand: chain 'Z' and resid 22 through 23 removed outlier: 5.681A pdb=" N ILE Z 91 " --> pdb=" O GLY Z 109 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N GLY Z 109 " --> pdb=" O ILE Z 91 " (cutoff:3.500A) removed outlier: 5.978A pdb=" N ASP Z 97 " --> pdb=" O VAL Z 103 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N VAL Z 103 " --> pdb=" O ASP Z 97 " (cutoff:3.500A) Processing sheet with id=87, first strand: chain 'Z' and resid 39 through 43 removed outlier: 6.434A pdb=" N THR Z 39 " --> pdb=" O HIS Z 52 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N HIS Z 52 " --> pdb=" O THR Z 39 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N VAL Z 41 " --> pdb=" O GLN Z 50 " (cutoff:3.500A) removed outlier: 5.276A pdb=" N GLU Z 43 " --> pdb=" O MET Z 48 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N MET Z 48 " --> pdb=" O GLU Z 43 " (cutoff:3.500A) Processing sheet with id=88, first strand: chain '0' and resid 57 through 60 removed outlier: 6.627A pdb=" N THR 0 57 " --> pdb=" O TYR 0 73 " (cutoff:3.500A) removed outlier: 7.701A pdb=" N ILE 0 75 " --> pdb=" O THR 0 57 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N GLY 0 59 " --> pdb=" O ILE 0 75 " (cutoff:3.500A) removed outlier: 8.426A pdb=" N LEU 0 77 " --> pdb=" O GLY 0 59 " (cutoff:3.500A) removed outlier: 5.582A pdb=" N TYR 0 73 " --> pdb=" O LEU 0 191 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N LEU 0 191 " --> pdb=" O TYR 0 73 " (cutoff:3.500A) removed outlier: 5.582A pdb=" N ILE 0 75 " --> pdb=" O VAL 0 189 " (cutoff:3.500A) removed outlier: 7.267A pdb=" N VAL 0 189 " --> pdb=" O ILE 0 75 " (cutoff:3.500A) removed outlier: 5.080A pdb=" N LEU 0 77 " --> pdb=" O THR 0 187 " (cutoff:3.500A) removed outlier: 5.947A pdb=" N THR 0 187 " --> pdb=" O LEU 0 77 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N GLN 0 79 " --> pdb=" O GLN 0 185 " (cutoff:3.500A) removed outlier: 7.144A pdb=" N THR 0 181 " --> pdb=" O THR 0 83 " (cutoff:3.500A) removed outlier: 7.250A pdb=" N GLY 0 175 " --> pdb=" O SER 0 93 " (cutoff:3.500A) removed outlier: 5.104A pdb=" N SER 0 93 " --> pdb=" O GLY 0 175 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N VAL 0 177 " --> pdb=" O GLN 0 91 " (cutoff:3.500A) Processing sheet with id=89, first strand: chain '0' and resid 57 through 60 removed outlier: 6.627A pdb=" N THR 0 57 " --> pdb=" O TYR 0 73 " (cutoff:3.500A) removed outlier: 7.701A pdb=" N ILE 0 75 " --> pdb=" O THR 0 57 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N GLY 0 59 " --> pdb=" O ILE 0 75 " (cutoff:3.500A) removed outlier: 8.426A pdb=" N LEU 0 77 " --> pdb=" O GLY 0 59 " (cutoff:3.500A) removed outlier: 5.582A pdb=" N TYR 0 73 " --> pdb=" O LEU 0 191 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N LEU 0 191 " --> pdb=" O TYR 0 73 " (cutoff:3.500A) removed outlier: 5.582A pdb=" N ILE 0 75 " --> pdb=" O VAL 0 189 " (cutoff:3.500A) removed outlier: 7.267A pdb=" N VAL 0 189 " --> pdb=" O ILE 0 75 " (cutoff:3.500A) removed outlier: 5.080A pdb=" N LEU 0 77 " --> pdb=" O THR 0 187 " (cutoff:3.500A) removed outlier: 5.947A pdb=" N THR 0 187 " --> pdb=" O LEU 0 77 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N GLN 0 79 " --> pdb=" O GLN 0 185 " (cutoff:3.500A) removed outlier: 7.144A pdb=" N THR 0 181 " --> pdb=" O THR 0 83 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N LYS 0 174 " --> pdb=" O ILE 0 262 " (cutoff:3.500A) removed outlier: 4.733A pdb=" N PHE 0 229 " --> pdb=" O PRO 0 247 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N ILE 0 249 " --> pdb=" O LEU 0 227 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N LEU 0 227 " --> pdb=" O ILE 0 249 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N LYS 0 251 " --> pdb=" O GLN 0 225 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N GLN 0 225 " --> pdb=" O LYS 0 251 " (cutoff:3.500A) Processing sheet with id=90, first strand: chain '0' and resid 123 through 129 removed outlier: 6.594A pdb=" N THR 0 167 " --> pdb=" O GLY 0 124 " (cutoff:3.500A) removed outlier: 5.291A pdb=" N LEU 0 126 " --> pdb=" O ILE 0 165 " (cutoff:3.500A) removed outlier: 7.741A pdb=" N ILE 0 165 " --> pdb=" O LEU 0 126 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N LYS 0 128 " --> pdb=" O ASN 0 163 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N ASN 0 163 " --> pdb=" O LYS 0 128 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N ALA 0 162 " --> pdb=" O SER 0 105 " (cutoff:3.500A) removed outlier: 4.752A pdb=" N SER 0 105 " --> pdb=" O ALA 0 162 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N ILE 0 164 " --> pdb=" O VAL 0 103 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N VAL 0 103 " --> pdb=" O ILE 0 164 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N PHE 0 166 " --> pdb=" O THR 0 101 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N THR 0 101 " --> pdb=" O PHE 0 166 " (cutoff:3.500A) removed outlier: 5.007A pdb=" N GLU 0 168 " --> pdb=" O GLY 0 99 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N ALA 0 97 " --> pdb=" O LYS 0 170 " (cutoff:3.500A) removed outlier: 5.784A pdb=" N THR 0 107 " --> pdb=" O THR 0 118 " (cutoff:3.500A) removed outlier: 4.728A pdb=" N THR 0 118 " --> pdb=" O THR 0 107 " (cutoff:3.500A) Processing sheet with id=91, first strand: chain '0' and resid 132 through 133 Processing sheet with id=92, first strand: chain '0' and resid 233 through 236 removed outlier: 6.667A pdb=" N ILE 0 243 " --> pdb=" O ILE 0 235 " (cutoff:3.500A) Processing sheet with id=93, first strand: chain '1' and resid 22 through 23 removed outlier: 6.888A pdb=" N ILE 1 93 " --> pdb=" O HIS 1 108 " (cutoff:3.500A) removed outlier: 5.381A pdb=" N HIS 1 108 " --> pdb=" O ILE 1 93 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N VAL 1 95 " --> pdb=" O SER 1 106 " (cutoff:3.500A) removed outlier: 5.316A pdb=" N SER 1 106 " --> pdb=" O VAL 1 95 " (cutoff:3.500A) removed outlier: 7.690A pdb=" N ASP 1 97 " --> pdb=" O ILE 1 104 " (cutoff:3.500A) removed outlier: 7.250A pdb=" N ILE 1 104 " --> pdb=" O ASP 1 97 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N GLU 1 130 " --> pdb=" O ASN 1 113 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N TYR 1 115 " --> pdb=" O GLU 1 128 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N GLU 1 128 " --> pdb=" O TYR 1 115 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N GLU 1 117 " --> pdb=" O THR 1 126 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N THR 1 126 " --> pdb=" O GLU 1 117 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N LEU 1 66 " --> pdb=" O ALA 1 27 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N ALA 1 27 " --> pdb=" O LEU 1 66 " (cutoff:3.500A) Processing sheet with id=94, first strand: chain '1' and resid 22 through 23 removed outlier: 6.888A pdb=" N ILE 1 93 " --> pdb=" O HIS 1 108 " (cutoff:3.500A) removed outlier: 5.381A pdb=" N HIS 1 108 " --> pdb=" O ILE 1 93 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N VAL 1 95 " --> pdb=" O SER 1 106 " (cutoff:3.500A) removed outlier: 5.316A pdb=" N SER 1 106 " --> pdb=" O VAL 1 95 " (cutoff:3.500A) removed outlier: 7.690A pdb=" N ASP 1 97 " --> pdb=" O ILE 1 104 " (cutoff:3.500A) removed outlier: 7.250A pdb=" N ILE 1 104 " --> pdb=" O ASP 1 97 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N THR 1 135 " --> pdb=" O HIS 1 108 " (cutoff:3.500A) Processing sheet with id=95, first strand: chain '1' and resid 39 through 41 removed outlier: 4.095A pdb=" N GLU 1 51 " --> pdb=" O VAL 1 41 " (cutoff:3.500A) Processing sheet with id=96, first strand: chain '3' and resid 177 through 178 removed outlier: 5.880A pdb=" N ILE 3 169 " --> pdb=" O LEU 3 207 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N LEU 3 207 " --> pdb=" O ILE 3 169 " (cutoff:3.500A) removed outlier: 5.343A pdb=" N VAL 3 214 " --> pdb=" O LYS 3 245 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N LYS 3 245 " --> pdb=" O VAL 3 214 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N LYS 3 241 " --> pdb=" O LEU 3 218 " (cutoff:3.500A) removed outlier: 9.602A pdb=" N LYS 3 57 " --> pdb=" O PRO 3 139 " (cutoff:3.500A) removed outlier: 11.015A pdb=" N ARG 3 135 " --> pdb=" O ASP 3 216 " (cutoff:3.500A) removed outlier: 12.601A pdb=" N ASP 3 216 " --> pdb=" O ARG 3 135 " (cutoff:3.500A) removed outlier: 12.112A pdb=" N THR 3 137 " --> pdb=" O VAL 3 214 " (cutoff:3.500A) removed outlier: 11.537A pdb=" N VAL 3 214 " --> pdb=" O THR 3 137 " (cutoff:3.500A) removed outlier: 12.067A pdb=" N TYR 3 212 " --> pdb=" O PRO 3 139 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N VAL 3 141 " --> pdb=" O LEU 3 210 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N HIS 3 200 " --> pdb=" O VAL 3 151 " (cutoff:3.500A) Processing sheet with id=97, first strand: chain '3' and resid 63 through 65 Processing sheet with id=98, first strand: chain '3' and resid 107 through 110 Processing sheet with id=99, first strand: chain '3' and resid 160 through 161 Processing sheet with id=100, first strand: chain '3' and resid 223 through 226 Processing sheet with id=101, first strand: chain '4' and resid 97 through 106 removed outlier: 6.514A pdb=" N TYR 4 105 " --> pdb=" O GLN 4 195 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N GLN 4 195 " --> pdb=" O TYR 4 105 " (cutoff:3.500A) removed outlier: 8.192A pdb=" N PHE 4 133 " --> pdb=" O PRO 4 194 " (cutoff:3.500A) removed outlier: 8.671A pdb=" N MET 4 196 " --> pdb=" O LEU 4 131 " (cutoff:3.500A) removed outlier: 4.834A pdb=" N LEU 4 131 " --> pdb=" O MET 4 196 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N ARG 4 198 " --> pdb=" O LEU 4 129 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N LEU 4 129 " --> pdb=" O ARG 4 198 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N GLU 4 200 " --> pdb=" O GLU 4 127 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLN 4 125 " --> pdb=" O VAL 4 202 " (cutoff:3.500A) removed outlier: 8.328A pdb=" N LEU 4 129 " --> pdb=" O LYS 4 140 " (cutoff:3.500A) removed outlier: 5.609A pdb=" N LYS 4 140 " --> pdb=" O LEU 4 129 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N LEU 4 131 " --> pdb=" O ILE 4 138 " (cutoff:3.500A) Processing sheet with id=102, first strand: chain '4' and resid 116 through 117 Processing sheet with id=103, first strand: chain '4' and resid 250 through 255 removed outlier: 6.782A pdb=" N THR 4 259 " --> pdb=" O LEU 5 253 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N LEU 5 253 " --> pdb=" O THR 4 259 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N THR 4 261 " --> pdb=" O LYS 5 251 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N LYS 5 251 " --> pdb=" O THR 4 261 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N GLY 4 263 " --> pdb=" O ALA 5 249 " (cutoff:3.500A) Processing sheet with id=104, first strand: chain '5' and resid 97 through 106 removed outlier: 6.512A pdb=" N TYR 5 105 " --> pdb=" O GLN 5 195 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N GLN 5 195 " --> pdb=" O TYR 5 105 " (cutoff:3.500A) removed outlier: 5.416A pdb=" N MET 5 196 " --> pdb=" O GLN 5 132 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N VAL 5 202 " --> pdb=" O VAL 5 126 " (cutoff:3.500A) removed outlier: 5.679A pdb=" N VAL 5 126 " --> pdb=" O VAL 5 202 " (cutoff:3.500A) removed outlier: 8.436A pdb=" N LEU 5 129 " --> pdb=" O LYS 5 140 " (cutoff:3.500A) removed outlier: 5.752A pdb=" N LYS 5 140 " --> pdb=" O LEU 5 129 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N LEU 5 131 " --> pdb=" O ILE 5 138 " (cutoff:3.500A) Processing sheet with id=105, first strand: chain '5' and resid 116 through 117 Processing sheet with id=106, first strand: chain '6' and resid 22 through 23 removed outlier: 5.681A pdb=" N ILE 6 91 " --> pdb=" O GLY 6 109 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N GLY 6 109 " --> pdb=" O ILE 6 91 " (cutoff:3.500A) removed outlier: 5.978A pdb=" N ASP 6 97 " --> pdb=" O VAL 6 103 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N VAL 6 103 " --> pdb=" O ASP 6 97 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N GLU 6 130 " --> pdb=" O ASN 6 113 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N TYR 6 115 " --> pdb=" O GLU 6 128 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N GLU 6 128 " --> pdb=" O TYR 6 115 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N GLU 6 117 " --> pdb=" O THR 6 126 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N THR 6 126 " --> pdb=" O GLU 6 117 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N LEU 6 66 " --> pdb=" O ALA 6 27 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N ALA 6 27 " --> pdb=" O LEU 6 66 " (cutoff:3.500A) Processing sheet with id=107, first strand: chain '6' and resid 22 through 23 removed outlier: 5.681A pdb=" N ILE 6 91 " --> pdb=" O GLY 6 109 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N GLY 6 109 " --> pdb=" O ILE 6 91 " (cutoff:3.500A) removed outlier: 5.978A pdb=" N ASP 6 97 " --> pdb=" O VAL 6 103 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N VAL 6 103 " --> pdb=" O ASP 6 97 " (cutoff:3.500A) Processing sheet with id=108, first strand: chain '6' and resid 39 through 43 removed outlier: 6.434A pdb=" N THR 6 39 " --> pdb=" O HIS 6 52 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N HIS 6 52 " --> pdb=" O THR 6 39 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N VAL 6 41 " --> pdb=" O GLN 6 50 " (cutoff:3.500A) removed outlier: 5.276A pdb=" N GLU 6 43 " --> pdb=" O MET 6 48 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N MET 6 48 " --> pdb=" O GLU 6 43 " (cutoff:3.500A) Processing sheet with id=109, first strand: chain '7' and resid 57 through 60 removed outlier: 6.627A pdb=" N THR 7 57 " --> pdb=" O TYR 7 73 " (cutoff:3.500A) removed outlier: 7.701A pdb=" N ILE 7 75 " --> pdb=" O THR 7 57 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N GLY 7 59 " --> pdb=" O ILE 7 75 " (cutoff:3.500A) removed outlier: 8.425A pdb=" N LEU 7 77 " --> pdb=" O GLY 7 59 " (cutoff:3.500A) removed outlier: 5.582A pdb=" N TYR 7 73 " --> pdb=" O LEU 7 191 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N LEU 7 191 " --> pdb=" O TYR 7 73 " (cutoff:3.500A) removed outlier: 5.581A pdb=" N ILE 7 75 " --> pdb=" O VAL 7 189 " (cutoff:3.500A) removed outlier: 7.266A pdb=" N VAL 7 189 " --> pdb=" O ILE 7 75 " (cutoff:3.500A) removed outlier: 5.080A pdb=" N LEU 7 77 " --> pdb=" O THR 7 187 " (cutoff:3.500A) removed outlier: 5.946A pdb=" N THR 7 187 " --> pdb=" O LEU 7 77 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N GLN 7 79 " --> pdb=" O GLN 7 185 " (cutoff:3.500A) removed outlier: 7.144A pdb=" N THR 7 181 " --> pdb=" O THR 7 83 " (cutoff:3.500A) removed outlier: 7.250A pdb=" N GLY 7 175 " --> pdb=" O SER 7 93 " (cutoff:3.500A) removed outlier: 5.103A pdb=" N SER 7 93 " --> pdb=" O GLY 7 175 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N VAL 7 177 " --> pdb=" O GLN 7 91 " (cutoff:3.500A) Processing sheet with id=110, first strand: chain '7' and resid 57 through 60 removed outlier: 6.627A pdb=" N THR 7 57 " --> pdb=" O TYR 7 73 " (cutoff:3.500A) removed outlier: 7.701A pdb=" N ILE 7 75 " --> pdb=" O THR 7 57 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N GLY 7 59 " --> pdb=" O ILE 7 75 " (cutoff:3.500A) removed outlier: 8.425A pdb=" N LEU 7 77 " --> pdb=" O GLY 7 59 " (cutoff:3.500A) removed outlier: 5.582A pdb=" N TYR 7 73 " --> pdb=" O LEU 7 191 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N LEU 7 191 " --> pdb=" O TYR 7 73 " (cutoff:3.500A) removed outlier: 5.581A pdb=" N ILE 7 75 " --> pdb=" O VAL 7 189 " (cutoff:3.500A) removed outlier: 7.266A pdb=" N VAL 7 189 " --> pdb=" O ILE 7 75 " (cutoff:3.500A) removed outlier: 5.080A pdb=" N LEU 7 77 " --> pdb=" O THR 7 187 " (cutoff:3.500A) removed outlier: 5.946A pdb=" N THR 7 187 " --> pdb=" O LEU 7 77 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N GLN 7 79 " --> pdb=" O GLN 7 185 " (cutoff:3.500A) removed outlier: 7.144A pdb=" N THR 7 181 " --> pdb=" O THR 7 83 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N LYS 7 174 " --> pdb=" O ILE 7 262 " (cutoff:3.500A) removed outlier: 4.733A pdb=" N PHE 7 229 " --> pdb=" O PRO 7 247 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N ILE 7 249 " --> pdb=" O LEU 7 227 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N LEU 7 227 " --> pdb=" O ILE 7 249 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N LYS 7 251 " --> pdb=" O GLN 7 225 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N GLN 7 225 " --> pdb=" O LYS 7 251 " (cutoff:3.500A) Processing sheet with id=111, first strand: chain '7' and resid 123 through 129 removed outlier: 6.594A pdb=" N THR 7 167 " --> pdb=" O GLY 7 124 " (cutoff:3.500A) removed outlier: 5.291A pdb=" N LEU 7 126 " --> pdb=" O ILE 7 165 " (cutoff:3.500A) removed outlier: 7.741A pdb=" N ILE 7 165 " --> pdb=" O LEU 7 126 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N LYS 7 128 " --> pdb=" O ASN 7 163 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N ASN 7 163 " --> pdb=" O LYS 7 128 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N ALA 7 162 " --> pdb=" O SER 7 105 " (cutoff:3.500A) removed outlier: 4.751A pdb=" N SER 7 105 " --> pdb=" O ALA 7 162 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N ILE 7 164 " --> pdb=" O VAL 7 103 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N VAL 7 103 " --> pdb=" O ILE 7 164 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N PHE 7 166 " --> pdb=" O THR 7 101 " (cutoff:3.500A) removed outlier: 4.688A pdb=" N THR 7 101 " --> pdb=" O PHE 7 166 " (cutoff:3.500A) removed outlier: 5.007A pdb=" N GLU 7 168 " --> pdb=" O GLY 7 99 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N ALA 7 97 " --> pdb=" O LYS 7 170 " (cutoff:3.500A) removed outlier: 5.785A pdb=" N THR 7 107 " --> pdb=" O THR 7 118 " (cutoff:3.500A) removed outlier: 4.728A pdb=" N THR 7 118 " --> pdb=" O THR 7 107 " (cutoff:3.500A) Processing sheet with id=112, first strand: chain '7' and resid 132 through 133 Processing sheet with id=113, first strand: chain '7' and resid 233 through 236 removed outlier: 6.667A pdb=" N ILE 7 243 " --> pdb=" O ILE 7 235 " (cutoff:3.500A) Processing sheet with id=114, first strand: chain '8' and resid 22 through 23 removed outlier: 6.888A pdb=" N ILE 8 93 " --> pdb=" O HIS 8 108 " (cutoff:3.500A) removed outlier: 5.382A pdb=" N HIS 8 108 " --> pdb=" O ILE 8 93 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N VAL 8 95 " --> pdb=" O SER 8 106 " (cutoff:3.500A) removed outlier: 5.316A pdb=" N SER 8 106 " --> pdb=" O VAL 8 95 " (cutoff:3.500A) removed outlier: 7.690A pdb=" N ASP 8 97 " --> pdb=" O ILE 8 104 " (cutoff:3.500A) removed outlier: 7.250A pdb=" N ILE 8 104 " --> pdb=" O ASP 8 97 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N GLU 8 130 " --> pdb=" O ASN 8 113 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N TYR 8 115 " --> pdb=" O GLU 8 128 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N GLU 8 128 " --> pdb=" O TYR 8 115 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N GLU 8 117 " --> pdb=" O THR 8 126 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N THR 8 126 " --> pdb=" O GLU 8 117 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N LEU 8 66 " --> pdb=" O ALA 8 27 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N ALA 8 27 " --> pdb=" O LEU 8 66 " (cutoff:3.500A) Processing sheet with id=115, first strand: chain '8' and resid 22 through 23 removed outlier: 6.888A pdb=" N ILE 8 93 " --> pdb=" O HIS 8 108 " (cutoff:3.500A) removed outlier: 5.382A pdb=" N HIS 8 108 " --> pdb=" O ILE 8 93 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N VAL 8 95 " --> pdb=" O SER 8 106 " (cutoff:3.500A) removed outlier: 5.316A pdb=" N SER 8 106 " --> pdb=" O VAL 8 95 " (cutoff:3.500A) removed outlier: 7.690A pdb=" N ASP 8 97 " --> pdb=" O ILE 8 104 " (cutoff:3.500A) removed outlier: 7.250A pdb=" N ILE 8 104 " --> pdb=" O ASP 8 97 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N THR 8 135 " --> pdb=" O HIS 8 108 " (cutoff:3.500A) Processing sheet with id=116, first strand: chain '8' and resid 39 through 41 removed outlier: 4.095A pdb=" N GLU 8 51 " --> pdb=" O VAL 8 41 " (cutoff:3.500A) Processing sheet with id=117, first strand: chain 'a' and resid 177 through 178 removed outlier: 5.880A pdb=" N ILE a 169 " --> pdb=" O LEU a 207 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N LEU a 207 " --> pdb=" O ILE a 169 " (cutoff:3.500A) removed outlier: 5.344A pdb=" N VAL a 214 " --> pdb=" O LYS a 245 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N LYS a 245 " --> pdb=" O VAL a 214 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N LYS a 241 " --> pdb=" O LEU a 218 " (cutoff:3.500A) removed outlier: 9.602A pdb=" N LYS a 57 " --> pdb=" O PRO a 139 " (cutoff:3.500A) removed outlier: 11.015A pdb=" N ARG a 135 " --> pdb=" O ASP a 216 " (cutoff:3.500A) removed outlier: 12.602A pdb=" N ASP a 216 " --> pdb=" O ARG a 135 " (cutoff:3.500A) removed outlier: 12.112A pdb=" N THR a 137 " --> pdb=" O VAL a 214 " (cutoff:3.500A) removed outlier: 11.538A pdb=" N VAL a 214 " --> pdb=" O THR a 137 " (cutoff:3.500A) removed outlier: 12.067A pdb=" N TYR a 212 " --> pdb=" O PRO a 139 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N VAL a 141 " --> pdb=" O LEU a 210 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N HIS a 200 " --> pdb=" O VAL a 151 " (cutoff:3.500A) Processing sheet with id=118, first strand: chain 'a' and resid 63 through 65 Processing sheet with id=119, first strand: chain 'a' and resid 107 through 110 Processing sheet with id=120, first strand: chain 'a' and resid 160 through 161 Processing sheet with id=121, first strand: chain 'a' and resid 223 through 226 Processing sheet with id=122, first strand: chain 'd' and resid 97 through 106 removed outlier: 6.514A pdb=" N TYR d 105 " --> pdb=" O GLN d 195 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N GLN d 195 " --> pdb=" O TYR d 105 " (cutoff:3.500A) removed outlier: 8.192A pdb=" N PHE d 133 " --> pdb=" O PRO d 194 " (cutoff:3.500A) removed outlier: 8.671A pdb=" N MET d 196 " --> pdb=" O LEU d 131 " (cutoff:3.500A) removed outlier: 4.834A pdb=" N LEU d 131 " --> pdb=" O MET d 196 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N ARG d 198 " --> pdb=" O LEU d 129 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N LEU d 129 " --> pdb=" O ARG d 198 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N GLU d 200 " --> pdb=" O GLU d 127 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLN d 125 " --> pdb=" O VAL d 202 " (cutoff:3.500A) removed outlier: 8.328A pdb=" N LEU d 129 " --> pdb=" O LYS d 140 " (cutoff:3.500A) removed outlier: 5.609A pdb=" N LYS d 140 " --> pdb=" O LEU d 129 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N LEU d 131 " --> pdb=" O ILE d 138 " (cutoff:3.500A) Processing sheet with id=123, first strand: chain 'd' and resid 116 through 117 Processing sheet with id=124, first strand: chain 'd' and resid 250 through 255 removed outlier: 6.782A pdb=" N THR d 259 " --> pdb=" O LEU e 253 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N LEU e 253 " --> pdb=" O THR d 259 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N THR d 261 " --> pdb=" O LYS e 251 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N LYS e 251 " --> pdb=" O THR d 261 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N GLY d 263 " --> pdb=" O ALA e 249 " (cutoff:3.500A) Processing sheet with id=125, first strand: chain 'e' and resid 97 through 106 removed outlier: 6.512A pdb=" N TYR e 105 " --> pdb=" O GLN e 195 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N GLN e 195 " --> pdb=" O TYR e 105 " (cutoff:3.500A) removed outlier: 5.416A pdb=" N MET e 196 " --> pdb=" O GLN e 132 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N VAL e 202 " --> pdb=" O VAL e 126 " (cutoff:3.500A) removed outlier: 5.679A pdb=" N VAL e 126 " --> pdb=" O VAL e 202 " (cutoff:3.500A) removed outlier: 8.436A pdb=" N LEU e 129 " --> pdb=" O LYS e 140 " (cutoff:3.500A) removed outlier: 5.752A pdb=" N LYS e 140 " --> pdb=" O LEU e 129 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N LEU e 131 " --> pdb=" O ILE e 138 " (cutoff:3.500A) Processing sheet with id=126, first strand: chain 'e' and resid 116 through 117 2628 hydrogen bonds defined for protein. 