Starting phenix.real_space_refine on Mon Mar 11 00:31:15 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ozn_13129/03_2024/7ozn_13129.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ozn_13129/03_2024/7ozn_13129.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ozn_13129/03_2024/7ozn_13129.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ozn_13129/03_2024/7ozn_13129.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ozn_13129/03_2024/7ozn_13129.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ozn_13129/03_2024/7ozn_13129.pdb" } resolution = 3.5 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= 0.924 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 10 6.06 5 S 312 5.16 5 C 34364 2.51 5 N 9406 2.21 5 O 10238 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 418": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 571": "OD1" <-> "OD2" Residue "B ASP 66": "OD1" <-> "OD2" Residue "B PHE 88": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 215": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 226": "OE1" <-> "OE2" Residue "B PHE 320": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 341": "OE1" <-> "OE2" Residue "B PHE 364": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 546": "OE1" <-> "OE2" Residue "B GLU 547": "OE1" <-> "OE2" Residue "B GLU 551": "OE1" <-> "OE2" Residue "B PHE 568": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 724": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 816": "OE1" <-> "OE2" Residue "C TYR 230": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 183": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 112": "OD1" <-> "OD2" Residue "G PHE 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 133": "OE1" <-> "OE2" Residue "H PHE 88": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 118": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 16": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 418": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ASP 571": "OD1" <-> "OD2" Residue "N ASP 66": "OD1" <-> "OD2" Residue "N PHE 88": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 215": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 226": "OE1" <-> "OE2" Residue "N PHE 320": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 341": "OE1" <-> "OE2" Residue "N PHE 364": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 546": "OE1" <-> "OE2" Residue "N GLU 547": "OE1" <-> "OE2" Residue "N GLU 551": "OE1" <-> "OE2" Residue "N PHE 568": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 724": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 816": "OE1" <-> "OE2" Residue "O TYR 230": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 183": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ASP 112": "OD1" <-> "OD2" Residue "S PHE 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S GLU 133": "OE1" <-> "OE2" Residue "T PHE 88": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T TYR 118": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U PHE 16": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U TYR 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U PHE 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W PHE 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 54330 Number of models: 1 Model: "" Number of chains: 32 Chain: "A" Number of atoms: 8233 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1033, 8233 Classifications: {'peptide': 1033} Link IDs: {'PCIS': 1, 'PTRANS': 42, 'TRANS': 989} Chain breaks: 6 Chain: "B" Number of atoms: 8179 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1023, 8179 Classifications: {'peptide': 1023} Link IDs: {'PTRANS': 48, 'TRANS': 974} Chain breaks: 2 Chain: "C" Number of atoms: 2059 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2059 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 15, 'TRANS': 241} Chain breaks: 1 Chain: "D" Number of atoms: 1063 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1063 Classifications: {'peptide': 129} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 125} Chain: "E" Number of atoms: 1720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1720 Classifications: {'peptide': 209} Link IDs: {'PTRANS': 11, 'TRANS': 197} Chain: "F" Number of atoms: 635 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 635 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 5, 'TRANS': 73} Chain: "G" Number of atoms: 1351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1351 Classifications: {'peptide': 171} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 160} Chain: "H" Number of atoms: 1186 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 1186 Classifications: {'peptide': 148} Link IDs: {'PTRANS': 4, 'TRANS': 143} Chain: "I" Number of atoms: 927 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 927 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 5, 'TRANS': 108} Chain: "J" Number of atoms: 515 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 515 Classifications: {'peptide': 65} Link IDs: {'PTRANS': 2, 'TRANS': 62} Chain: "K" Number of atoms: 920 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 920 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 8, 'TRANS': 106} Chain: "L" Number of atoms: 372 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 372 Classifications: {'peptide': 44} Link IDs: {'PTRANS': 1, 'TRANS': 42} Chain: "M" Number of atoms: 8233 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1033, 8233 Classifications: {'peptide': 1033} Link IDs: {'PCIS': 1, 'PTRANS': 42, 'TRANS': 989} Chain breaks: 6 Chain: "N" Number of atoms: 8179 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1023, 8179 Classifications: {'peptide': 1023} Link IDs: {'PTRANS': 48, 'TRANS': 974} Chain breaks: 2 Chain: "O" Number of atoms: 2059 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2059 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 15, 'TRANS': 241} Chain breaks: 1 Chain: "P" Number of atoms: 1063 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1063 Classifications: {'peptide': 129} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 125} Chain: "Q" Number of atoms: 1720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1720 Classifications: {'peptide': 209} Link IDs: {'PTRANS': 11, 'TRANS': 197} Chain: "R" Number of atoms: 635 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 635 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 5, 'TRANS': 73} Chain: "S" Number of atoms: 1351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1351 Classifications: {'peptide': 171} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 160} Chain: "T" Number of atoms: 1186 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 1186 Classifications: {'peptide': 148} Link IDs: {'PTRANS': 4, 'TRANS': 143} Chain: "U" Number of atoms: 927 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 927 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 5, 'TRANS': 108} Chain: "V" Number of atoms: 515 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 515 Classifications: {'peptide': 65} Link IDs: {'PTRANS': 2, 'TRANS': 62} Chain: "W" Number of atoms: 920 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 920 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 8, 'TRANS': 106} Chain: "X" Number of atoms: 372 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 372 Classifications: {'peptide': 44} Link IDs: {'PTRANS': 1, 'TRANS': 42} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 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: "U" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "V" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "X" 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 17106 SG CYS C 88 106.686 62.021 14.254 1.00 76.47 S ATOM 17119 SG CYS C 90 103.784 64.186 12.951 1.00 78.53 S ATOM 17154 SG CYS C 94 103.665 60.867 11.758 1.00 69.42 S ATOM 17176 SG CYS C 97 103.204 60.868 15.187 1.00 69.04 S ATOM 24473 SG CYS I 17 24.719 43.565 103.716 1.00 90.76 S ATOM 24497 SG CYS I 20 23.480 46.706 102.167 1.00 93.03 S ATOM 24658 SG CYS I 39 26.168 46.823 105.024 1.00 93.86 S ATOM 24683 SG CYS I 42 22.567 46.036 105.751 1.00 99.62 S ATOM 25035 SG CYS I 86 48.753 11.251 88.909 1.00 81.94 S ATOM 25059 SG CYS I 89 45.920 9.647 86.816 1.00 84.58 S ATOM 25263 SG CYS I 114 48.304 12.339 85.320 1.00 73.45 S ATOM 25298 SG CYS I 119 45.644 13.181 87.837 1.00 82.35 S ATOM 25408 SG CYS J 7 92.166 38.102 35.042 1.00 31.83 S ATOM 25432 SG CYS J 10 95.590 37.053 33.591 1.00 25.96 S ATOM 25696 SG CYS J 44 93.989 35.211 36.583 1.00 22.89 S ATOM 25702 SG CYS J 45 92.643 34.838 33.067 1.00 29.29 S ATOM 26830 SG CYS L 19 57.232 62.318 22.359 1.00 72.62 S ATOM 26849 SG CYS L 22 57.191 61.011 18.829 1.00 73.72 S ATOM 26966 SG CYS L 36 55.604 64.420 19.702 1.00 74.67 S ATOM 26992 SG CYS L 39 53.932 61.133 20.639 1.00 74.38 S ATOM 44266 SG CYS O 88 50.164 152.033 14.252 1.00 74.51 S ATOM 44279 SG CYS O 90 53.066 149.869 12.949 1.00 77.94 S ATOM 44314 SG CYS O 94 53.184 153.187 11.756 1.00 68.90 S ATOM 44336 SG CYS O 97 53.646 153.187 15.184 1.00 68.51 S ATOM 51633 SG CYS U 17 132.150 170.500 103.695 1.00 90.75 S ATOM 51657 SG CYS U 20 