6894 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: 27.02 Time building geometry restraints manager: 15.81 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 21266 1.34 - 1.46: 11799 1.46 - 1.58: 33391 1.58 - 1.69: 0 1.69 - 1.81: 462 Bond restraints: 66918 Sorted by residual: bond pdb=" N LEU P 17 " pdb=" CA LEU P 17 " ideal model delta sigma weight residual 1.458 1.492 -0.034 1.90e-02 2.77e+03 3.19e+00 bond pdb=" N LEU d 17 " pdb=" CA LEU d 17 " ideal model delta sigma weight residual 1.458 1.492 -0.034 1.90e-02 2.77e+03 3.19e+00 bond pdb=" N LEU b 17 " pdb=" CA LEU b 17 " ideal model delta sigma weight residual 1.458 1.492 -0.034 1.90e-02 2.77e+03 3.17e+00 bond pdb=" N LEU X 17 " pdb=" CA LEU X 17 " ideal model delta sigma weight residual 1.458 1.492 -0.034 1.90e-02 2.77e+03 3.17e+00 bond pdb=" N LEU H 17 " pdb=" CA LEU H 17 " ideal model delta sigma weight residual 1.458 1.492 -0.034 1.90e-02 2.77e+03 3.14e+00 ... (remaining 66913 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.15: 81788 1.15 - 2.31: 7552 2.31 - 3.46: 828 3.46 - 4.61: 353 4.61 - 5.76: 79 Bond angle restraints: 90600 Sorted by residual: angle pdb=" N PHE C 62 " pdb=" CA PHE C 62 " pdb=" C PHE C 62 " ideal model delta sigma weight residual 109.81 115.57 -5.76 2.21e+00 2.05e-01 6.80e+00 angle pdb=" N PHE 0 62 " pdb=" CA PHE 0 62 " pdb=" C PHE 0 62 " ideal model delta sigma weight residual 109.81 115.57 -5.76 2.21e+00 2.05e-01 6.80e+00 angle pdb=" N PHE 7 62 " pdb=" CA PHE 7 62 " pdb=" C PHE 7 62 " ideal model delta sigma weight residual 109.81 115.55 -5.74 2.21e+00 2.05e-01 6.75e+00 angle pdb=" N PHE K 62 " pdb=" CA PHE K 62 " pdb=" C PHE K 62 " ideal model delta sigma weight residual 109.81 115.55 -5.74 2.21e+00 2.05e-01 6.75e+00 angle pdb=" N PHE M 62 " pdb=" CA PHE M 62 " pdb=" C PHE M 62 " ideal model delta sigma weight residual 109.81 115.53 -5.72 2.21e+00 2.05e-01 6.69e+00 ... (remaining 90595 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.85: 37334 17.85 - 35.70: 2068 35.70 - 53.54: 522 53.54 - 71.39: 204 71.39 - 89.24: 78 Dihedral angle restraints: 40206 sinusoidal: 16452 harmonic: 23754 Sorted by residual: dihedral pdb=" CA GLU P 20 " pdb=" C GLU P 20 " pdb=" N TYR P 21 " pdb=" CA TYR P 21 " ideal model delta harmonic sigma weight residual -180.00 -153.82 -26.18 0 5.00e+00 4.00e-02 2.74e+01 dihedral pdb=" CA GLU d 20 " pdb=" C GLU d 20 " pdb=" N TYR d 21 " pdb=" CA TYR d 21 " ideal model delta harmonic sigma weight residual 180.00 -153.82 -26.18 0 5.00e+00 4.00e-02 2.74e+01 dihedral pdb=" CA GLU X 20 " pdb=" C GLU X 20 " pdb=" N TYR X 21 " pdb=" CA TYR X 21 " ideal model delta harmonic sigma weight residual -180.00 -153.83 -26.17 0 5.00e+00 4.00e-02 2.74e+01 ... (remaining 40203 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 5738 0.036 - 0.072: 2918 0.072 - 0.109: 901 0.109 - 0.145: 353 0.145 - 0.181: 50 Chirality restraints: 9960 Sorted by residual: chirality pdb=" CA ILE X 244 " pdb=" N ILE X 244 " pdb=" C ILE X 244 " pdb=" CB ILE X 244 " both_signs ideal model delta sigma weight residual False 2.43 2.61 -0.18 2.00e-01 2.50e+01 8.20e-01 chirality pdb=" CA ILE b 244 " pdb=" N ILE b 244 " pdb=" C ILE b 244 " pdb=" CB ILE b 244 " both_signs ideal model delta sigma weight residual False 2.43 2.61 -0.18 2.00e-01 2.50e+01 8.20e-01 chirality pdb=" CA ILE H 244 " pdb=" N ILE H 244 " pdb=" C ILE H 244 " pdb=" CB ILE H 244 " both_signs ideal model delta sigma weight residual False 2.43 2.61 -0.18 2.00e-01 2.50e+01 8.19e-01 ... (remaining 9957 not shown) Planarity restraints: 11694 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG Y 88 " -0.263 9.50e-02 1.11e+02 1.18e-01 1.03e+01 pdb=" NE ARG Y 88 " 0.023 2.00e-02 2.50e+03 pdb=" CZ ARG Y 88 " -0.020 2.00e-02 2.50e+03 pdb=" NH1 ARG Y 88 " 0.010 2.00e-02 2.50e+03 pdb=" NH2 ARG Y 88 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG c 88 " -0.263 9.50e-02 1.11e+02 1.18e-01 1.03e+01 pdb=" NE ARG c 88 " 0.023 2.00e-02 2.50e+03 pdb=" CZ ARG c 88 " -0.020 2.00e-02 2.50e+03 pdb=" NH1 ARG c 88 " 0.010 2.00e-02 2.50e+03 pdb=" NH2 ARG c 88 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG Q 88 " -0.263 9.50e-02 1.11e+02 1.19e-01 1.03e+01 pdb=" NE ARG Q 88 " 0.023 2.00e-02 2.50e+03 pdb=" CZ ARG Q 88 " -0.020 2.00e-02 2.50e+03 pdb=" NH1 ARG Q 88 " 0.010 2.00e-02 2.50e+03 pdb=" NH2 ARG Q 88 " -0.002 2.00e-02 2.50e+03 ... (remaining 11691 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.79: 14058 2.79 - 3.32: 60125 3.32 - 3.85: 103270 3.85 - 4.37: 126302 4.37 - 4.90: 222999 Nonbonded interactions: 526754 Sorted by model distance: nonbonded pdb=" OD2 ASP Z 97 " pdb=" OG1 THR Z 100 " model vdw 2.266 3.040 nonbonded pdb=" OD2 ASP B 97 " pdb=" OG1 THR B 100 " model vdw 2.266 3.040 nonbonded pdb=" OD2 ASP R 97 " pdb=" OG1 THR R 100 " model vdw 2.266 3.040 nonbonded pdb=" OD2 ASP A 97 " pdb=" OG1 THR A 100 " model vdw 2.266 3.040 nonbonded pdb=" OD2 ASP 6 97 " pdb=" OG1 THR 6 100 " model vdw 2.266 3.040 ... (remaining 526749 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 '0' selection = chain '7' selection = chain 'C' selection = chain 'K' selection = chain 'M' selection = chain 'T' } ncs_group { reference = (chain '1' and resid 2 through 140) selection = chain '6' selection = (chain '8' and resid 2 through 140) selection = chain 'A' selection = chain 'B' selection = (chain 'D' and resid 2 through 140) selection = (chain 'G' and resid 2 through 140) selection = chain 'J' selection = (chain 'L' and resid 2 through 140) selection = chain 'R' selection = (chain 'U' and resid 2 through 140) selection = chain 'Z' } ncs_group { reference = chain '2' selection = chain '9' selection = chain 'E' selection = chain 'N' selection = chain 'V' selection = chain 'r' } ncs_group { reference = chain '3' selection = chain 'F' selection = chain 'O' selection = chain 'S' selection = chain 'W' selection = chain 'a' } ncs_group { reference = chain '4' selection = chain '5' selection = chain 'H' selection = chain 'I' selection = chain 'P' selection = chain 'Q' selection = chain 'X' selection = chain 'Y' selection = chain 'b' selection = chain 'c' selection = chain 'd' selection = chain 'e' } 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=0.01 max=1.00 mean=0.98 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 1.040 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: 0.050 Extract box with map and model: 1.760 Check model and map are aligned: 0.350 Set scattering table: 0.440 Process input model: 124.210 Find NCS groups from input model: 2.450 Set up NCS constraints: 0.590 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:2.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 133.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7433 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 : 0.005 0.048 66918 Z= 0.349 Angle : 0.727 5.763 90600 Z= 0.399 Chirality : 0.049 0.181 9960 Planarity : 0.008 0.119 11694 Dihedral : 13.860 89.241 25014 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 0.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -0.16 (0.09), residues: 8010 helix: -0.23 (0.11), residues: 1644 sheet: 0.30 (0.11), residues: 2130 loop : -0.15 (0.09), residues: 4236 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP Q 239 HIS 0.007 0.002 HIS 5 77 PHE 0.022 0.003 PHE L 131 TYR 0.028 0.003 TYR a 132 ARG 0.023 0.003 ARG Y 88 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16020 Ramachandran restraints generated. 8010 Oldfield, 0 Emsley, 8010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16020 Ramachandran restraints generated. 8010 Oldfield, 0 Emsley, 8010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1787 residues out of total 7134 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1787 time to evaluate : 7.167 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 LYS cc_start: 0.8852 (mttm) cc_final: 0.8502 (mttp) REVERT: A 31 SER cc_start: 0.8716 (t) cc_final: 0.8459 (m) REVERT: A 35 GLU cc_start: 0.7981 (tt0) cc_final: 0.7616 (tt0) REVERT: M 48 CYS cc_start: 0.8448 (t) cc_final: 0.8177 (t) REVERT: M 50 LYS cc_start: 0.7466 (pttt) cc_final: 0.7135 (mmtt) REVERT: M 70 GLU cc_start: 0.7484 (tt0) cc_final: 0.7281 (tt0) REVERT: M 102 LEU cc_start: 0.7354 (mt) cc_final: 0.7126 (mt) REVERT: M 137 TYR cc_start: 0.8003 (t80) cc_final: 0.7214 (t80) REVERT: M 138 ASP cc_start: 0.7803 (m-30) cc_final: 0.7482 (m-30) REVERT: M 146 LYS cc_start: 0.6889 (mtmm) cc_final: 0.6065 (mmtm) REVERT: M 184 GLU cc_start: 0.7769 (tt0) cc_final: 0.7166 (tt0) REVERT: G 18 MET cc_start: 0.8009 (mtp) cc_final: 0.7678 (mtp) REVERT: G 35 GLU cc_start: 0.7304 (mt-10) cc_final: 0.7098 (mt-10) REVERT: G 48 MET cc_start: 0.8386 (mtp) cc_final: 0.8087 (mtt) REVERT: G 87 LYS cc_start: 0.8204 (mtmm) cc_final: 0.7860 (mttm) REVERT: S 108 ASN cc_start: 0.7864 (m110) cc_final: 0.7228 (m110) REVERT: S 149 TYR cc_start: 0.8561 (m-80) cc_final: 0.7917 (m-80) REVERT: S 187 LYS cc_start: 0.7856 (mtpt) cc_final: 0.7477 (mmmt) REVERT: S 227 LYS cc_start: 0.7968 (tptm) cc_final: 0.7386 (mttp) REVERT: S 254 ASP cc_start: 0.7689 (m-30) cc_final: 0.7195 (m-30) REVERT: b 37 ILE cc_start: 0.7349 (pt) cc_final: 0.6671 (mt) REVERT: b 136 ARG cc_start: 0.6564 (mtt180) cc_final: 0.6121 (mmt180) REVERT: b 147 LYS cc_start: 0.7587 (mmtt) cc_final: 0.7078 (mptt) REVERT: b 196 MET cc_start: 0.7408 (mmm) cc_final: 0.7003 (mmt) REVERT: b 217 TRP cc_start: 0.8362 (p90) cc_final: 0.8091 (p90) REVERT: b 225 GLN cc_start: 0.7246 (tt0) cc_final: 0.6857 (tt0) REVERT: c 93 SER cc_start: 0.8566 (t) cc_final: 0.8270 (t) REVERT: c 114 MET cc_start: 0.8776 (tpt) cc_final: 0.8293 (tpp) REVERT: c 138 ILE cc_start: 0.7842 (mm) cc_final: 0.7398 (mt) REVERT: c 269 MET cc_start: 0.7391 (tpp) cc_final: 0.7104 (tpp) REVERT: c 285 LYS cc_start: 0.7260 (ttpt) cc_final: 0.6904 (tmmt) REVERT: B 20 LYS cc_start: 0.8798 (mttm) cc_final: 0.8554 (mttp) REVERT: B 35 GLU cc_start: 0.7879 (tt0) cc_final: 0.7604 (tt0) REVERT: C 137 TYR cc_start: 0.7997 (t80) cc_final: 0.7197 (t80) REVERT: C 138 ASP cc_start: 0.7414 (m-30) cc_final: 0.7193 (m-30) REVERT: C 146 LYS cc_start: 0.6905 (mtmm) cc_final: 0.6071 (mmtp) REVERT: C 266 ILE cc_start: 0.7534 (mt) cc_final: 0.7227 (mt) REVERT: D 29 SER cc_start: 0.7809 (p) cc_final: 0.7586 (p) REVERT: D 68 MET cc_start: 0.7907 (mtm) cc_final: 0.7663 (mtm) REVERT: D 115 TYR cc_start: 0.8804 (t80) cc_final: 0.8586 (t80) REVERT: D 128 GLU cc_start: 0.7708 (tt0) cc_final: 0.7000 (pt0) REVERT: D 139 LYS cc_start: 0.7909 (ptpt) cc_final: 0.7664 (mmtp) REVERT: F 70 ASN cc_start: 0.8257 (t0) cc_final: 0.8009 (t0) REVERT: F 143 MET cc_start: 0.8622 (mmp) cc_final: 0.8237 (mmt) REVERT: F 153 LYS cc_start: 0.7814 (tttm) cc_final: 0.7613 (pttt) REVERT: F 185 GLU cc_start: 0.7456 (tt0) cc_final: 0.7251 (tt0) REVERT: F 187 LYS cc_start: 0.7658 (mtpt) cc_final: 0.7224 (tttt) REVERT: F 227 LYS cc_start: 0.8407 (tptm) cc_final: 0.7669 (mttp) REVERT: F 228 PHE cc_start: 0.8787 (t80) cc_final: 0.8176 (t80) REVERT: F 254 ASP cc_start: 0.7699 (m-30) cc_final: 0.7367 (m-30) REVERT: H 37 ILE cc_start: 0.7386 (pt) cc_final: 0.6730 (mt) REVERT: H 62 GLN cc_start: 0.7608 (pt0) cc_final: 0.7329 (pt0) REVERT: H 114 MET cc_start: 0.8244 (tpt) cc_final: 0.7973 (tpp) REVERT: H 136 ARG cc_start: 0.6956 (mtt180) cc_final: 0.6534 (ptm160) REVERT: H 147 LYS cc_start: 0.7745 (mmtt) cc_final: 0.7427 (mmtm) REVERT: H 196 MET cc_start: 0.6944 (mmm) cc_final: 0.6663 (mmt) REVERT: H 198 ARG cc_start: 0.7640 (ttt-90) cc_final: 0.7337 (ttt180) REVERT: H 208 ARG cc_start: 0.7051 (ptt-90) cc_final: 0.6543 (ptt-90) REVERT: H 209 LYS cc_start: 0.7459 (tppt) cc_final: 0.6908 (mmtm) REVERT: H 217 TRP cc_start: 0.8220 (p90) cc_final: 0.7950 (p90) REVERT: H 225 GLN cc_start: 0.7238 (tt0) cc_final: 0.6981 (tt0) REVERT: H 282 GLU cc_start: 0.7427 (tt0) cc_final: 0.7177 (tt0) REVERT: I 110 PHE cc_start: 0.8034 (t80) cc_final: 0.7586 (t80) REVERT: I 114 MET cc_start: 0.8718 (tpt) cc_final: 0.8168 (tpp) REVERT: I 138 ILE cc_start: 0.7608 (mm) cc_final: 0.7239 (mt) REVERT: J 20 LYS cc_start: 0.8864 (mttm) cc_final: 0.8582 (mttp) REVERT: J 76 LEU cc_start: 0.8060 (mt) cc_final: 0.7773 (mt) REVERT: J 87 LYS cc_start: 0.8280 (mtmt) cc_final: 0.7759 (mttm) REVERT: K 26 TYR cc_start: 0.6948 (p90) cc_final: 0.6131 (t80) REVERT: K 38 GLN cc_start: 0.7518 (mt0) cc_final: 0.7188 (mt0) REVERT: K 95 PHE cc_start: 0.8491 (m-80) cc_final: 0.8230 (m-80) REVERT: K 137 TYR cc_start: 0.7847 (t80) cc_final: 0.7436 (t80) REVERT: K 138 ASP cc_start: 0.7538 (m-30) cc_final: 0.7301 (m-30) REVERT: K 184 GLU cc_start: 0.7759 (tt0) cc_final: 0.7486 (tt0) REVERT: K 276 ASP cc_start: 0.7089 (t0) cc_final: 0.6717 (t70) REVERT: L 18 MET cc_start: 0.8062 (mtp) cc_final: 0.7847 (mtp) REVERT: L 48 MET cc_start: 0.8517 (mtp) cc_final: 0.8274 (mtt) REVERT: L 56 ARG cc_start: 0.7748 (ptm160) cc_final: 0.5625 (mpt180) REVERT: L 87 LYS cc_start: 0.8092 (mtmm) cc_final: 0.7751 (mttp) REVERT: L 115 TYR cc_start: 0.8669 (t80) cc_final: 0.8450 (t80) REVERT: L 128 GLU cc_start: 0.7620 (tt0) cc_final: 0.7411 (tt0) REVERT: L 139 LYS cc_start: 0.8001 (ptpt) cc_final: 0.7741 (ptpt) REVERT: O 108 ASN cc_start: 0.7840 (m110) cc_final: 0.7597 (m110) REVERT: O 187 LYS cc_start: 0.7737 (mtpt) cc_final: 0.7192 (tttt) REVERT: O 227 LYS cc_start: 0.8191 (tptm) cc_final: 0.7429 (mttp) REVERT: O 254 ASP cc_start: 0.7534 (m-30) cc_final: 0.7163 (m-30) REVERT: P 37 ILE cc_start: 0.7353 (pt) cc_final: 0.6731 (mt) REVERT: P 114 MET cc_start: 0.8299 (tpt) cc_final: 0.8036 (tpp) REVERT: P 136 ARG cc_start: 0.6413 (mtt180) cc_final: 0.6193 (ptm160) REVERT: P 147 LYS cc_start: 0.7470 (mmtt) cc_final: 0.7104 (mmtm) REVERT: P 198 ARG cc_start: 0.7797 (ttt-90) cc_final: 0.7568 (ttt180) REVERT: P 199 LEU cc_start: 0.7995 (tp) cc_final: 0.7700 (tp) REVERT: Q 102 MET cc_start: 0.8043 (mmt) cc_final: 0.7641 (mmm) REVERT: Q 110 PHE cc_start: 0.8179 (t80) cc_final: 0.7734 (t80) REVERT: Q 114 MET cc_start: 0.8714 (tpt) cc_final: 0.7834 (tpt) REVERT: Q 138 ILE cc_start: 0.8128 (mm) cc_final: 0.7735 (mt) REVERT: Q 209 LYS cc_start: 0.8099 (tppt) cc_final: 0.7895 (ttmm) REVERT: Q 248 ILE cc_start: 0.8582 (mm) cc_final: 0.8252 (mt) REVERT: Q 269 MET cc_start: 0.7076 (tpp) cc_final: 0.6849 (tpp) REVERT: Q 299 MET cc_start: 0.8718 (tmm) cc_final: 0.8132 (tmm) REVERT: R 20 LYS cc_start: 0.8851 (mttm) cc_final: 0.8503 (mttp) REVERT: R 31 SER cc_start: 0.8724 (t) cc_final: 0.8463 (m) REVERT: R 35 GLU cc_start: 0.7977 (tt0) cc_final: 0.7609 (tt0) REVERT: T 48 CYS cc_start: 0.8456 (t) cc_final: 0.8175 (t) REVERT: T 50 LYS cc_start: 0.7464 (pttt) cc_final: 0.7137 (mmtt) REVERT: T 102 LEU cc_start: 0.7357 (mt) cc_final: 0.7129 (mt) REVERT: T 137 TYR cc_start: 0.8002 (t80) cc_final: 0.7212 (t80) REVERT: T 138 ASP cc_start: 0.7805 (m-30) cc_final: 0.7484 (m-30) REVERT: T 146 LYS cc_start: 0.6892 (mtmm) cc_final: 0.6066 (mmtm) REVERT: T 184 GLU cc_start: 0.7770 (tt0) cc_final: 0.7163 (tt0) REVERT: U 18 MET cc_start: 0.8013 (mtp) cc_final: 0.7681 (mtp) REVERT: U 35 GLU cc_start: 0.7300 (mt-10) cc_final: 0.7095 (mt-10) REVERT: U 48 MET cc_start: 0.8389 (mtp) cc_final: 0.8093 (mtt) REVERT: U 87 LYS cc_start: 0.8210 (mtmm) cc_final: 0.7864 (mttm) REVERT: W 108 ASN cc_start: 0.7854 (m110) cc_final: 0.7223 (m110) REVERT: W 149 TYR cc_start: 0.8553 (m-80) cc_final: 0.7917 (m-80) REVERT: W 187 LYS cc_start: 0.7854 (mtpt) cc_final: 0.7476 (mmmt) REVERT: W 227 LYS cc_start: 0.7967 (tptm) cc_final: 0.7386 (mttp) REVERT: W 254 ASP cc_start: 0.7673 (m-30) cc_final: 0.7192 (m-30) REVERT: X 37 ILE cc_start: 0.7349 (pt) cc_final: 0.6676 (mt) REVERT: X 136 ARG cc_start: 0.6564 (mtt180) cc_final: 0.6121 (mmt180) REVERT: X 147 LYS cc_start: 0.7588 (mmtt) cc_final: 0.7079 (mptt) REVERT: X 196 MET cc_start: 0.7412 (mmm) cc_final: 0.7009 (mmt) REVERT: X 217 TRP cc_start: 0.8362 (p90) cc_final: 0.8092 (p90) REVERT: X 225 GLN cc_start: 0.7262 (tt0) cc_final: 0.6875 (tt0) REVERT: Y 93 SER cc_start: 0.8560 (t) cc_final: 0.8261 (t) REVERT: Y 114 MET cc_start: 0.8779 (tpt) cc_final: 0.8299 (tpp) REVERT: Y 138 ILE cc_start: 0.7841 (mm) cc_final: 0.7394 (mt) REVERT: Y 269 MET cc_start: 0.7391 (tpp) cc_final: 0.7111 (tpp) REVERT: Y 285 LYS cc_start: 0.7260 (ttpt) cc_final: 0.6902 (tmmt) REVERT: Z 20 LYS cc_start: 0.8801 (mttm) cc_final: 0.8557 (mttp) REVERT: Z 35 GLU cc_start: 0.7880 (tt0) cc_final: 0.7607 (tt0) REVERT: 0 137 TYR cc_start: 0.8001 (t80) cc_final: 0.7196 (t80) REVERT: 0 138 ASP cc_start: 0.7416 (m-30) cc_final: 0.7194 (m-30) REVERT: 0 146 LYS cc_start: 0.6896 (mtmm) cc_final: 0.6070 (mmtp) REVERT: 0 266 ILE cc_start: 0.7533 (mt) cc_final: 0.7230 (mt) REVERT: 1 29 SER cc_start: 0.7811 (p) cc_final: 0.7587 (p) REVERT: 1 68 MET cc_start: 0.7910 (mtm) cc_final: 0.7667 (mtm) REVERT: 1 115 TYR cc_start: 0.8808 (t80) cc_final: 0.8589 (t80) REVERT: 1 128 GLU cc_start: 0.7707 (tt0) cc_final: 0.7005 (pt0) REVERT: 1 139 LYS cc_start: 0.7910 (ptpt) cc_final: 0.7659 (mmtp) REVERT: 3 70 ASN cc_start: 0.8262 (t0) cc_final: 0.8014 (t0) REVERT: 3 143 MET cc_start: 0.8622 (mmp) cc_final: 0.8232 (mmt) REVERT: 3 185 GLU cc_start: 0.7455 (tt0) cc_final: 0.7251 (tt0) REVERT: 3 187 LYS cc_start: 0.7659 (mtpt) cc_final: 0.7225 (tttt) REVERT: 3 227 LYS cc_start: 0.8408 (tptm) cc_final: 0.7671 (mttp) REVERT: 3 228 PHE cc_start: 0.8790 (t80) cc_final: 0.8179 (t80) REVERT: 3 254 ASP cc_start: 0.7704 (m-30) cc_final: 0.7367 (m-30) REVERT: 4 37 ILE cc_start: 0.7386 (pt) cc_final: 0.6730 (mt) REVERT: 4 62 GLN cc_start: 0.7607 (pt0) cc_final: 0.7326 (pt0) REVERT: 4 114 MET cc_start: 0.8240 (tpt) cc_final: 0.7967 (tpp) REVERT: 4 136 ARG cc_start: 0.6957 (mtt180) cc_final: 0.6535 (ptm160) REVERT: 4 147 LYS cc_start: 0.7739 (mmtt) cc_final: 0.7423 (mmtm) REVERT: 4 196 MET cc_start: 0.6946 (mmm) cc_final: 0.6668 (mmt) REVERT: 4 198 ARG cc_start: 0.7647 (ttt-90) cc_final: 0.7342 (ttt180) REVERT: 4 208 ARG cc_start: 0.7050 (ptt-90) cc_final: 0.6545 (ptt-90) REVERT: 4 209 LYS cc_start: 0.7461 (tppt) cc_final: 0.6909 (mmtm) REVERT: 4 217 TRP cc_start: 0.8215 (p90) cc_final: 0.7944 (p90) REVERT: 4 225 GLN cc_start: 0.7236 (tt0) cc_final: 0.6974 (tt0) REVERT: 4 282 GLU cc_start: 0.7427 (tt0) cc_final: 0.7180 (tt0) REVERT: 5 110 PHE cc_start: 0.8035 (t80) cc_final: 0.7588 (t80) REVERT: 5 114 MET cc_start: 0.8719 (tpt) cc_final: 0.8170 (tpp) REVERT: 5 138 ILE cc_start: 0.7607 (mm) cc_final: 0.7235 (mt) REVERT: 6 20 LYS cc_start: 0.8865 (mttm) cc_final: 0.8583 (mttp) REVERT: 6 76 LEU cc_start: 0.8061 (mt) cc_final: 0.7773 (mt) REVERT: 6 87 LYS cc_start: 0.8282 (mtmt) cc_final: 0.7760 (mttm) REVERT: 7 26 TYR cc_start: 0.6949 (p90) cc_final: 0.6133 (t80) REVERT: 7 38 GLN cc_start: 0.7521 (mt0) cc_final: 0.7191 (mt0) REVERT: 7 95 PHE cc_start: 0.8492 (m-80) cc_final: 0.8232 (m-80) REVERT: 7 137 TYR cc_start: 0.7850 (t80) cc_final: 0.7438 (t80) REVERT: 7 138 ASP cc_start: 0.7542 (m-30) cc_final: 0.7304 (m-30) REVERT: 7 184 GLU cc_start: 0.7737 (tt0) cc_final: 0.7469 (tt0) REVERT: 7 276 ASP cc_start: 0.7093 (t0) cc_final: 0.6726 (t70) REVERT: 8 18 MET cc_start: 0.8059 (mtp) cc_final: 0.7843 (mtp) REVERT: 8 29 SER cc_start: 0.7949 (p) cc_final: 0.7747 (p) REVERT: 8 48 MET cc_start: 0.8514 (mtp) cc_final: 0.8275 (mtt) REVERT: 8 56 ARG cc_start: 0.7751 (ptm160) cc_final: 0.5626 (mpt180) REVERT: 8 87 LYS cc_start: 0.8095 (mtmm) cc_final: 0.7757 (mttp) REVERT: 8 115 TYR cc_start: 0.8673 (t80) cc_final: 0.8453 (t80) REVERT: 8 128 GLU cc_start: 0.7620 (tt0) cc_final: 0.7412 (tt0) REVERT: 8 139 LYS cc_start: 0.7996 (ptpt) cc_final: 0.7741 (ptpt) REVERT: a 108 ASN cc_start: 0.7849 (m110) cc_final: 0.7606 (m110) REVERT: a 187 LYS cc_start: 0.7739 (mtpt) cc_final: 0.7191 (tttt) REVERT: a 227 LYS cc_start: 0.8189 (tptm) cc_final: 0.7426 (mttp) REVERT: a 254 ASP cc_start: 0.7544 (m-30) cc_final: 0.7173 (m-30) REVERT: d 37 ILE cc_start: 0.7351 (pt) cc_final: 0.6734 (mt) REVERT: d 114 MET cc_start: 0.8303 (tpt) cc_final: 0.8042 (tpp) REVERT: d 136 ARG cc_start: 0.6414 (mtt180) cc_final: 0.6194 (ptm160) REVERT: d 147 LYS cc_start: 0.7466 (mmtt) cc_final: 0.7100 (mmtm) REVERT: d 198 ARG cc_start: 0.7805 (ttt-90) cc_final: 0.7567 (ttt180) REVERT: d 199 LEU cc_start: 0.7994 (tp) cc_final: 0.7695 (tp) REVERT: e 102 MET cc_start: 0.8045 (mmt) cc_final: 0.7644 (mmm) REVERT: e 110 PHE cc_start: 0.8183 (t80) cc_final: 0.7739 (t80) REVERT: e 114 MET cc_start: 0.8716 (tpt) cc_final: 0.7833 (tpt) REVERT: e 138 ILE cc_start: 0.8128 (mm) cc_final: 0.7736 (mt) REVERT: e 248 ILE cc_start: 0.8583 (mm) cc_final: 0.8253 (mt) REVERT: e 269 MET cc_start: 0.7076 (tpp) cc_final: 0.6856 (tpp) REVERT: e 299 MET cc_start: 0.8722 (tmm) cc_final: 0.8137 (tmm) outliers start: 0 outliers final: 0 residues processed: 1787 average time/residue: 0.7285 time to fit residues: 2138.2613 Evaluate side-chains 1095 residues out of total 7134 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1095 time to evaluate : 7.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 786 random chunks: chunk 663 optimal weight: 5.9990 chunk 595 optimal weight: 2.9990 chunk 330 optimal weight: 0.6980 chunk 203 optimal weight: 3.9990 chunk 401 optimal weight: 2.9990 chunk 318 optimal weight: 10.0000 chunk 616 optimal weight: 10.0000 chunk 238 optimal weight: 9.9990 chunk 374 optimal weight: 9.9990 chunk 458 optimal weight: 5.9990 chunk 713 optimal weight: 20.0000 overall best weight: 3.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 13 ASN A 120 GLN M 81 GLN M 159 ASN M 185 GLN G 10 HIS b 298 ASN c 68 GLN B 13 ASN B 120 GLN C 141 GLN C 185 GLN C 220 GLN E 519 ASN F 145 GLN ** F 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 77 HIS I 130 GLN J 10 HIS J 120 GLN K 159 ASN K 185 GLN K 220 GLN L 10 HIS N 519 ASN ** O 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 298 ASN Q 28 ASN Q 68 GLN R 13 ASN R 120 GLN T 81 GLN T 159 ASN T 185 GLN U 10 HIS X 298 ASN Y 68 GLN Z 13 ASN Z 120 GLN 0 141 GLN 0 185 GLN 0 220 GLN 2 519 ASN 3 145 GLN ** 3 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 77 HIS 5 130 GLN 6 10 HIS 6 120 GLN 7 159 ASN 7 185 GLN 7 220 GLN 8 10 HIS 9 519 ASN ** a 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 298 ASN e 28 ASN e 68 GLN Total number of N/Q/H flips: 54 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7486 moved from start: 0.1721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 66918 Z= 0.280 Angle : 0.599 7.533 90600 Z= 0.323 Chirality : 0.046 0.171 9960 Planarity : 0.004 0.051 11694 Dihedral : 6.080 48.052 8898 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 2.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.85 % Favored : 99.15 % Rotamer: Outliers : 1.28 % Allowed : 6.80 % Favored : 91.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 0.24 (0.09), residues: 8010 helix: 0.84 (0.12), residues: 1626 sheet: 0.18 (0.11), residues: 2160 loop : -0.00 (0.10), residues: 4224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP e 239 HIS 0.007 0.001 HIS c 77 PHE 0.017 0.002 PHE M 117 TYR 0.022 0.002 TYR C 26 ARG 0.007 0.001 ARG H 103 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16020 Ramachandran restraints generated. 8010 Oldfield, 0 Emsley, 8010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16020 Ramachandran restraints generated. 