133.389 167.358 102.145 1.00 92.58 S ATOM 51818 SG CYS U 39 130.702 167.241 105.004 1.00 94.29 S ATOM 51843 SG CYS U 42 134.303 168.029 105.729 1.00 99.95 S ATOM 52195 SG CYS U 86 108.109 202.810 88.894 1.00 82.62 S ATOM 52219 SG CYS U 89 110.942 204.415 86.800 1.00 87.20 S ATOM 52423 SG CYS U 114 108.557 201.723 85.304 1.00 73.15 S ATOM 52458 SG CYS U 119 111.218 200.880 87.821 1.00 81.74 S ATOM 52568 SG CYS V 7 64.686 175.954 35.037 1.00 31.58 S ATOM 52592 SG CYS V 10 61.262 177.002 33.587 1.00 26.01 S ATOM 52856 SG CYS V 44 62.864 178.845 36.579 1.00 23.59 S ATOM 52862 SG CYS V 45 64.209 179.218 33.062 1.00 28.35 S ATOM 53990 SG CYS X 19 99.620 151.742 22.346 1.00 73.61 S ATOM 54009 SG CYS X 22 99.660 153.049 18.816 1.00 74.90 S ATOM 54126 SG CYS X 36 101.248 149.640 19.688 1.00 76.85 S ATOM 54152 SG CYS X 39 102.920 152.928 20.625 1.00 77.78 S Time building chain proxies: 20.62, per 1000 atoms: 0.38 Number of scatterers: 54330 At special positions: 0 Unit cell: (157.681, 214.871, 149.511, 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 10 29.99 S 312 16.00 O 10238 8.00 N 9406 7.00 C 34364 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 - 3.50 Amino acid : False - 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: 16.28 Conformation dependent library (CDL) restraints added in 7.5 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN C 301 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 94 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 90 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 97 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 88 " pdb=" ZN I 201 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 17 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 42 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 20 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 39 " pdb=" ZN I 202 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 119 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 114 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 86 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 89 " pdb=" ZN J 101 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 45 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 44 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 10 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 7 " pdb=" ZN L 101 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 22 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 36 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 19 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 39 " pdb=" ZN O 301 " pdb="ZN ZN O 301 " - pdb=" SG CYS O 94 " pdb="ZN ZN O 301 " - pdb=" SG CYS O 90 " pdb="ZN ZN O 301 " - pdb=" SG CYS O 97 " pdb="ZN ZN O 301 " - pdb=" SG CYS O 88 " pdb=" ZN U 201 " pdb="ZN ZN U 201 " - pdb=" SG CYS U 42 " pdb="ZN ZN U 201 " - pdb=" SG CYS U 17 " pdb="ZN ZN U 201 " - pdb=" SG CYS U 20 " pdb="ZN ZN U 201 " - pdb=" SG CYS U 39 " pdb=" ZN U 202 " pdb="ZN ZN U 202 " - pdb=" SG CYS U 119 " pdb="ZN ZN U 202 " - pdb=" SG CYS U 114 " pdb="ZN ZN U 202 " - pdb=" SG CYS U 86 " pdb="ZN ZN U 202 " - pdb=" SG CYS U 89 " pdb=" ZN V 101 " pdb="ZN ZN V 101 " - pdb=" SG CYS V 45 " pdb="ZN ZN V 101 " - pdb=" SG CYS V 44 " pdb="ZN ZN V 101 " - pdb=" SG CYS V 7 " pdb="ZN ZN V 101 " - pdb=" SG CYS V 10 " pdb=" ZN X 101 " pdb="ZN ZN X 101 " - pdb=" SG CYS X 22 " pdb="ZN ZN X 101 " - pdb=" SG CYS X 36 " pdb="ZN ZN X 101 " - pdb=" SG CYS X 19 " pdb="ZN ZN X 101 " - pdb=" SG CYS X 39 " Number of angles added : 60 13380 Ramachandran restraints generated. 6690 Oldfield, 0 Emsley, 6690 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 12796 Finding SS restraints... Secondary structure from input PDB file: 234 helices and 80 sheets defined 39.2% alpha, 19.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.24 Creating SS restraints... Processing helix chain 'A' and resid 382 through 388 Processing helix chain 'A' and resid 395 through 397 No H-bonds generated for 'chain 'A' and resid 395 through 397' Processing helix chain 'A' and resid 398 through 409 removed outlier: 3.810A pdb=" N GLY A 409 " --> pdb=" O LEU A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 434 through 439 Processing helix chain 'A' and resid 508 through 519 Processing helix chain 'A' and resid 520 through 525 Processing helix chain 'A' and resid 538 through 549 removed outlier: 3.653A pdb=" N THR A 543 " --> pdb=" O GLN A 539 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N ALA A 544 " --> pdb=" O ASP A 540 " (cutoff:3.500A) Processing helix chain 'A' and resid 556 through 566 removed outlier: 3.661A pdb=" N ASN A 562 " --> pdb=" O GLY A 558 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N PHE A 566 " --> pdb=" O ASN A 562 " (cutoff:3.500A) Processing helix chain 'A' and resid 588 through 596 removed outlier: 3.645A pdb=" N LEU A 594 " --> pdb=" O GLN A 590 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ILE A 595 " --> pdb=" O ILE A 591 " (cutoff:3.500A) Processing helix chain 'A' and resid 610 through 616 removed outlier: 4.047A pdb=" N ASP A 614 " --> pdb=" O PRO A 610 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N SER A 615 " --> pdb=" O ASP A 611 " (cutoff:3.500A) Processing helix chain 'A' and resid 651 through 660 Processing helix chain 'A' and resid 661 through 684 removed outlier: 3.951A pdb=" N ILE A 682 " --> pdb=" O ASN A 678 " (cutoff:3.500A) Processing helix chain 'A' and resid 688 through 693 removed outlier: 3.754A pdb=" N SER A 692 " --> pdb=" O GLY A 688 " (cutoff:3.500A) Processing helix chain 'A' and resid 695 through 722 Processing helix chain 'A' and resid 732 through 760 Processing helix chain 'A' and resid 764 through 773 removed outlier: 3.505A pdb=" N VAL A 770 " --> pdb=" O PHE A 766 " (cutoff:3.500A) Processing helix chain 'A' and resid 777 through 786 Processing helix chain 'A' and resid 832 through 869 removed outlier: 3.571A pdb=" N PHE A 837 " --> pdb=" O PRO A 833 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ALA A 855 " --> pdb=" O ALA A 851 " (cutoff:3.500A) Processing helix chain 'A' and resid 890 through 894 Processing helix chain 'A' and resid 914 through 921 removed outlier: 3.520A pdb=" N LYS A 918 " --> pdb=" O LYS A 914 " (cutoff:3.500A) Processing helix chain 'A' and resid 926 through 934 Processing helix chain 'A' and resid 935 through 945 removed outlier: 3.738A pdb=" N ASN A 945 " --> pdb=" O ASP A 941 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 970 removed outlier: 3.972A pdb=" N GLN A 949 " --> pdb=" O ASN A 945 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ARG A 967 " --> pdb=" O ARG A 963 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N VAL A 968 " --> pdb=" O GLU A 964 " (cutoff:3.500A) Processing helix chain 'A' and resid 982 through 994 Processing helix chain 'A' and resid 1005 through 1020 removed outlier: 3.509A pdb=" N VAL A1009 " --> pdb=" O HIS A1005 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N VAL A1010 " --> pdb=" O PRO A1006 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LYS A1018 " --> pdb=" O LYS A1014 " (cutoff:3.500A) Processing helix chain 'A' and resid 1027 through 1038 Processing helix chain 'A' and resid 1038 through 1049 Processing helix chain 'A' and resid 1050 through 1057 Processing helix chain 'A' and resid 1061 through 1080 Processing helix chain 'A' and resid 1086 through 1101 Proline residue: A1098 - end of helix removed outlier: 4.184A pdb=" N GLN A1101 " --> pdb=" O GLU A1097 " (cutoff:3.500A) Processing helix chain 'A' and resid 1120 through 1129 Processing helix chain 'A' and resid 1145 through 1149 Processing helix chain 'A' and resid 1151 through 1153 No H-bonds generated for 'chain 'A' and resid 1151 through 1153' Processing helix chain 'A' and resid 1154 through 1162 Processing helix chain 'A' and resid 1165 through 1169 removed outlier: 3.588A pdb=" N VAL A1169 " --> pdb=" O THR A1165 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1165 through 1169' Processing helix chain 'A' and resid 1189 through 1199 removed outlier: 3.532A pdb=" N ASN A1194 " --> pdb=" O GLN A1190 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N VAL A1195 " --> pdb=" O GLU A1191 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N MET A1199 " --> pdb=" O VAL A1195 " (cutoff:3.500A) Processing helix chain 'A' and resid 1217 through 1225 Processing helix chain 'A' and resid 1227 through 1240 Processing helix chain 'A' and resid 1262 through 1267 Processing helix chain 'A' and resid 1281 through 1295 Processing helix chain 'A' and resid 1342 through 1348 removed outlier: 3.918A pdb=" N SER A1348 " --> pdb=" O MET A1344 " (cutoff:3.500A) Processing helix chain 'A' and resid 1361 through 1369 Processing helix chain 'A' and resid 1370 through 1389 removed outlier: 3.741A pdb=" N LYS A1376 " --> pdb=" O GLU A1372 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N ASP A1389 " --> pdb=" O VAL A1385 " (cutoff:3.500A) Processing helix chain 'A' and resid 1394 through 1406 Processing helix chain 'A' and resid 1478 through 1482 removed outlier: 4.001A pdb=" N TYR A1482 " --> pdb=" O LYS A1479 " (cutoff:3.500A) Processing helix chain 'B' and