8010 Oldfield, 0 Emsley, 8010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1249 residues out of total 7134 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 1158 time to evaluate : 7.335 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 LYS cc_start: 0.8672 (mttm) cc_final: 0.8237 (mttp) REVERT: A 31 SER cc_start: 0.8723 (t) cc_final: 0.8422 (m) REVERT: M 48 CYS cc_start: 0.7867 (t) cc_final: 0.7666 (t) REVERT: M 50 LYS cc_start: 0.7565 (pttt) cc_final: 0.7207 (mmtt) REVERT: M 70 GLU cc_start: 0.7622 (tt0) cc_final: 0.7393 (tt0) REVERT: M 96 GLU cc_start: 0.7326 (tt0) cc_final: 0.7120 (tt0) REVERT: M 137 TYR cc_start: 0.7932 (t80) cc_final: 0.7324 (t80) REVERT: M 146 LYS cc_start: 0.7070 (mtmm) cc_final: 0.6101 (mmtp) REVERT: M 154 ASN cc_start: 0.6839 (m-40) cc_final: 0.6447 (m-40) REVERT: M 159 ASN cc_start: 0.7443 (OUTLIER) cc_final: 0.7103 (t0) REVERT: G 18 MET cc_start: 0.7931 (mtp) cc_final: 0.7532 (mtp) REVERT: G 48 MET cc_start: 0.8506 (mtp) cc_final: 0.8156 (mtt) REVERT: G 56 ARG cc_start: 0.7752 (ptm160) cc_final: 0.5459 (mpt180) REVERT: S 98 MET cc_start: 0.8959 (ttp) cc_final: 0.8677 (ttm) REVERT: S 108 ASN cc_start: 0.7873 (m110) cc_final: 0.7316 (m110) REVERT: S 254 ASP cc_start: 0.7822 (m-30) cc_final: 0.7550 (m-30) REVERT: b 37 ILE cc_start: 0.7538 (pt) cc_final: 0.6817 (mt) REVERT: b 44 ASP cc_start: 0.8500 (m-30) cc_final: 0.8026 (t0) REVERT: b 136 ARG cc_start: 0.6502 (mtt180) cc_final: 0.6036 (mmt180) REVERT: b 196 MET cc_start: 0.7300 (mmm) cc_final: 0.6904 (mmt) REVERT: b 217 TRP cc_start: 0.8289 (p90) cc_final: 0.8041 (p90) REVERT: c 62 GLN cc_start: 0.7603 (tt0) cc_final: 0.7391 (tt0) REVERT: c 93 SER cc_start: 0.8478 (t) cc_final: 0.8187 (t) REVERT: c 138 ILE cc_start: 0.8166 (mm) cc_final: 0.7799 (mt) REVERT: c 285 LYS cc_start: 0.7268 (ttpt) cc_final: 0.6700 (tmmt) REVERT: B 20 LYS cc_start: 0.8758 (mttm) cc_final: 0.8533 (mttp) REVERT: C 24 ASN cc_start: 0.7890 (t0) cc_final: 0.7666 (t0) REVERT: C 48 CYS cc_start: 0.8318 (OUTLIER) cc_final: 0.7872 (t) REVERT: C 137 TYR cc_start: 0.8103 (t80) cc_final: 0.7568 (t80) REVERT: C 154 ASN cc_start: 0.6781 (m-40) cc_final: 0.6454 (m110) REVERT: C 157 TYR cc_start: 0.7192 (m-80) cc_final: 0.6823 (m-80) REVERT: C 169 LYS cc_start: 0.7950 (ptmm) cc_final: 0.7653 (ttpt) REVERT: D 56 ARG cc_start: 0.7886 (ptm160) cc_final: 0.5470 (mpt180) REVERT: D 139 LYS cc_start: 0.7901 (ptpt) cc_final: 0.7602 (mmtp) REVERT: F 70 ASN cc_start: 0.8534 (t0) cc_final: 0.8268 (t0) REVERT: F 94 LYS cc_start: 0.7718 (mttt) cc_final: 0.7407 (mtmt) REVERT: F 153 LYS cc_start: 0.8036 (tttm) cc_final: 0.7715 (pttt) REVERT: F 185 GLU cc_start: 0.7353 (tt0) cc_final: 0.7018 (tt0) REVERT: H 37 ILE cc_start: 0.7396 (pt) cc_final: 0.6790 (mt) REVERT: H 44 ASP cc_start: 0.8085 (m-30) cc_final: 0.7678 (t0) REVERT: H 80 GLU cc_start: 0.7998 (tt0) cc_final: 0.7740 (tt0) REVERT: H 114 MET cc_start: 0.8115 (tpt) cc_final: 0.7879 (tpp) REVERT: H 136 ARG cc_start: 0.6920 (mtt180) cc_final: 0.6462 (ptm160) REVERT: H 198 ARG cc_start: 0.7738 (ttt-90) cc_final: 0.7178 (ttt180) REVERT: H 217 TRP cc_start: 0.8207 (p90) cc_final: 0.7958 (p90) REVERT: H 219 MET cc_start: 0.8469 (ttp) cc_final: 0.8253 (ttp) REVERT: H 225 GLN cc_start: 0.7183 (tt0) cc_final: 0.6923 (tt0) REVERT: I 110 PHE cc_start: 0.8010 (t80) cc_final: 0.7796 (t80) REVERT: I 114 MET cc_start: 0.8763 (tpt) cc_final: 0.8451 (tpp) REVERT: I 138 ILE cc_start: 0.8199 (mm) cc_final: 0.7866 (mt) REVERT: I 209 LYS cc_start: 0.8619 (OUTLIER) cc_final: 0.7903 (mtmm) REVERT: J 20 LYS cc_start: 0.8814 (mttm) cc_final: 0.8567 (mttp) REVERT: J 87 LYS cc_start: 0.8261 (mtmt) cc_final: 0.7843 (mttm) REVERT: K 48 CYS cc_start: 0.8127 (t) cc_final: 0.7802 (t) REVERT: K 137 TYR cc_start: 0.8056 (t80) cc_final: 0.7615 (t80) REVERT: K 159 ASN cc_start: 0.7607 (OUTLIER) cc_final: 0.7316 (t0) REVERT: K 183 GLU cc_start: 0.7748 (tt0) cc_final: 0.7472 (tt0) REVERT: K 184 GLU cc_start: 0.7783 (tt0) cc_final: 0.7445 (tt0) REVERT: K 276 ASP cc_start: 0.7254 (t0) cc_final: 0.6899 (t70) REVERT: L 48 MET cc_start: 0.8520 (mtp) cc_final: 0.8123 (mtt) REVERT: L 56 ARG cc_start: 0.7756 (ptm160) cc_final: 0.5478 (mpt180) REVERT: O 108 ASN cc_start: 0.7925 (m110) cc_final: 0.7642 (m110) REVERT: O 227 LYS cc_start: 0.8121 (tptm) cc_final: 0.7351 (mttp) REVERT: O 254 ASP cc_start: 0.7637 (m-30) cc_final: 0.7335 (m-30) REVERT: P 28 ASN cc_start: 0.7937 (t0) cc_final: 0.7558 (t0) REVERT: P 37 ILE cc_start: 0.7363 (pt) cc_final: 0.6870 (mt) REVERT: P 114 MET cc_start: 0.8151 (tpt) cc_final: 0.7782 (tpp) REVERT: P 136 ARG cc_start: 0.6380 (mtt180) cc_final: 0.6102 (ptm160) REVERT: P 198 ARG cc_start: 0.7945 (ttt-90) cc_final: 0.7487 (ttt180) REVERT: Q 102 MET cc_start: 0.7740 (mmt) cc_final: 0.7161 (mmm) REVERT: Q 108 THR cc_start: 0.7755 (OUTLIER) cc_final: 0.7466 (p) REVERT: Q 114 MET cc_start: 0.8780 (tpt) cc_final: 0.8477 (tpt) REVERT: Q 138 ILE cc_start: 0.8240 (mm) cc_final: 0.7873 (mt) REVERT: Q 248 ILE cc_start: 0.8612 (mm) cc_final: 0.8243 (mt) REVERT: Q 299 MET cc_start: 0.8625 (tmm) cc_final: 0.8282 (tmm) REVERT: R 20 LYS cc_start: 0.8674 (mttm) cc_final: 0.8239 (mttp) REVERT: R 31 SER cc_start: 0.8722 (t) cc_final: 0.8420 (m) REVERT: T 48 CYS cc_start: 0.7881 (t) cc_final: 0.7666 (t) REVERT: T 50 LYS cc_start: 0.7558 (pttt) cc_final: 0.7205 (mmtt) REVERT: T 96 GLU cc_start: 0.7330 (tt0) cc_final: 0.7123 (tt0) REVERT: T 137 TYR cc_start: 0.7932 (t80) cc_final: 0.7319 (t80) REVERT: T 146 LYS cc_start: 0.7070 (mtmm) cc_final: 0.6101 (mmtp) REVERT: T 154 ASN cc_start: 0.6835 (m-40) cc_final: 0.6444 (m-40) REVERT: T 159 ASN cc_start: 0.7441 (OUTLIER) cc_final: 0.7101 (t0) REVERT: U 18 MET cc_start: 0.7934 (mtp) cc_final: 0.7533 (mtp) REVERT: U 48 MET cc_start: 0.8510 (mtp) cc_final: 0.8160 (mtt) REVERT: U 56 ARG cc_start: 0.7758 (ptm160) cc_final: 0.5464 (mpt180) REVERT: W 98 MET cc_start: 0.8961 (ttp) cc_final: 0.8683 (ttm) REVERT: W 108 ASN cc_start: 0.7859 (m110) cc_final: 0.7306 (m110) REVERT: W 254 ASP cc_start: 0.7819 (m-30) cc_final: 0.7546 (m-30) REVERT: X 37 ILE cc_start: 0.7539 (pt) cc_final: 0.6821 (mt) REVERT: X 44 ASP cc_start: 0.8495 (m-30) cc_final: 0.8026 (t0) REVERT: X 88 ARG cc_start: 0.7127 (mmt-90) cc_final: 0.6845 (mmt-90) REVERT: X 136 ARG cc_start: 0.6502 (mtt180) cc_final: 0.6038 (mmt180) REVERT: X 196 MET cc_start: 0.7268 (mmm) cc_final: 0.6876 (mmt) REVERT: X 217 TRP cc_start: 0.8287 (p90) cc_final: 0.8047 (p90) REVERT: Y 62 GLN cc_start: 0.7599 (tt0) cc_final: 0.7388 (tt0) REVERT: Y 93 SER cc_start: 0.8477 (t) cc_final: 0.8186 (t) REVERT: Y 138 ILE cc_start: 0.8164 (mm) cc_final: 0.7797 (mt) REVERT: Y 285 LYS cc_start: 0.7265 (ttpt) cc_final: 0.6694 (tmmt) REVERT: Z 20 LYS cc_start: 0.8759 (mttm) cc_final: 0.8532 (mttp) REVERT: 0 24 ASN cc_start: 0.7883 (t0) cc_final: 0.7664 (t0) REVERT: 0 48 CYS cc_start: 0.8317 (OUTLIER) cc_final: 0.7873 (t) REVERT: 0 137 TYR cc_start: 0.8102 (t80) cc_final: 0.7565 (t80) REVERT: 0 154 ASN cc_start: 0.6779 (m-40) cc_final: 0.6451 (m110) REVERT: 0 157 TYR cc_start: 0.7191 (m-80) cc_final: 0.6824 (m-80) REVERT: 0 169 LYS cc_start: 0.7949 (ptmm) cc_final: 0.7650 (ttpt) REVERT: 1 56 ARG cc_start: 0.7882 (ptm160) cc_final: 0.5471 (mpt180) REVERT: 1 139 LYS cc_start: 0.7899 (ptpt) cc_final: 0.7596 (mmtp) REVERT: 3 70 ASN cc_start: 0.8543 (t0) cc_final: 0.8275 (t0) REVERT: 3 94 LYS cc_start: 0.7718 (mttt) cc_final: 0.7408 (mtmt) REVERT: 3 185 GLU cc_start: 0.7360 (tt0) cc_final: 0.7027 (tt0) REVERT: 4 37 ILE cc_start: 0.7400 (pt) cc_final: 0.6794 (mt) REVERT: 4 44 ASP cc_start: 0.8088 (m-30) cc_final: 0.7668 (t0) REVERT: 4 114 MET cc_start: 0.8104 (tpt) cc_final: 0.7867 (tpp) REVERT: 4 136 ARG cc_start: 0.6920 (mtt180) cc_final: 0.6461 (ptm160) REVERT: 4 198 ARG cc_start: 0.7735 (ttt-90) cc_final: 0.7178 (ttt180) REVERT: 4 217 TRP cc_start: 0.8203 (p90) cc_final: 0.7950 (p90) REVERT: 4 219 MET cc_start: 0.8470 (ttp) cc_final: 0.8257 (ttp) REVERT: 4 225 GLN cc_start: 0.7196 (tt0) cc_final: 0.6927 (tt0) REVERT: 5 110 PHE cc_start: 0.8010 (t80) cc_final: 0.7799 (t80) REVERT: 5 114 MET cc_start: 0.8764 (tpt) cc_final: 0.8453 (tpp) REVERT: 5 138 ILE cc_start: 0.8198 (mm) cc_final: 0.7865 (mt) REVERT: 5 209 LYS cc_start: 0.8619 (OUTLIER) cc_final: 0.7900 (mtmm) REVERT: 6 20 LYS cc_start: 0.8815 (mttm) cc_final: 0.8570 (mttp) REVERT: 6 87 LYS cc_start: 0.8260 (mtmt) cc_final: 0.7844 (mttm) REVERT: 7 48 CYS cc_start: 0.8130 (t) cc_final: 0.7803 (t) REVERT: 7 137 TYR cc_start: 0.8058 (t80) cc_final: 0.7614 (t80) REVERT: 7 159 ASN cc_start: 0.7605 (OUTLIER) cc_final: 0.7316 (t0) REVERT: 7 183 GLU cc_start: 0.7746 (tt0) cc_final: 0.7471 (tt0) REVERT: 7 184 GLU cc_start: 0.7762 (tt0) cc_final: 0.7430 (tt0) REVERT: 7 276 ASP cc_start: 0.7264 (t0) cc_final: 0.6910 (t70) REVERT: 8 48 MET cc_start: 0.8520 (mtp) cc_final: 0.8127 (mtt) REVERT: 8 56 ARG cc_start: 0.7762 (ptm160) cc_final: 0.5482 (mpt180) REVERT: a 108 ASN cc_start: 0.7936 (m110) cc_final: 0.7652 (m110) REVERT: a 227 LYS cc_start: 0.8108 (tptm) cc_final: 0.7347 (mttp) REVERT: a 254 ASP cc_start: 0.7651 (m-30) cc_final: 0.7343 (m-30) REVERT: d 28 ASN cc_start: 0.7935 (t0) cc_final: 0.7556 (t0) REVERT: d 37 ILE cc_start: 0.7365 (pt) cc_final: 0.6870 (mt) REVERT: d 44 ASP cc_start: 0.7824 (m-30) cc_final: 0.7465 (t0) REVERT: d 114 MET cc_start: 0.8154 (tpt) cc_final: 0.7788 (tpp) REVERT: d 136 ARG cc_start: 0.6381 (mtt180) cc_final: 0.6100 (ptm160) REVERT: d 198 ARG cc_start: 0.7949 (ttt-90) cc_final: 0.7479 (ttt180) REVERT: e 102 MET cc_start: 0.7734 (mmt) cc_final: 0.7158 (mmm) REVERT: e 108 THR cc_start: 0.7750 (OUTLIER) cc_final: 0.7462 (p) REVERT: e 114 MET cc_start: 0.8777 (tpt) cc_final: 0.8476 (tpt) REVERT: e 138 ILE cc_start: 0.8242 (mm) cc_final: 0.7874 (mt) REVERT: e 248 ILE cc_start: 0.8610 (mm) cc_final: 0.8243 (mt) REVERT: e 299 MET cc_start: 0.8626 (tmm) cc_final: 0.8283 (tmm) outliers start: 91 outliers final: 67 residues processed: 1218 average time/residue: 0.7752 time to fit residues: 1579.3147 Evaluate side-chains 1070 residues out of total 7134 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 993 time to evaluate : 7.679 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 105 SER Chi-restraints excluded: chain M residue 107 THR Chi-restraints excluded: chain M residue 159 ASN Chi-restraints excluded: chain M residue 161 ASN Chi-restraints excluded: chain G residue 100 THR Chi-restraints excluded: chain G residue 118 THR Chi-restraints excluded: chain S residue 215 SER Chi-restraints excluded: chain c residue 87 GLU Chi-restraints excluded: chain c residue 98 THR Chi-restraints excluded: chain c residue 191 THR Chi-restraints excluded: chain B residue 117 GLU Chi-restraints excluded: chain C residue 25 CYS Chi-restraints excluded: chain C residue 48 CYS Chi-restraints excluded: chain C residue 57 THR Chi-restraints excluded: chain C residue 105 SER Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain E residue 550 VAL Chi-restraints excluded: chain F residue 215 SER Chi-restraints excluded: chain F residue 233 SER Chi-restraints excluded: chain F residue 251 VAL Chi-restraints excluded: chain I residue 98 THR Chi-restraints excluded: chain I residue 191 THR Chi-restraints excluded: chain I residue 209 LYS Chi-restraints excluded: chain K residue 57 THR Chi-restraints excluded: chain K residue 107 THR Chi-restraints excluded: chain K residue 159 ASN Chi-restraints excluded: chain L residue 8 THR Chi-restraints excluded: chain L residue 61 ILE Chi-restraints excluded: chain L residue 118 THR Chi-restraints excluded: chain O residue 153 LYS Chi-restraints excluded: chain O residue 154 ASP Chi-restraints excluded: chain O residue 215 SER Chi-restraints excluded: chain O residue 233 SER Chi-restraints excluded: chain O residue 251 VAL Chi-restraints excluded: chain P residue 215 LYS Chi-restraints excluded: chain Q residue 98 THR Chi-restraints excluded: chain Q residue 108 THR Chi-restraints excluded: chain Q residue 278 LEU Chi-restraints excluded: chain T residue 105 SER Chi-restraints excluded: chain T residue 107 THR Chi-restraints excluded: chain T residue 159 ASN Chi-restraints excluded: chain T residue 161 ASN Chi-restraints excluded: chain U residue 100 THR Chi-restraints excluded: chain U residue 118 THR Chi-restraints excluded: chain W residue 215 SER Chi-restraints excluded: chain Y residue 87 GLU Chi-restraints excluded: chain Y residue 98 THR Chi-restraints excluded: chain Y residue 191 THR Chi-restraints excluded: chain Z residue 117 GLU Chi-restraints excluded: chain 0 residue 25 CYS Chi-restraints excluded: chain 0 residue 48 CYS Chi-restraints excluded: chain 0 residue 57 THR Chi-restraints excluded: chain 0 residue 105 SER Chi-restraints excluded: chain 0 residue 107 THR Chi-restraints excluded: chain 2 residue 550 VAL Chi-restraints excluded: chain 3 residue 153 LYS Chi-restraints excluded: chain 3 residue 215 SER Chi-restraints excluded: chain 3 residue 233 SER Chi-restraints excluded: chain 3 residue 251 VAL Chi-restraints excluded: chain 5 residue 98 THR Chi-restraints excluded: chain 5 residue 191 THR Chi-restraints excluded: chain 5 residue 209 LYS Chi-restraints excluded: chain 7 residue 57 THR Chi-restraints excluded: chain 7 residue 107 THR Chi-restraints excluded: chain 7 residue 159 ASN Chi-restraints excluded: chain 8 residue 8 THR Chi-restraints excluded: chain 8 residue 61 ILE Chi-restraints excluded: chain 8 residue 118 THR Chi-restraints excluded: chain a residue 153 LYS Chi-restraints excluded: chain a residue 154 ASP Chi-restraints excluded: chain a residue 215 SER Chi-restraints excluded: chain a residue 233 SER Chi-restraints excluded: chain a residue 251 VAL Chi-restraints excluded: chain d residue 215 LYS Chi-restraints excluded: chain e residue 98 THR Chi-restraints excluded: chain e residue 108 THR Chi-restraints excluded: chain e residue 278 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 786 random chunks: chunk 396 optimal weight: 1.9990 chunk 221 optimal weight: 6.9990 chunk 594 optimal weight: 6.9990 chunk 486 optimal weight: 20.0000 chunk 196 optimal weight: 9.9990 chunk 715 optimal weight: 7.9990 chunk 772 optimal weight: 10.0000 chunk 636 optimal weight: 10.0000 chunk 709 optimal weight: 20.0000 chunk 243 optimal weight: 8.9990 chunk 573 optimal weight: 9.9990 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 81 GLN r 530 GLN r 551 GLN S 145 GLN S 199 ASN b 28 ASN c 68 GLN C 81 GLN C 264 GLN E 530 GLN ** F 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 154 ASN K 264 GLN N 519 ASN N 530 GLN ** O 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 62 GLN Q 68 GLN T 81 GLN V 530 GLN V 551 GLN W 145 GLN X 28 ASN Y 68 GLN 0 81 GLN 0 264 GLN 2 530 GLN 7 154 ASN 7 264 GLN 9 519 ASN 9 530 GLN ** a 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 62 GLN e 68 GLN Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7554 moved from start: 0.2438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.057 66918 Z= 0.491 Angle : 0.692 8.443 90600 Z= 0.369 Chirality : 0.049 0.166 9960 Planarity : 0.005 0.049 11694 Dihedral : 6.175 51.011 8898 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 3.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 2.35 % Allowed : 9.48 % Favored : 88.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -0.14 (0.09), residues: 8010 helix: 0.48 (0.12), residues: 1674 sheet: -0.12 (0.11), residues: 2214 loop : -0.19 (0.09), residues: 4122 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP H 217 HIS 0.011 0.002 HIS Y 77 PHE 0.022 0.003 PHE M 117 TYR 0.026 0.002 TYR T 160 ARG 0.006 0.001 ARG W 135 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16020 Ramachandran restraints generated. 8010 Oldfield, 0 Emsley, 8010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16020 Ramachandran restraints generated. 8010 Oldfield, 0 Emsley, 8010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1179 residues out of total 7134 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 168 poor density : 1011 time to evaluate : 6.323 Fit side-chains REVERT: A 20 LYS cc_start: 0.8715 (mttm) cc_final: 0.8291 (mttp) REVERT: A 31 SER cc_start: 0.8731 (t) cc_final: 0.8417 (m) REVERT: M 48 CYS cc_start: 0.8168 (t) cc_final: 0.7968 (t) REVERT: M 70 GLU cc_start: 0.7787 (tt0) cc_final: 0.7513 (tt0) REVERT: M 137 TYR cc_start: 0.7752 (t80) cc_final: 0.7391 (t80) REVERT: M 146 LYS cc_start: 0.7088 (mtmm) cc_final: 0.6145 (mmtt) REVERT: M 154 ASN cc_start: 0.6907 (m-40) cc_final: 0.6418 (m-40) REVERT: M 159 ASN cc_start: 0.7510 (t0) cc_final: 0.7247 (t0) REVERT: G 18 MET cc_start: 0.7955 (mtp) cc_final: 0.7587 (mtp) REVERT: G 48 MET cc_start: 0.8484 (mtp) cc_final: 0.8132 (mtt) REVERT: G 56 ARG cc_start: 0.7968 (ptm160) cc_final: 0.5454 (mpt180) REVERT: G 71 GLU cc_start: 0.7451 (OUTLIER) cc_final: 0.6954 (pm20) REVERT: S 98 MET cc_start: 0.9028 (ttp) cc_final: 0.8806 (ttm) REVERT: S 218 LEU cc_start: 0.8816 (OUTLIER) cc_final: 0.8532 (mp) REVERT: S 254 ASP cc_start: 0.7942 (m-30) cc_final: 0.7638 (m-30) REVERT: b 37 ILE cc_start: 0.7586 (pt) cc_final: 0.6840 (mt) REVERT: b 44 ASP cc_start: 0.8144 (m-30) cc_final: 0.7454 (m-30) REVERT: b 70 MET cc_start: 0.8546 (ttm) cc_final: 0.8335 (ttp) REVERT: b 136 ARG cc_start: 0.6459 (mtt180) cc_final: 0.5928 (mmt180) REVERT: b 196 MET cc_start: 0.7445 (mmm) cc_final: 0.6887 (mmt) REVERT: c 93 SER cc_start: 0.8428 (t) cc_final: 0.8168 (t) REVERT: c 138 ILE cc_start: 0.8240 (mm) cc_final: 0.7880 (mt) REVERT: c 285 LYS cc_start: 0.7443 (ttpt) cc_final: 0.6730 (tmmt) REVERT: B 20 LYS cc_start: 0.8777 (mttm) cc_final: 0.8503 (mttp) REVERT: C 24 ASN cc_start: 0.7848 (t0) cc_final: 0.6857 (m-40) REVERT: C 137 TYR cc_start: 0.8001 (t80) cc_final: 0.7604 (t80) REVERT: C 146 LYS cc_start: 0.7025 (mtmm) cc_final: 0.5940 (mmtp) REVERT: C 154 ASN cc_start: 0.6755 (m-40) cc_final: 0.6421 (m110) REVERT: C 169 LYS cc_start: 0.8080 (ptmm) cc_final: 0.7863 (ttpt) REVERT: D 56 ARG cc_start: 0.8097 (ptm160) cc_final: 0.5355 (mpt180) REVERT: D 139 LYS cc_start: 0.7838 (ptpt) cc_final: 0.7606 (mmtp) REVERT: F 143 MET cc_start: 0.8569 (mmp) cc_final: 0.8262 (mmt) REVERT: F 153 LYS cc_start: 0.8279 (tttm) cc_final: 0.7898 (pttt) REVERT: F 185 GLU cc_start: 0.6950 (tt0) cc_final: 0.6671 (tt0) REVERT: H 37 ILE cc_start: 0.7263 (pt) cc_final: 0.6652 (mt) REVERT: H 198 ARG cc_start: 0.7667 (ttt-90) cc_final: 0.7168 (ttt180) REVERT: I 114 MET cc_start: 0.8742 (tpt) cc_final: 0.8379 (tpt) REVERT: I 138 ILE cc_start: 0.8243 (mm) cc_final: 0.7915 (mt) REVERT: I 209 LYS cc_start: 0.8596 (OUTLIER) cc_final: 0.7948 (mtmm) REVERT: J 20 LYS cc_start: 0.8784 (mttm) cc_final: 0.8439 (mttp) REVERT: J 87 LYS cc_start: 0.8346 (mtmt) cc_final: 0.7860 (mttm) REVERT: J 117 GLU cc_start: 0.8466 (OUTLIER) cc_final: 0.8251 (pm20) REVERT: K 137 TYR cc_start: 0.7970 (t80) cc_final: 0.7458 (t80) REVERT: K 146 LYS cc_start: 0.7122 (mtmm) cc_final: 0.6219 (mtpp) REVERT: K 183 GLU cc_start: 0.7816 (tt0) cc_final: 0.7563 (tt0) REVERT: K 184 GLU cc_start: 0.7937 (tt0) cc_final: 0.7502 (tt0) REVERT: L 48 MET cc_start: 0.8552 (mtp) cc_final: 0.8168 (mtt) REVERT: L 56 ARG cc_start: 0.7978 (ptm160) cc_final: 0.5565 (mpt180) REVERT: O 108 ASN cc_start: 0.8226 (m110) cc_final: 0.7915 (m110) REVERT: O 218 LEU cc_start: 0.8722 (OUTLIER) cc_final: 0.8305 (mp) REVERT: O 254 ASP cc_start: 0.7791 (m-30) cc_final: 0.7451 (m-30) REVERT: P 37 ILE cc_start: 0.7371 (pt) cc_final: 0.6784 (mt) REVERT: P 68 GLN cc_start: 0.7959 (mm-40) cc_final: 0.7474 (mt0) REVERT: P 198 ARG cc_start: 0.7966 (ttt-90) cc_final: 0.7456 (ttt180) REVERT: Q 33 ASP cc_start: 0.6820 (t70) cc_final: 0.6342 (p0) REVERT: Q 56 MET cc_start: 0.8446 (mtm) cc_final: 0.8217 (mtm) REVERT: Q 88 ARG cc_start: 0.6564 (OUTLIER) cc_final: 0.6330 (mpt180) REVERT: Q 102 MET cc_start: 0.7768 (mmt) cc_final: 0.6996 (mmm) REVERT: Q 108 THR cc_start: 0.7808 (OUTLIER) cc_final: 0.7444 (p) REVERT: Q 114 MET cc_start: 0.8854 (tpt) cc_final: 0.8517 (tpp) REVERT: Q 138 ILE cc_start: 0.8206 (mm) cc_final: 0.7826 (mt) REVERT: Q 209 LYS cc_start: 0.8240 (OUTLIER) cc_final: 0.7414 (mtmm) REVERT: Q 299 MET cc_start: 0.8389 (tmm) cc_final: 0.7995 (tmm) REVERT: R 20 LYS cc_start: 0.8717 (mttm) cc_final: 0.8294 (mttp) REVERT: R 31 SER cc_start: 0.8725 (t) cc_final: 0.8408 (m) REVERT: T 48 CYS cc_start: 0.8170 (t) cc_final: 0.7965 (t) REVERT: T 137 TYR cc_start: 0.7752 (t80) cc_final: 0.7389 (t80) REVERT: T 146 LYS cc_start: 0.7088 (mtmm) cc_final: 0.6144 (mmtt) REVERT: T 154 ASN cc_start: 0.6902 (m-40) cc_final: 0.6414 (m-40) REVERT: T 159 ASN cc_start: 0.7511 (t0) cc_final: 0.7248 (t0) REVERT: U 18 MET cc_start: 0.7957 (mtp) cc_final: 0.7585 (mtp) REVERT: U 48 MET cc_start: 0.8489 (mtp) cc_final: 0.8137 (mtt) REVERT: U 56 ARG cc_start: 0.7969 (ptm160) cc_final: 0.5455 (mpt180) REVERT: U 71 GLU cc_start: 0.7438 (OUTLIER) cc_final: 0.6936 (pm20) REVERT: W 98 MET cc_start: 0.9026 (ttp) cc_final: 0.8812 (ttm) REVERT: W 218 LEU cc_start: 0.8816 (OUTLIER) cc_final: 0.8536 (mp) REVERT: W 254 ASP cc_start: 0.7936 (m-30) cc_final: 0.7636 (m-30) REVERT: X 37 ILE cc_start: 0.7584 (pt) cc_final: 0.6845 (mt) REVERT: X 44 ASP cc_start: 0.8142 (m-30) cc_final: 0.7457 (m-30) REVERT: X 70 MET cc_start: 0.8544 (ttm) cc_final: 0.8332 (ttp) REVERT: X 136 ARG cc_start: 0.6461 (mtt180) cc_final: 0.5929 (mmt180) REVERT: X 196 MET cc_start: 0.7446 (mmm) cc_final: 0.6890 (mmt) REVERT: Y 93 SER cc_start: 0.8428 (t) cc_final: 0.8172 (t) REVERT: Y 138 ILE cc_start: 0.8238 (mm) cc_final: 0.7876 (mt) REVERT: Y 285 LYS cc_start: 0.7441 (ttpt) cc_final: 0.6727 (tmmt) REVERT: Z 20 LYS cc_start: 0.8778 (mttm) cc_final: 0.8503 (mttp) REVERT: 0 24 ASN cc_start: 0.7769 (t0) cc_final: 0.6856 (m-40) REVERT: 0 137 TYR cc_start: 0.7999 (t80) cc_final: 0.7601 (t80) REVERT: 0 146 LYS cc_start: 0.7023 (mtmm) cc_final: 0.5937 (mmtp) REVERT: 0 154 ASN cc_start: 0.6753 (m-40) cc_final: 0.6419 (m110) REVERT: 0 169 LYS cc_start: 0.8075 (ptmm) cc_final: 0.7859 (ttpt) REVERT: 1 56 ARG cc_start: 0.8098 (ptm160) cc_final: 0.5361 (mpt180) REVERT: 1 139 LYS cc_start: 0.7835 (ptpt) cc_final: 0.7601 (mmtp) REVERT: 3 143 MET cc_start: 0.8567 (mmp) cc_final: 0.8262 (mmt) REVERT: 3 185 GLU cc_start: 0.6954 (tt0) cc_final: 0.6674 (tt0) REVERT: 4 37 ILE cc_start: 0.7265 (pt) cc_final: 0.6646 (mt) REVERT: 4 198 ARG cc_start: 0.7673 (ttt-90) cc_final: 0.7177 (ttt180) REVERT: 5 114 MET cc_start: 0.8741 (tpt) cc_final: 0.8376 (tpt) REVERT: 5 138 ILE cc_start: 0.8241 (mm) cc_final: 0.7912 (mt) REVERT: 5 209 LYS cc_start: 0.8601 (OUTLIER) cc_final: 0.7950 (mtmm) REVERT: 6 20 LYS cc_start: 0.8783 (mttm) cc_final: 0.8439 (mttp) REVERT: 6 87 LYS cc_start: 0.8347 (mtmt) cc_final: 0.7860 (mttm) REVERT: 6 117 GLU cc_start: 0.8468 (OUTLIER) cc_final: 0.8252 (pm20) REVERT: 7 137 TYR cc_start: 0.7970 (t80) cc_final: 0.7461 (t80) REVERT: 7 146 LYS cc_start: 0.7121 (mtmm) cc_final: 0.6218 (mtpp) REVERT: 7 183 GLU cc_start: 0.7810 (tt0) cc_final: 0.7550 (tt0) REVERT: 8 48 MET cc_start: 0.8549 (mtp) cc_final: 0.8087 (mtt) REVERT: 8 56 ARG cc_start: 0.7974 (ptm160) cc_final: 0.5562 (mpt180) REVERT: a 108 ASN cc_start: 0.8228 (m110) cc_final: 0.7918 (m110) REVERT: a 218 LEU cc_start: 0.8728 (OUTLIER) cc_final: 0.8313 (mp) REVERT: a 254 ASP cc_start: 0.7806 (m-30) cc_final: 0.7462 (m-30) REVERT: d 37 ILE cc_start: 0.7370 (pt) cc_final: 0.6790 (mt) REVERT: d 68 GLN cc_start: 0.7967 (mm-40) cc_final: 0.7476 (mt0) REVERT: d 198 ARG cc_start: 0.7967 (ttt-90) cc_final: 0.7665 (ttt180) REVERT: e 33 ASP cc_start: 0.6824 (t70) cc_final: 0.6344 (p0) REVERT: e 56 MET cc_start: 0.8441 (mtm) cc_final: 0.8211 (mtm) REVERT: e 88 ARG cc_start: 0.6556 (OUTLIER) cc_final: 0.6327 (mpt180) REVERT: e 102 MET cc_start: 0.7762 (mmt) cc_final: 0.6996 (mmm) REVERT: e 108 THR cc_start: 0.7802 (OUTLIER) cc_final: 0.7439 (p) REVERT: e 114 MET cc_start: 0.8853 (tpt) cc_final: 0.8518 (tpp) REVERT: e 138 ILE cc_start: 0.8206 (mm) cc_final: 0.7826 (mt) REVERT: e 299 MET cc_start: 0.8394 (tmm) cc_final: 0.8001 (tmm) outliers start: 168 outliers final: 113 residues processed: 1130 average time/residue: 0.7789 time to fit residues: 1487.8328 Evaluate side-chains 1080 residues out of total 7134 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 128 poor density : 952 time to evaluate : 7.086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 SER Chi-restraints excluded: chain M residue 57 THR Chi-restraints excluded: chain M residue 74 LEU Chi-restraints excluded: chain M residue 82 GLU Chi-restraints excluded: chain M residue 105 SER Chi-restraints excluded: chain M residue 107 THR Chi-restraints excluded: chain M residue 221 THR Chi-restraints excluded: chain G residue 39 THR Chi-restraints excluded: chain G residue 71 GLU Chi-restraints excluded: chain G residue 100 THR Chi-restraints excluded: chain S residue 199 ASN Chi-restraints excluded: chain S residue 215 SER Chi-restraints excluded: chain S residue 218 LEU Chi-restraints excluded: chain S residue 251 VAL Chi-restraints excluded: chain b residue 197 ILE Chi-restraints excluded: chain b residue 203 SER Chi-restraints excluded: chain c residue 98 THR Chi-restraints excluded: chain c residue 191 THR Chi-restraints excluded: chain B residue 15 VAL Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain B residue 117 GLU Chi-restraints excluded: chain C residue 57 THR Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 82 GLU Chi-restraints excluded: chain C residue 105 SER Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain D residue 39 THR Chi-restraints excluded: chain D residue 100 THR Chi-restraints excluded: chain E residue 550 VAL Chi-restraints excluded: chain F residue 47 MET Chi-restraints excluded: chain F residue 97 ILE Chi-restraints excluded: chain F residue 198 GLU Chi-restraints excluded: chain F residue 215 SER Chi-restraints excluded: chain F residue 233 SER Chi-restraints excluded: chain F residue 251 VAL Chi-restraints excluded: chain H residue 131 LEU Chi-restraints excluded: chain I residue 98 THR Chi-restraints excluded: chain I residue 191 THR Chi-restraints excluded: chain I residue 209 LYS Chi-restraints excluded: chain I residue 264 THR Chi-restraints excluded: chain J residue 15 VAL Chi-restraints excluded: chain J residue 117 GLU Chi-restraints excluded: chain K residue 57 THR Chi-restraints excluded: chain K residue 82 GLU Chi-restraints excluded: chain K residue 98 THR Chi-restraints excluded: chain K residue 107 THR Chi-restraints excluded: chain K residue 216 ILE Chi-restraints excluded: chain K residue 221 THR Chi-restraints excluded: chain L residue 61 ILE Chi-restraints excluded: chain L residue 100 THR Chi-restraints excluded: chain N residue 550 VAL Chi-restraints excluded: chain O residue 53 ASP Chi-restraints excluded: chain O residue 153 LYS Chi-restraints excluded: chain O residue 215 SER Chi-restraints excluded: chain O residue 218 LEU Chi-restraints excluded: chain O residue 233 SER Chi-restraints excluded: chain O residue 251 VAL Chi-restraints excluded: chain P residue 203 SER Chi-restraints excluded: chain P residue 215 LYS Chi-restraints excluded: chain Q residue 88 ARG Chi-restraints excluded: chain Q residue 98 THR Chi-restraints excluded: chain Q residue 108 THR Chi-restraints excluded: chain Q residue 209 LYS Chi-restraints excluded: chain Q residue 288 LEU Chi-restraints excluded: chain R residue 137 SER Chi-restraints excluded: chain T residue 57 THR Chi-restraints excluded: chain T residue 74 LEU Chi-restraints excluded: chain T residue 82 GLU Chi-restraints excluded: chain T residue 105 SER Chi-restraints excluded: chain T residue 107 THR Chi-restraints excluded: chain T residue 221 THR Chi-restraints excluded: chain U residue 39 THR Chi-restraints excluded: chain U residue 71 GLU Chi-restraints excluded: chain U residue 100 THR Chi-restraints excluded: chain W residue 215 SER Chi-restraints excluded: chain W residue 218 LEU Chi-restraints excluded: chain W residue 251 VAL Chi-restraints excluded: chain X residue 197 ILE Chi-restraints excluded: chain X residue 203 SER Chi-restraints excluded: chain Y residue 98 THR Chi-restraints excluded: chain Y residue 191 THR Chi-restraints excluded: chain Z residue 15 VAL Chi-restraints excluded: chain Z residue 76 LEU Chi-restraints excluded: chain Z residue 117 GLU Chi-restraints excluded: chain 0 residue 57 THR Chi-restraints excluded: chain 0 residue 58 VAL Chi-restraints excluded: chain 0 residue 82 GLU Chi-restraints excluded: chain 0 residue 105 SER Chi-restraints excluded: chain 0 residue 107 THR Chi-restraints excluded: chain 1 residue 39 THR Chi-restraints excluded: chain 1 residue 100 THR Chi-restraints excluded: chain 2 residue 550 VAL Chi-restraints excluded: chain 3 residue 47 MET Chi-restraints excluded: chain 3 residue 97 ILE Chi-restraints excluded: chain 3 residue 153 LYS Chi-restraints excluded: chain 3 residue 198 GLU Chi-restraints excluded: chain 3 residue 215 SER Chi-restraints excluded: chain 3 residue 233 SER Chi-restraints excluded: chain 3 residue 251 VAL Chi-restraints excluded: chain 4 residue 131 LEU Chi-restraints excluded: chain 5 residue 98 THR Chi-restraints excluded: chain 5 residue 191 THR Chi-restraints excluded: chain 5 residue 209 LYS Chi-restraints excluded: chain 5 residue 264 THR Chi-restraints excluded: chain 6 residue 15 VAL Chi-restraints excluded: chain 6 residue 117 GLU Chi-restraints excluded: chain 7 residue 57 THR Chi-restraints excluded: chain 7 residue 82 GLU Chi-restraints excluded: chain 7 residue 98 THR Chi-restraints excluded: chain 7 residue 107 THR Chi-restraints excluded: chain 7 residue 216 ILE Chi-restraints excluded: chain 7 residue 221 THR Chi-restraints excluded: chain 8 residue 61 ILE Chi-restraints excluded: chain 8 residue 100 THR Chi-restraints excluded: chain 9 residue 550 VAL Chi-restraints excluded: chain a residue 53 ASP Chi-restraints excluded: chain a residue 153 LYS Chi-restraints excluded: chain a residue 215 SER Chi-restraints excluded: chain a residue 218 LEU Chi-restraints excluded: chain a residue 233 SER Chi-restraints excluded: chain a residue 251 VAL Chi-restraints excluded: chain d residue 196 MET Chi-restraints excluded: chain d residue 203 SER Chi-restraints excluded: chain d residue 215 LYS Chi-restraints excluded: chain e residue 88 ARG Chi-restraints excluded: chain e residue 98 THR Chi-restraints excluded: chain e residue 108 THR Chi-restraints excluded: chain e residue 288 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 786 random chunks: chunk 706 optimal weight: 7.9990 chunk 537 optimal weight: 1.9990 chunk 371 optimal weight: 0.9980 chunk 79 optimal weight: 10.0000 chunk 341 optimal weight: 4.9990 chunk 480 optimal weight: 5.9990 chunk 717 optimal weight: 2.9990 chunk 759 optimal weight: 1.9990 chunk 374 optimal weight: 1.9990 chunk 680 optimal weight: 4.9990 chunk 204 optimal weight: 5.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 81 GLN r 551 GLN c 62 GLN c 68 GLN ** F 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 28 ASN H 63 ASN I 62 GLN J 72 ASN N 519 ASN ** O 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 81 GLN V 551 GLN Y 62 GLN Y 68 GLN 4 28 ASN 4 63 ASN 6 72 ASN 7 159 ASN 9 519 ASN ** a 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 100 HIS Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7505 moved from start: 0.2605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 66918 Z= 0.189 Angle : 0.519 7.030 90600 Z= 0.280 Chirality : 0.044 0.147 9960 Planarity : 0.004 0.040 11694 Dihedral : 5.612 49.454 8898 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 3.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Rotamer: Outliers : 1.67 % Allowed : 11.68 % Favored : 86.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 0.07 (0.09), residues: 8010 helix: 1.09 (0.13), residues: 1614 sheet: -0.10 (0.11), residues: 2286 loop : -0.18 (0.09), residues: 4110 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP H 217 HIS 0.007 0.001 HIS 5 77 PHE 0.023 0.001 PHE M 149 TYR 0.012 0.001 TYR L 115 ARG 0.004 0.000 ARG e 81 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16020 Ramachandran restraints generated. 8010 Oldfield, 0 Emsley, 8010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16020 Ramachandran restraints generated. 8010 Oldfield, 0 Emsley, 8010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1171 residues out of total 7134 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 119 poor density : 1052 time to evaluate : 5.630 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 20 LYS cc_start: 0.8696 (mttm) cc_final: 0.8365 (mttp) REVERT: A 31 SER cc_start: 0.8693 (t) cc_final: 0.8361 (m) REVERT: A 48 MET cc_start: 0.8891 (mmm) cc_final: 0.8404 (mmm) REVERT: M 137 TYR cc_start: 0.7654 (t80) cc_final: 0.7312 (t80) REVERT: M 146 LYS cc_start: 0.7061 (mtmm) cc_final: 0.6114 (mmtt) REVERT: M 154 ASN cc_start: 0.6386 (m-40) cc_final: 0.6145 (m110) REVERT: M 159 ASN cc_start: 0.7410 (t0) cc_final: 0.7162 (t0) REVERT: M 183 GLU cc_start: 0.7631 (tt0) cc_final: 0.7363 (tt0) REVERT: G 18 MET cc_start: 0.7957 (mtp) cc_final: 0.7617 (mtp) REVERT: G 48 MET cc_start: 0.8479 (mtp) cc_final: 0.8081 (mtt) REVERT: G 56 ARG cc_start: 0.7963 (ptm160) cc_final: 0.5523 (mpt180) REVERT: G 71 GLU cc_start: 0.7293 (OUTLIER) cc_final: 0.6764 (pm20) REVERT: S 254 ASP cc_start: 0.7968 (m-30) cc_final: 0.7697 (m-30) REVERT: b 37 ILE cc_start: 0.7640 (pt) cc_final: 0.6874 (mt) REVERT: b 44 ASP cc_start: 0.8174 (m-30) cc_final: 0.7556 (m-30) REVERT: b 196 MET cc_start: 0.7277 (mmm) cc_final: 0.6852 (tpp) REVERT: b 208 ARG cc_start: 0.7206 (ptt-90) cc_final: 0.6841 (ptp90) REVERT: c 62 GLN cc_start: 0.7403 (tt0) cc_final: 0.7187 (tt0) REVERT: c 93 SER cc_start: 0.8460 (t) cc_final: 0.8214 (t) REVERT: c 138 ILE cc_start: 0.8231 (mm) cc_final: 0.7877 (mt) REVERT: c 285 LYS cc_start: 0.7376 (ttpt) cc_final: 0.6680 (tmmt) REVERT: B 20 LYS cc_start: 0.8755 (mttm) cc_final: 0.8498 (mttp) REVERT: C 24 ASN cc_start: 0.7683 (t0) cc_final: 0.7006 (m-40) REVERT: C 137 TYR cc_start: 0.7889 (t80) cc_final: 0.7667 (t80) REVERT: C 169 LYS cc_start: 0.8066 (ptmm) cc_final: 0.7823 (ttpt) REVERT: C 251 LYS cc_start: 0.8581 (ttpp) cc_final: 0.8305 (ttpp) REVERT: D 56 ARG cc_start: 0.8058 (ptm160) cc_final: 0.5354 (mpt180) REVERT: D 101 LYS cc_start: 0.7999 (mptt) cc_final: 0.7769 (mmtt) REVERT: F 70 ASN cc_start: 0.8293 (t0) cc_final: 0.8090 (t0) REVERT: F 143 MET cc_start: 0.8531 (mmp) cc_final: 0.8176 (mmt) REVERT: F 153 LYS cc_start: 0.8249 (tttm) cc_final: 0.7793 (pttt) REVERT: F 185 GLU cc_start: 0.6960 (tt0) cc_final: 0.6697 (tt0) REVERT: H 37 ILE cc_start: 0.7315 (pt) cc_final: 0.6694 (mt) REVERT: H 68 GLN cc_start: 0.8144 (mm-40) cc_final: 0.6944 (mp10) REVERT: H 88 ARG cc_start: 0.7527 (mmp80) cc_final: 0.6689 (mmt-90) REVERT: H 198 ARG cc_start: 0.7660 (ttt-90) cc_final: 0.7285 (ttt180) REVERT: H 225 GLN cc_start: 0.7035 (tt0) cc_final: 0.6805 (tt0) REVERT: I 88 ARG cc_start: 0.7265 (OUTLIER) cc_final: 0.6858 (mtm-85) REVERT: I 110 PHE cc_start: 0.8046 (t80) cc_final: 0.7711 (t80) REVERT: I 114 MET cc_start: 0.8739 (tpt) cc_final: 0.8060 (tpt) REVERT: I 138 ILE cc_start: 0.8186 (mm) cc_final: 0.7840 (mt) REVERT: I 209 LYS cc_start: 0.8593 (OUTLIER) cc_final: 0.7946 (mtmm) REVERT: J 20 LYS cc_start: 0.8735 (mttm) cc_final: 0.8426 (mttp) REVERT: J 61 ILE cc_start: 0.8228 (OUTLIER) cc_final: 0.7953 (tp) REVERT: J 87 LYS cc_start: 0.8256 (mtmt) cc_final: 0.7806 (mttm) REVERT: K 137 TYR cc_start: 0.7981 (t80) cc_final: 0.7521 (t80) REVERT: K 146 LYS cc_start: 0.6973 (mtmm) cc_final: 0.5920 (mmtt) REVERT: K 183 GLU cc_start: 0.7627 (tt0) cc_final: 0.7138 (tt0) REVERT: K 184 GLU cc_start: 0.7804 (tt0) cc_final: 0.7455 (tt0) REVERT: K 251 LYS cc_start: 0.8334 (ttpp) cc_final: 0.7935 (tttp) REVERT: L 6 LYS cc_start: 0.8213 (mtpt) cc_final: 0.7826 (mtpp) REVERT: L 56 ARG cc_start: 0.7987 (ptm160) cc_final: 0.5626 (mpt180) REVERT: L 99 LEU cc_start: 0.7548 (tp) cc_final: 0.7043 (mp) REVERT: N 555 GLU cc_start: 0.6477 (tt0) cc_final: 0.5839 (pt0) REVERT: O 108 ASN cc_start: 0.8092 (m110) cc_final: 0.7788 (m110) REVERT: O 254 ASP cc_start: 0.7718 (m-30) cc_final: 0.7385 (m-30) REVERT: P 37 ILE cc_start: 0.7313 (pt) cc_final: 0.6739 (mt) REVERT: P 68 GLN cc_start: 0.7932 (mm-40) cc_final: 0.6962 (mp10) REVERT: P 198 ARG cc_start: 0.7975 (ttt-90) cc_final: 0.7537 (ttt180) REVERT: Q 33 ASP cc_start: 0.6771 (t70) cc_final: 0.6187 (p0) REVERT: Q 102 MET cc_start: 0.7638 (mmt) cc_final: 0.7300 (mmm) REVERT: Q 108 THR cc_start: 0.7773 (m) cc_final: 0.7510 (p) REVERT: Q 138 ILE cc_start: 0.8172 (mm) cc_final: 0.7785 (mt) REVERT: Q 191 THR cc_start: 0.7623 (m) cc_final: 0.7411 (p) REVERT: Q 269 MET cc_start: 0.7106 (tpp) cc_final: 0.6760 (mtm) REVERT: Q 299 MET cc_start: 0.8375 (tmm) cc_final: 0.7920 (tmm) REVERT: R 20 LYS cc_start: 0.8699 (mttm) cc_final: 0.8366 (mttp) REVERT: R 31 SER cc_start: 0.8685 (t) cc_final: 0.8352 (m) REVERT: R 48 MET cc_start: 0.8890 (mmm) cc_final: 0.8402 (mmm) REVERT: T 137 TYR cc_start: 0.7655 (t80) cc_final: 0.7312 (t80) REVERT: T 146 LYS cc_start: 0.7064 (mtmm) cc_final: 0.6114 (mmtt) REVERT: T 154 ASN cc_start: 0.6383 (m-40) cc_final: 0.6145 (m110) REVERT: T 159 ASN cc_start: 0.7413 (t0) cc_final: 0.7167 (t0) REVERT: T 183 GLU cc_start: 0.7638 (tt0) cc_final: 0.7373 (tt0) REVERT: U 18 MET cc_start: 0.7958 (mtp) cc_final: 0.7618 (mtp) REVERT: U 48 MET cc_start: 0.8482 (mtp) cc_final: 0.8083 (mtt) REVERT: U 56 ARG cc_start: 0.7965 (ptm160) cc_final: 0.5524 (mpt180) REVERT: U 71 GLU cc_start: 0.7282 (OUTLIER) cc_final: 0.6756 (pm20) REVERT: W 254 ASP cc_start: 0.7970 (m-30) cc_final: 0.7702 (m-30) REVERT: X 37 ILE cc_start: 0.7642 (pt) cc_final: 0.6881 (mt) REVERT: X 44 ASP cc_start: 0.8175 (m-30) cc_final: 0.7560 (m-30) REVERT: X 88 ARG cc_start: 0.7365 (mmp80) cc_final: 0.7028 (mmt-90) REVERT: X 196 MET cc_start: 0.7277 (mmm) cc_final: 0.6854 (tpp) REVERT: X 208 ARG cc_start: 0.7216 (ptt-90) cc_final: 0.6845 (ptp90) REVERT: Y 62 GLN cc_start: 0.7400 (tt0) cc_final: 0.7186 (tt0) REVERT: Y 93 SER cc_start: 0.8460 (t) cc_final: 0.8218 (t) REVERT: Y 138 ILE cc_start: 0.8228 (mm) cc_final: 0.7876 (mt) REVERT: Y 285 LYS cc_start: 0.7374 (ttpt) cc_final: 0.6677 (tmmt) REVERT: Z 20 LYS cc_start: 0.8754 (mttm) cc_final: 0.8496 (mttp) REVERT: 0 24 ASN cc_start: 0.7591 (t0) cc_final: 0.6969 (m-40) REVERT: 0 137 TYR cc_start: 0.7889 (t80) cc_final: 0.7665 (t80) REVERT: 0 169 LYS cc_start: 0.8062 (ptmm) cc_final: 0.7823 (ttpt) REVERT: 0 251 LYS cc_start: 0.8573 (ttpp) cc_final: 0.8313 (ttpp) REVERT: 1 56 ARG cc_start: 0.8059 (ptm160) cc_final: 0.5360 (mpt180) REVERT: 1 101 LYS cc_start: 0.8001 (mptt) cc_final: 0.7769 (mmtt) REVERT: 3 70 ASN cc_start: 0.8295 (t0) cc_final: 0.8091 (t0) REVERT: 3 143 MET cc_start: 0.8528 (mmp) cc_final: 0.8174 (mmt) REVERT: 3 185 GLU cc_start: 0.6964 (tt0) cc_final: 0.6699 (tt0) REVERT: 4 37 ILE cc_start: 0.7319 (pt) cc_final: 0.6691 (mt) REVERT: 4 68 GLN cc_start: 0.8144 (mm-40) cc_final: 0.6943 (mp10) REVERT: 4 88 ARG cc_start: 0.7524 (mmp80) cc_final: 0.6684 (mmt-90) REVERT: 4 198 ARG cc_start: 0.7666 (ttt-90) cc_final: 0.7293 (ttt180) REVERT: 4 225 GLN cc_start: 0.7039 (tt0) cc_final: 0.6809 (tt0) REVERT: 5 88 ARG cc_start: 0.7262 (OUTLIER) cc_final: 0.6859 (mtm-85) REVERT: 5 110 PHE cc_start: 0.8039 (t80) cc_final: 0.7705 (t80) REVERT: 5 114 MET cc_start: 0.8736 (tpt) cc_final: 0.8054 (tpt) REVERT: 5 138 ILE cc_start: 0.8184 (mm) cc_final: 0.7840 (mt) REVERT: 5 209 LYS cc_start: 0.8601 (OUTLIER) cc_final: 0.7948 (mtmm) REVERT: 6 20 LYS cc_start: 0.8736 (mttm) cc_final: 0.8429 (mttp) REVERT: 6 61 ILE cc_start: 0.8244 (OUTLIER) cc_final: 0.7963 (tp) REVERT: 6 87 LYS cc_start: 0.8255 (mtmt) cc_final: 0.7805 (mttm) REVERT: 7 137 TYR cc_start: 0.7980 (t80) cc_final: 0.7522 (t80) REVERT: 7 146 LYS cc_start: 0.6974 (mtmm) cc_final: 0.5921 (mmtt) REVERT: 7 159 ASN cc_start: 0.7320 (OUTLIER) cc_final: 0.7093 (t0) REVERT: 7 183 GLU cc_start: 0.7595 (tt0) cc_final: 0.7094 (tt0) REVERT: 7 251 LYS cc_start: 0.8337 (ttpp) cc_final: 0.7939 (tttp) REVERT: 8 56 ARG cc_start: 0.7987 (ptm160) cc_final: 0.5626 (mpt180) REVERT: 8 99 LEU cc_start: 0.7553 (tp) cc_final: 0.7047 (mp) REVERT: 9 555 GLU cc_start: 0.6482 (tt0) cc_final: 0.5842 (pt0) REVERT: a 108 ASN cc_start: 0.8093 (m110) cc_final: 0.7789 (m110) REVERT: a 254 ASP cc_start: 0.7729 (m-30) cc_final: 0.7391 (m-30) REVERT: d 37 ILE cc_start: 0.7318 (pt) cc_final: 0.6746 (mt) REVERT: d 68 GLN cc_start: 0.7937 (mm-40) cc_final: 0.6963 (mp10) REVERT: d 198 ARG cc_start: 0.7998 (ttt-90) cc_final: 0.7614 (ttt180) REVERT: e 33 ASP cc_start: 0.6772 (t70) cc_final: 0.6185 (p0) REVERT: e 102 MET cc_start: 0.7636 (mmt) cc_final: 0.7300 (mmm) REVERT: e 108 THR cc_start: 0.7780 (m) cc_final: 0.7519 (p) REVERT: e 138 ILE cc_start: 0.8172 (mm) cc_final: 0.7785 (mt) REVERT: e 191 THR cc_start: 0.7623 (m) cc_final: 0.7411 (p) REVERT: e 209 LYS cc_start: 0.8306 (OUTLIER) cc_final: 0.7473 (mtmm) REVERT: e 269 MET cc_start: 0.7114 (tpp) cc_final: 0.6769 (mtm) REVERT: e 299 MET cc_start: 0.8380 (tmm) cc_final: 0.7925 (tmm) outliers start: 119 outliers final: 81 residues processed: 1126 average time/residue: 0.7888 time to fit residues: 1479.8160 Evaluate side-chains 1080 residues out of total 7134 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 989 time to evaluate : 6.906 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 VAL Chi-restraints excluded: chain M residue 24 ASN Chi-restraints excluded: chain M residue 105 SER Chi-restraints excluded: chain M residue 221 THR Chi-restraints excluded: chain G residue 71 GLU Chi-restraints excluded: chain G residue 118 THR Chi-restraints excluded: chain G residue 121 THR Chi-restraints excluded: chain c residue 98 THR Chi-restraints excluded: chain c residue 191 THR Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 117 GLU Chi-restraints excluded: chain C residue 48 CYS Chi-restraints excluded: chain C residue 74 LEU Chi-restraints excluded: chain C residue 82 GLU Chi-restraints excluded: chain C residue 149 PHE Chi-restraints excluded: chain C residue 221 THR Chi-restraints excluded: chain D residue 39 THR Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain E residue 550 VAL Chi-restraints excluded: chain F residue 233 SER Chi-restraints excluded: chain H residue 20 GLU Chi-restraints excluded: chain H residue 131 LEU Chi-restraints excluded: chain I residue 88 ARG Chi-restraints excluded: chain I residue 98 THR Chi-restraints excluded: chain I residue 191 THR Chi-restraints excluded: chain I residue 209 LYS Chi-restraints excluded: chain J residue 61 ILE Chi-restraints excluded: chain K residue 45 GLU Chi-restraints excluded: chain K residue 48 CYS Chi-restraints excluded: chain K residue 57 THR Chi-restraints excluded: chain K residue 82 GLU Chi-restraints excluded: chain K residue 216 ILE Chi-restraints excluded: chain K residue 221 THR Chi-restraints excluded: chain L residue 61 ILE Chi-restraints excluded: chain L residue 118 THR Chi-restraints excluded: chain L residue 121 THR Chi-restraints excluded: chain N residue 550 VAL Chi-restraints excluded: chain O residue 53 ASP Chi-restraints excluded: chain O residue 153 LYS Chi-restraints excluded: chain O residue 154 ASP Chi-restraints excluded: chain O residue 233 SER Chi-restraints excluded: chain P residue 215 LYS Chi-restraints excluded: chain Q residue 98 THR Chi-restraints excluded: chain Q residue 288 LEU Chi-restraints excluded: chain R residue 15 VAL Chi-restraints excluded: chain T residue 24 ASN Chi-restraints excluded: chain T residue 105 SER Chi-restraints excluded: chain T residue 221 THR Chi-restraints excluded: chain U residue 71 GLU Chi-restraints excluded: chain U residue 118 THR Chi-restraints excluded: chain U residue 121 THR Chi-restraints excluded: chain Y residue 98 THR Chi-restraints excluded: chain Y residue 191 THR Chi-restraints excluded: chain Z residue 8 THR Chi-restraints excluded: chain Z residue 117 GLU Chi-restraints excluded: chain 0 residue 48 CYS Chi-restraints excluded: chain 0 residue 74 LEU Chi-restraints excluded: chain 0 residue 82 GLU Chi-restraints excluded: chain 0 residue 149 PHE Chi-restraints excluded: chain 0 residue 221 THR Chi-restraints excluded: chain 1 residue 39 THR Chi-restraints excluded: chain 1 residue 121 THR Chi-restraints excluded: chain 2 residue 550 VAL Chi-restraints excluded: chain 3 residue 153 LYS Chi-restraints excluded: chain 3 residue 233 SER Chi-restraints excluded: chain 4 residue 20 GLU Chi-restraints excluded: chain 4 residue 131 LEU Chi-restraints excluded: chain 5 residue 88 ARG Chi-restraints excluded: chain 5 residue 98 THR Chi-restraints excluded: chain 5 residue 191 THR Chi-restraints excluded: chain 5 residue 209 LYS Chi-restraints excluded: chain 6 residue 61 ILE Chi-restraints excluded: chain 7 residue 45 GLU Chi-restraints excluded: chain 7 residue 48 CYS Chi-restraints excluded: chain 7 residue 57 THR Chi-restraints excluded: chain 7 residue 82 GLU Chi-restraints excluded: chain 7 residue 159 ASN Chi-restraints excluded: chain 7 residue 216 ILE Chi-restraints excluded: chain 7 residue 221 THR Chi-restraints excluded: chain 8 residue 61 ILE Chi-restraints excluded: chain 8 residue 118 THR Chi-restraints excluded: chain 8 residue 121 THR Chi-restraints excluded: chain 9 residue 550 VAL Chi-restraints excluded: chain a residue 53 ASP Chi-restraints excluded: chain a residue 153 LYS Chi-restraints excluded: chain a residue 154 ASP Chi-restraints excluded: chain a residue 233 SER Chi-restraints excluded: chain d residue 215 LYS Chi-restraints excluded: chain e residue 98 THR Chi-restraints excluded: chain e residue 209 LYS Chi-restraints excluded: chain e residue 288 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 786 random chunks: chunk 632 optimal weight: 7.9990 chunk 431 optimal weight: 1.9990 chunk 11 optimal weight: 9.9990 chunk 565 optimal weight: 9.9990 chunk 313 optimal weight: 9.9990 chunk 648 optimal weight: 10.0000 chunk 525 optimal weight: 0.6980 chunk 0 optimal weight: 10.0000 chunk 387 optimal weight: 10.0000 chunk 681 optimal weight: 9.9990 chunk 191 optimal weight: 10.0000 overall best weight: 6.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 81 GLN r 551 GLN c 68 GLN C 154 ASN D 10 HIS H 28 ASN H 39 ASN J 13 ASN ** O 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 81 GLN V 551 GLN Y 68 GLN 0 154 ASN 1 10 HIS 4 28 ASN 4 39 ASN 6 13 ASN ** a 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 100 HIS Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7557 moved from start: 0.2840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.055 66918 Z= 0.454 Angle : 0.630 8.715 90600 Z= 0.336 Chirality : 0.048 0.154 9960 Planarity : 0.005 0.045 11694 Dihedral : 5.821 53.883 8898 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 3.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 2.87 % Allowed : 12.73 % Favored : 84.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -0.28 (0.09), residues: 8010 helix: 0.65 (0.12), residues: 1674 sheet: -0.26 (0.11), residues: 2244 loop : -0.39 (0.09), residues: 4092 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP S 60 HIS 0.013 0.002 HIS Y 77 PHE 0.023 0.002 PHE M 149 TYR 0.016 0.002 TYR K 157 ARG 0.007 0.001 ARG Q 81 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16020 Ramachandran restraints generated. 8010 Oldfield, 0 Emsley, 8010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16020 Ramachandran restraints generated. 8010 Oldfield, 0 Emsley, 8010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1176 residues out of total 7134 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 205 poor density : 971 time to evaluate : 7.230 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 LYS cc_start: 0.8857 (mttm) cc_final: 0.8533 (mttp) REVERT: A 31 SER cc_start: 0.8737 (t) cc_final: 0.8419 (m) REVERT: A 48 MET cc_start: 0.8844 (mmm) cc_final: 0.8308 (mmm) REVERT: M 70 GLU cc_start: 0.7836 (tt0) cc_final: 0.7538 (tt0) REVERT: M 137 TYR cc_start: 0.7833 (t80) cc_final: 0.7458 (t80) REVERT: M 146 LYS cc_start: 0.7102 (mtmm) cc_final: 0.6163 (mmtt) REVERT: M 154 ASN cc_start: 0.6820 (m-40) cc_final: 0.6484 (m110) REVERT: M 157 TYR cc_start: 0.7287 (m-80) cc_final: 0.7002 (m-80) REVERT: M 159 ASN cc_start: 0.7398 (t0) cc_final: 0.7174 (t0) REVERT: M 183 GLU cc_start: 0.7723 (tt0) cc_final: 0.7445 (tt0) REVERT: G 18 MET cc_start: 0.8080 (mtp) cc_final: 0.7770 (mtp) REVERT: G 26 ARG cc_start: 0.8475 (OUTLIER) cc_final: 0.8265 (mmt-90) REVERT: G 48 MET cc_start: 0.8392 (mtp) cc_final: 0.8044 (mtt) REVERT: G 56 ARG cc_start: 0.8088 (ptm160) cc_final: 0.5344 (mpt180) REVERT: G 71 GLU cc_start: 0.7427 (OUTLIER) cc_final: 0.7030 (pm20) REVERT: S 98 MET cc_start: 0.9012 (ttp) cc_final: 0.8797 (ttm) REVERT: S 254 ASP cc_start: 0.7961 (m-30) cc_final: 0.7690 (m-30) REVERT: b 37 ILE cc_start: 0.7435 (pt) cc_final: 0.6697 (mt) REVERT: b 44 ASP cc_start: 0.7999 (m-30) cc_final: 0.7290 (m-30) REVERT: b 68 GLN cc_start: 0.7785 (mm-40) cc_final: 0.7583 (mt0) REVERT: b 234 GLU cc_start: 0.6808 (OUTLIER) cc_final: 0.6087 (mm-30) REVERT: c 112 SER cc_start: 0.7652 (m) cc_final: 0.7444 (m) REVERT: c 138 ILE cc_start: 0.8224 (mm) cc_final: 0.7868 (mt) REVERT: c 285 LYS cc_start: 0.7608 (ttpt) cc_final: 0.6895 (tmmt) REVERT: B 20 LYS cc_start: 0.8785 (mttm) cc_final: 0.8397 (mttp) REVERT: B 84 GLU cc_start: 0.8901 (OUTLIER) cc_final: 0.8683 (pm20) REVERT: C 24 ASN cc_start: 0.7596 (t0) cc_final: 0.7073 (m-40) REVERT: C 137 TYR cc_start: 0.7885 (t80) cc_final: 0.7643 (t80) REVERT: C 146 LYS cc_start: 0.7030 (mtmm) cc_final: 0.6002 (mmtp) REVERT: C 157 TYR cc_start: 0.7340 (m-80) cc_final: 0.7002 (m-80) REVERT: C 169 LYS cc_start: 0.8109 (ptmm) cc_final: 0.7856 (ttpt) REVERT: D 26 ARG cc_start: 0.8466 (OUTLIER) cc_final: 0.8000 (mmt90) REVERT: D 56 ARG cc_start: 0.8157 (ptm160) cc_final: 0.5396 (mpt180) REVERT: F 153 LYS cc_start: 0.8284 (tttm) cc_final: 0.7887 (pttt) REVERT: H 37 ILE cc_start: 0.7366 (pt) cc_final: 0.6644 (mt) REVERT: H 68 GLN cc_start: 0.8130 (mm-40) cc_final: 0.7002 (mp10) REVERT: H 198 ARG cc_start: 0.7712 (ttt-90) cc_final: 0.7383 (ttt180) REVERT: I 88 ARG cc_start: 0.7297 (OUTLIER) cc_final: 0.6812 (mtm-85) REVERT: I 114 MET cc_start: 0.8678 (tpt) cc_final: 0.8263 (tpp) REVERT: I 138 ILE cc_start: 0.8051 (mm) cc_final: 0.7717 (mt) REVERT: I 209 LYS cc_start: 0.8572 (OUTLIER) cc_final: 0.7948 (mtmm) REVERT: I 269 MET cc_start: 0.7016 (OUTLIER) cc_final: 0.6519 (tpt) REVERT: J 20 LYS cc_start: 0.8705 (mttm) cc_final: 0.8360 (mttp) REVERT: J 61 ILE cc_start: 0.8238 (OUTLIER) cc_final: 0.7941 (tp) REVERT: J 87 LYS cc_start: 0.8377 (mtmt) cc_final: 0.7885 (mttm) REVERT: J 117 GLU cc_start: 0.8440 (OUTLIER) cc_final: 0.8212 (pm20) REVERT: K 137 TYR cc_start: 0.7977 (t80) cc_final: 0.7486 (t80) REVERT: K 183 GLU cc_start: 0.7779 (tt0) cc_final: 0.7568 (tt0) REVERT: K 184 GLU cc_start: 0.7853 (tt0) cc_final: 0.7492 (tt0) REVERT: L 6 LYS cc_start: 0.8143 (mtpt) cc_final: 0.7790 (mtpp) REVERT: L 56 ARG cc_start: 0.8055 (ptm160) cc_final: 0.5583 (mpt180) REVERT: N 555 GLU cc_start: 0.6391 (tt0) cc_final: 0.5761 (pt0) REVERT: O 218 LEU cc_start: 0.8711 (OUTLIER) cc_final: 0.8280 (mp) REVERT: O 254 ASP cc_start: 0.7816 (m-30) cc_final: 0.7437 (m-30) REVERT: P 37 ILE cc_start: 0.7307 (pt) cc_final: 0.6737 (mt) REVERT: P 68 GLN cc_start: 0.7838 (mm-40) cc_final: 0.6929 (mp10) REVERT: P 198 ARG cc_start: 