resid 18 through 37 removed outlier: 4.307A pdb=" N GLN B 23 " --> pdb=" O PRO B 19 " (cutoff:3.500A) removed outlier: 5.809A pdb=" N GLU B 24 " --> pdb=" O ASP B 20 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N TRP B 27 " --> pdb=" O GLN B 23 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ILE B 30 " --> pdb=" O CYS B 26 " (cutoff:3.500A) Processing helix chain 'B' and resid 40 through 53 removed outlier: 3.604A pdb=" N SER B 46 " --> pdb=" O GLN B 42 " (cutoff:3.500A) Processing helix chain 'B' and resid 53 through 61 Processing helix chain 'B' and resid 109 through 117 removed outlier: 3.572A pdb=" N ARG B 114 " --> pdb=" O PRO B 110 " (cutoff:3.500A) Processing helix chain 'B' and resid 167 through 174 Processing helix chain 'B' and resid 248 through 253 Processing helix chain 'B' and resid 269 through 277 Processing helix chain 'B' and resid 280 through 289 removed outlier: 3.646A pdb=" N ILE B 284 " --> pdb=" O SER B 280 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 310 removed outlier: 4.157A pdb=" N MET B 298 " --> pdb=" O ASP B 294 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N MET B 300 " --> pdb=" O GLU B 296 " (cutoff:3.500A) Proline residue: B 303 - end of helix removed outlier: 3.548A pdb=" N ASP B 306 " --> pdb=" O LYS B 302 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N GLU B 307 " --> pdb=" O PRO B 303 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ALA B 308 " --> pdb=" O SER B 304 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N VAL B 310 " --> pdb=" O ASP B 306 " (cutoff:3.500A) Processing helix chain 'B' and resid 313 through 324 removed outlier: 4.147A pdb=" N ARG B 324 " --> pdb=" O PHE B 320 " (cutoff:3.500A) Processing helix chain 'B' and resid 331 through 345 removed outlier: 3.696A pdb=" N ARG B 335 " --> pdb=" O THR B 331 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ILE B 336 " --> pdb=" O LYS B 332 " (cutoff:3.500A) Processing helix chain 'B' and resid 357 through 378 Processing helix chain 'B' and resid 387 through 389 No H-bonds generated for 'chain 'B' and resid 387 through 389' Processing helix chain 'B' and resid 395 through 426 removed outlier: 3.597A pdb=" N ARG B 405 " --> pdb=" O ALA B 401 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N GLY B 406 " --> pdb=" O PHE B 402 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N MET B 407 " --> pdb=" O LEU B 403 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N LYS B 421 " --> pdb=" O ILE B 417 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N PHE B 422 " --> pdb=" O TYR B 418 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ARG B 425 " --> pdb=" O LYS B 421 " (cutoff:3.500A) Processing helix chain 'B' and resid 430 through 435 removed outlier: 3.545A pdb=" N ALA B 434 " --> pdb=" O ASN B 430 " (cutoff:3.500A) Processing helix chain 'B' and resid 436 through 451 removed outlier: 4.137A pdb=" N ILE B 440 " --> pdb=" O LYS B 436 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N LEU B 444 " --> pdb=" O ILE B 440 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N SER B 447 " --> pdb=" O GLY B 443 " (cutoff:3.500A) Processing helix chain 'B' and resid 474 through 483 Processing helix chain 'B' and resid 490 through 496 Processing helix chain 'B' and resid 502 through 506 removed outlier: 3.511A pdb=" N LEU B 505 " --> pdb=" O HIS B 502 " (cutoff:3.500A) Processing helix chain 'B' and resid 538 through 548 removed outlier: 3.727A pdb=" N GLU B 546 " --> pdb=" O LEU B 542 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N GLU B 547 " --> pdb=" O GLU B 543 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N TRP B 548 " --> pdb=" O PHE B 544 " (cutoff:3.500A) Processing helix chain 'B' and resid 557 through 562 removed outlier: 3.550A pdb=" N ALA B 562 " --> pdb=" O ALA B 559 " (cutoff:3.500A) Processing helix chain 'B' and resid 579 through 593 removed outlier: 3.877A pdb=" N LEU B 583 " --> pdb=" O ASP B 579 " (cutoff:3.500A) Processing helix chain 'B' and resid 607 through 609 No H-bonds generated for 'chain 'B' and resid 607 through 609' Processing helix chain 'B' and resid 636 through 645 Processing helix chain 'B' and resid 652 through 659 removed outlier: 3.985A pdb=" N LEU B 656 " --> pdb=" O SER B 652 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N VAL B 657 " --> pdb=" O TRP B 653 " (cutoff:3.500A) Processing helix chain 'B' and resid 667 through 671 Processing helix chain 'B' and resid 678 through 684 removed outlier: 3.727A pdb=" N LEU B 682 " --> pdb=" O THR B 678 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N GLU B 684 " --> pdb=" O ASP B 680 " (cutoff:3.500A) Processing helix chain 'B' and resid 699 through 704 Processing helix chain 'B' and resid 705 through 710 removed outlier: 3.863A pdb=" N ILE B 710 " --> pdb=" O VAL B 706 " (cutoff:3.500A) Processing helix chain 'B' and resid 718 through 732 removed outlier: 3.535A pdb=" N ALA B 727 " --> pdb=" O THR B 723 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LYS B 730 " --> pdb=" O SER B 726 " (cutoff:3.500A) Processing helix chain 'B' and resid 762 through 767 removed outlier: 4.348A pdb=" N TYR B 766 " --> pdb=" O ARG B 762 " (cutoff:3.500A) Processing helix chain 'B' and resid 798 through 803 Processing helix chain 'B' and resid 969 through 972 Processing helix chain 'B' and resid 977 through 994 removed outlier: 4.242A pdb=" N LEU B 981 " --> pdb=" O THR B 977 " (cutoff:3.500A) Processing helix chain 'B' and resid 1007 through 1017 removed outlier: 3.529A pdb=" N ASP B1017 " --> pdb=" O ASN B1013 " (cutoff:3.500A) Processing helix chain 'B' and resid 1054 through 1061 removed outlier: 3.662A pdb=" N LYS B1058 " --> pdb=" O MET B1054 " (cutoff:3.500A) Processing helix chain 'C' and resid 27 through 40 removed outlier: 3.769A pdb=" N ILE C 39 " --> pdb=" O ARG C 35 " (cutoff:3.500A) Processing helix chain 'C' and resid 60 through 71 removed outlier: 3.686A pdb=" N LEU C 68 " --> pdb=" O ILE C 64 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N GLY C 69 " --> pdb=" O ALA C 65 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N LEU C 70 " --> pdb=" O HIS C 66 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ILE C 71 " --> pdb=" O ARG C 67 " (cutoff:3.500A) Processing helix chain 'C' and resid 77 through 82 Processing helix chain 'C' and resid 118 through 120 No H-bonds generated for 'chain 'C' and resid 118 through 120' Processing helix chain 'C' and resid 173 through 177 Processing helix chain 'C' and resid 240 through 271 removed outlier: 4.143A pdb=" N VAL C 245 " --> pdb=" O PRO C 241 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N LEU C 246 " --> pdb=" O GLU C 242 " (cutoff:3.500A) Processing helix chain 'D' and resid 23 through 28 Processing helix chain 'D' and resid 33 through 51 Processing helix chain 'D' and resid 58 through 71 Processing helix chain 'D' and resid 76 through 89 Processing helix chain 'D' and resid 93 through 104 removed outlier: 3.680A pdb=" N ALA D 98 " --> pdb=" O LYS D 94 " (cutoff:3.500A) Processing helix chain 'D' and resid 107 through 115 Processing helix chain 'D' and resid 115 through 122 removed outlier: 4.098A pdb=" N GLU D 119 " --> pdb=" O ILE D 115 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N GLY D 120 " --> pdb=" O PRO D 116 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N ARG D 121 " --> pdb=" O SER D 117 " (cutoff:3.500A) Processing helix chain 'D' and resid 127 through 138 removed outlier: 3.886A pdb=" N ASP D 133 " --> pdb=" O GLN D 129 " (cutoff:3.500A) Processing helix chain 'E' and resid 3 through 25 removed outlier: 3.644A pdb=" N TYR E 8 " --> pdb=" O GLU E 4 " (cutoff:3.500A) Processing helix chain 'E' and resid 29 through 34 removed outlier: 3.560A pdb=" N LEU E 33 " --> pdb=" O THR E 29 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ASP E 34 " --> pdb=" O GLN E 30 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 29 through 34' Processing helix chain 'E' and resid 36 through 45 removed outlier: 3.540A pdb=" N LYS E 41 " --> pdb=" O LEU E 37 " (cutoff:3.500A) Processing helix chain 'E' and resid 83 through 98 removed outlier: 3.806A pdb=" N GLU E 96 " --> pdb=" O GLN E 92 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N GLU E 97 " --> pdb=" O ARG E 93 " (cutoff:3.500A) Processing helix chain 'E' and resid 111 through 121 removed outlier: 3.594A pdb=" N GLN E 116 " --> pdb=" O PRO E 112 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N SER E 117 " --> pdb=" O SER E 113 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N LEU E 118 " --> pdb=" O ALA E 114 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N VAL E 119 " --> pdb=" O LYS E 115 " (cutoff:3.500A) Processing helix chain 'E' and resid 132 through 136 Processing helix chain 'E' and resid 152 through 164 Processing helix chain 'E' and resid 177 through 184 Processing helix chain 'F' and resid 58 through 75 Processing helix chain 'F' and resid 88 through 100 Processing helix chain 'G' and resid 14 through 18 Processing helix chain 'G' and resid 21 through 34 removed outlier: 3.964A pdb=" N THR G 25 " --> pdb=" O ASN G 21 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N PHE