0.7980 (ttt-90) cc_final: 0.7611 (ttt180) REVERT: Q 33 ASP cc_start: 0.6557 (t70) cc_final: 0.6013 (p0) REVERT: Q 88 ARG cc_start: 0.7445 (mtm-85) cc_final: 0.6972 (mtm-85) REVERT: Q 102 MET cc_start: 0.7654 (mmt) cc_final: 0.7260 (mmm) REVERT: Q 108 THR cc_start: 0.7771 (m) cc_final: 0.7517 (p) REVERT: Q 138 ILE cc_start: 0.8049 (mm) cc_final: 0.7724 (mt) REVERT: Q 299 MET cc_start: 0.8334 (tmm) cc_final: 0.7957 (tmm) REVERT: R 20 LYS cc_start: 0.8858 (mttm) cc_final: 0.8511 (mttp) REVERT: R 31 SER cc_start: 0.8734 (t) cc_final: 0.8408 (m) REVERT: R 48 MET cc_start: 0.8856 (mmm) cc_final: 0.8321 (mmm) REVERT: T 137 TYR cc_start: 0.7834 (t80) cc_final: 0.7458 (t80) REVERT: T 146 LYS cc_start: 0.7102 (mtmm) cc_final: 0.6164 (mmtt) REVERT: T 154 ASN cc_start: 0.6817 (m-40) cc_final: 0.6481 (m110) REVERT: T 157 TYR cc_start: 0.7285 (m-80) cc_final: 0.7001 (m-80) REVERT: T 159 ASN cc_start: 0.7401 (t0) cc_final: 0.7178 (t0) REVERT: T 183 GLU cc_start: 0.7725 (tt0) cc_final: 0.7454 (tt0) REVERT: U 18 MET cc_start: 0.8081 (mtp) cc_final: 0.7770 (mtp) REVERT: U 26 ARG cc_start: 0.8479 (OUTLIER) cc_final: 0.8264 (mmt-90) REVERT: U 48 MET cc_start: 0.8397 (mtp) cc_final: 0.8048 (mtt) REVERT: U 56 ARG cc_start: 0.8090 (ptm160) cc_final: 0.5347 (mpt180) REVERT: U 71 GLU cc_start: 0.7422 (OUTLIER) cc_final: 0.7030 (pm20) REVERT: W 98 MET cc_start: 0.9018 (ttp) cc_final: 0.8803 (ttm) REVERT: W 254 ASP cc_start: 0.7960 (m-30) cc_final: 0.7689 (m-30) REVERT: X 37 ILE cc_start: 0.7439 (pt) cc_final: 0.6700 (mt) REVERT: X 44 ASP cc_start: 0.7996 (m-30) cc_final: 0.7288 (m-30) REVERT: X 68 GLN cc_start: 0.7784 (mm-40) cc_final: 0.7583 (mt0) REVERT: X 234 GLU cc_start: 0.6816 (OUTLIER) cc_final: 0.6088 (mm-30) REVERT: Y 112 SER cc_start: 0.7653 (m) cc_final: 0.7440 (m) REVERT: Y 138 ILE cc_start: 0.8223 (mm) cc_final: 0.7866 (mt) REVERT: Y 285 LYS cc_start: 0.7605 (ttpt) cc_final: 0.6891 (tmmt) REVERT: Z 20 LYS cc_start: 0.8784 (mttm) cc_final: 0.8398 (mttp) REVERT: Z 84 GLU cc_start: 0.8900 (OUTLIER) cc_final: 0.8682 (pm20) REVERT: 0 24 ASN cc_start: 0.7569 (t0) cc_final: 0.7001 (m-40) REVERT: 0 137 TYR cc_start: 0.7886 (t80) cc_final: 0.7643 (t80) REVERT: 0 146 LYS cc_start: 0.7031 (mtmm) cc_final: 0.6001 (mmtp) REVERT: 0 157 TYR cc_start: 0.7342 (m-80) cc_final: 0.7005 (m-80) REVERT: 0 169 LYS cc_start: 0.8104 (ptmm) cc_final: 0.7856 (ttpt) REVERT: 1 26 ARG cc_start: 0.8468 (OUTLIER) cc_final: 0.8002 (mmt90) REVERT: 1 56 ARG cc_start: 0.8161 (ptm160) cc_final: 0.5402 (mpt180) REVERT: 4 37 ILE cc_start: 0.7367 (pt) cc_final: 0.6640 (mt) REVERT: 4 68 GLN cc_start: 0.8130 (mm-40) cc_final: 0.7003 (mp10) REVERT: 4 198 ARG cc_start: 0.7717 (ttt-90) cc_final: 0.7387 (ttt180) REVERT: 5 88 ARG cc_start: 0.7298 (OUTLIER) cc_final: 0.6812 (mtm-85) REVERT: 5 114 MET cc_start: 0.8673 (tpt) cc_final: 0.8257 (tpp) REVERT: 5 138 ILE cc_start: 0.8051 (mm) cc_final: 0.7716 (mt) REVERT: 5 209 LYS cc_start: 0.8577 (OUTLIER) cc_final: 0.7949 (mtmm) REVERT: 5 269 MET cc_start: 0.7014 (OUTLIER) cc_final: 0.6510 (tpt) REVERT: 6 20 LYS cc_start: 0.8705 (mttm) cc_final: 0.8360 (mttp) REVERT: 6 61 ILE cc_start: 0.8243 (OUTLIER) cc_final: 0.7938 (tp) REVERT: 6 87 LYS cc_start: 0.8376 (mtmt) cc_final: 0.7885 (mttm) REVERT: 6 117 GLU cc_start: 0.8445 (OUTLIER) cc_final: 0.8216 (pm20) REVERT: 7 137 TYR cc_start: 0.7978 (t80) cc_final: 0.7487 (t80) REVERT: 7 183 GLU cc_start: 0.7736 (tt0) cc_final: 0.7527 (tt0) REVERT: 8 56 ARG cc_start: 0.8048 (ptm160) cc_final: 0.5572 (mpt180) REVERT: 9 555 GLU cc_start: 0.6375 (tt0) cc_final: 0.5755 (pt0) REVERT: a 218 LEU cc_start: 0.8724 (OUTLIER) cc_final: 0.8298 (mp) REVERT: a 254 ASP cc_start: 0.7828 (m-30) cc_final: 0.7446 (m-30) REVERT: d 37 ILE cc_start: 0.7309 (pt) cc_final: 0.6745 (mt) REVERT: d 68 GLN cc_start: 0.7849 (mm-40) cc_final: 0.6932 (mp10) REVERT: d 198 ARG cc_start: 0.7941 (ttt-90) cc_final: 0.7672 (ttt180) REVERT: e 33 ASP cc_start: 0.6555 (t70) cc_final: 0.6013 (p0) REVERT: e 88 ARG cc_start: 0.7444 (mtm-85) cc_final: 0.6968 (mtm-85) REVERT: e 102 MET cc_start: 0.7650 (mmt) cc_final: 0.7261 (mmm) REVERT: e 108 THR cc_start: 0.7772 (m) cc_final: 0.7519 (p) REVERT: e 138 ILE cc_start: 0.8049 (mm) cc_final: 0.7723 (mt) REVERT: e 209 LYS cc_start: 0.8221 (OUTLIER) cc_final: 0.7464 (mtmm) REVERT: e 299 MET cc_start: 0.8338 (tmm) cc_final: 0.7962 (tmm) outliers start: 205 outliers final: 141 residues processed: 1115 average time/residue: 0.7705 time to fit residues: 1448.7958 Evaluate side-chains 1099 residues out of total 7134 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 164 poor density : 935 time to evaluate : 7.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 VAL Chi-restraints excluded: chain A residue 84 GLU Chi-restraints excluded: chain A residue 137 SER Chi-restraints excluded: chain M residue 28 ILE Chi-restraints excluded: chain M residue 57 THR Chi-restraints excluded: chain M residue 74 LEU Chi-restraints excluded: chain M residue 105 SER Chi-restraints excluded: chain M residue 216 ILE Chi-restraints excluded: chain M residue 221 THR Chi-restraints excluded: chain G residue 26 ARG Chi-restraints excluded: chain G residue 71 GLU Chi-restraints excluded: chain G residue 100 THR Chi-restraints excluded: chain G residue 118 THR Chi-restraints excluded: chain G residue 121 THR Chi-restraints excluded: chain S residue 215 SER Chi-restraints excluded: chain S residue 251 VAL Chi-restraints excluded: chain b residue 197 ILE Chi-restraints excluded: chain b residue 203 SER Chi-restraints excluded: chain b residue 234 GLU Chi-restraints excluded: chain c residue 98 THR Chi-restraints excluded: chain c residue 191 THR Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 61 ILE Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain B residue 84 GLU Chi-restraints excluded: chain B residue 117 GLU Chi-restraints excluded: chain C residue 48 CYS Chi-restraints excluded: chain C residue 57 THR Chi-restraints excluded: chain C residue 74 LEU Chi-restraints excluded: chain C residue 82 GLU Chi-restraints excluded: chain C residue 149 PHE Chi-restraints excluded: chain C residue 221 THR Chi-restraints excluded: chain C residue 250 ILE Chi-restraints excluded: chain D residue 26 ARG Chi-restraints excluded: chain D residue 39 THR Chi-restraints excluded: chain D residue 100 THR Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain F residue 97 ILE Chi-restraints excluded: chain F residue 156 ILE Chi-restraints excluded: chain F residue 198 GLU Chi-restraints excluded: chain F residue 215 SER Chi-restraints excluded: chain F residue 233 SER Chi-restraints excluded: chain F residue 251 VAL Chi-restraints excluded: chain H residue 20 GLU Chi-restraints excluded: chain H residue 131 LEU Chi-restraints excluded: chain I residue 88 ARG Chi-restraints excluded: chain I residue 98 THR Chi-restraints excluded: chain I residue 191 THR Chi-restraints excluded: chain I residue 209 LYS Chi-restraints excluded: chain I residue 269 MET Chi-restraints excluded: chain J residue 61 ILE Chi-restraints excluded: chain J residue 117 GLU Chi-restraints excluded: chain K residue 25 CYS Chi-restraints excluded: chain K residue 45 GLU Chi-restraints excluded: chain K residue 48 CYS Chi-restraints excluded: chain K residue 57 THR Chi-restraints excluded: chain K residue 82 GLU Chi-restraints excluded: chain K residue 98 THR Chi-restraints excluded: chain K residue 107 THR Chi-restraints excluded: chain K residue 216 ILE Chi-restraints excluded: chain K residue 221 THR Chi-restraints excluded: chain L residue 61 ILE Chi-restraints excluded: chain L residue 100 THR Chi-restraints excluded: chain L residue 118 THR Chi-restraints excluded: chain L residue 121 THR Chi-restraints excluded: chain N residue 550 VAL Chi-restraints excluded: chain O residue 53 ASP Chi-restraints excluded: chain O residue 97 ILE Chi-restraints excluded: chain O residue 110 LEU Chi-restraints excluded: chain O residue 153 LYS Chi-restraints excluded: chain O residue 154 ASP Chi-restraints excluded: chain O residue 156 ILE Chi-restraints excluded: chain O residue 215 SER Chi-restraints excluded: chain O residue 218 LEU Chi-restraints excluded: chain O residue 233 SER Chi-restraints excluded: chain O residue 251 VAL Chi-restraints excluded: chain P residue 196 MET Chi-restraints excluded: chain P residue 203 SER Chi-restraints excluded: chain P residue 215 LYS Chi-restraints excluded: chain Q residue 98 THR Chi-restraints excluded: chain Q residue 288 LEU Chi-restraints excluded: chain R residue 15 VAL Chi-restraints excluded: chain R residue 84 GLU Chi-restraints excluded: chain R residue 137 SER Chi-restraints excluded: chain T residue 28 ILE Chi-restraints excluded: chain T residue 57 THR Chi-restraints excluded: chain T residue 74 LEU Chi-restraints excluded: chain T residue 105 SER Chi-restraints excluded: chain T residue 216 ILE Chi-restraints excluded: chain T residue 221 THR Chi-restraints excluded: chain U residue 26 ARG Chi-restraints excluded: chain U residue 71 GLU Chi-restraints excluded: chain U residue 100 THR Chi-restraints excluded: chain U residue 118 THR Chi-restraints excluded: chain U residue 121 THR Chi-restraints excluded: chain W residue 215 SER Chi-restraints excluded: chain W residue 251 VAL Chi-restraints excluded: chain X residue 197 ILE Chi-restraints excluded: chain X residue 203 SER Chi-restraints excluded: chain X residue 234 GLU Chi-restraints excluded: chain Y residue 98 THR Chi-restraints excluded: chain Y residue 191 THR Chi-restraints excluded: chain Z residue 8 THR Chi-restraints excluded: chain Z residue 61 ILE Chi-restraints excluded: chain Z residue 76 LEU Chi-restraints excluded: chain Z residue 84 GLU Chi-restraints excluded: chain Z residue 117 GLU Chi-restraints excluded: chain 0 residue 48 CYS Chi-restraints excluded: chain 0 residue 57 THR Chi-restraints excluded: chain 0 residue 74 LEU Chi-restraints excluded: chain 0 residue 82 GLU Chi-restraints excluded: chain 0 residue 149 PHE Chi-restraints excluded: chain 0 residue 221 THR Chi-restraints excluded: chain 0 residue 250 ILE Chi-restraints excluded: chain 1 residue 26 ARG Chi-restraints excluded: chain 1 residue 39 THR Chi-restraints excluded: chain 1 residue 100 THR Chi-restraints excluded: chain 1 residue 121 THR Chi-restraints excluded: chain 3 residue 97 ILE Chi-restraints excluded: chain 3 residue 153 LYS Chi-restraints excluded: chain 3 residue 156 ILE Chi-restraints excluded: chain 3 residue 198 GLU Chi-restraints excluded: chain 3 residue 215 SER Chi-restraints excluded: chain 3 residue 233 SER Chi-restraints excluded: chain 3 residue 251 VAL Chi-restraints excluded: chain 4 residue 20 GLU Chi-restraints excluded: chain 4 residue 131 LEU Chi-restraints excluded: chain 5 residue 88 ARG Chi-restraints excluded: chain 5 residue 98 THR Chi-restraints excluded: chain 5 residue 191 THR Chi-restraints excluded: chain 5 residue 209 LYS Chi-restraints excluded: chain 5 residue 269 MET Chi-restraints excluded: chain 6 residue 61 ILE Chi-restraints excluded: chain 6 residue 117 GLU Chi-restraints excluded: chain 7 residue 25 CYS Chi-restraints excluded: chain 7 residue 45 GLU Chi-restraints excluded: chain 7 residue 48 CYS Chi-restraints excluded: chain 7 residue 57 THR Chi-restraints excluded: chain 7 residue 82 GLU Chi-restraints excluded: chain 7 residue 98 THR Chi-restraints excluded: chain 7 residue 107 THR Chi-restraints excluded: chain 7 residue 184 GLU Chi-restraints excluded: chain 7 residue 216 ILE Chi-restraints excluded: chain 7 residue 221 THR Chi-restraints excluded: chain 8 residue 61 ILE Chi-restraints excluded: chain 8 residue 100 THR Chi-restraints excluded: chain 8 residue 118 THR Chi-restraints excluded: chain 8 residue 121 THR Chi-restraints excluded: chain 9 residue 550 VAL Chi-restraints excluded: chain a residue 53 ASP Chi-restraints excluded: chain a residue 97 ILE Chi-restraints excluded: chain a residue 110 LEU Chi-restraints excluded: chain a residue 153 LYS Chi-restraints excluded: chain a residue 154 ASP Chi-restraints excluded: chain a residue 156 ILE Chi-restraints excluded: chain a residue 215 SER Chi-restraints excluded: chain a residue 218 LEU Chi-restraints excluded: chain a residue 233 SER Chi-restraints excluded: chain a residue 251 VAL Chi-restraints excluded: chain d residue 203 SER Chi-restraints excluded: chain d residue 215 LYS Chi-restraints excluded: chain e residue 98 THR Chi-restraints excluded: chain e residue 209 LYS Chi-restraints excluded: chain e residue 288 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 786 random chunks: chunk 255 optimal weight: 0.7980 chunk 684 optimal weight: 2.9990 chunk 150 optimal weight: 2.9990 chunk 446 optimal weight: 5.9990 chunk 187 optimal weight: 6.9990 chunk 760 optimal weight: 7.9990 chunk 631 optimal weight: 10.0000 chunk 352 optimal weight: 5.9990 chunk 63 optimal weight: 4.9990 chunk 251 optimal weight: 9.9990 chunk 399 optimal weight: 4.9990 overall best weight: 3.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 81 GLN r 551 GLN c 68 GLN I 62 GLN ** O 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 39 ASN T 81 GLN V 551 GLN Y 68 GLN 5 62 GLN ** a 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 39 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7533 moved from start: 0.2948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 66918 Z= 0.270 Angle : 0.543 7.749 90600 Z= 0.291 Chirality : 0.045 0.169 9960 Planarity : 0.004 0.045 11694 Dihedral : 5.600 55.159 8898 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 2.83 % Allowed : 13.36 % Favored : 83.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -0.19 (0.09), residues: 8010 helix: 0.94 (0.13), residues: 1638 sheet: -0.23 (0.11), residues: 2232 loop : -0.41 (0.09), residues: 4140 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP H 217 HIS 0.008 0.001 HIS Y 77 PHE 0.018 0.002 PHE M 149 TYR 0.012 0.001 TYR 7 157 ARG 0.005 0.000 ARG Q 81 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16020 Ramachandran restraints generated. 8010 Oldfield, 0 Emsley, 8010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16020 Ramachandran restraints generated. 8010 Oldfield, 0 Emsley, 8010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1193 residues out of total 7134 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 202 poor density : 991 time to evaluate : 7.806 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: A 20 LYS cc_start: 0.8830 (mttm) cc_final: 0.8485 (mttp) REVERT: A 31 SER cc_start: 0.8664 (t) cc_final: 0.8396 (m) REVERT: A 48 MET cc_start: 0.8838 (mmm) cc_final: 0.8376 (mmm) REVERT: M 81 GLN cc_start: 0.7452 (tt0) cc_final: 0.7002 (tp40) REVERT: M 137 TYR cc_start: 0.7689 (t80) cc_final: 0.7312 (t80) REVERT: M 146 LYS cc_start: 0.7102 (mtmm) cc_final: 0.6166 (mmtt) REVERT: M 154 ASN cc_start: 0.6805 (m-40) cc_final: 0.6472 (m110) REVERT: M 159 ASN cc_start: 0.7402 (t0) cc_final: 0.7152 (t0) REVERT: M 183 GLU cc_start: 0.7658 (tt0) cc_final: 0.7434 (tt0) REVERT: G 18 MET cc_start: 0.8052 (mtp) cc_final: 0.7752 (mtp) REVERT: G 48 MET cc_start: 0.8332 (mtp) cc_final: 0.8028 (mtt) REVERT: G 56 ARG cc_start: 0.8075 (ptm160) cc_final: 0.5322 (mpt180) REVERT: G 71 GLU cc_start: 0.7377 (OUTLIER) cc_final: 0.7029 (pm20) REVERT: G 99 LEU cc_start: 0.7485 (tp) cc_final: 0.7035 (mp) REVERT: S 98 MET cc_start: 0.8960 (ttp) cc_final: 0.8745 (ttm) REVERT: S 254 ASP cc_start: 0.7942 (m-30) cc_final: 0.7664 (m-30) REVERT: b 37 ILE cc_start: 0.7264 (pt) cc_final: 0.6586 (mt) REVERT: b 44 ASP cc_start: 0.7816 (m-30) cc_final: 0.7077 (m-30) REVERT: b 68 GLN cc_start: 0.7737 (mm-40) cc_final: 0.6925 (mp10) REVERT: b 208 ARG cc_start: 0.7374 (ptt-90) cc_final: 0.6970 (ptp90) REVERT: b 234 GLU cc_start: 0.6746 (OUTLIER) cc_final: 0.6043 (mm-30) REVERT: c 88 ARG cc_start: 0.7266 (mtm-85) cc_final: 0.6892 (mtm-85) REVERT: c 112 SER cc_start: 0.7628 (m) cc_final: 0.7416 (m) REVERT: c 138 ILE cc_start: 0.8134 (mm) cc_final: 0.7782 (mt) REVERT: c 285 LYS cc_start: 0.7603 (ttpt) cc_final: 0.6881 (tmmt) REVERT: B 20 LYS cc_start: 0.8748 (mttm) cc_final: 0.8372 (mttp) REVERT: B 84 GLU cc_start: 0.8868 (OUTLIER) cc_final: 0.8480 (pm20) REVERT: C 24 ASN cc_start: 0.7534 (t0) cc_final: 0.7047 (m-40) REVERT: C 137 TYR cc_start: 0.7882 (t80) cc_final: 0.7606 (t80) REVERT: C 169 LYS cc_start: 0.8101 (ptmm) cc_final: 0.7743 (tttm) REVERT: D 56 ARG cc_start: 0.8137 (ptm160) cc_final: 0.5279 (mpt180) REVERT: D 139 LYS cc_start: 0.8390 (pttt) cc_final: 0.8128 (pttt) REVERT: F 70 ASN cc_start: 0.8441 (t0) cc_final: 0.8184 (t0) REVERT: F 153 LYS cc_start: 0.8229 (tttm) cc_final: 0.7785 (pttt) REVERT: H 37 ILE cc_start: 0.7357 (pt) cc_final: 0.6654 (mt) REVERT: H 68 GLN cc_start: 0.8067 (mm-40) cc_final: 0.7006 (mp10) REVERT: H 198 ARG cc_start: 0.7779 (ttt-90) cc_final: 0.7485 (ttt180) REVERT: H 234 GLU cc_start: 0.6796 (OUTLIER) cc_final: 0.6058 (mm-30) REVERT: I 88 ARG cc_start: 0.7291 (OUTLIER) cc_final: 0.6912 (mtm-85) REVERT: I 138 ILE cc_start: 0.7961 (mm) cc_final: 0.7587 (mt) REVERT: I 209 LYS cc_start: 0.8648 (OUTLIER) cc_final: 0.7970 (mtmm) REVERT: J 20 LYS cc_start: 0.8688 (mttm) cc_final: 0.8369 (mttp) REVERT: J 61 ILE cc_start: 0.8227 (OUTLIER) cc_final: 0.7928 (tp) REVERT: J 87 LYS cc_start: 0.8358 (mtmt) cc_final: 0.7861 (mttm) REVERT: K 137 TYR cc_start: 0.7988 (t80) cc_final: 0.7481 (t80) REVERT: K 183 GLU cc_start: 0.7630 (tt0) cc_final: 0.7410 (tt0) REVERT: K 184 GLU cc_start: 0.7782 (tt0) cc_final: 0.7417 (tt0) REVERT: L 6 LYS cc_start: 0.8177 (mtpt) cc_final: 0.7831 (mtpp) REVERT: L 56 ARG cc_start: 0.8048 (ptm160) cc_final: 0.5541 (mpt180) REVERT: L 99 LEU cc_start: 0.7575 (tp) cc_final: 0.7097 (mp) REVERT: N 555 GLU cc_start: 0.6372 (tt0) cc_final: 0.5739 (pt0) REVERT: O 254 ASP cc_start: 0.7755 (m-30) cc_final: 0.7386 (m-30) REVERT: P 37 ILE cc_start: 0.7247 (pt) cc_final: 0.6775 (mt) REVERT: P 68 GLN cc_start: 0.7873 (mm-40) cc_final: 0.6978 (mp10) REVERT: P 198 ARG cc_start: 0.7854 (ttt-90) cc_final: 0.7498 (ttt180) REVERT: Q 33 ASP cc_start: 0.6647 (t70) cc_final: 0.6309 (p0) REVERT: Q 88 ARG cc_start: 0.7427 (mtm-85) cc_final: 0.7189 (mtm-85) REVERT: Q 102 MET cc_start: 0.7602 (mmt) cc_final: 0.7221 (mmm) REVERT: Q 108 THR cc_start: 0.7765 (OUTLIER) cc_final: 0.7526 (p) REVERT: Q 138 ILE cc_start: 0.8087 (mm) cc_final: 0.7513 (mp) REVERT: Q 299 MET cc_start: 0.8316 (tmm) cc_final: 0.7949 (tmm) REVERT: R 20 LYS cc_start: 0.8832 (mttm) cc_final: 0.8479 (mttp) REVERT: R 31 SER cc_start: 0.8664 (t) cc_final: 0.8394 (m) REVERT: R 48 MET cc_start: 0.8847 (mmm) cc_final: 0.8377 (mmm) REVERT: T 81 GLN cc_start: 0.7454 (tt0) cc_final: 0.7009 (tp40) REVERT: T 137 TYR cc_start: 0.7691 (t80) cc_final: 0.7311 (t80) REVERT: T 146 LYS cc_start: 0.7103 (mtmm) cc_final: 0.6166 (mmtt) REVERT: T 154 ASN cc_start: 0.6802 (m-40) cc_final: 0.6467 (m110) REVERT: T 159 ASN cc_start: 0.7405 (t0) cc_final: 0.7155 (t0) REVERT: T 183 GLU cc_start: 0.7662 (tt0) cc_final: 0.7437 (tt0) REVERT: U 18 MET cc_start: 0.8051 (mtp) cc_final: 0.7753 (mtp) REVERT: U 48 MET cc_start: 0.8336 (mtp) cc_final: 0.8034 (mtt) REVERT: U 56 ARG cc_start: 0.8078 (ptm160) cc_final: 0.5323 (mpt180) REVERT: U 71 GLU cc_start: 0.7370 (OUTLIER) cc_final: 0.7027 (pm20) REVERT: U 99 LEU cc_start: 0.7483 (tp) cc_final: 0.7031 (mp) REVERT: W 98 MET cc_start: 0.8959 (ttp) cc_final: 0.8746 (ttm) REVERT: W 254 ASP cc_start: 0.7941 (m-30) cc_final: 0.7667 (m-30) REVERT: X 37 ILE cc_start: 0.7268 (pt) cc_final: 0.6588 (mt) REVERT: X 44 ASP cc_start: 0.7814 (m-30) cc_final: 0.7069 (m-30) REVERT: X 68 GLN cc_start: 0.7734 (mm-40) cc_final: 0.6923 (mp10) REVERT: X 88 ARG cc_start: 0.7492 (mmp80) cc_final: 0.7075 (mmt-90) REVERT: X 208 ARG cc_start: 0.7384 (ptt-90) cc_final: 0.6984 (ptp90) REVERT: X 234 GLU cc_start: 0.6750 (OUTLIER) cc_final: 0.6040 (mm-30) REVERT: Y 88 ARG cc_start: 0.7260 (mtm-85) cc_final: 0.6886 (mtm-85) REVERT: Y 112 SER cc_start: 0.7627 (m) cc_final: 0.7412 (m) REVERT: Y 138 ILE cc_start: 0.8130 (mm) cc_final: 0.7778 (mt) REVERT: Y 285 LYS cc_start: 0.7601 (ttpt) cc_final: 0.6877 (tmmt) REVERT: Z 20 LYS cc_start: 0.8746 (mttm) cc_final: 0.8371 (mttp) REVERT: Z 84 GLU cc_start: 0.8867 (OUTLIER) cc_final: 0.8478 (pm20) REVERT: 0 24 ASN cc_start: 0.7547 (t0) cc_final: 0.7043 (m-40) REVERT: 0 137 TYR cc_start: 0.7883 (t80) cc_final: 0.7604 (t80) REVERT: 0 169 LYS cc_start: 0.8099 (ptmm) cc_final: 0.7741 (tttm) REVERT: 1 56 ARG cc_start: 0.8139 (ptm160) cc_final: 0.5286 (mpt180) REVERT: 1 139 LYS cc_start: 0.8389 (pttt) cc_final: 0.8127 (pttt) REVERT: 3 70 ASN cc_start: 0.8445 (t0) cc_final: 0.8188 (t0) REVERT: 4 37 ILE cc_start: 0.7359 (pt) cc_final: 0.6649 (mt) REVERT: 4 68 GLN cc_start: 0.8067 (mm-40) cc_final: 0.7004 (mp10) REVERT: 4 198 ARG cc_start: 0.7782 (ttt-90) cc_final: 0.7489 (ttt180) REVERT: 4 234 GLU cc_start: 0.6798 (OUTLIER) cc_final: 0.6061 (mm-30) REVERT: 5 88 ARG cc_start: 0.7290 (OUTLIER) cc_final: 0.6909 (mtm-85) REVERT: 5 138 ILE cc_start: 0.7958 (mm) cc_final: 0.7584 (mt) REVERT: 5 209 LYS cc_start: 0.8650 (OUTLIER) cc_final: 0.7969 (mtmm) REVERT: 6 20 LYS cc_start: 0.8690 (mttm) cc_final: 0.8368 (mttp) REVERT: 6 61 ILE cc_start: 0.8240 (OUTLIER) cc_final: 0.7936 (tp) REVERT: 6 87 LYS cc_start: 0.8359 (mtmt) cc_final: 0.7862 (mttm) REVERT: 7 137 TYR cc_start: 0.7988 (t80) cc_final: 0.7483 (t80) REVERT: 7 159 ASN cc_start: 0.7227 (t0) cc_final: 0.6934 (t0) REVERT: 8 56 ARG cc_start: 0.8044 (ptm160) cc_final: 0.5534 (mpt180) REVERT: 8 99 LEU cc_start: 0.7582 (tp) cc_final: 0.7099 (mp) REVERT: 9 555 GLU cc_start: 0.6360 (tt0) cc_final: 0.5738 (pt0) REVERT: a 254 ASP cc_start: 0.7768 (m-30) cc_final: 0.7396 (m-30) REVERT: d 37 ILE cc_start: 0.7271 (pt) cc_final: 0.6795 (mt) REVERT: d 68 GLN cc_start: 0.7878 (mm-40) cc_final: 0.6982 (mp10) REVERT: d 198 ARG cc_start: 0.7952 (ttt-90) cc_final: 0.7701 (ttt180) REVERT: e 33 ASP cc_start: 0.6646 (t70) cc_final: 0.6308 (p0) REVERT: e 88 ARG cc_start: 0.7428 (mtm-85) cc_final: 0.7206 (mtm-85) REVERT: e 102 MET cc_start: 0.7600 (mmt) cc_final: 0.7221 (mmm) REVERT: e 108 THR cc_start: 0.7767 (OUTLIER) cc_final: 0.7530 (p) REVERT: e 138 ILE cc_start: 0.8087 (mm) cc_final: 0.7514 (mp) REVERT: e 209 LYS cc_start: 0.8229 (OUTLIER) cc_final: 0.7513 (mtmm) REVERT: e 299 MET cc_start: 0.8319 (tmm) cc_final: 0.7886 (tmm) outliers start: 202 outliers final: 141 residues processed: 1146 average time/residue: 0.7659 time to fit residues: 1467.5314 Evaluate side-chains 1106 residues out of total 7134 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 158 poor density : 948 time to evaluate : 5.