G 31 " --> pdb=" O LYS G 27 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N THR G 32 " --> pdb=" O GLN G 28 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N VAL G 34 " --> pdb=" O LEU G 30 " (cutoff:3.500A) Processing helix chain 'I' and resid 69 through 73 removed outlier: 3.523A pdb=" N VAL I 72 " --> pdb=" O ILE I 69 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N SER I 73 " --> pdb=" O ALA I 70 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 69 through 73' Processing helix chain 'I' and resid 102 through 107 removed outlier: 4.301A pdb=" N ASP I 106 " --> pdb=" O ARG I 103 " (cutoff:3.500A) Processing helix chain 'J' and resid 14 through 26 removed outlier: 4.175A pdb=" N GLU J 19 " --> pdb=" O GLY J 15 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N ALA J 20 " --> pdb=" O ASN J 16 " (cutoff:3.500A) Processing helix chain 'J' and resid 30 through 39 removed outlier: 3.765A pdb=" N LEU J 35 " --> pdb=" O GLU J 31 " (cutoff:3.500A) Processing helix chain 'J' and resid 42 through 51 removed outlier: 3.664A pdb=" N MET J 48 " --> pdb=" O CYS J 44 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LEU J 49 " --> pdb=" O CYS J 45 " (cutoff:3.500A) Processing helix chain 'J' and resid 55 through 60 Processing helix chain 'K' and resid 5 through 10 removed outlier: 3.778A pdb=" N SER K 9 " --> pdb=" O ALA K 6 " (cutoff:3.500A) Processing helix chain 'K' and resid 39 through 53 removed outlier: 4.214A pdb=" N ILE K 45 " --> pdb=" O THR K 41 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ILE K 46 " --> pdb=" O LEU K 42 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N GLN K 49 " --> pdb=" O ILE K 45 " (cutoff:3.500A) Processing helix chain 'K' and resid 65 through 68 Processing helix chain 'K' and resid 82 through 115 removed outlier: 3.855A pdb=" N LYS K 110 " --> pdb=" O ARG K 106 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ASP K 111 " --> pdb=" O VAL K 107 " (cutoff:3.500A) Processing helix chain 'M' and resid 382 through 388 Processing helix chain 'M' and resid 395 through 397 No H-bonds generated for 'chain 'M' and resid 395 through 397' Processing helix chain 'M' and resid 398 through 409 removed outlier: 3.809A pdb=" N GLY M 409 " --> pdb=" O LEU M 405 " (cutoff:3.500A) Processing helix chain 'M' and resid 434 through 439 Processing helix chain 'M' and resid 508 through 519 Processing helix chain 'M' and resid 520 through 525 Processing helix chain 'M' and resid 538 through 549 removed outlier: 3.653A pdb=" N THR M 543 " --> pdb=" O GLN M 539 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N ALA M 544 " --> pdb=" O ASP M 540 " (cutoff:3.500A) Processing helix chain 'M' and resid 556 through 566 removed outlier: 3.661A pdb=" N ASN M 562 " --> pdb=" O GLY M 558 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N PHE M 566 " --> pdb=" O ASN M 562 " (cutoff:3.500A) Processing helix chain 'M' and resid 588 through 596 removed outlier: 3.646A pdb=" N LEU M 594 " --> pdb=" O GLN M 590 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ILE M 595 " --> pdb=" O ILE M 591 " (cutoff:3.500A) Processing helix chain 'M' and resid 610 through 616 removed outlier: 4.047A pdb=" N ASP M 614 " --> pdb=" O PRO M 610 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N SER M 615 " --> pdb=" O ASP M 611 " (cutoff:3.500A) Processing helix chain 'M' and resid 651 through 660 Processing helix chain 'M' and resid 661 through 684 removed outlier: 3.950A pdb=" N ILE M 682 " --> pdb=" O ASN M 678 " (cutoff:3.500A) Processing helix chain 'M' and resid 688 through 693 removed outlier: 3.754A pdb=" N SER M 692 " --> pdb=" O GLY M 688 " (cutoff:3.500A) Processing helix chain 'M' and resid 695 through 722 Processing helix chain 'M' and resid 732 through 760 Processing helix chain 'M' and resid 764 through 773 removed outlier: 3.505A pdb=" N VAL M 770 " --> pdb=" O PHE M 766 " (cutoff:3.500A) Processing helix chain 'M' and resid 777 through 786 Processing helix chain 'M' and resid 832 through 869 removed outlier: 3.571A pdb=" N PHE M 837 " --> pdb=" O PRO M 833 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ALA M 855 " --> pdb=" O ALA M 851 " (cutoff:3.500A) Processing helix chain 'M' and resid 890 through 894 Processing helix chain 'M' and resid 914 through 921 removed outlier: 3.520A pdb=" N LYS M 918 " --> pdb=" O LYS M 914 " (cutoff:3.500A) Processing helix chain 'M' and resid 926 through 934 Processing helix chain 'M' and resid 935 through 945 removed outlier: 3.738A pdb=" N ASN M 945 " --> pdb=" O ASP M 941 " (cutoff:3.500A) Processing helix chain 'M' and resid 945 through 970 removed outlier: 3.972A pdb=" N GLN M 949 " --> pdb=" O ASN M 945 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ARG M 967 " --> pdb=" O ARG M 963 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N VAL M 968 " --> pdb=" O GLU M 964 " (cutoff:3.500A) Processing helix chain 'M' and resid 982 through 994 Processing helix chain 'M' and resid 1005 through 1020 removed outlier: 3.509A pdb=" N VAL M1009 " --> pdb=" O HIS M1005 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N VAL M1010 " --> pdb=" O PRO M1006 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LYS M1018 " --> pdb=" O LYS M1014 " (cutoff:3.500A) Processing helix chain 'M' and resid 1027 through 1038 Processing helix chain 'M' and resid 1038 through 1049 Processing helix chain 'M' and resid 1050 through 1057 Processing helix chain 'M' and resid 1061 through 1080 Processing helix chain 'M' and resid 1086 through 1101 Proline residue: M1098 - end of helix removed outlier: 4.184A pdb=" N GLN M1101 " --> pdb=" O GLU M1097 " (cutoff:3.500A) Processing helix chain 'M' and resid 1120 through 1129 Processing helix chain 'M' and resid 1145 through 1149 Processing helix chain 'M' and resid 1151 through 1153 No H-bonds generated for 'chain 'M' and resid 1151 through 1153' Processing helix chain 'M' and resid 1154 through 1162 Processing helix chain 'M' and resid 1165 through 1169 removed outlier: 3.588A pdb=" N VAL M1169 " --> pdb=" O THR M1165 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 1165 through 1169' Processing helix chain 'M' and resid 1189 through 1199 removed outlier: 3.531A pdb=" N ASN M1194 " --> pdb=" O GLN M1190 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N VAL M1195 " --> pdb=" O GLU M1191 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N MET M1199 " --> pdb=" O VAL M1195 " (cutoff:3.500A) Processing helix chain 'M' and resid 1217 through 1225 Processing helix chain 'M' and resid 1227 through 1240 Processing helix chain 'M' and resid 1262 through 1267 Processing helix chain 'M' and resid 1281 through 1295 Processing helix chain 'M' and resid 1342 through 1348 removed outlier: 3.917A pdb=" N SER M1348 " --> pdb=" O MET M1344 " (cutoff:3.500A) Processing helix chain 'M' and resid 1361 through 1369 Processing helix chain 'M' and resid 1370 through 1389 removed outlier: 3.741A pdb=" N LYS M1376 " --> pdb=" O GLU M1372 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N ASP M1389 " --> pdb=" O VAL M1385 " (cutoff:3.500A) Processing helix chain 'M' and resid 1394 through 1406 Processing helix chain 'M' and resid 1478 through 1482 removed outlier: 4.001A pdb=" N TYR M1482 " --> pdb=" O LYS M1479 " (cutoff:3.500A) Processing helix chain 'N' and resid 18 through 37 removed outlier: 4.307A pdb=" N GLN N 23 " --> pdb=" O PRO N 19 " (cutoff:3.500A) removed outlier: 5.809A pdb=" N GLU N 24 " --> pdb=" O ASP N 20 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N TRP N 27 " --> pdb=" O GLN N 23 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ILE N 30 " --> pdb=" O CYS N 26 " (cutoff:3.500A) Processing helix chain 'N' and resid 40 through 53 removed outlier: 3.604A pdb=" N SER N 46 " --> pdb=" O GLN N 42 " (cutoff:3.500A) Processing helix chain 'N' and resid 53 through 61 Processing helix chain 'N' and resid 109 through 117 removed outlier: 3.572A pdb=" N ARG N 114 " --> pdb=" O PRO N 110 " (cutoff:3.500A) Processing helix chain 'N' and resid 167 through 174 Processing helix chain 'N' and resid 248 through 253 Processing helix chain 'N' and resid 269 through 277 Processing helix chain 'N' and resid 280 through 289 removed outlier: 3.646A pdb=" N ILE N 284 " --> pdb=" O SER N 280 " (cutoff:3.500A) Processing helix chain 'N' and resid 294 through 310 removed outlier: 4.156A pdb=" N MET N 298 " --> pdb=" O ASP N 294 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N MET N 300 " --> pdb=" O GLU N 296 " (cutoff:3.500A) Proline residue: N 303 - end of helix removed outlier: 3.548A pdb=" N ASP N 306 " --> pdb=" O LYS N 302 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N GLU N 307 " --> pdb=" O PRO N 303 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ALA N 308 " --> pdb=" O SER N 304 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N VAL N 310 " --> pdb=" O ASP N 306 " (cutoff:3.500A) Processing helix chain 'N' and resid 313 through 324 removed outlier: 4.146A pdb=" N ARG N 324 " --> pdb=" O PHE N 320 " (cutoff:3.500A) Processing helix chain 'N' and resid 331 through 345 removed outlier: 3.696A pdb=" N ARG N 335 " --> pdb=" O THR N 331 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ILE N 336 " --> pdb=" O LYS N 332 " (cutoff:3.500A) Processing helix chain 'N' and resid 357 through 378 Processing helix chain 'N' and resid 387 through 389 No H-bonds generated for 'chain 'N' and resid 387 through 389' Processing helix chain 'N' and resid 395 through 426 removed outlier: 3.598A pdb=" N ARG N 405 " --> pdb=" O ALA N 401 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N GLY N 406 " --> pdb=" O PHE N 402 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N MET N 407 " --> pdb=" O LEU N 403 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N LYS N 421 " --> pdb=" O ILE N 417 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N PHE N 422 " --> pdb=" O TYR N 418 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ARG N 425 " --> pdb=" O LYS N 421 " (cutoff:3.500A) Processing helix chain 'N' and resid 430 through 435 removed outlier: 3.546A pdb=" N ALA N 434 " --> pdb=" O ASN N 430 " (cutoff:3.500A) Processing helix chain 'N' and resid 436 through 451 removed outlier: 4.136A pdb=" N ILE N 440 " --> pdb=" O LYS N 436 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LEU N 444 " --> pdb=" O ILE N 440 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N SER N 447 " --> pdb=" O GLY N 443 " (cutoff:3.500A) Processing helix chain 'N' and resid 474 through 483 Processing helix chain 'N' and resid 490 through 496 Processing helix chain 'N' and resid 502 through 506 removed outlier: 3.511A pdb=" N LEU N 505 " --> pdb=" O HIS N 502 " (cutoff:3.500A) Processing helix chain 'N' and resid 538 through 548 removed outlier: 3.727A pdb=" N GLU N 546 " --> pdb=" O LEU N 542 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N GLU N 547 " --> pdb=" O GLU N 543 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N TRP N 548 " --> pdb=" O PHE N 544 " (cutoff:3.500A) Processing helix chain 'N' and resid 557 through 562 removed outlier: 3.549A pdb=" N ALA N 562 " --> pdb=" O ALA N 559 " (cutoff:3.500A) Processing helix chain 'N' and resid 579 through 593 removed outlier: 3.877A pdb=" N LEU N 583 " --> pdb=" O ASP N 579 " (cutoff:3.500A) Processing helix chain 'N' and resid 607 through 609 No H-bonds generated for 'chain 'N' and resid 607 through 609' Processing helix chain 'N' and resid 636 through 645 Processing helix chain 'N' and resid 652 through 659 removed outlier: 3.985A pdb=" N LEU N 656 " --> pdb=" O SER N 652 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N VAL N 657 " --> pdb=" O TRP N 653 " (cutoff:3.500A) Processing helix chain 'N' and resid 667 through 671 Processing helix chain 'N' and resid 678 through 684 removed outlier: 3.726A pdb=" N LEU N 682 " --> pdb=" O THR N 678 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N GLU N 684 " --> pdb=" O ASP N 680 " (cutoff:3.500A) Processing helix chain 'N' and resid 699 through 704 Processing helix chain 'N' and resid 705 through 710 removed outlier: 3.863A pdb=" N ILE N 710 " --> pdb=" O VAL N 706 " (cutoff:3.500A) Processing helix chain 'N' and resid 718 through 732 removed outlier: 3.535A pdb=" N ALA N 727 " --> pdb=" O THR N 723 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LYS N 730 " --> pdb=" O SER N 726 " (cutoff:3.500A) Processing helix chain 'N' and resid 762 through 767 removed outlier: 4.348A pdb=" N TYR N 766 " --> pdb=" O ARG N 762 " (cutoff:3.500A) Processing helix chain 'N' and resid 798 through 803 Processing helix chain 'N' and resid 969 through 972 Processing helix chain 'N' and resid 977 through 994 removed outlier: 4.242A pdb=" N LEU N 981 " --> pdb=" O THR N 977 " (cutoff:3.500A) Processing helix chain 'N' and resid 1007 through 1017 removed outlier: 3.528A pdb=" N ASP N1017 " --> pdb=" O ASN N1013 " (cutoff:3.500A) Processing helix chain 'N' and resid 1054 through 1061 removed outlier: 3.662A pdb=" N LYS N1058 " --> pdb=" O MET N1054 " (cutoff:3.500A) Processing helix chain 'O' and resid 27 through 40 removed outlier: 3.769A pdb=" N ILE O 39 " --> pdb=" O ARG O 35 " (cutoff:3.500A) Processing helix chain 'O' and resid 60 through 71 removed outlier: 3.685A pdb=" N LEU O 68 " --> pdb=" O ILE O 64 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N GLY O 69 " --> pdb=" O ALA O 65 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N LEU O 70 " --> pdb=" O HIS O 66 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ILE O 71 " --> pdb=" O ARG O 67 " (cutoff:3.500A) Processing helix chain 'O' and resid 77 through 82 Processing helix chain 'O' and resid 118 through 120 No H-bonds generated for 'chain 'O' and resid 118 through 120' Processing helix chain 'O' and resid 173 through 177 Processing helix chain 'O' and resid 240 through 271 removed outlier: 4.143A pdb=" N VAL O 245 " --> pdb=" O PRO O 241 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N LEU O 246 " --> pdb=" O GLU O 242 " (cutoff:3.500A) Processing helix chain 'P' and resid 23 through 28 Processing helix chain 'P' and resid 33 through 51 Processing helix chain 'P' and resid 58 through 71 Processing helix chain 'P' and resid 76 through 89 Processing helix chain 'P' and resid 93 through 104 removed outlier: 3.680A pdb=" N ALA P 98 " --> pdb=" O LYS P 94 " (cutoff:3.500A) Processing helix chain 'P' and resid 107 through 115 Processing helix chain 'P' and resid 115 through 122 removed outlier: 4.098A pdb=" N GLU P 119 " --> pdb=" O ILE P 115 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N GLY P 120 " --> pdb=" O PRO P 116 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N ARG P 121 " --> pdb=" O SER P 117 " (cutoff:3.500A) Processing helix chain 'P' and resid 127 through 138 removed outlier: 3.887A pdb=" N ASP P 133 " --> pdb=" O GLN P 129 " (cutoff:3.500A) Processing helix chain 'Q' and resid 3 through 25 removed outlier: 3.644A pdb=" N TYR Q 8 " --> pdb=" O GLU Q 4 " (cutoff:3.500A) Processing helix chain 'Q' and resid 29 through 34 removed outlier: 3.560A pdb=" N LEU Q 33 " --> pdb=" O THR Q 29 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ASP Q 34 " --> pdb=" O GLN Q 30 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 29 through 34' Processing helix chain 'Q' and resid 36 through 45 removed outlier: 3.539A pdb=" N LYS Q 41 " --> pdb=" O LEU Q 37 " (cutoff:3.500A) Processing helix chain 'Q' and resid 83 through 98 removed outlier: 3.807A pdb=" N GLU Q 96 " --> pdb=" O GLN Q 92 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N GLU Q 97 " --> pdb=" O ARG Q 93 " (cutoff:3.500A) Processing helix chain 'Q' and resid 111 through 121 removed outlier: 3.593A pdb=" N GLN Q 116 " --> pdb=" O PRO Q 112 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N SER Q 117 " --> pdb=" O SER Q 113 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N LEU Q 118 " --> pdb=" O ALA Q 114 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N VAL Q 119 " --> pdb=" O LYS Q 115 " (cutoff:3.500A) Processing helix chain 'Q' and resid 132 through 136 Processing helix chain 'Q' and resid 152 through 164 Processing helix chain 'Q' and resid 177 through 184 Processing helix chain 'R' and resid 58 through 75 Processing helix chain 'R' and resid 88 through 100 Processing helix chain 'S' and resid 14 through 18 Processing helix chain 'S' and resid 21 through 34 removed outlier: 3.964A pdb=" N THR S 25 " --> pdb=" O ASN S 21 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N PHE S 31 " --> pdb=" O LYS S 27 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N THR S 32 " --> pdb=" O GLN S 28 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N VAL S 34 " --> pdb=" O LEU S 30 " (cutoff:3.500A) Processing helix chain 'U' and resid 69 through 73 removed outlier: 3.523A pdb=" N VAL U 72 " --> pdb=" O ILE U 69 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N SER U 73 " --> pdb=" O ALA U 70 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 69 through 73' Processing helix chain 'U' and resid 102 through 107 removed outlier: 4.301A pdb=" N ASP U 106 " --> pdb=" O ARG U 103 " (cutoff:3.500A) Processing helix chain 'V' and resid 14 through 26 removed outlier: 4.176A pdb=" N GLU V 19 " --> pdb=" O GLY V 15 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N ALA V 20 " --> pdb=" O ASN V 16 " (cutoff:3.500A) Processing helix chain 'V' and resid 30 through 39 removed outlier: 3.765A pdb=" N LEU V 35 " --> pdb=" O GLU V 31 " (cutoff:3.500A) Processing helix chain 'V' and resid 42 through 51 removed outlier: 3.665A pdb=" N MET V 48 " --> pdb=" O CYS V 44 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LEU V 49 " --> pdb=" O CYS V 45 " (cutoff:3.500A) Processing helix chain 'V' and resid 55 through 60 Processing helix chain 'W' and resid 5 through 10 removed outlier: 3.778A pdb=" N SER W 9 " --> pdb=" O ALA W 6 " (cutoff:3.500A) Processing helix chain 'W' and resid 39 through 53 removed outlier: 4.214A pdb=" N ILE W 45 " --> pdb=" O THR W 41 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ILE W 46 " --> pdb=" O LEU W 42 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N GLN W 49 " --> pdb=" O ILE W 45 " (cutoff:3.500A) Processing helix chain 'W' and resid 65 through 68 Processing helix chain 'W' and resid 82 through 115 removed outlier: 3.855A pdb=" N LYS W 110 " --> pdb=" O ARG W 106 