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 VAL Chi-restraints excluded: chain A residue 117 GLU Chi-restraints excluded: chain A residue 137 SER Chi-restraints excluded: chain M residue 24 ASN Chi-restraints excluded: chain M residue 28 ILE Chi-restraints excluded: chain M residue 221 THR Chi-restraints excluded: chain G residue 35 GLU Chi-restraints excluded: chain G residue 71 GLU Chi-restraints excluded: chain G residue 100 THR Chi-restraints excluded: chain G residue 118 THR Chi-restraints excluded: chain G residue 121 THR Chi-restraints excluded: chain S residue 153 LYS Chi-restraints excluded: chain S residue 156 ILE Chi-restraints excluded: chain S residue 215 SER Chi-restraints excluded: chain S residue 226 THR Chi-restraints excluded: chain S residue 251 VAL Chi-restraints excluded: chain b residue 197 ILE Chi-restraints excluded: chain b residue 234 GLU Chi-restraints excluded: chain c residue 98 THR Chi-restraints excluded: chain c residue 191 THR Chi-restraints excluded: chain c residue 264 THR Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 15 VAL Chi-restraints excluded: chain B residue 61 ILE Chi-restraints excluded: chain B residue 84 GLU Chi-restraints excluded: chain B residue 117 GLU Chi-restraints excluded: chain C residue 57 THR Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 74 LEU Chi-restraints excluded: chain C residue 82 GLU Chi-restraints excluded: chain C residue 149 PHE Chi-restraints excluded: chain C residue 221 THR Chi-restraints excluded: chain D residue 39 THR Chi-restraints excluded: chain D residue 100 THR Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain F residue 97 ILE Chi-restraints excluded: chain F residue 156 ILE Chi-restraints excluded: chain F residue 215 SER Chi-restraints excluded: chain F residue 233 SER Chi-restraints excluded: chain F residue 251 VAL Chi-restraints excluded: chain H residue 20 GLU Chi-restraints excluded: chain H residue 131 LEU Chi-restraints excluded: chain H residue 222 GLU Chi-restraints excluded: chain H residue 234 GLU Chi-restraints excluded: chain I residue 88 ARG Chi-restraints excluded: chain I residue 98 THR Chi-restraints excluded: chain I residue 191 THR Chi-restraints excluded: chain I residue 209 LYS Chi-restraints excluded: chain I residue 264 THR Chi-restraints excluded: chain J residue 15 VAL Chi-restraints excluded: chain J residue 61 ILE Chi-restraints excluded: chain K residue 45 GLU Chi-restraints excluded: chain K residue 48 CYS Chi-restraints excluded: chain K residue 57 THR Chi-restraints excluded: chain K residue 74 LEU Chi-restraints excluded: chain K residue 82 GLU Chi-restraints excluded: chain K residue 149 PHE Chi-restraints excluded: chain K residue 216 ILE Chi-restraints excluded: chain K residue 221 THR Chi-restraints excluded: chain L residue 61 ILE Chi-restraints excluded: chain L residue 100 THR Chi-restraints excluded: chain L residue 118 THR Chi-restraints excluded: chain L residue 121 THR Chi-restraints excluded: chain N residue 550 VAL Chi-restraints excluded: chain O residue 53 ASP Chi-restraints excluded: chain O residue 97 ILE Chi-restraints excluded: chain O residue 110 LEU Chi-restraints excluded: chain O residue 137 THR Chi-restraints excluded: chain O residue 153 LYS Chi-restraints excluded: chain O residue 154 ASP Chi-restraints excluded: chain O residue 156 ILE Chi-restraints excluded: chain O residue 215 SER Chi-restraints excluded: chain O residue 233 SER Chi-restraints excluded: chain O residue 251 VAL Chi-restraints excluded: chain P residue 203 SER Chi-restraints excluded: chain P residue 215 LYS Chi-restraints excluded: chain Q residue 98 THR Chi-restraints excluded: chain Q residue 108 THR Chi-restraints excluded: chain Q residue 288 LEU Chi-restraints excluded: chain R residue 15 VAL Chi-restraints excluded: chain R residue 117 GLU Chi-restraints excluded: chain R residue 137 SER Chi-restraints excluded: chain T residue 24 ASN Chi-restraints excluded: chain T residue 28 ILE Chi-restraints excluded: chain T residue 221 THR Chi-restraints excluded: chain U residue 71 GLU Chi-restraints excluded: chain U residue 100 THR Chi-restraints excluded: chain U residue 118 THR Chi-restraints excluded: chain U residue 121 THR Chi-restraints excluded: chain W residue 156 ILE Chi-restraints excluded: chain W residue 215 SER Chi-restraints excluded: chain W residue 226 THR Chi-restraints excluded: chain W residue 251 VAL Chi-restraints excluded: chain X residue 197 ILE Chi-restraints excluded: chain X residue 234 GLU Chi-restraints excluded: chain Y residue 98 THR Chi-restraints excluded: chain Y residue 191 THR Chi-restraints excluded: chain Y residue 264 THR Chi-restraints excluded: chain Z residue 8 THR Chi-restraints excluded: chain Z residue 15 VAL Chi-restraints excluded: chain Z residue 61 ILE Chi-restraints excluded: chain Z residue 84 GLU Chi-restraints excluded: chain Z residue 117 GLU Chi-restraints excluded: chain 0 residue 57 THR Chi-restraints excluded: chain 0 residue 58 VAL Chi-restraints excluded: chain 0 residue 74 LEU Chi-restraints excluded: chain 0 residue 82 GLU Chi-restraints excluded: chain 0 residue 149 PHE Chi-restraints excluded: chain 0 residue 221 THR Chi-restraints excluded: chain 1 residue 39 THR Chi-restraints excluded: chain 1 residue 100 THR Chi-restraints excluded: chain 1 residue 121 THR Chi-restraints excluded: chain 3 residue 97 ILE Chi-restraints excluded: chain 3 residue 153 LYS Chi-restraints excluded: chain 3 residue 156 ILE Chi-restraints excluded: chain 3 residue 215 SER Chi-restraints excluded: chain 3 residue 233 SER Chi-restraints excluded: chain 3 residue 251 VAL Chi-restraints excluded: chain 4 residue 20 GLU Chi-restraints excluded: chain 4 residue 131 LEU Chi-restraints excluded: chain 4 residue 222 GLU Chi-restraints excluded: chain 4 residue 234 GLU Chi-restraints excluded: chain 5 residue 88 ARG Chi-restraints excluded: chain 5 residue 98 THR Chi-restraints excluded: chain 5 residue 191 THR Chi-restraints excluded: chain 5 residue 209 LYS Chi-restraints excluded: chain 5 residue 264 THR Chi-restraints excluded: chain 6 residue 15 VAL Chi-restraints excluded: chain 6 residue 61 ILE Chi-restraints excluded: chain 7 residue 45 GLU Chi-restraints excluded: chain 7 residue 48 CYS Chi-restraints excluded: chain 7 residue 57 THR Chi-restraints excluded: chain 7 residue 74 LEU Chi-restraints excluded: chain 7 residue 82 GLU Chi-restraints excluded: chain 7 residue 149 PHE Chi-restraints excluded: chain 7 residue 184 GLU Chi-restraints excluded: chain 7 residue 216 ILE Chi-restraints excluded: chain 7 residue 221 THR Chi-restraints excluded: chain 8 residue 61 ILE Chi-restraints excluded: chain 8 residue 100 THR Chi-restraints excluded: chain 8 residue 118 THR Chi-restraints excluded: chain 8 residue 121 THR Chi-restraints excluded: chain 9 residue 550 VAL Chi-restraints excluded: chain a residue 53 ASP Chi-restraints excluded: chain a residue 97 ILE Chi-restraints excluded: chain a residue 110 LEU Chi-restraints excluded: chain a residue 137 THR Chi-restraints excluded: chain a residue 153 LYS Chi-restraints excluded: chain a residue 154 ASP Chi-restraints excluded: chain a residue 156 ILE Chi-restraints excluded: chain a residue 233 SER Chi-restraints excluded: chain a residue 251 VAL Chi-restraints excluded: chain d residue 203 SER Chi-restraints excluded: chain d residue 215 LYS Chi-restraints excluded: chain e residue 98 THR Chi-restraints excluded: chain e residue 108 THR Chi-restraints excluded: chain e residue 209 LYS Chi-restraints excluded: chain e residue 288 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 786 random chunks: chunk 733 optimal weight: 5.9990 chunk 85 optimal weight: 6.9990 chunk 433 optimal weight: 4.9990 chunk 555 optimal weight: 4.9990 chunk 430 optimal weight: 8.9990 chunk 640 optimal weight: 10.0000 chunk 424 optimal weight: 4.9990 chunk 757 optimal weight: 1.9990 chunk 474 optimal weight: 10.0000 chunk 461 optimal weight: 10.0000 chunk 349 optimal weight: 9.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: r 551 GLN b 39 ASN c 68 GLN I 62 GLN ** O 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 39 ASN Y 68 GLN 5 62 GLN ** a 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7550 moved from start: 0.3085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 66918 Z= 0.359 Angle : 0.583 8.522 90600 Z= 0.312 Chirality : 0.046 0.158 9960 Planarity : 0.004 0.046 11694 Dihedral : 5.659 59.153 8898 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 3.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 3.10 % Allowed : 13.34 % Favored : 83.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -0.26 (0.09), residues: 8010 helix: 0.94 (0.12), residues: 1626 sheet: -0.26 (0.11), residues: 2232 loop : -0.50 (0.09), residues: 4152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP a 60 HIS 0.011 0.001 HIS Y 77 PHE 0.021 0.002 PHE M 149 TYR 0.015 0.001 TYR R 133 ARG 0.006 0.001 ARG P 103 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16020 Ramachandran restraints generated. 8010 Oldfield, 0 Emsley, 8010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16020 Ramachandran restraints generated. 8010 Oldfield, 0 Emsley, 8010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1207 residues out of total 7134 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 221 poor density : 986 time to evaluate : 7.403 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 LYS cc_start: 0.8848 (mttm) cc_final: 0.8486 (mttp) REVERT: A 48 MET cc_start: 0.8830 (mmm) cc_final: 0.8368 (mmm) REVERT: M 81 GLN cc_start: 0.7374 (tt0) cc_final: 0.6931 (tp40) REVERT: M 137 TYR cc_start: 0.7694 (t80) cc_final: 0.7297 (t80) REVERT: M 146 LYS cc_start: 0.7105 (mtmm) cc_final: 0.6202 (mmtt) REVERT: M 154 ASN cc_start: 0.6713 (m-40) cc_final: 0.6381 (m110) REVERT: M 159 ASN cc_start: 0.7400 (t0) cc_final: 0.7163 (t0) REVERT: M 183 GLU cc_start: 0.7697 (tt0) cc_final: 0.7474 (tt0) REVERT: M 266 ILE cc_start: 0.7513 (mt) cc_final: 0.7308 (mm) REVERT: G 18 MET cc_start: 0.8102 (mtp) cc_final: 0.7794 (mtp) REVERT: G 48 MET cc_start: 0.8327 (mtp) cc_final: 0.8005 (mtt) REVERT: G 71 GLU cc_start: 0.7387 (OUTLIER) cc_final: 0.7067 (pm20) REVERT: G 99 LEU cc_start: 0.7494 (tp) cc_final: 0.7037 (mp) REVERT: S 98 MET cc_start: 0.8985 (ttp) cc_final: 0.8763 (ttm) REVERT: S 254 ASP cc_start: 0.7952 (m-30) cc_final: 0.7703 (m-30) REVERT: b 37 ILE cc_start: 0.7170 (pt) cc_final: 0.6532 (mt) REVERT: b 44 ASP cc_start: 0.7777 (m-30) cc_final: 0.7018 (m-30) REVERT: b 68 GLN cc_start: 0.7752 (mm-40) cc_final: 0.6899 (mp10) REVERT: b 208 ARG cc_start: 0.7200 (ptt-90) cc_final: 0.6809 (ptp90) REVERT: b 234 GLU cc_start: 0.6793 (OUTLIER) cc_final: 0.6096 (mm-30) REVERT: c 88 ARG cc_start: 0.7233 (OUTLIER) cc_final: 0.6911 (mtm-85) REVERT: c 112 SER cc_start: 0.7707 (m) cc_final: 0.7502 (m) REVERT: c 138 ILE cc_start: 0.8132 (mm) cc_final: 0.7780 (mt) REVERT: c 285 LYS cc_start: 0.7597 (ttpt) cc_final: 0.6883 (tmmt) REVERT: B 20 LYS cc_start: 0.8754 (mttm) cc_final: 0.8366 (mttp) REVERT: B 84 GLU cc_start: 0.8885 (OUTLIER) cc_final: 0.8602 (pm20) REVERT: C 24 ASN cc_start: 0.7492 (t0) cc_final: 0.7076 (m-40) REVERT: C 137 TYR cc_start: 0.7865 (t80) cc_final: 0.7562 (t80) REVERT: C 146 LYS cc_start: 0.7008 (mtmm) cc_final: 0.6011 (mmtp) REVERT: C 169 LYS cc_start: 0.8112 (ptmm) cc_final: 0.7742 (tttm) REVERT: D 139 LYS cc_start: 0.8396 (pttt) cc_final: 0.8145 (pttt) REVERT: F 153 LYS cc_start: 0.8303 (tttm) cc_final: 0.7883 (pttt) REVERT: H 37 ILE cc_start: 0.7376 (pt) cc_final: 0.6644 (mt) REVERT: H 68 GLN cc_start: 0.8079 (mm-40) cc_final: 0.7042 (mp10) REVERT: H 198 ARG cc_start: 0.7720 (ttt-90) cc_final: 0.7314 (ttt180) REVERT: H 208 ARG cc_start: 0.7288 (OUTLIER) cc_final: 0.6377 (ptt90) REVERT: H 234 GLU cc_start: 0.6822 (OUTLIER) cc_final: 0.6082 (mm-30) REVERT: I 33 ASP cc_start: 0.6545 (t70) cc_final: 0.6284 (p0) REVERT: I 138 ILE cc_start: 0.7940 (mm) cc_final: 0.7578 (mt) REVERT: I 201 TYR cc_start: 0.8302 (p90) cc_final: 0.8081 (p90) REVERT: I 209 LYS cc_start: 0.8643 (OUTLIER) cc_final: 0.7957 (mtmm) REVERT: I 269 MET cc_start: 0.6865 (OUTLIER) cc_final: 0.6360 (tpt) REVERT: J 20 LYS cc_start: 0.8712 (mttm) cc_final: 0.8364 (mttp) REVERT: J 61 ILE cc_start: 0.8234 (OUTLIER) cc_final: 0.7936 (tp) REVERT: J 87 LYS cc_start: 0.8481 (mtmt) cc_final: 0.7978 (mttm) REVERT: K 137 TYR cc_start: 0.7984 (t80) cc_final: 0.7737 (t80) REVERT: K 184 GLU cc_start: 0.7756 (tt0) cc_final: 0.7400 (tt0) REVERT: L 6 LYS cc_start: 0.8191 (mtpt) cc_final: 0.7853 (mtpp) REVERT: L 99 LEU cc_start: 0.7531 (tp) cc_final: 0.7081 (mp) REVERT: N 555 GLU cc_start: 0.6430 (tt0) cc_final: 0.5808 (pt0) REVERT: O 218 LEU cc_start: 0.8693 (OUTLIER) cc_final: 0.8289 (mp) REVERT: O 254 ASP cc_start: 0.7791 (m-30) cc_final: 0.7398 (m-30) REVERT: P 37 ILE cc_start: 0.7308 (OUTLIER) cc_final: 0.6819 (mt) REVERT: P 68 GLN cc_start: 0.7881 (mm-40) cc_final: 0.6908 (mp10) REVERT: P 209 LYS cc_start: 0.7751 (OUTLIER) cc_final: 0.7407 (mmtm) REVERT: Q 33 ASP cc_start: 0.6530 (t70) cc_final: 0.6249 (p0) REVERT: Q 88 ARG cc_start: 0.7357 (mtm-85) cc_final: 0.7060 (mtm-85) REVERT: Q 102 MET cc_start: 0.7608 (mmt) cc_final: 0.7225 (mmm) REVERT: Q 108 THR cc_start: 0.7768 (OUTLIER) cc_final: 0.7528 (p) REVERT: Q 138 ILE cc_start: 0.8080 (mm) cc_final: 0.7705 (mt) REVERT: Q 299 MET cc_start: 0.8266 (tmm) cc_final: 0.7837 (tmm) REVERT: R 20 LYS cc_start: 0.8851 (mttm) cc_final: 0.8492 (mttp) REVERT: R 31 SER cc_start: 0.8688 (t) cc_final: 0.8404 (m) REVERT: R 48 MET cc_start: 0.8839 (mmm) cc_final: 0.8365 (mmm) REVERT: T 81 GLN cc_start: 0.7366 (tt0) cc_final: 0.6935 (tp40) REVERT: T 137 TYR cc_start: 0.7695 (t80) cc_final: 0.7298 (t80) REVERT: T 146 LYS cc_start: 0.7108 (mtmm) cc_final: 0.6204 (mmtt) REVERT: T 154 ASN cc_start: 0.6713 (m-40) cc_final: 0.6374 (m110) REVERT: T 159 ASN cc_start: 0.7406 (t0) cc_final: 0.7171 (t0) REVERT: T 183 GLU cc_start: 0.7689 (tt0) cc_final: 0.7477 (tt0) REVERT: U 18 MET cc_start: 0.8102 (mtp) cc_final: 0.7793 (mtp) REVERT: U 48 MET cc_start: 0.8330 (mtp) cc_final: 0.8011 (mtt) REVERT: U 71 GLU cc_start: 0.7379 (OUTLIER) cc_final: 0.7063 (pm20) REVERT: U 99 LEU cc_start: 0.7495 (tp) cc_final: 0.7034 (mp) REVERT: W 98 MET cc_start: 0.8985 (ttp) cc_final: 0.8765 (ttm) REVERT: W 254 ASP cc_start: 0.7952 (m-30) cc_final: 0.7704 (m-30) REVERT: X 37 ILE cc_start: 0.7172 (pt) cc_final: 0.6532 (mt) REVERT: X 44 ASP cc_start: 0.7775 (m-30) cc_final: 0.7017 (m-30) REVERT: X 68 GLN cc_start: 0.7750 (mm-40) cc_final: 0.6901 (mp10) REVERT: X 208 ARG cc_start: 0.7220 (ptt-90) cc_final: 0.6823 (ptp90) REVERT: X 234 GLU cc_start: 0.6796 (OUTLIER) cc_final: 0.6097 (mm-30) REVERT: Y 88 ARG cc_start: 0.7230 (OUTLIER) cc_final: 0.6908 (mtm-85) REVERT: Y 112 SER cc_start: 0.7707 (m) cc_final: 0.7497 (m) REVERT: Y 138 ILE cc_start: 0.8129 (mm) cc_final: 0.7775 (mt) REVERT: Y 285 LYS cc_start: 0.7594 (ttpt) cc_final: 0.6881 (tmmt) REVERT: Z 20 LYS cc_start: 0.8752 (mttm) cc_final: 0.8367 (mttp) REVERT: Z 84 GLU cc_start: 0.8884 (OUTLIER) cc_final: 0.8604 (pm20) REVERT: 0 24 ASN cc_start: 0.7499 (t0) cc_final: 0.7076 (m-40) REVERT: 0 137 TYR cc_start: 0.7868 (t80) cc_final: 0.7559 (t80) REVERT: 0 146 LYS cc_start: 0.7006 (mtmm) cc_final: 0.6009 (mmtp) REVERT: 0 169 LYS cc_start: 0.8112 (ptmm) cc_final: 0.7739 (tttm) REVERT: 1 139 LYS cc_start: 0.8395 (pttt) cc_final: 0.8145 (pttt) REVERT: 4 37 ILE cc_start: 0.7378 (pt) cc_final: 0.6642 (mt) REVERT: 4 68 GLN cc_start: 0.8081 (mm-40) cc_final: 0.7041 (mp10) REVERT: 4 198 ARG cc_start: 0.7719 (ttt-90) cc_final: 0.7311 (ttt180) REVERT: 4 208 ARG cc_start: 0.7292 (OUTLIER) cc_final: 0.6378 (ptt90) REVERT: 4 234 GLU cc_start: 0.6824 (OUTLIER) cc_final: 0.6083 (mm-30) REVERT: 5 33 ASP cc_start: 0.6546 (t70) cc_final: 0.6284 (p0) REVERT: 5 138 ILE cc_start: 0.7939 (mm) cc_final: 0.7577 (mt) REVERT: 5 201 TYR cc_start: 0.8308 (p90) cc_final: 0.8086 (p90) REVERT: 5 209 LYS cc_start: 0.8645 (OUTLIER) cc_final: 0.7959 (mtmm) REVERT: 5 269 MET cc_start: 0.6862 (OUTLIER) cc_final: 0.6357 (tpt) REVERT: 6 20 LYS cc_start: 0.8714 (mttm) cc_final: 0.8363 (mttp) REVERT: 6 61 ILE cc_start: 0.8244 (OUTLIER) cc_final: 0.7945 (tp) REVERT: 6 87 LYS cc_start: 0.8482 (mtmt) cc_final: 0.7979 (mttm) REVERT: 7 137 TYR cc_start: 0.7983 (t80) cc_final: 0.7736 (t80) REVERT: 7 159 ASN cc_start: 0.7247 (t0) cc_final: 0.7010 (t0) REVERT: 8 99 LEU cc_start: 0.7537 (tp) cc_final: 0.7082 (mp) REVERT: 9 555 GLU cc_start: 0.6427 (tt0) cc_final: 0.5812 (pt0) REVERT: a 218 LEU cc_start: 0.8704 (OUTLIER) cc_final: 0.8304 (mp) REVERT: a 254 ASP cc_start: 0.7806 (m-30) cc_final: 0.7407 (m-30) REVERT: d 37 ILE cc_start: 0.7309 (OUTLIER) cc_final: 0.6825 (mt) REVERT: d 68 GLN cc_start: 0.7885 (mm-40) cc_final: 0.6911 (mp10) REVERT: d 209 LYS cc_start: 0.7754 (OUTLIER) cc_final: 0.7409 (mmtm) REVERT: e 33 ASP cc_start: 0.6533 (t70) cc_final: 0.6251 (p0) REVERT: e 88 ARG cc_start: 0.7355 (mtm-85) cc_final: 0.7058 (mtm-85) REVERT: e 102 MET cc_start: 0.7604 (mmt) cc_final: 0.7223 (mmm) REVERT: e 108 THR cc_start: 0.7769 (OUTLIER) cc_final: 0.7531 (p) REVERT: e 138 ILE cc_start: 0.8079 (mm) cc_final: 0.7704 (mt) REVERT: e 209 LYS cc_start: 0.8225 (OUTLIER) cc_final: 0.7538 (mtmm) REVERT: e 299 MET cc_start: 0.8271 (tmm) cc_final: 0.7840 (tmm) outliers start: 221 outliers final: 163 residues processed: 1149 average time/residue: 0.7721 time to fit residues: 1509.9131 Evaluate side-chains 1155 residues out of total 7134 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 190 poor density : 965 time to evaluate : 7.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 VAL Chi-restraints excluded: chain A residue 117 GLU Chi-restraints excluded: chain A residue 137 SER Chi-restraints excluded: chain M residue 24 ASN Chi-restraints excluded: chain M residue 28 ILE Chi-restraints excluded: chain M residue 221 THR Chi-restraints excluded: chain G residue 35 GLU Chi-restraints excluded: chain G residue 71 GLU Chi-restraints excluded: chain G residue 100 THR Chi-restraints excluded: chain G residue 118 THR Chi-restraints excluded: chain G residue 121 THR Chi-restraints excluded: chain S residue 137 THR Chi-restraints excluded: chain S residue 153 LYS Chi-restraints excluded: chain S residue 156 ILE Chi-restraints excluded: chain S residue 215 SER Chi-restraints excluded: chain S residue 226 THR Chi-restraints excluded: chain S residue 251 VAL Chi-restraints excluded: chain b residue 197 ILE Chi-restraints excluded: chain b residue 203 SER Chi-restraints excluded: chain b residue 234 GLU Chi-restraints excluded: chain c residue 88 ARG Chi-restraints excluded: chain c residue 98 THR Chi-restraints excluded: chain c residue 191 THR Chi-restraints excluded: chain c residue 264 THR Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 15 VAL Chi-restraints excluded: chain B residue 61 ILE Chi-restraints excluded: chain B residue 84 GLU Chi-restraints excluded: chain B residue 117 GLU Chi-restraints excluded: chain C residue 48 CYS Chi-restraints excluded: chain C residue 57 THR Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 74 LEU Chi-restraints excluded: chain C residue 82 GLU Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain C residue 149 PHE Chi-restraints excluded: chain C residue 250 ILE Chi-restraints excluded: chain D residue 39 THR Chi-restraints excluded: chain D residue 100 THR Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain F residue 97 ILE Chi-restraints excluded: chain F residue 119 THR Chi-restraints excluded: chain F residue 137 THR Chi-restraints excluded: chain F residue 156 ILE Chi-restraints excluded: chain F residue 198 GLU Chi-restraints excluded: chain F residue 215 SER Chi-restraints excluded: chain F residue 233 SER Chi-restraints excluded: chain F residue 251 VAL Chi-restraints excluded: chain H residue 20 GLU Chi-restraints excluded: chain H residue 131 LEU Chi-restraints excluded: chain H residue 208 ARG Chi-restraints excluded: chain H residue 234 GLU Chi-restraints excluded: chain I residue 61 VAL Chi-restraints excluded: chain I residue 98 THR Chi-restraints excluded: chain I residue 191 THR Chi-restraints excluded: chain I residue 209 LYS Chi-restraints excluded: chain I residue 264 THR Chi-restraints excluded: chain I residue 269 MET Chi-restraints excluded: chain J residue 15 VAL Chi-restraints excluded: chain J residue 61 ILE Chi-restraints excluded: chain K residue 45 GLU Chi-restraints excluded: chain K residue 48 CYS Chi-restraints excluded: chain K residue 57 THR Chi-restraints excluded: chain K residue 74 LEU Chi-restraints excluded: chain K residue 82 GLU Chi-restraints excluded: chain K residue 98 THR Chi-restraints excluded: chain K residue 107 THR Chi-restraints excluded: chain K residue 149 PHE Chi-restraints excluded: chain K residue 216 ILE Chi-restraints excluded: chain K residue 221 THR Chi-restraints excluded: chain L residue 61 ILE Chi-restraints excluded: chain L residue 100 THR Chi-restraints excluded: chain L residue 118 THR Chi-restraints excluded: chain L residue 121 THR Chi-restraints excluded: chain N residue 550 VAL Chi-restraints excluded: chain O residue 53 ASP Chi-restraints excluded: chain O residue 97 ILE Chi-restraints excluded: chain O residue 110 LEU Chi-restraints excluded: chain O residue 137 THR Chi-restraints excluded: chain O residue 153 LYS Chi-restraints excluded: chain O residue 154 ASP Chi-restraints excluded: chain O residue 156 ILE Chi-restraints excluded: chain O residue 215 SER Chi-restraints excluded: chain O residue 218 LEU Chi-restraints excluded: chain O residue 233 SER Chi-restraints excluded: chain O residue 251 VAL Chi-restraints excluded: chain P residue 37 ILE Chi-restraints excluded: chain P residue 203 SER Chi-restraints excluded: chain P residue 209 LYS Chi-restraints excluded: chain P residue 215 LYS Chi-restraints excluded: chain Q residue 98 THR Chi-restraints excluded: chain Q residue 108 THR Chi-restraints excluded: chain Q residue 288 LEU Chi-restraints excluded: chain R residue 15 VAL Chi-restraints excluded: chain R residue 117 GLU Chi-restraints excluded: chain R residue 137 SER Chi-restraints excluded: chain T residue 24 ASN Chi-restraints excluded: chain T residue 28 ILE Chi-restraints excluded: chain T residue 221 THR Chi-restraints excluded: chain U residue 35 GLU Chi-restraints excluded: chain U residue 71 GLU Chi-restraints excluded: chain U residue 100 THR Chi-restraints excluded: chain U residue 118 THR Chi-restraints excluded: chain U residue 121 THR Chi-restraints excluded: chain W residue 137 THR Chi-restraints excluded: chain W residue 153 LYS Chi-restraints excluded: chain W residue 156 ILE Chi-restraints excluded: chain W residue 201 THR Chi-restraints excluded: chain W residue 215 SER Chi-restraints excluded: chain W residue 226 THR Chi-restraints excluded: chain W residue 251 VAL Chi-restraints excluded: chain X residue 197 ILE Chi-restraints excluded: chain X residue 203 SER Chi-restraints excluded: chain X residue 234 GLU Chi-restraints excluded: chain Y residue 88 ARG Chi-restraints excluded: chain Y residue 98 THR Chi-restraints excluded: chain Y residue 191 THR Chi-restraints excluded: chain Y residue 264 THR Chi-restraints excluded: chain Z residue 8 THR Chi-restraints excluded: chain Z residue 15 VAL Chi-restraints excluded: chain Z residue 61 ILE Chi-restraints excluded: chain Z residue 84 GLU Chi-restraints excluded: chain Z residue 117 GLU Chi-restraints excluded: chain 0 residue 48 CYS Chi-restraints excluded: chain 0 residue 57 THR Chi-restraints excluded: chain 0 residue 58 VAL Chi-restraints excluded: chain 0 residue 74 LEU Chi-restraints excluded: chain 0 residue 82 GLU Chi-restraints excluded: chain 0 residue 107 THR Chi-restraints excluded: chain 0 residue 149 PHE Chi-restraints excluded: chain 0 residue 250 ILE Chi-restraints excluded: chain 1 residue 39 THR Chi-restraints excluded: chain 1 residue 100 THR Chi-restraints excluded: chain 1 residue 121 THR Chi-restraints excluded: chain 3 residue 97 ILE Chi-restraints excluded: chain 3 residue 119 THR Chi-restraints excluded: chain 3 residue 137 THR Chi-restraints excluded: chain 3 residue 153 LYS Chi-restraints excluded: chain 3 residue 156 ILE Chi-restraints excluded: chain 3 residue 198 GLU Chi-restraints excluded: chain 3 residue 215 SER Chi-restraints excluded: chain 3 residue 233 SER Chi-restraints excluded: chain 3 residue 251 VAL Chi-restraints excluded: chain 4 residue 20 GLU Chi-restraints excluded: chain 4 residue 131 LEU Chi-restraints excluded: chain 4 residue 208 ARG Chi-restraints excluded: chain 4 residue 234 GLU Chi-restraints excluded: chain 5 residue 61 VAL Chi-restraints excluded: chain 5 residue 98 THR Chi-restraints excluded: chain 5 residue 191 THR Chi-restraints excluded: chain 5 residue 209 LYS Chi-restraints excluded: chain 5 residue 264 THR Chi-restraints excluded: chain 5 residue 269 MET Chi-restraints excluded: chain 6 residue 15 VAL Chi-restraints excluded: chain 6 residue 61 ILE Chi-restraints excluded: chain 7 residue 45 GLU Chi-restraints excluded: chain 7 residue 48 CYS Chi-restraints excluded: chain 7 residue 57 THR Chi-restraints excluded: chain 7 residue 74 LEU Chi-restraints excluded: chain 7 residue 82 GLU Chi-restraints excluded: chain 7 residue 98 THR Chi-restraints excluded: chain 7 residue 107 THR Chi-restraints excluded: chain 7 residue 149 PHE Chi-restraints excluded: chain 7 residue 184 GLU Chi-restraints excluded: chain 7 residue 216 ILE Chi-restraints excluded: chain 7 residue 221 THR Chi-restraints excluded: chain 8 residue 61 ILE Chi-restraints excluded: chain 8 residue 100 THR Chi-restraints excluded: chain 8 residue 118 THR Chi-restraints excluded: chain 8 residue 121 THR Chi-restraints excluded: chain 9 residue 550 VAL Chi-restraints excluded: chain a residue 53 ASP Chi-restraints excluded: chain a residue 97 ILE Chi-restraints excluded: chain a residue 110 LEU Chi-restraints excluded: chain a residue 137 THR Chi-restraints excluded: chain a residue 153 LYS Chi-restraints excluded: chain a residue 154 ASP Chi-restraints excluded: chain a residue 156 ILE Chi-restraints excluded: chain a residue 215 SER Chi-restraints excluded: chain a residue 218 LEU Chi-restraints excluded: chain a residue 233 SER Chi-restraints excluded: chain a residue 251 VAL Chi-restraints excluded: chain d residue 37 ILE Chi-restraints excluded: chain d residue 203 SER Chi-restraints excluded: chain d residue 209 LYS Chi-restraints excluded: chain d residue 215 LYS Chi-restraints excluded: chain e residue 98 THR Chi-restraints excluded: chain e residue 108 THR Chi-restraints excluded: chain e residue 209 LYS Chi-restraints excluded: chain e residue 288 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 786 random chunks: chunk 468 optimal weight: 2.9990 chunk 302 optimal weight: 3.9990 chunk 452 optimal weight: 0.0570 chunk 228 optimal weight: 8.9990 chunk 148 optimal weight: 7.9990 chunk 146 optimal weight: 0.9990 chunk 481 optimal weight: 6.9990 chunk 516 optimal weight: 3.9990 chunk 374 optimal weight: 5.9990 chunk 70 optimal weight: 0.9990 chunk 595 optimal weight: 0.9990 overall best weight: 1.2106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: r 551 GLN c 68 GLN F 253 GLN ** O 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 551 GLN Y 68 GLN 3 253 GLN ** a 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7498 moved from start: 0.3184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 66918 Z= 0.144 Angle : 0.477 6.784 90600 Z= 0.258 Chirality : 0.043 0.158 9960 Planarity : 0.004 0.042 11694 Dihedral : 5.240 56.472 8898 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % Rotamer: Outliers : 1.84 % Allowed : 15.10 % Favored : 83.