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ASP W 111 " --> pdb=" O VAL W 107 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 367 through 369 removed outlier: 6.010A pdb=" N THR A 368 " --> pdb=" O LEU A 484 " (cutoff:3.500A) removed outlier: 6.101A pdb=" N VAL A 378 " --> pdb=" O ARG A 475 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N LEU A 477 " --> pdb=" O VAL A 378 " (cutoff:3.500A) removed outlier: 5.921A pdb=" N VAL A 380 " --> pdb=" O LEU A 477 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 389 through 393 removed outlier: 4.110A pdb=" N TYR A 418 " --> pdb=" O GLU A 447 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N HIS A 449 " --> pdb=" O ALA A 416 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N ALA A 416 " --> pdb=" O HIS A 449 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 554 through 555 Processing sheet with id=AA4, first strand: chain 'A' and resid 579 through 581 removed outlier: 5.383A pdb=" N ILE A 579 " --> pdb=" O TYR H 93 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N TYR H 93 " --> pdb=" O ILE A 579 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N VAL H 91 " --> pdb=" O LYS A 581 " (cutoff:3.500A) removed outlier: 5.764A pdb=" N VAL H 96 " --> pdb=" O SER H 117 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N SER H 117 " --> pdb=" O VAL H 96 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ARG H 98 " --> pdb=" O TYR H 115 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N ARG H 111 " --> pdb=" O ASP H 102 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 579 through 581 removed outlier: 5.383A pdb=" N ILE A 579 " --> pdb=" O TYR H 93 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N TYR H 93 " --> pdb=" O ILE A 579 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N VAL H 91 " --> pdb=" O LYS A 581 " (cutoff:3.500A) removed outlier: 7.109A pdb=" N PHE H 56 " --> pdb=" O ILE H 9 " (cutoff:3.500A) removed outlier: 5.452A pdb=" N ILE H 9 " --> pdb=" O PHE H 56 " (cutoff:3.500A) removed outlier: 7.676A pdb=" N LEU H 58 " --> pdb=" O GLU H 7 " (cutoff:3.500A) removed outlier: 5.110A pdb=" N GLU H 7 " --> pdb=" O LEU H 58 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N ILE H 60 " --> pdb=" O LEU H 5 " (cutoff:3.500A) removed outlier: 5.811A pdb=" N VAL H 12 " --> pdb=" O GLU H 31 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N GLU H 31 " --> pdb=" O VAL H 12 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ASP H 14 " --> pdb=" O HIS H 29 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LEU H 41 " --> pdb=" O LEU H 28 " (cutoff:3.500A) removed outlier: 5.683A pdb=" N LEU H 122 " --> pdb=" O ASP H 42 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N ARG H 111 " --> pdb=" O ASP H 102 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 602 through 605 removed outlier: 3.514A pdb=" N CYS A 602 " --> pdb=" O VAL A 630 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N VAL A 629 " --> pdb=" O ILE A 636 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 789 through 790 Processing sheet with id=AA8, first strand: chain 'A' and resid 872 through 873 Processing sheet with id=AA9, first strand: chain 'A' and resid 902 through 905 Processing sheet with id=AB1, first strand: chain 'A' and resid 1139 through 1142 removed outlier: 3.933A pdb=" N ILE A1335 " --> pdb=" O HIS A1310 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 1243 through 1247 removed outlier: 4.368A pdb=" N LEU A1255 " --> pdb=" O LEU A1216 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ASN A1172 " --> pdb=" O GLU A1215 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N TYR I 54 " --> pdb=" O ILE A1175 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 1320 through 1322 removed outlier: 3.741A pdb=" N LYS A1329 " --> pdb=" O ILE A1321 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 30 through 31 removed outlier: 3.668A pdb=" N GLU D 30 " --> pdb=" O HIS G 4 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N VAL G 76 " --> pdb=" O TYR G 3 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N GLY G 57 " --> pdb=" O LEU A1475 " (cutoff:3.500A) removed outlier: 5.076A pdb=" N LEU A1473 " --> pdb=" O ILE G 59 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 30 through 31 removed outlier: 3.668A pdb=" N GLU D 30 " --> pdb=" O HIS G 4 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N VAL G 76 " --> pdb=" O TYR G 3 " (cutoff:3.500A) removed outlier: 5.130A pdb=" N ILE G 54 " --> pdb=" O PRO G 69 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N LYS G 71 " --> pdb=" O ASP G 52 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N ILE G 75 " --> pdb=" O VAL G 48 " (cutoff:3.500A) removed outlier: 5.861A pdb=" N VAL G 48 " --> pdb=" O ILE G 75 " (cutoff:3.500A) removed outlier: 8.650A pdb=" N PHE G 77 " --> pdb=" O ILE G 46 " (cutoff:3.500A) removed outlier: 7.443A pdb=" N ILE G 46 " --> pdb=" O PHE G 77 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 65 through 67 removed outlier: 3.601A pdb=" N TYR B 84 " --> pdb=" O LEU B 67 " (cutoff:3.500A) removed outlier: 5.437A pdb=" N TYR B 84 " --> pdb=" O ILE B 133 " (cutoff:3.500A) removed outlier: 7.511A pdb=" N ILE B 133 " --> pdb=" O TYR B 84 " (cutoff:3.500A) removed outlier: 5.415A pdb=" N LEU B 86 " --> pdb=" O THR B 131 " (cutoff:3.500A) removed outlier: 7.242A pdb=" N THR B 131 " --> pdb=" O LEU B 86 " (cutoff:3.500A) removed outlier: 5.315A pdb=" N PHE B 88 " --> pdb=" O THR B 129 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N THR B 129 " --> pdb=" O PHE B 88 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N GLN B 90 " --> pdb=" O ASP B 127 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N VAL B 126 " --> pdb=" O PHE B 148 " (cutoff:3.500A) removed outlier: 5.294A pdb=" N PHE B 148 " --> pdb=" O VAL B 126 " (cutoff:3.500A) removed outlier: 7.809A pdb=" N ILE B 128 " --> pdb=" O LYS B 146 " (cutoff:3.500A) removed outlier: 7.292A pdb=" N LYS B 146 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 8.055A pdb=" N LYS B 130 " --> pdb=" O HIS B 144 " (cutoff:3.500A) removed outlier: 7.958A pdb=" N HIS B 144 " --> pdb=" O LYS B 130 " (cutoff:3.500A) removed outlier: 8.260A pdb=" N VAL B 132 " --> pdb=" O THR B 142 " (cutoff:3.500A) removed outlier: 8.188A pdb=" N THR B 142 " --> pdb=" O VAL B 132 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 97 through 98 removed outlier: 3.538A pdb=" N SER B 106 " --> pdb=" O HIS B 98 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 185 through 187 Processing sheet with id=AB9, first strand: chain 'B' and resid 391 through 394 removed outlier: 3.734A pdb=" N ALA B 196 " --> pdb=" O ARG B 484 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 206 through 209 removed outlier: 3.570A pdb=" N PHE B 208 " --> pdb=" O THR B 218 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ILE B 235 " --> pdb=" O CYS B 221 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N SER B 233 " --> pdb=" O SER B 223 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N TRP B 236 " --> pdb=" O THR B 259 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 531 through 532 Processing sheet with id=AC3, first strand: chain 'B' and resid 531 through 532 Processing sheet with id=AC4, first strand: chain 'B' and resid 572 through 573 removed outlier: 5.988A pdb=" N LYS B 566 " --> pdb=" O ILE B 612 " (cutoff:3.500A) removed outlier: 7.244A pdb=" N ILE B 614 " --> pdb=" O LYS B 566 " (cutoff:3.500A) removed outlier: 5.882A pdb=" N PHE B 568 " --> pdb=" O ILE B 614 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 748 through 751 removed outlier: 3.695A pdb=" N SER B 808 " --> pdb=" O ARG B 927 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N LYS B 917 " --> pdb=" O GLU B 818 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N GLN B 906 " --> pdb=" O ARG B 922 " (cutoff:3.500A) removed outlier: 5.628A pdb=" N ARG B 924 " --> pdb=" O VAL B 904 " (cutoff:3.500A) removed outlier: 4.703A pdb=" N VAL B 904 " --> pdb=" O ARG B 924 " (cutoff:3.500A) removed outlier: 7.673A pdb=" N VAL B 926 " --> pdb=" O GLY B 902 " (cutoff:3.500A) removed outlier: 7.342A pdb=" N GLY B 902 " --> pdb=" O VAL B 926 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 748 through 751 removed outlier: 3.695A pdb=" N SER B 808 " --> pdb=" O ARG B 927 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N LYS B 917 " --> pdb=" O GLU B 818 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N GLN B 906 " --> pdb=" O ARG B 922 " (cutoff:3.500A) removed outlier: 5.628A pdb=" N ARG B 924 " --> pdb=" O VAL B 904 " (cutoff:3.500A) removed outlier: 4.703A pdb=" N VAL B 904 " --> pdb=" O ARG B 924 " (cutoff:3.500A) removed outlier: 7.673A pdb=" N VAL B 926 " --> pdb=" O GLY B 902 " (cutoff:3.500A) removed outlier: 7.342A pdb=" N GLY B 902 " --> pdb=" O VAL B 926 " (cutoff:3.500A) removed outlier: 5.038A pdb=" N VAL B 907 " --> pdb=" O LYS L 46 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 759 through 760 Processing sheet with id=AC8, first strand: chain 'B' and resid 1025 through 1026 removed outlier: 7.043A pdb=" N VAL B 794 " --> pdb=" O GLY B 946 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N