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 0.04 (0.09), residues: 8010 helix: 1.30 (0.13), residues: 1626 sheet: -0.14 (0.11), residues: 2292 loop : -0.31 (0.10), residues: 4092 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.000 TRP U 119 HIS 0.006 0.001 HIS I 77 PHE 0.015 0.001 PHE 4 110 TYR 0.011 0.001 TYR 4 270 ARG 0.005 0.000 ARG e 81 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16020 Ramachandran restraints generated. 8010 Oldfield, 0 Emsley, 8010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16020 Ramachandran restraints generated. 8010 Oldfield, 0 Emsley, 8010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1149 residues out of total 7134 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 131 poor density : 1018 time to evaluate : 7.301 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 LYS cc_start: 0.8838 (mttm) cc_final: 0.8491 (mttp) REVERT: A 31 SER cc_start: 0.8633 (t) cc_final: 0.8372 (m) REVERT: A 48 MET cc_start: 0.8834 (mmm) cc_final: 0.8393 (mmm) REVERT: M 81 GLN cc_start: 0.7260 (tt0) cc_final: 0.6944 (tp40) REVERT: M 82 GLU cc_start: 0.7986 (OUTLIER) cc_final: 0.7679 (tt0) REVERT: M 137 TYR cc_start: 0.7674 (t80) cc_final: 0.7275 (t80) REVERT: M 146 LYS cc_start: 0.7129 (mtmm) cc_final: 0.6241 (mmtt) REVERT: M 159 ASN cc_start: 0.7441 (t0) cc_final: 0.7155 (t0) REVERT: M 183 GLU cc_start: 0.7599 (tt0) cc_final: 0.7273 (mt-10) REVERT: G 18 MET cc_start: 0.8035 (mtp) cc_final: 0.7739 (mtp) REVERT: G 48 MET cc_start: 0.8321 (mtp) cc_final: 0.8026 (mtt) REVERT: G 71 GLU cc_start: 0.7237 (OUTLIER) cc_final: 0.7006 (pm20) REVERT: G 99 LEU cc_start: 0.7433 (tp) cc_final: 0.7032 (mp) REVERT: S 98 MET cc_start: 0.8873 (ttp) cc_final: 0.8638 (ttm) REVERT: S 254 ASP cc_start: 0.7884 (m-30) cc_final: 0.7643 (m-30) REVERT: b 37 ILE cc_start: 0.7207 (pt) cc_final: 0.6607 (mt) REVERT: b 44 ASP cc_start: 0.7806 (m-30) cc_final: 0.7165 (m-30) REVERT: b 68 GLN cc_start: 0.7668 (mm-40) cc_final: 0.6912 (mp10) REVERT: b 196 MET cc_start: 0.7159 (mmm) cc_final: 0.6743 (tpp) REVERT: b 208 ARG cc_start: 0.7078 (ptt-90) cc_final: 0.6556 (ptp90) REVERT: b 234 GLU cc_start: 0.6673 (OUTLIER) cc_final: 0.5984 (mm-30) REVERT: c 112 SER cc_start: 0.7590 (m) cc_final: 0.7375 (m) REVERT: c 138 ILE cc_start: 0.8035 (mm) cc_final: 0.7686 (mt) REVERT: c 285 LYS cc_start: 0.7484 (ttpt) cc_final: 0.6809 (tmmt) REVERT: B 20 LYS cc_start: 0.8747 (mttm) cc_final: 0.8400 (mttp) REVERT: B 97 ASP cc_start: 0.8420 (t70) cc_final: 0.8168 (t70) REVERT: C 24 ASN cc_start: 0.7487 (t0) cc_final: 0.7001 (m-40) REVERT: C 137 TYR cc_start: 0.7875 (t80) cc_final: 0.7561 (t80) REVERT: C 146 LYS cc_start: 0.7022 (mtmm) cc_final: 0.6072 (mmtt) REVERT: C 218 GLU cc_start: 0.8076 (pt0) cc_final: 0.7617 (tt0) REVERT: D 139 LYS cc_start: 0.8359 (pttt) cc_final: 0.8092 (pttt) REVERT: F 70 ASN cc_start: 0.8407 (t0) cc_final: 0.8154 (t0) REVERT: F 153 LYS cc_start: 0.8266 (tttm) cc_final: 0.7783 (pttt) REVERT: H 37 ILE cc_start: 0.7414 (pt) cc_final: 0.6717 (mt) REVERT: H 68 GLN cc_start: 0.7955 (mm-40) cc_final: 0.6962 (mp10) REVERT: H 88 ARG cc_start: 0.7556 (mmp80) cc_final: 0.6812 (mmt-90) REVERT: H 198 ARG cc_start: 0.7743 (ttt-90) cc_final: 0.7295 (ttt180) REVERT: H 225 GLN cc_start: 0.6956 (tt0) cc_final: 0.6649 (tt0) REVERT: H 234 GLU cc_start: 0.6752 (OUTLIER) cc_final: 0.5990 (mm-30) REVERT: H 269 MET cc_start: 0.7941 (tpp) cc_final: 0.6553 (mpp) REVERT: I 88 ARG cc_start: 0.7269 (OUTLIER) cc_final: 0.7009 (mtm-85) REVERT: I 138 ILE cc_start: 0.7947 (mm) cc_final: 0.7572 (mt) REVERT: I 209 LYS cc_start: 0.8638 (OUTLIER) cc_final: 0.7862 (mtpt) REVERT: I 269 MET cc_start: 0.6932 (tpp) cc_final: 0.6669 (mtt) REVERT: J 20 LYS cc_start: 0.8676 (mttm) cc_final: 0.8363 (mttp) REVERT: J 61 ILE cc_start: 0.8195 (OUTLIER) cc_final: 0.7910 (tp) REVERT: J 75 ASP cc_start: 0.7956 (t0) cc_final: 0.7746 (t0) REVERT: J 87 LYS cc_start: 0.8374 (mtmt) cc_final: 0.7871 (mttm) REVERT: K 137 TYR cc_start: 0.7955 (t80) cc_final: 0.7448 (t80) REVERT: K 184 GLU cc_start: 0.7717 (tt0) cc_final: 0.7425 (tt0) REVERT: L 6 LYS cc_start: 0.8172 (mtpt) cc_final: 0.7801 (mtpp) REVERT: L 99 LEU cc_start: 0.7530 (tp) cc_final: 0.7109 (mp) REVERT: N 555 GLU cc_start: 0.6510 (tt0) cc_final: 0.5875 (pt0) REVERT: O 254 ASP cc_start: 0.7786 (m-30) cc_final: 0.7433 (m-30) REVERT: P 28 ASN cc_start: 0.8094 (t0) cc_final: 0.7866 (t0) REVERT: P 37 ILE cc_start: 0.7308 (pt) cc_final: 0.6834 (mt) REVERT: P 68 GLN cc_start: 0.7872 (mm-40) cc_final: 0.6906 (mp10) REVERT: P 209 LYS cc_start: 0.7656 (OUTLIER) cc_final: 0.7377 (mmtm) REVERT: Q 102 MET cc_start: 0.7587 (mmt) cc_final: 0.7265 (mmm) REVERT: Q 138 ILE cc_start: 0.8076 (mm) cc_final: 0.7697 (mt) REVERT: Q 299 MET cc_start: 0.8267 (tmm) cc_final: 0.7783 (tmm) REVERT: R 20 LYS cc_start: 0.8843 (mttm) cc_final: 0.8497 (mttp) REVERT: R 31 SER cc_start: 0.8631 (t) cc_final: 0.8362 (m) REVERT: R 48 MET cc_start: 0.8834 (mmm) cc_final: 0.8377 (mmm) REVERT: T 81 GLN cc_start: 0.7257 (tt0) cc_final: 0.6954 (tp40) REVERT: T 82 GLU cc_start: 0.7971 (OUTLIER) cc_final: 0.7664 (tt0) REVERT: T 137 TYR cc_start: 0.7676 (t80) cc_final: 0.7278 (t80) REVERT: T 146 LYS cc_start: 0.7130 (mtmm) cc_final: 0.6239 (mmtt) REVERT: T 154 ASN cc_start: 0.6804 (m-40) cc_final: 0.6597 (m110) REVERT: T 159 ASN cc_start: 0.7443 (t0) cc_final: 0.7158 (t0) REVERT: T 183 GLU cc_start: 0.7600 (tt0) cc_final: 0.7290 (mt-10) REVERT: U 18 MET cc_start: 0.8035 (mtp) cc_final: 0.7739 (mtp) REVERT: U 48 MET cc_start: 0.8320 (mtp) cc_final: 0.8032 (mtt) REVERT: U 71 GLU cc_start: 0.7232 (OUTLIER) cc_final: 0.7008 (pm20) REVERT: U 99 LEU cc_start: 0.7434 (tp) cc_final: 0.7029 (mp) REVERT: W 98 MET cc_start: 0.8866 (ttp) cc_final: 0.8636 (ttm) REVERT: W 254 ASP cc_start: 0.7886 (m-30) cc_final: 0.7647 (m-30) REVERT: X 37 ILE cc_start: 0.7211 (pt) cc_final: 0.6610 (mt) REVERT: X 44 ASP cc_start: 0.7823 (m-30) cc_final: 0.7179 (m-30) REVERT: X 68 GLN cc_start: 0.7668 (mm-40) cc_final: 0.6912 (mp10) REVERT: X 88 ARG cc_start: 0.7514 (mmp80) cc_final: 0.6985 (mmt-90) REVERT: X 196 MET cc_start: 0.7159 (mmm) cc_final: 0.6749 (tpp) REVERT: X 208 ARG cc_start: 0.7104 (ptt-90) cc_final: 0.6552 (ptp90) REVERT: X 234 GLU cc_start: 0.6671 (OUTLIER) cc_final: 0.5980 (mm-30) REVERT: Y 112 SER cc_start: 0.7586 (m) cc_final: 0.7368 (m) REVERT: Y 138 ILE cc_start: 0.8033 (mm) cc_final: 0.7681 (mt) REVERT: Y 285 LYS cc_start: 0.7479 (ttpt) cc_final: 0.6806 (tmmt) REVERT: Z 20 LYS cc_start: 0.8746 (mttm) cc_final: 0.8399 (mttp) REVERT: Z 97 ASP cc_start: 0.8418 (t70) cc_final: 0.8172 (t70) REVERT: 0 24 ASN cc_start: 0.7484 (t0) cc_final: 0.6984 (m-40) REVERT: 0 137 TYR cc_start: 0.7876 (t80) cc_final: 0.7560 (t80) REVERT: 0 146 LYS cc_start: 0.7020 (mtmm) cc_final: 0.6069 (mmtt) REVERT: 0 218 GLU cc_start: 0.8075 (pt0) cc_final: 0.7627 (tt0) REVERT: 1 139 LYS cc_start: 0.8358 (pttt) cc_final: 0.8092 (pttt) REVERT: 3 70 ASN cc_start: 0.8412 (t0) cc_final: 0.8159 (t0) REVERT: 4 37 ILE cc_start: 0.7414 (pt) cc_final: 0.6712 (mt) REVERT: 4 68 GLN cc_start: 0.7957 (mm-40) cc_final: 0.6965 (mp10) REVERT: 4 88 ARG cc_start: 0.7550 (mmp80) cc_final: 0.6800 (mmt-90) REVERT: 4 198 ARG cc_start: 0.7744 (ttt-90) cc_final: 0.7297 (ttt180) REVERT: 4 225 GLN cc_start: 0.6961 (tt0) cc_final: 0.6653 (tt0) REVERT: 4 234 GLU cc_start: 0.6755 (OUTLIER) cc_final: 0.5996 (mm-30) REVERT: 4 269 MET cc_start: 0.7939 (tpp) cc_final: 0.6554 (mpp) REVERT: 5 88 ARG cc_start: 0.7266 (OUTLIER) cc_final: 0.7006 (mtm-85) REVERT: 5 138 ILE cc_start: 0.7948 (mm) cc_final: 0.7572 (mt) REVERT: 5 209 LYS cc_start: 0.8641 (OUTLIER) cc_final: 0.7863 (mtpt) REVERT: 5 269 MET cc_start: 0.6927 (tpp) cc_final: 0.6665 (mtt) REVERT: 6 20 LYS cc_start: 0.8676 (mttm) cc_final: 0.8362 (mttp) REVERT: 6 61 ILE cc_start: 0.8212 (OUTLIER) cc_final: 0.7953 (tp) REVERT: 6 75 ASP cc_start: 0.7954 (t0) cc_final: 0.7746 (t0) REVERT: 6 87 LYS cc_start: 0.8376 (mtmt) cc_final: 0.7872 (mttm) REVERT: 7 79 GLN cc_start: 0.7698 (mt0) cc_final: 0.7451 (mt0) REVERT: 7 137 TYR cc_start: 0.7954 (t80) cc_final: 0.7449 (t80) REVERT: 7 159 ASN cc_start: 0.7253 (t0) cc_final: 0.7001 (t0) REVERT: 8 99 LEU cc_start: 0.7536 (tp) cc_final: 0.7111 (mp) REVERT: 9 555 GLU cc_start: 0.6506 (tt0) cc_final: 0.5876 (pt0) REVERT: a 254 ASP cc_start: 0.7795 (m-30) cc_final: 0.7439 (m-30) REVERT: d 28 ASN cc_start: 0.8098 (t0) cc_final: 0.7866 (t0) REVERT: d 37 ILE cc_start: 0.7309 (pt) cc_final: 0.6844 (mt) REVERT: d 68 GLN cc_start: 0.7872 (mm-40) cc_final: 0.6908 (mp10) REVERT: d 209 LYS cc_start: 0.7659 (OUTLIER) cc_final: 0.7378 (mmtm) REVERT: e 102 MET cc_start: 0.7586 (mmt) cc_final: 0.7266 (mmm) REVERT: e 138 ILE cc_start: 0.8076 (mm) cc_final: 0.7696 (mt) REVERT: e 209 LYS cc_start: 0.8189 (OUTLIER) cc_final: 0.7615 (mtmm) REVERT: e 299 MET cc_start: 0.8268 (tmm) cc_final: 0.7785 (tmm) outliers start: 131 outliers final: 91 residues processed: 1107 average time/residue: 0.8078 time to fit residues: 1506.6620 Evaluate side-chains 1055 residues out of total 7134 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 947 time to evaluate : 7.688 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 VAL Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 137 SER Chi-restraints excluded: chain M residue 24 ASN Chi-restraints excluded: chain M residue 28 ILE Chi-restraints excluded: chain M residue 82 GLU Chi-restraints excluded: chain M residue 221 THR Chi-restraints excluded: chain G residue 35 GLU Chi-restraints excluded: chain G residue 71 GLU Chi-restraints excluded: chain S residue 156 ILE Chi-restraints excluded: chain S residue 215 SER Chi-restraints excluded: chain S residue 251 VAL Chi-restraints excluded: chain b residue 197 ILE Chi-restraints excluded: chain b residue 203 SER Chi-restraints excluded: chain b residue 234 GLU Chi-restraints excluded: chain c residue 88 ARG Chi-restraints excluded: chain c residue 200 GLU Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 15 VAL Chi-restraints excluded: chain B residue 61 ILE Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain B residue 117 GLU Chi-restraints excluded: chain C residue 57 THR Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 149 PHE Chi-restraints excluded: chain D residue 39 THR Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain F residue 156 ILE Chi-restraints excluded: chain F residue 251 VAL Chi-restraints excluded: chain H residue 20 GLU Chi-restraints excluded: chain H residue 131 LEU Chi-restraints excluded: chain H residue 234 GLU Chi-restraints excluded: chain I residue 88 ARG Chi-restraints excluded: chain I residue 209 LYS Chi-restraints excluded: chain J residue 15 VAL Chi-restraints excluded: chain J residue 61 ILE Chi-restraints excluded: chain K residue 45 GLU Chi-restraints excluded: chain K residue 107 THR Chi-restraints excluded: chain K residue 149 PHE Chi-restraints excluded: chain K residue 216 ILE Chi-restraints excluded: chain K residue 221 THR Chi-restraints excluded: chain L residue 61 ILE Chi-restraints excluded: chain L residue 121 THR Chi-restraints excluded: chain N residue 550 VAL Chi-restraints excluded: chain O residue 110 LEU Chi-restraints excluded: chain O residue 153 LYS Chi-restraints excluded: chain O residue 154 ASP Chi-restraints excluded: chain O residue 156 ILE Chi-restraints excluded: chain O residue 251 VAL Chi-restraints excluded: chain P residue 203 SER Chi-restraints excluded: chain P residue 209 LYS Chi-restraints excluded: chain Q residue 278 LEU Chi-restraints excluded: chain Q residue 288 LEU Chi-restraints excluded: chain R residue 15 VAL Chi-restraints excluded: chain R residue 61 ILE Chi-restraints excluded: chain R residue 137 SER Chi-restraints excluded: chain T residue 24 ASN Chi-restraints excluded: chain T residue 28 ILE Chi-restraints excluded: chain T residue 82 GLU Chi-restraints excluded: chain T residue 221 THR Chi-restraints excluded: chain U residue 35 GLU Chi-restraints excluded: chain U residue 71 GLU Chi-restraints excluded: chain W residue 215 SER Chi-restraints excluded: chain W residue 251 VAL Chi-restraints excluded: chain X residue 197 ILE Chi-restraints excluded: chain X residue 234 GLU Chi-restraints excluded: chain Y residue 88 ARG Chi-restraints excluded: chain Y residue 200 GLU Chi-restraints excluded: chain Z residue 8 THR Chi-restraints excluded: chain Z residue 15 VAL Chi-restraints excluded: chain Z residue 61 ILE Chi-restraints excluded: chain Z residue 76 LEU Chi-restraints excluded: chain Z residue 117 GLU Chi-restraints excluded: chain 0 residue 57 THR Chi-restraints excluded: chain 0 residue 58 VAL Chi-restraints excluded: chain 0 residue 149 PHE Chi-restraints excluded: chain 1 residue 39 THR Chi-restraints excluded: chain 1 residue 121 THR Chi-restraints excluded: chain 3 residue 153 LYS Chi-restraints excluded: chain 3 residue 156 ILE Chi-restraints excluded: chain 3 residue 251 VAL Chi-restraints excluded: chain 4 residue 20 GLU Chi-restraints excluded: chain 4 residue 131 LEU Chi-restraints excluded: chain 4 residue 234 GLU Chi-restraints excluded: chain 5 residue 88 ARG Chi-restraints excluded: chain 5 residue 209 LYS Chi-restraints excluded: chain 6 residue 15 VAL Chi-restraints excluded: chain 6 residue 61 ILE Chi-restraints excluded: chain 7 residue 45 GLU Chi-restraints excluded: chain 7 residue 107 THR Chi-restraints excluded: chain 7 residue 149 PHE Chi-restraints excluded: chain 7 residue 184 GLU Chi-restraints excluded: chain 7 residue 216 ILE Chi-restraints excluded: chain 7 residue 221 THR Chi-restraints excluded: chain 8 residue 61 ILE Chi-restraints excluded: chain 8 residue 121 THR Chi-restraints excluded: chain 9 residue 550 VAL Chi-restraints excluded: chain a residue 110 LEU Chi-restraints excluded: chain a residue 153 LYS Chi-restraints excluded: chain a residue 154 ASP Chi-restraints excluded: chain a residue 156 ILE Chi-restraints excluded: chain a residue 233 SER Chi-restraints excluded: chain a residue 251 VAL Chi-restraints excluded: chain d residue 203 SER Chi-restraints excluded: chain d residue 209 LYS Chi-restraints excluded: chain e residue 209 LYS Chi-restraints excluded: chain e residue 278 LEU Chi-restraints excluded: chain e residue 288 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 786 random chunks: chunk 689 optimal weight: 8.9990 chunk 725 optimal weight: 0.6980 chunk 662 optimal weight: 0.9990 chunk 705 optimal weight: 7.9990 chunk 424 optimal weight: 7.9990 chunk 307 optimal weight: 10.0000 chunk 554 optimal weight: 10.0000 chunk 216 optimal weight: 6.9990 chunk 637 optimal weight: 7.9990 chunk 667 optimal weight: 6.9990 chunk 703 optimal weight: 10.0000 overall best weight: 4.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 154 ASN r 551 GLN ** c 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 237 GLN ** O 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 551 GLN ** Y 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 5 237 GLN ** a 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7548 moved from start: 0.3240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 66918 Z= 0.362 Angle : 0.578 7.882 90600 Z= 0.309 Chirality : 0.046 0.183 9960 Planarity : 0.004 0.044 11694 Dihedral : 5.496 60.425 8898 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 2.47 % Allowed : 14.72 % Favored : 82.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -0.14 (0.09), residues: 8010 helix: 1.11 (0.13), residues: 1626 sheet: -0.19 (0.11), residues: 2202 loop : -0.44 (0.09), residues: 4182 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP I 239 HIS 0.010 0.001 HIS Y 77 PHE 0.023 0.002 PHE M 149 TYR 0.016 0.001 TYR A 133 ARG 0.007 0.001 ARG Q 81 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16020 Ramachandran restraints generated. 8010 Oldfield, 0 Emsley, 8010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16020 Ramachandran restraints generated. 8010 Oldfield, 0 Emsley, 8010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1139 residues out of total 7134 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 176 poor density : 963 time to evaluate : 5.710 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 LYS cc_start: 0.8861 (mttm) cc_final: 0.8502 (mttp) REVERT: A 31 SER cc_start: 0.8687 (t) cc_final: 0.8424 (m) REVERT: A 48 MET cc_start: 0.8798 (mmm) cc_final: 0.8336 (mmm) REVERT: M 81 GLN cc_start: 0.7345 (tt0) cc_final: 0.6948 (tp40) REVERT: M 137 TYR cc_start: 0.7717 (t80) cc_final: 0.7304 (t80) REVERT: M 146 LYS cc_start: 0.7112 (mtmm) cc_final: 0.6193 (mmtm) REVERT: M 159 ASN cc_start: 0.7402 (t0) cc_final: 0.7127 (t0) REVERT: M 183 GLU cc_start: 0.7660 (tt0) cc_final: 0.7352 (mt-10) REVERT: G 18 MET cc_start: 0.8111 (mtp) cc_final: 0.7798 (mtp) REVERT: G 48 MET cc_start: 0.8315 (mtp) cc_final: 0.8001 (mtt) REVERT: G 99 LEU cc_start: 0.7480 (tp) cc_final: 0.7047 (mp) REVERT: S 98 MET cc_start: 0.8980 (ttp) cc_final: 0.8758 (ttm) REVERT: S 254 ASP cc_start: 0.7914 (m-30) cc_final: 0.7693 (m-30) REVERT: b 37 ILE cc_start: 0.7176 (pt) cc_final: 0.6579 (mt) REVERT: b 44 ASP cc_start: 0.7758 (m-30) cc_final: 0.7041 (m-30) REVERT: b 68 GLN cc_start: 0.7732 (mm-40) cc_final: 0.6929 (mp10) REVERT: b 208 ARG cc_start: 0.6982 (ptt-90) cc_final: 0.6628 (ptp90) REVERT: b 234 GLU cc_start: 0.6807 (OUTLIER) cc_final: 0.6090 (mm-30) REVERT: c 112 SER cc_start: 0.7734 (m) cc_final: 0.7525 (m) REVERT: c 138 ILE cc_start: 0.8117 (mm) cc_final: 0.7816 (mt) REVERT: c 209 LYS cc_start: 0.8170 (mmmt) cc_final: 0.7953 (mmtp) REVERT: c 285 LYS cc_start: 0.7577 (ttpt) cc_final: 0.6856 (tmmt) REVERT: B 20 LYS cc_start: 0.8759 (mttm) cc_final: 0.8311 (mttp) REVERT: B 84 GLU cc_start: 0.8893 (OUTLIER) cc_final: 0.8457 (pm20) REVERT: C 24 ASN cc_start: 0.7412 (t0) cc_final: 0.7008 (m-40) REVERT: C 137 TYR cc_start: 0.7788 (t80) cc_final: 0.7465 (t80) REVERT: C 146 LYS cc_start: 0.7007 (mtmm) cc_final: 0.6013 (mmtp) REVERT: F 153 LYS cc_start: 0.8294 (tttm) cc_final: 0.7891 (pttt) REVERT: H 37 ILE cc_start: 0.7401 (pt) cc_final: 0.6668 (mt) REVERT: H 68 GLN cc_start: 0.7985 (mm-40) cc_final: 0.6983 (mp10) REVERT: H 198 ARG cc_start: 0.7697 (ttt-90) cc_final: 0.7333 (ttt180) REVERT: H 225 GLN cc_start: 0.7086 (tt0) cc_final: 0.6860 (tt0) REVERT: H 234 GLU cc_start: 0.6818 (OUTLIER) cc_final: 0.6066 (mm-30) REVERT: H 269 MET cc_start: 0.7742 (tpp) cc_final: 0.7415 (tpp) REVERT: I 33 ASP cc_start: 0.6613 (t70) cc_final: 0.6212 (p0) REVERT: I 88 ARG cc_start: 0.7252 (OUTLIER) cc_final: 0.6934 (mtm-85) REVERT: I 138 ILE cc_start: 0.7974 (mm) cc_final: 0.7529 (mt) REVERT: I 209 LYS cc_start: 0.8630 (OUTLIER) cc_final: 0.7853 (mtpt) REVERT: I 269 MET cc_start: 0.6979 (OUTLIER) cc_final: 0.6469 (tpt) REVERT: J 20 LYS cc_start: 0.8703 (mttm) cc_final: 0.8371 (mttp) REVERT: J 61 ILE cc_start: 0.8229 (OUTLIER) cc_final: 0.7930 (tp) REVERT: J 87 LYS cc_start: 0.8484 (mtmt) cc_final: 0.7976 (mttm) REVERT: K 137 TYR cc_start: 0.7992 (t80) cc_final: 0.7421 (t80) REVERT: K 184 GLU cc_start: 0.7772 (tt0) cc_final: 0.7447 (tt0) REVERT: L 6 LYS cc_start: 0.8227 (mtpt) cc_final: 0.7897 (mtpp) REVERT: L 99 LEU cc_start: 0.7473 (tp) cc_final: 0.6990 (mp) REVERT: L 113 ASN cc_start: 0.7055 (m-40) cc_final: 0.6798 (m-40) REVERT: N 555 GLU cc_start: 0.6432 (tt0) cc_final: 0.5860 (pt0) REVERT: O 254 ASP cc_start: 0.7765 (m-30) cc_final: 0.7389 (m-30) REVERT: P 37 ILE cc_start: 0.7317 (pt) cc_final: 0.6825 (mt) REVERT: P 68 GLN cc_start: 0.7865 (mm-40) cc_final: 0.6895 (mp10) REVERT: P 209 LYS cc_start: 0.7650 (OUTLIER) cc_final: 0.7376 (mmtm) REVERT: Q 33 ASP cc_start: 0.6577 (t70) cc_final: 0.6332 (p0) REVERT: Q 102 MET cc_start: 0.7622 (mmt) cc_final: 0.7240 (mmm) REVERT: Q 138 ILE cc_start: 0.8030 (mm) cc_final: 0.7642 (mt) REVERT: Q 299 MET cc_start: 0.8251 (tmm) cc_final: 0.7809 (tmm) REVERT: R 20 LYS cc_start: 0.8867 (mttm) cc_final: 0.8507 (mttp) REVERT: R 31 SER cc_start: 0.8684 (t) cc_final: 0.8414 (m) REVERT: R 48 MET cc_start: 0.8816 (mmm) cc_final: 0.8354 (mmm) REVERT: T 81 GLN cc_start: 0.7369 (tt0) cc_final: 0.7004 (tp40) REVERT: T 137 TYR cc_start: 0.7713 (t80) cc_final: 0.7298 (t80) REVERT: T 146 LYS cc_start: 0.7112 (mtmm) cc_final: 0.6191 (mmtm) REVERT: T 154 ASN cc_start: 0.6794 (m-40) cc_final: 0.6530 (m110) REVERT: T 159 ASN cc_start: 0.7403 (t0) cc_final: 0.7149 (t0) REVERT: T 183 GLU cc_start: 0.7655 (tt0) cc_final: 0.7358 (mt-10) REVERT: U 18 MET cc_start: 0.8114 (mtp) cc_final: 0.7799 (mtp) REVERT: U 48 MET cc_start: 0.8314 (mtp) cc_final: 0.8002 (mtt) REVERT: U 99 LEU cc_start: 0.7479 (tp) cc_final: 0.7044 (mp) REVERT: W 98 MET cc_start: 0.8979 (ttp) cc_final: 0.8757 (ttm) REVERT: W 254 ASP cc_start: 0.7915 (m-30) cc_final: 0.7693 (m-30) REVERT: X 37 ILE cc_start: 0.7185 (pt) cc_final: 0.6581 (mt) REVERT: X 44 ASP cc_start: 0.7759 (m-30) cc_final: 0.7013 (m-30) REVERT: X 68 GLN cc_start: 0.7732 (mm-40) cc_final: 0.6931 (mp10) REVERT: X 208 ARG cc_start: 0.6990 (ptt-90) cc_final: 0.6635 (ptp90) REVERT: X 234 GLU cc_start: 0.6807 (OUTLIER) cc_final: 0.6092 (mm-30) REVERT: Y 112 SER cc_start: 0.7733 (m) cc_final: 0.7521 (m) REVERT: Y 138 ILE cc_start: 0.8114 (mm) cc_final: 0.7814 (mt) REVERT: Y 209 LYS cc_start: 0.8174 (mmmt) cc_final: 0.7957 (mmtp) REVERT: Y 285 LYS cc_start: 0.7572 (ttpt) cc_final: 0.6853 (tmmt) REVERT: Z 20 LYS cc_start: 0.8758 (mttm) cc_final: 0.8309 (mttp) REVERT: Z 84 GLU cc_start: 0.8893 (OUTLIER) cc_final: 0.8455 (pm20) REVERT: 0 24 ASN cc_start: 0.7397 (t0) cc_final: 0.6978 (m-40) REVERT: 0 137 TYR cc_start: 0.7859 (t80) cc_final: 0.7547 (t80) REVERT: 0 146 LYS cc_start: 0.7006 (mtmm) cc_final: 0.6012 (mmtp) REVERT: 4 37 ILE cc_start: 0.7417 (pt) cc_final: 0.6690 (mt) REVERT: 4 68 GLN cc_start: 0.7988 (mm-40) cc_final: 0.6984 (mp10) REVERT: 4 198 ARG cc_start: 0.7693 (ttt-90) cc_final: 0.7329 (ttt180) REVERT: 4 225 GLN cc_start: 0.7087 (tt0) cc_final: 0.6861 (tt0) REVERT: 4 234 GLU cc_start: 0.6819 (OUTLIER) cc_final: 0.6070 (mm-30) REVERT: 4 269 MET cc_start: 0.7752 (tpp) cc_final: 0.7446 (tpp) REVERT: 5 33 ASP cc_start: 0.6612 (t70) cc_final: 0.6209 (p0) REVERT: 5 88 ARG cc_start: 0.7239 (OUTLIER) cc_final: 0.6924 (mtm-85) REVERT: 5 138 ILE cc_start: 0.7975 (mm) cc_final: 0.7531 (mt) REVERT: 5 209 LYS cc_start: 0.8635 (OUTLIER) cc_final: 0.7854 (mtpt) REVERT: 5 269 MET cc_start: 0.6978 (OUTLIER) cc_final: 0.6467 (tpt) REVERT: 6 20 LYS cc_start: 0.8703 (mttm) cc_final: 0.8372 (mttp) REVERT: 6 61 ILE cc_start: 0.8240 (OUTLIER) cc_final: 0.7938 (tp) REVERT: 6 87 LYS cc_start: 0.8486 (mtmt) cc_final: 0.7976 (mttm) REVERT: 7 137 TYR cc_start: 0.7993 (t80) cc_final: 0.7421 (t80) REVERT: 7 159 ASN cc_start: 0.7273 (t0) cc_final: 0.7036 (t0) REVERT: 8 99 LEU cc_start: 0.7480 (tp) cc_final: 0.6992 (mp) REVERT: 8 113 ASN cc_start: 0.7059 (m-40) cc_final: 0.6804 (m-40) REVERT: 9 555 GLU cc_start: 0.6430 (tt0) cc_final: 0.5864 (pt0) REVERT: a 254 ASP cc_start: 0.7774 (m-30) cc_final: 0.7396 (m-30) REVERT: d 37 ILE cc_start: 0.7321 (pt) cc_final: 0.6832 (mt) REVERT: d 68 GLN cc_start: 0.7867 (mm-40) cc_final: 0.6898 (mp10) REVERT: d 209 LYS cc_start: 0.7655 (OUTLIER) cc_final: 0.7379 (mmtm) REVERT: e 33 ASP cc_start: 0.6577 (t70) cc_final: 0.6336 (p0) REVERT: e 102 MET cc_start: 0.7622 (mmt) cc_final: 0.7241 (mmm) REVERT: e 138 ILE cc_start: 0.8031 (mm) cc_final: 0.7642 (mt) REVERT: e 299 MET cc_start: 0.8253 (tmm) cc_final: 0.7810 (tmm) outliers start: 176 outliers final: 132 residues processed: 1083 average time/residue: 0.6170 time to fit residues: 1130.4655 Evaluate side-chains 1087 residues out of total 7134 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 148 poor density : 939 time to evaluate : 5.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 VAL Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 137 SER Chi-restraints excluded: chain M residue 24 ASN Chi-restraints excluded: chain M residue 28 ILE Chi-restraints excluded: chain M residue 74 LEU Chi-restraints excluded: chain M residue 221 THR Chi-restraints excluded: chain G residue 35 GLU Chi-restraints excluded: chain G residue 100 THR Chi-restraints excluded: chain G residue 121 THR Chi-restraints excluded: chain S residue 137 THR Chi-restraints excluded: chain S residue 156 ILE Chi-restraints excluded: chain S residue 215 SER Chi-restraints excluded: chain S residue 226 THR Chi-restraints excluded: chain S residue 251 VAL Chi-restraints excluded: chain b residue 197 ILE Chi-restraints excluded: chain b residue 203 SER Chi-restraints excluded: chain b residue 234 GLU Chi-restraints excluded: chain c residue 88 ARG Chi-restraints excluded: chain c residue 98 THR Chi-restraints excluded: chain c residue 200 GLU Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 15 VAL Chi-restraints excluded: chain B residue 61 ILE Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain B residue 84 GLU Chi-restraints excluded: chain B residue 117 GLU Chi-restraints excluded: chain C residue 57 THR Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain C residue 149 PHE Chi-restraints excluded: chain C residue 189 VAL Chi-restraints excluded: chain D residue 39 THR Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain F residue 137 THR Chi-restraints excluded: chain F residue 156 ILE Chi-restraints excluded: chain F residue 233 SER Chi-restraints excluded: chain F residue 251 VAL Chi-restraints excluded: chain H residue 20 GLU Chi-restraints excluded: chain H residue 131 LEU Chi-restraints excluded: chain H residue 234 GLU Chi-restraints excluded: chain H residue 262 ILE Chi-restraints excluded: chain I residue 61 VAL Chi-restraints excluded: chain I residue 88 ARG Chi-restraints excluded: chain I residue 98 THR Chi-restraints excluded: chain I residue 209 LYS Chi-restraints excluded: chain I residue 269 MET Chi-restraints excluded: chain J residue 15 VAL Chi-restraints excluded: chain J residue 61 ILE Chi-restraints excluded: chain K residue 45 GLU Chi-restraints excluded: chain K residue 57 THR Chi-restraints excluded: chain K residue 98 THR Chi-restraints excluded: chain K residue 107 THR Chi-restraints excluded: chain K residue 216 ILE Chi-restraints excluded: chain K residue 221 THR Chi-restraints excluded: chain L residue 61 ILE Chi-restraints excluded: chain L residue 117 GLU Chi-restraints excluded: chain L residue 121 THR Chi-restraints excluded: chain N residue 550 VAL Chi-restraints excluded: chain O residue 53 ASP Chi-restraints excluded: chain O residue 97 ILE Chi-restraints excluded: chain O residue 110 LEU Chi-restraints excluded: chain O residue 137 THR Chi-restraints excluded: chain O residue 153 LYS Chi-restraints excluded: chain O residue 154 ASP Chi-restraints excluded: chain O residue 156 ILE Chi-restraints excluded: chain O residue 233 SER Chi-restraints excluded: chain O residue 251 VAL Chi-restraints excluded: chain P residue 203 SER Chi-restraints excluded: chain P residue 209 LYS Chi-restraints excluded: chain Q residue 288 LEU Chi-restraints excluded: chain R residue 15 VAL Chi-restraints excluded: chain R residue 61 ILE Chi-restraints excluded: chain R residue 137 SER Chi-restraints excluded: chain T residue 24 ASN Chi-restraints excluded: chain T residue 28 ILE Chi-restraints excluded: chain T residue 74 LEU Chi-restraints excluded: chain T residue 149 PHE Chi-restraints excluded: chain T residue 221 THR Chi-restraints excluded: chain U residue 35 GLU Chi-restraints excluded: chain U residue 100 THR Chi-restraints excluded: chain U residue 121 THR Chi-restraints excluded: chain W residue 137 THR Chi-restraints excluded: chain W residue 153 LYS Chi-restraints excluded: chain W residue 156 ILE Chi-restraints excluded: chain W residue 201 THR Chi-restraints excluded: chain W residue 215 SER Chi-restraints excluded: chain W residue 226 THR Chi-restraints excluded: chain W residue 251 VAL Chi-restraints excluded: chain X residue 197 ILE Chi-restraints excluded: chain X residue 203 SER Chi-restraints excluded: chain X residue 234 GLU Chi-restraints excluded: chain Y residue 88 ARG Chi-restraints excluded: chain Y residue 98 THR Chi-restraints excluded: chain Y residue 200 GLU Chi-restraints excluded: chain Z residue 8 THR Chi-restraints excluded: chain Z residue 15 VAL Chi-restraints excluded: chain Z residue 61 ILE Chi-restraints excluded: chain Z residue 76 LEU Chi-restraints excluded: chain Z residue 84 GLU Chi-restraints excluded: chain Z residue 117 GLU Chi-restraints excluded: chain 0 residue 57 THR Chi-restraints excluded: chain 0 residue 58 VAL Chi-restraints excluded: chain 0 residue 149 PHE Chi-restraints excluded: chain 0 residue 189 VAL Chi-restraints excluded: chain 0 residue 221 THR Chi-restraints excluded: chain 1 residue 35 GLU Chi-restraints excluded: chain 1 residue 39 THR Chi-restraints excluded: chain 1 residue 121 THR Chi-restraints excluded: chain 3 residue 137 THR Chi-restraints excluded: chain 3 residue 153 LYS Chi-restraints excluded: chain 3 residue 156 ILE Chi-restraints excluded: chain 3 residue 198 GLU Chi-restraints excluded: chain 3 residue 233 SER Chi-restraints excluded: chain 3 residue 251 VAL Chi-restraints excluded: chain 4 residue 20 GLU Chi-restraints excluded: chain 4 residue 131 LEU Chi-restraints excluded: chain 4 residue 234 GLU Chi-restraints excluded: chain 4 residue 262 ILE Chi-restraints excluded: chain 5 residue 88 ARG Chi-restraints excluded: chain 5 residue 98 THR Chi-restraints excluded: chain 5 residue 209 LYS Chi-restraints excluded: chain 5 residue 269 MET Chi-restraints excluded: chain 6 residue 15 VAL Chi-restraints excluded: chain 6 residue 61 ILE Chi-restraints excluded: chain 7 residue 45 GLU Chi-restraints excluded: chain 7 residue 57 THR Chi-restraints excluded: chain 7 residue 98 THR Chi-restraints excluded: chain 7 residue 107 THR Chi-restraints excluded: chain 7 residue 184 GLU Chi-restraints excluded: chain 7 residue 216 ILE Chi-restraints excluded: chain 7 residue 221 THR Chi-restraints excluded: chain 8 residue 61 ILE Chi-restraints excluded: chain 8 residue 117 GLU Chi-restraints excluded: chain 8 residue 121 THR Chi-restraints excluded: chain 9 residue 550 VAL Chi-restraints excluded: chain a residue 53 ASP Chi-restraints excluded: chain a residue 97 ILE Chi-restraints excluded: chain a residue 110 LEU Chi-restraints excluded: chain a residue 137 THR Chi-restraints excluded: chain a residue 153 LYS Chi-restraints excluded: chain a residue 154 ASP Chi-restraints excluded: chain a residue 156 ILE Chi-restraints excluded: chain a residue 233 SER Chi-restraints excluded: chain a residue 251 VAL Chi-restraints excluded: chain d residue 203 SER Chi-restraints excluded: chain d residue 209 LYS Chi-restraints excluded: chain e residue 288 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 786 random chunks: chunk 463 optimal weight: 0.9990 chunk 746 optimal weight: 6.9990 chunk 455 optimal weight: 4.9990 chunk 354 optimal weight: 5.9990 chunk 518 optimal weight: 3.9990 chunk 783 optimal weight: 0.6980 chunk 720 optimal weight: 0.9990 chunk 623 optimal weight: 3.9990 chunk 64 optimal weight: 10.0000 chunk 481 optimal weight: 10.0000 chunk 382 optimal weight: 5.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 38 GLN c 68 GLN K 154 ASN ** O 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 38 GLN Y 68 GLN ** Y 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 7 154 ASN ** a 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7517 moved from start: 0.3280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 66918 Z= 0.195 Angle : 0.501 7.943 90600 Z= 0.270 Chirality : 0.043 0.155 9960 Planarity : 0.004 0.043 11694 Dihedral : 5.297 60.001 8898 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer: Outliers : 1.84 % Allowed : 15.52 % Favored : 82.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 0.02 (0.09), residues: 8010 helix: 1.27 (0.13), residues: 1626 sheet: -0.13 (0.11), residues: 2262 loop : -0.33 (0.10), residues: 4122 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP U 119 HIS 0.006 0.001 HIS c 77 PHE 0.017 0.001 PHE 7 149 TYR 0.011 0.001 TYR Y 270 ARG 0.010 0.000 ARG e 81 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16020 Ramachandran restraints generated. 8010 Oldfield, 0 Emsley, 8010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16020 Ramachandran restraints generated. 8010 Oldfield, 0 Emsley, 8010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1083 residues out of total 7134 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 131 poor density : 952 time to evaluate : 5.583 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 LYS cc_start: 0.8888 (mttm) cc_final: 0.8539 (mttp) REVERT: A 31 SER cc_start: 0.8666 (t) cc_final: 0.8394 (m) REVERT: A 48 MET cc_start: 0.8821 (mmm) cc_final: 0.8376 (mmm) REVERT: M 81 GLN cc_start: 0.7258 (tt0) cc_final: 0.6962 (tp40) REVERT: M 137 TYR cc_start: 0.7720 (t80) cc_final: 0.7301 (t80) REVERT: M 146 LYS cc_start: 0.7084 (mtmm) cc_final: 0.6155 (mmtm) REVERT: M 159 ASN cc_start: 0.7378 (t0) cc_final: 0.7055 (t0) REVERT: M 183 GLU cc_start: 0.7607 (tt0) cc_final: 0.7195 (mt-10) REVERT: G 18 MET cc_start: 0.8054 (mtp) cc_final: 0.7749 (mtp) REVERT: G 48 MET cc_start: 0.8288 (mtp) cc_final: 0.7993 (mtt) REVERT: G 71 GLU cc_start: 0.7048 (pm20) cc_final: 0.6625 (pm20) REVERT: G 99 LEU cc_start: 0.7474 (tp) cc_final: 0.7087 (mp) REVERT: S 98 MET cc_start: 0.8925 (ttp) cc_final: 0.8704 (ttm) REVERT: S 254 ASP cc_start: 0.7926 (m-30) cc_final: 0.7699 (m-30) REVERT: b 37 ILE cc_start: 0.7194 (pt) cc_final: 0.6593 (mt) REVERT: b 44 ASP cc_start: 0.7769 (m-30) cc_final: 0.7104 (m-30) REVERT: b 68 GLN cc_start: 0.7730 (mm-40) cc_final: 0.6952 (mp10) REVERT: b 196 MET cc_start: 0.7126 (mmm) cc_final: 0.6826 (tpp) REVERT: b 208 ARG cc_start: 0.6971 (ptt-90) cc_final: 0.6749 (ptp90) REVERT: b 234 GLU cc_start: 0.6683 (OUTLIER) cc_final: 0.5986 (mm-30) REVERT: c 112 SER cc_start: 0.7693 (m) cc_final: 0.7486 (m) REVERT: c 138 ILE cc_start: 0.8101 (mm) cc_final: 0.7805 (mt) REVERT: c 209 LYS cc_start: 0.8128 (mmmt) cc_final: 0.7926 (mmtp) REVERT: c 285 LYS cc_start: 0.7557 (ttpt) cc_final: 0.6839 (tmmt) REVERT: B 20 LYS cc_start: 0.8753 (mttm) cc_final: 0.8382 (mttp) REVERT: B 84 GLU cc_start: 0.8845 (OUTLIER) cc_final: 0.8351 (pm20) REVERT: C 24 ASN cc_start: 0.7463 (t0) cc_final: 0.6972 (m-40) REVERT: C 137 TYR cc_start: 0.7807 (t80) cc_final: 0.7460 (t80) REVERT: C 146 LYS cc_start: 0.7034 (mtmm) cc_final: 0.6076 (mmtt) REVERT: C 218 GLU cc_start: 0.8106 (pt0) cc_final: 0.7647 (tt0) REVERT: F 70 ASN cc_start: 0.8436 (t0) cc_final: 0.8182 (t0) REVERT: F 153 LYS cc_start: 0.8193 (tttm) cc_final: 0.7745 (pttt) REVERT: H 37 ILE cc_start: 0.7440 (pt) cc_final: 0.6728 (mt) REVERT: H 68 GLN cc_start: 0.8001 (mm-40) cc_final: 0.6971 (mp10) REVERT: H 88 ARG cc_start: 0.7544 (mmp80) cc_final: 0.6776 (mmt-90) REVERT: H 198 ARG cc_start: 0.7761 (ttt-90) cc_final: 0.7300 (ttt180) REVERT: H 225 GLN cc_start: 0.6987 (tt0) cc_final: 0.6668 (tt0) REVERT: H 234 GLU cc_start: 0.6782 (OUTLIER) cc_final: 0.6026 (mm-30) REVERT: H 269 MET cc_start: 0.7691 (tpp) cc_final: 0.7466 (tpp) REVERT: I 33 ASP cc_start: 0.6557 (t70) cc_final: 0.6168 (p0) REVERT: I 138 ILE cc_start: 0.7909 (mm) cc_final: 0.7526 (mt) REVERT: I 209 LYS cc_start: 0.8618 (OUTLIER) cc_final: 0.7859 (mtpt) REVERT: I 269 MET cc_start: 0.6929 (tpp) cc_final: 0.6653 (mtt) REVERT: J 20 LYS cc_start: 0.8683 (mttm) cc_final: 0.8362 (mttp) REVERT: J 61 ILE cc_start: 0.8208 (OUTLIER) cc_final: 0.7900 (tp) REVERT: J 87 LYS cc_start: 0.8394 (mtmt) cc_final: 0.7886 (mttm) REVERT: K 137 TYR cc_start: 0.7969 (t80) cc_final: 0.7707 (t80) REVERT: K 184 GLU cc_start: 0.7742 (tt0) cc_final: 0.7436 (tt0) REVERT: K 218 GLU cc_start: 0.7916 (tt0) cc_final: 0.7556 (tt0) REVERT: L 6 LYS cc_start: 0.8291 (mtpt) cc_final: 0.7933 (mtpp) REVERT: L 56 ARG cc_start: 0.8055 (ptm160) cc_final: 0.5541 (mpt180) REVERT: L 99 LEU cc_start: 0.7489 (tp) cc_final: 0.7097 (mp) REVERT: N 555 GLU cc_start: 0.6513 (tt0) cc_final: 0.5868 (pt0) REVERT: O 254 ASP cc_start: 0.7744 (m-30) cc_final: 0.7400 (m-30) REVERT: P 37 ILE cc_start: 0.7326 (pt) cc_final: 0.6839 (mt) REVERT: P 68 GLN cc_start: 0.7859 (mm-40) cc_final: 0.6889 (mp10) REVERT: P 209 LYS cc_start: 0.7619 (OUTLIER) cc_final: 0.7357 (mmtm) REVERT: Q 102 MET cc_start: 0.7627 (mmt) cc_final: 0.7287 (mmm) REVERT: Q 138 ILE cc_start: 0.8093 (mm) cc_final: 0.7482 (mp) REVERT: R 20 LYS cc_start: 0.8893 (mttm) cc_final: 0.8544 (mttp) REVERT: R 31 SER cc_start: 0.8664 (t) cc_final: 0.8385 (m) REVERT: R 48 MET cc_start: 0.8829 (mmm) cc_final: 0.8374 (mmm) REVERT: T 81 GLN cc_start: 0.7246 (tt0) cc_final: 0.6961 (tp40) REVERT: T 137 TYR cc_start: 0.7715 (t80) cc_final: 0.7301 (t80) REVERT: T 146 LYS cc_start: 0.7087 (mtmm) cc_final: 0.6152 (mmtm) REVERT: T 154 ASN cc_start: 0.6727 (m-40) cc_final: 0.6492 (m110) REVERT: T 159 ASN cc_start: 0.7378 (t0) cc_final: 0.7054 (t0) REVERT: T 183 GLU cc_start: 0.7606 (tt0) cc_final: 0.7196 (mt-10) REVERT: U 18 MET cc_start: 0.8052 (mtp) cc_final: 0.7747 (mtp) REVERT: U 48 MET cc_start: 0.8291 (mtp) cc_final: 0.7996 (mtt) REVERT: U 71 GLU cc_start: 0.7043 (pm20) cc_final: 0.6624 (pm20) REVERT: U 99 LEU cc_start: 0.7472 (tp) cc_final: 0.7083 (mp) REVERT: W 98 MET cc_start: 0.8920 (ttp) cc_final: 0.8704 (ttm) REVERT: W 254 ASP cc_start: 0.7927 (m-30) cc_final: 0.7704 (m-30) REVERT: X 37 ILE cc_start: 0.7195 (pt) cc_final: 0.6595 (mt) REVERT: X 44 ASP cc_start: 0.7775 (m-30) cc_final: 0.7115 (m-30) REVERT: X 68 GLN cc_start: 0.7731 (mm-40) cc_final: 0.6952 (mp10) REVERT: X 88 ARG cc_start: 0.7543 (mmp80) cc_final: 0.6965 (mmt-90) REVERT: X 196 MET cc_start: 0.7127 (mmm) cc_final: 0.6831 (tpp) REVERT: X 208 ARG cc_start: 0.6984 (ptt-90) cc_final: 0.6763 (ptp90) REVERT: X 234 GLU cc_start: 0.6685 (OUTLIER) cc_final: 0.5987 (mm-30) REVERT: Y 112 SER cc_start: 0.7690 (m) cc_final: 0.7481 (m) REVERT: Y 138 ILE cc_start: 0.8097 (mm) cc_final: 0.7803 (mt) REVERT: Y 209 LYS cc_start: 0.8135 (mmmt) cc_final: 0.7931 (mmtp) REVERT: Y 285 LYS cc_start: 0.7554 (ttpt) cc_final: 0.6837 (tmmt) REVERT: Z 20 LYS cc_start: 0.8751 (mttm) cc_final: 0.8379 (mttp) REVERT: Z 84 GLU cc_start: 0.8845 (OUTLIER) cc_final: 0.8349 (pm20) REVERT: 0 24 ASN cc_start: 0.7324 (t0) cc_final: 0.6935 (m-40) REVERT: 0 137 TYR cc_start: 0.7808 (t80) cc_final: 0.7459 (t80) REVERT: 0 146 LYS cc_start: 0.7034 (mtmm) cc_final: 0.6076 (mmtt) REVERT: 3 70 ASN cc_start: 0.8440 (t0) cc_final: 0.8185 (t0) REVERT: 4 37 ILE cc_start: 0.7455 (pt) cc_final: 0.6749 (mt) REVERT: 4 68 GLN cc_start: 0.8003 (mm-40) cc_final: 0.6972 (mp10) REVERT: 4 88 ARG cc_start: 0.7534 (mmp80) cc_final: 0.6764 (mmt-90) REVERT: 4 198 ARG cc_start: 0.7754 (ttt-90) cc_final: 0.7296 (ttt180) REVERT: 4 225 GLN cc_start: 0.6988 (tt0) cc_final: 0.6669 (tt0) REVERT: 4 234 GLU cc_start: 0.6782 (OUTLIER) cc_final: 0.6034 (mm-30) REVERT: 4 269 MET cc_start: 0.7695 (tpp) cc_final: 0.7465 (tpp) REVERT: 5 33 ASP cc_start: 0.6555 (t70) cc_final: 0.6166 (p0) REVERT: 5 138 ILE cc_start: 0.7909 (mm) cc_final: 0.7528 (mt) REVERT: 5 209 LYS cc_start: 0.8623 (OUTLIER) cc_final: 0.7862 (mtpt) REVERT: 5 269 MET cc_start: 0.6921 (tpp) cc_final: 0.6652 (mtt) REVERT: 6 20 LYS cc_start: 0.8684 (mttm) cc_final: 0.8362 (mttp) REVERT: 6 61 ILE cc_start: 0.8222 (OUTLIER) cc_final: 0.7910 (tp) REVERT: 6 87 LYS cc_start: 0.8396 (mtmt) cc_final: 0.7886 (mttm) REVERT: 7 137 TYR cc_start: 0.7969 (t80) cc_final: 0.7709 (t80) REVERT: 7 159 ASN cc_start: 0.7274 (t0) cc_final: 0.7036 (t0) REVERT: 7 169 LYS cc_start: 0.8100 (ttpt) cc_final: 0.7815 (tptt) REVERT: 7 218 GLU cc_start: 0.7910 (tt0) cc_final: 0.7559 (tt0) REVERT: 8 99 LEU cc_start: 0.7495 (tp) cc_final: 0.7098 (mp) REVERT: 9 555 GLU cc_start: 0.6513 (tt0) cc_final: 0.5873 (pt0) REVERT: a 254 ASP cc_start: 0.7709 (m-30) cc_final: 0.7355 (m-30) REVERT: d 37 ILE cc_start: 0.7329 (pt) cc_final: 0.6846 (mt) REVERT: d 68 GLN cc_start: 0.7861 (mm-40) cc_final: 0.6893 (mp10) REVERT: d 209 LYS cc_start: 0.7626 (OUTLIER) cc_final: 0.7363 (mmtm) REVERT: e 102 MET cc_start: 0.7624 (mmt) cc_final: 0.7290 (mmm) REVERT: e 138 ILE cc_start: 0.8093 (mm) cc_final: 0.7712 (mt) outliers start: 131 outliers final: 109 residues processed: 1049 average time/residue: 0.6259 time to fit residues: 1104.2848 Evaluate side-chains 1056 residues out of total 7134 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 121 poor density : 935 time to evaluate : 5.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 VAL Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 117 GLU Chi-restraints excluded: chain A residue 137 SER Chi-restraints excluded: chain M residue 24 ASN Chi-restraints excluded: chain M residue 28 ILE Chi-restraints excluded: chain M residue 221 THR Chi-restraints excluded: chain G residue 100 THR Chi-restraints excluded: chain G residue 121 THR Chi-restraints excluded: chain S residue 156 ILE Chi-restraints excluded: chain S residue 215 SER Chi-restraints excluded: chain S residue 251 VAL Chi-restraints excluded: chain b residue 197 ILE Chi-restraints excluded: chain b residue 203 SER Chi-restraints excluded: chain b residue 234 GLU Chi-restraints excluded: chain c residue 88 ARG Chi-restraints excluded: chain c residue 98 THR Chi-restraints excluded: chain c residue 200 GLU Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 15 VAL Chi-restraints excluded: chain B residue 61 ILE Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain B residue 84 GLU Chi-restraints excluded: chain B residue 117 GLU Chi-restraints excluded: chain C residue 57 THR Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 149 PHE Chi-restraints excluded: chain C residue 189 VAL Chi-restraints excluded: chain C residue 250 ILE Chi-restraints excluded: chain D residue 39 THR Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain F residue 156 ILE Chi-restraints excluded: chain F residue 251 VAL Chi-restraints excluded: chain H residue 20 GLU Chi-restraints excluded: chain H residue 131 LEU Chi-restraints excluded: chain H residue 234 GLU Chi-restraints excluded: chain H residue 262 ILE Chi-restraints excluded: chain I residue 61 VAL Chi-restraints excluded: chain I residue 209 LYS Chi-restraints excluded: chain J residue 15 VAL Chi-restraints excluded: chain J residue 61 ILE Chi-restraints excluded: chain K residue 45 GLU Chi-restraints excluded: chain K residue 57 THR Chi-restraints excluded: chain K residue 216 ILE Chi-restraints excluded: chain K residue 221 THR Chi-restraints excluded: chain L residue 61 ILE Chi-restraints excluded: chain L residue 117 GLU Chi-restraints excluded: chain L residue 121 THR Chi-restraints excluded: chain N residue 550 VAL Chi-restraints excluded: chain O residue 110 LEU Chi-restraints excluded: chain O residue 153 LYS Chi-restraints excluded: chain O residue 154 ASP Chi-restraints excluded: chain O residue 156 ILE Chi-restraints excluded: chain O residue 233 SER Chi-restraints excluded: chain O residue 251 VAL Chi-restraints excluded: chain P residue 203 SER Chi-restraints excluded: chain P residue 209 LYS Chi-restraints excluded: chain Q residue 98 THR Chi-restraints excluded: chain Q residue 288 LEU Chi-restraints excluded: chain R residue 15 VAL Chi-restraints excluded: chain R residue 61 ILE Chi-restraints excluded: chain R residue 117 GLU Chi-restraints excluded: chain R residue 137 SER Chi-restraints excluded: chain T residue 24 ASN Chi-restraints excluded: chain T residue 28 ILE Chi-restraints excluded: chain T residue 221 THR Chi-restraints excluded: chain U residue 100 THR Chi-restraints excluded: chain U residue 121 THR Chi-restraints excluded: chain W residue 156 ILE Chi-restraints excluded: chain W residue 215 SER Chi-restraints excluded: chain W residue 251 VAL Chi-restraints excluded: chain X residue 197 ILE Chi-restraints excluded: chain X residue 203 SER Chi-restraints excluded: chain X residue 234 GLU Chi-restraints excluded: chain Y residue 88 ARG Chi-restraints excluded: chain Y residue 98 THR Chi-restraints excluded: chain Y residue 200 GLU Chi-restraints excluded: chain Z residue 8 THR Chi-restraints excluded: chain Z residue 15 VAL Chi-restraints excluded: chain Z residue 61 ILE Chi-restraints excluded: chain Z residue 76 LEU Chi-restraints excluded: chain Z residue 84 GLU Chi-restraints excluded: chain Z residue 117 GLU Chi-restraints excluded: chain 0 residue 57 THR Chi-restraints excluded: chain 0 residue 58 VAL Chi-restraints excluded: chain 0 residue 107 THR Chi-restraints excluded: chain 0 residue 149 PHE Chi-restraints excluded: chain 0 residue 250 ILE Chi-restraints excluded: chain 1 residue 35 GLU Chi-restraints excluded: chain 1 residue 39 THR Chi-restraints excluded: chain 1 residue 121 THR Chi-restraints excluded: chain 3 residue 153 LYS Chi-restraints excluded: chain 3 residue 156 ILE Chi-restraints excluded: chain 3 residue 198 GLU Chi-restraints excluded: chain 3 residue 251 VAL Chi-restraints excluded: chain 4 residue 20 GLU Chi-restraints excluded: chain 4 residue 131 LEU Chi-restraints excluded: chain 4 residue 234 GLU Chi-restraints excluded: chain 4 residue 262 ILE Chi-restraints excluded: chain 5 residue 209 LYS Chi-restraints excluded: chain 6 residue 15 VAL Chi-restraints excluded: chain 6 residue 61 ILE Chi-restraints excluded: chain 7 residue 45 GLU Chi-restraints excluded: chain 7 residue 57 THR Chi-restraints excluded: chain 7 residue 184 GLU Chi-restraints excluded: chain 7 residue 216 ILE Chi-restraints excluded: chain 7 residue 221 THR Chi-restraints excluded: chain 8 residue 61 ILE Chi-restraints excluded: chain 8 residue 117 GLU Chi-restraints excluded: chain 8 residue 121 THR Chi-restraints excluded: chain 9 residue 550 VAL Chi-restraints excluded: chain a residue 110 LEU Chi-restraints excluded: chain a residue 153 LYS Chi-restraints excluded: chain a residue 154 ASP Chi-restraints excluded: chain a residue 156 ILE Chi-restraints excluded: chain a residue 233 SER Chi-restraints excluded: chain a residue 251 VAL Chi-restraints excluded: chain d residue 203 SER Chi-restraints excluded: chain d residue 209 LYS Chi-restraints excluded: chain e residue 98 THR Chi-restraints excluded: chain e residue 288 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 786 random chunks: chunk 495 optimal weight: 0.0670 chunk 664 optimal weight: 10.0000 chunk 191 optimal weight: 9.9990 chunk 574 optimal weight: 5.9990 chunk 92 optimal weight: 5.9990 chunk 173 optimal weight: 20.0000 chunk 624 optimal weight: 0.8980 chunk 261 optimal weight: 10.0000 chunk 641 optimal weight: 10.0000 chunk 79 optimal weight: 0.2980 chunk 115 optimal weight: 9.9990 overall best weight: 2.6522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 159 ASN ** O 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.114291 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2805 r_free = 0.2805 target = 0.090112 restraints weight = 89020.482| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2808 r_free = 0.2808 target = 0.090432 restraints weight = 63160.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2816 r_free = 0.2816 target = 0.091001 restraints weight = 52027.513| |-----------------------------------------------------------------------------| r_work (final): 0.2817 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2813 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2813 r_free = 0.2813 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 1068 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2766 r_free = 0.2766 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 86 | |-----------------------------------------------------------------------------| r_final: 0.2766 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8238 moved from start: 0.3316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 66918 Z= 0.229 Angle : 0.512 8.120 90600 Z= 0.274 Chirality : 0.044 0.154 9960 Planarity : 0.004 0.042 11694 Dihedral : 5.260 60.573 8898 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 2.19 % Allowed : 15.31 % Favored : 82.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 0.03 (0.09), residues: 8010 helix: 1.22 (0.13), residues: 1638 sheet: -0.11 (0.11), residues: 2262 loop : -0.31 (0.10), residues: 4110 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP U 119 HIS 0.007 0.001 HIS c 77 PHE 0.019 0.001 PHE M 149 TYR 0.012 0.001 TYR T 26 ARG 0.009 0.000 ARG Q 81 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 20270.03 seconds wall clock time: 374 minutes 58.00 seconds (22498.00 seconds total)