GLN B 948 " --> pdb=" O VAL B 794 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N MET B 796 " --> pdb=" O GLN B 948 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ILE B 965 " --> pdb=" O ILE B 779 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ILE B 967 " --> pdb=" O ALA B 781 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N PHE B1042 " --> pdb=" O ILE B 782 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 827 through 828 removed outlier: 4.804A pdb=" N CYS B 837 " --> pdb=" O LYS B 889 " (cutoff:3.500A) removed outlier: 7.141A pdb=" N ASP B 891 " --> pdb=" O CYS B 837 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N GLY B 839 " --> pdb=" O ASP B 891 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 865 through 867 removed outlier: 3.610A pdb=" N ILE B 866 " --> pdb=" O THR B 894 " (cutoff:3.500A) removed outlier: 7.481A pdb=" N THR B 894 " --> pdb=" O ILE B 866 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD1 Processing sheet with id=AD2, first strand: chain 'B' and resid 956 through 957 Processing sheet with id=AD3, first strand: chain 'C' and resid 8 through 14 removed outlier: 6.743A pdb=" N LYS C 20 " --> pdb=" O THR C 12 " (cutoff:3.500A) removed outlier: 5.069A pdb=" N LEU C 14 " --> pdb=" O ASN C 18 " (cutoff:3.500A) removed outlier: 7.286A pdb=" N ASN C 18 " --> pdb=" O LEU C 14 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N ASN C 232 " --> pdb=" O VAL C 182 " (cutoff:3.500A) removed outlier: 4.792A pdb=" N VAL C 182 " --> pdb=" O ASN C 232 " (cutoff:3.500A) removed outlier: 5.366A pdb=" N GLU C 234 " --> pdb=" O ALA C 180 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 121 through 122 removed outlier: 6.878A pdb=" N GLU C 158 " --> pdb=" O ASN C 55 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N ASN C 55 " --> pdb=" O GLU C 158 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N ARG C 160 " --> pdb=" O ASP C 53 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N LYS C 166 " --> pdb=" O ILE C 47 " (cutoff:3.500A) removed outlier: 5.738A pdb=" N ILE C 47 " --> pdb=" O LYS C 166 " (cutoff:3.500A) removed outlier: 7.337A pdb=" N GLY C 168 " --> pdb=" O ILE C 45 " (cutoff:3.500A) removed outlier: 5.835A pdb=" N ILE C 45 " --> pdb=" O GLY C 168 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 113 through 116 Processing sheet with id=AD6, first strand: chain 'E' and resid 26 through 27 removed outlier: 4.250A pdb=" N ALA E 63 " --> pdb=" O LEU E 27 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N VAL E 60 " --> pdb=" O VAL E 74 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N VAL E 74 " --> pdb=" O VAL E 60 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N VAL E 62 " --> pdb=" O MET E 72 " (cutoff:3.500A) removed outlier: 4.666A pdb=" N ARG E 101 " --> pdb=" O GLN E 71 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N GLU E 128 " --> pdb=" O ALA E 102 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'E' and resid 81 through 82 removed outlier: 4.082A pdb=" N VAL E 82 " --> pdb=" O GLY E 109 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD7 Processing sheet with id=AD8, first strand: chain 'E' and resid 147 through 151 removed outlier: 3.913A pdb=" N GLU E 147 " --> pdb=" O ILE E 194 " (cutoff:3.500A) removed outlier: 4.723A pdb=" N VAL E 190 " --> pdb=" O MET E 151 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'G' and resid 83 through 92 removed outlier: 7.301A pdb=" N PHE G 98 " --> pdb=" O THR G 90 " (cutoff:3.500A) removed outlier: 5.141A pdb=" N SER G 105 " --> pdb=" O ILE G 157 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N ALA G 159 " --> pdb=" O SER G 105 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N SER G 162 " --> pdb=" O ILE G 147 " (cutoff:3.500A) removed outlier: 5.586A pdb=" N ILE G 147 " --> pdb=" O SER G 162 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N GLU G 83 " --> pdb=" O ILE G 147 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'G' and resid 117 through 118 Processing sheet with id=AE2, first strand: chain 'I' and resid 25 through 28 removed outlier: 3.690A pdb=" N TYR I 25 " --> pdb=" O ALA I 38 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'I' and resid 80 through 81 Processing sheet with id=AE4, first strand: chain 'K' and resid 21 through 23 Processing sheet with id=AE5, first strand: chain 'M' and resid 367 through 369 removed outlier: 6.009A pdb=" N THR M 368 " --> pdb=" O LEU M 484 " (cutoff:3.500A) removed outlier: 6.100A pdb=" N VAL M 378 " --> pdb=" O ARG M 475 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N LEU M 477 " --> pdb=" O VAL M 378 " (cutoff:3.500A) removed outlier: 5.921A pdb=" N VAL M 380 " --> pdb=" O LEU M 477 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'M' and resid 389 through 393 removed outlier: 4.110A pdb=" N TYR M 418 " --> pdb=" O GLU M 447 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N HIS M 449 " --> pdb=" O ALA M 416 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N ALA M 416 " --> pdb=" O HIS M 449 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'M' and resid 554 through 555 Processing sheet with id=AE8, first strand: chain 'M' and resid 579 through 581 removed outlier: 5.382A pdb=" N ILE M 579 " --> pdb=" O TYR T 93 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N TYR T 93 " --> pdb=" O ILE M 579 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N VAL T 91 " --> pdb=" O LYS M 581 " (cutoff:3.500A) removed outlier: 5.764A pdb=" N VAL T 96 " --> pdb=" O SER T 117 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N SER T 117 " --> pdb=" O VAL T 96 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ARG T 98 " --> pdb=" O TYR T 115 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N ARG T 111 " --> pdb=" O ASP T 102 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'M' and resid 579 through 581 removed outlier: 5.382A pdb=" N ILE M 579 " --> pdb=" O TYR T 93 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N TYR T 93 " --> pdb=" O ILE M 579 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N VAL T 91 " --> pdb=" O LYS M 581 " (cutoff:3.500A) removed outlier: 7.108A pdb=" N PHE T 56 " --> pdb=" O ILE T 9 " (cutoff:3.500A) removed outlier: 5.451A pdb=" N ILE T 9 " --> pdb=" O PHE T 56 " (cutoff:3.500A) removed outlier: 7.675A pdb=" N LEU T 58 " --> pdb=" O GLU T 7 " (cutoff:3.500A) removed outlier: 5.110A pdb=" N GLU T 7 " --> pdb=" O LEU T 58 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N ILE T 60 " --> pdb=" O LEU T 5 " (cutoff:3.500A) removed outlier: 5.811A pdb=" N VAL T 12 " --> pdb=" O GLU T 31 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N GLU T 31 " --> pdb=" O VAL T 12 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ASP T 14 " --> pdb=" O HIS T 29 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LEU T 41 " --> pdb=" O LEU T 28 " (cutoff:3.500A) removed outlier: 5.683A pdb=" N LEU T 122 " --> pdb=" O ASP T 42 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N ARG T 111 " --> pdb=" O ASP T 102 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'M' and resid 602 through 605 removed outlier: 3.514A pdb=" N CYS M 602 " --> pdb=" O VAL M 630 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N VAL M 629 " --> pdb=" O ILE M 636 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'M' and resid 789 through 790 Processing sheet with id=AF3, first strand: chain 'M' and resid 872 through 873 Processing sheet with id=AF4, first strand: chain 'M' and resid 902 through 905 Processing sheet with id=AF5, first strand: chain 'M' and resid 1139 through 1142 removed outlier: 3.933A pdb=" N ILE M1335 " --> pdb=" O HIS M1310 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'M' and resid 1243 through 1247 removed outlier: 4.368A pdb=" N LEU M1255 " --> pdb=" O LEU M1216 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ASN M1172 " --> pdb=" O GLU M1215 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N TYR U 54 " --> pdb=" O ILE M1175 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'M' and resid 1320 through 1322 removed outlier: 3.742A pdb=" N LYS M1329 " --> pdb=" O ILE M1321 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'P' and resid 30 through 31 removed outlier: 3.669A pdb=" N GLU P 30 " --> pdb=" O HIS S 4 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N VAL S 76 " --> pdb=" O TYR S 3 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N GLY S 57 " --> pdb=" O LEU M1475 " (cutoff:3.500A) removed outlier: 5.077A pdb=" N LEU M1473 " --> pdb=" O ILE S 59 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'P' and resid 30 through 31 removed outlier: 3.669A pdb=" N GLU P 30 " --> pdb=" O HIS S 4 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N VAL S 76 " --> pdb=" O TYR S 3 " (cutoff:3.500A) removed outlier: 5.130A pdb=" N ILE S 54 " --> pdb=" O PRO S 69 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N LYS S 71 " --> pdb=" O ASP S 52 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N ILE S 75 " --> pdb=" O VAL S 48 " (cutoff:3.500A) removed outlier: 5.861A pdb=" N VAL S 48 " --> pdb=" O ILE S 75 " (cutoff:3.500A) removed outlier: 8.650A pdb=" N PHE S 77 " --> pdb=" O ILE S 46 " (cutoff:3.500A) removed outlier: 7.443A pdb=" N ILE S 46 " --> pdb=" O PHE S 77 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'N' and resid 65 through 67 removed outlier: 3.602A pdb=" N TYR N 84 " --> pdb=" O LEU N 67 " (cutoff:3.500A) removed outlier: 5.438A pdb=" N TYR N 84 " --> pdb=" O ILE N 133 " (cutoff:3.500A) removed outlier: 7.510A pdb=" N ILE N 133 " --> pdb=" O TYR N 84 " (cutoff:3.500A) removed outlier: 5.416A pdb=" N LEU N 86 " --> pdb=" O THR N 131 " (cutoff:3.500A) removed outlier: 7.242A pdb=" N THR N 131 " --> pdb=" O LEU N 86 " (cutoff:3.500A) removed outlier: 5.315A pdb=" N PHE N 88 " --> pdb=" O THR N 129 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N THR N 129 " --> pdb=" O PHE N 88 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N GLN N 90 " --> pdb=" O ASP N 127 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N VAL N 126 " --> pdb=" O PHE N 148 " (cutoff:3.500A) removed outlier: 5.294A pdb=" N PHE N 148 " --> pdb=" O VAL N 126 " (cutoff:3.500A) removed outlier: 7.808A pdb=" N ILE N 128 " --> pdb=" O LYS N 146 " (cutoff:3.500A) removed outlier: 7.292A pdb=" N LYS N 146 " --> pdb=" O ILE N 128 " (cutoff:3.500A) removed outlier: 8.054A pdb=" N LYS N 130 " --> pdb=" O HIS N 144 " (cutoff:3.500A) removed outlier: 7.958A pdb=" N HIS N 144 " --> pdb=" O LYS N 130 " (cutoff:3.500A) removed outlier: 8.259A pdb=" N VAL N 132 " --> pdb=" O THR N 142 " (cutoff:3.500A) removed outlier: 8.188A pdb=" N THR N 142 " --> pdb=" O VAL N 132 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'N' and resid 97 through 98 removed outlier: 3.538A pdb=" N SER N 106 " --> pdb=" O HIS N 98 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'N' and resid 185 through 187 Processing sheet with id=AG4, first strand: chain 'N' and resid 391 through 394 removed outlier: 3.734A pdb=" N ALA N 196 " --> pdb=" O ARG N 484 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'N' and resid 206 through 209 removed outlier: 3.571A pdb=" N PHE N 208 " --> pdb=" O THR N 218 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ILE N 235 " --> pdb=" O CYS N 221 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N SER N 233 " --> pdb=" O SER N 223 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N TRP N 236 " --> pdb=" O THR N 259 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'N' and resid 531 through 532 Processing sheet with id=AG7, first strand: chain 'N' and resid 531 through 532 Processing sheet with id=AG8, first strand: chain 'N' and resid 572 through 573 removed outlier: 5.990A pdb=" N LYS N 566 " --> pdb=" O ILE N 612 " (cutoff:3.500A) removed outlier: 7.244A pdb=" N ILE N 614 " --> pdb=" O LYS N 566 " (cutoff:3.500A) removed outlier: 5.882A pdb=" N PHE N 568 " --> pdb=" O ILE N 614 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'N' and resid 748 through 751 removed outlier: 3.695A pdb=" N SER N 808 " --> pdb=" O ARG N 927 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N LYS N 917 " --> pdb=" O GLU N 818 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N GLN N 906 " --> pdb=" O ARG N 922 " (cutoff:3.500A) removed outlier: 5.628A pdb=" N ARG N 924 " --> pdb=" O VAL N 904 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N VAL N 904 " --> pdb=" O ARG N 924 " (cutoff:3.500A) removed outlier: 7.674A pdb=" N VAL N 926 " --> pdb=" O GLY N 902 " (cutoff:3.500A) removed outlier: 7.342A pdb=" N GLY N 902 " --> pdb=" O VAL N 926 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'N' and resid 748 through 751 removed outlier: 3.695A pdb=" N SER N 808 " --> pdb=" O ARG N 927 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N LYS N 917 " --> pdb=" O GLU N 818 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N GLN N 906 " --> pdb=" O ARG N 922 " (cutoff:3.500A) removed outlier: 5.628A pdb=" N ARG N 924 " --> pdb=" O VAL N 904 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N VAL N 904 " --> pdb=" O ARG N 924 " (cutoff:3.500A) removed outlier: 7.674A pdb=" N VAL N 926 " --> pdb=" O GLY N 902 " (cutoff:3.500A) removed outlier: 7.342A pdb=" N GLY N 902 " --> pdb=" O VAL N 926 " (cutoff:3.500A) removed outlier: 5.038A pdb=" N VAL N 907 " --> pdb=" O LYS X 46 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'N' and resid 759 through 760 Processing sheet with id=AH3, first strand: chain 'N' and resid 1025 through 1026 removed outlier: 7.045A pdb=" N VAL N 794 " --> pdb=" O GLY N 946 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N GLN N 948 " --> pdb=" O VAL N 794 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N MET N 796 " --> pdb=" O GLN N 948 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ILE N 965 " --> pdb=" O ILE N 779 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ILE N 967 " --> pdb=" O ALA N 781 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N PHE N1042 " --> pdb=" O ILE N 782 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'N' and resid 827 through 828 removed outlier: 4.803A pdb=" N CYS N 837 " --> pdb=" O LYS N 889 " (cutoff:3.500A) removed outlier: 7.141A pdb=" N ASP N 891 " --> pdb=" O CYS N 837 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N GLY N 839 " --> pdb=" O ASP N 891 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'N' and resid 865 through 867 removed outlier: 3.609A pdb=" N ILE N 866 " --> pdb=" O THR N 894 " (cutoff:3.500A) removed outlier: 7.480A pdb=" N THR N 894 " --> pdb=" O ILE N 866 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH5 Processing sheet with id=AH6, first strand: chain 'N' and resid 956 through 957 Processing sheet with id=AH7, first strand: chain 'O' and resid 8 through 14 removed outlier: 6.743A pdb=" N LYS O 20 " --> pdb=" O THR O 12 " (cutoff:3.500A) removed outlier: 5.068A pdb=" N LEU O 14 " --> pdb=" O ASN O 18 " (cutoff:3.500A) removed outlier: 7.286A pdb=" N ASN O 18 " --> pdb=" O LEU O 14 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N ASN O 232 " --> pdb=" O VAL O 182 " (cutoff:3.500A) removed outlier: 4.792A pdb=" N VAL O 182 " --> pdb=" O ASN O 232 " (cutoff:3.500A) removed outlier: 5.366A pdb=" N GLU O 234 " --> pdb=" O ALA O 180 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'O' and resid 121 through 122 removed outlier: 6.877A pdb=" N GLU O 158 " --> pdb=" O ASN O 55 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N ASN O 55 " --> pdb=" O GLU O 158 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N ARG O 160 " --> pdb=" O ASP O 53 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N LYS O 166 " --> pdb=" O ILE O 47 " (cutoff:3.500A) removed outlier: 5.738A pdb=" N ILE O 47 " --> pdb=" O LYS O 166 " (cutoff:3.500A) removed outlier: 7.337A pdb=" N GLY O 168 " --> pdb=" O ILE O 45 " (cutoff:3.500A) removed outlier: 5.835A pdb=" N ILE O 45 " --> pdb=" O GLY O 168 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'O' and resid 113 through 116 Processing sheet with id=AI1, first strand: chain 'Q' and resid 26 through 27 removed outlier: 4.250A pdb=" N ALA Q 63 " --> pdb=" O LEU Q 27 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N VAL Q 60 " --> pdb=" O VAL Q 74 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N VAL Q 74 " --> pdb=" O VAL Q 60 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N VAL Q 62 " --> pdb=" O MET Q 72 " (cutoff:3.500A) removed outlier: 4.666A pdb=" N ARG Q 101 " --> pdb=" O GLN Q 71 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N GLU Q 128 " --> pdb=" O ALA Q 102 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'Q' and resid 81 through 82 removed outlier: 4.082A pdb=" N VAL Q 82 " --> pdb=" O GLY Q 109 " (cutoff:3.500A) No H-bonds generated for sheet with id=AI2 Processing sheet with id=AI3, first strand: chain 'Q' and resid 147 through 151 removed outlier: 3.913A pdb=" N GLU Q 147 " --> pdb=" O ILE Q 194 " (cutoff:3.500A) removed outlier: 4.721A pdb=" N VAL Q 190 " --> pdb=" O MET Q 151 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'S' and resid 83 through 92 removed outlier: 7.301A pdb=" N PHE S 98 " --> pdb=" O THR S 90 " (cutoff:3.500A) removed outlier: 5.140A pdb=" N SER S 105 " --> pdb=" O ILE S 157 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N ALA S 159 " --> pdb=" O SER S 105 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N SER S 162 " --> pdb=" O ILE S 147 " (cutoff:3.500A) removed outlier: 5.586A pdb=" N ILE S 147 " --> pdb=" O SER S 162 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N GLU S 83 " --> pdb=" O ILE S 147 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'S' and resid 117 through 118 Processing sheet with id=AI6, first strand: chain 'U' and resid 25 through 28 removed outlier: 3.690A pdb=" N TYR U 25 " --> pdb=" O ALA U 38 " (cutoff:3.500A) Processing sheet with id=AI7, first strand: chain 'U' and resid 80 through 81 Processing sheet with id=AI8, first strand: chain 'W' and resid 21 through 23 2248 hydrogen bonds defined for protein. 6306 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: 22.52 Time building geometry restraints manager: 17.97 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 18153 1.35 - 1.47: 11840 1.47 - 1.58: 24863 1.58 - 1.70: 0 1.70 - 1.82: 496 Bond restraints: 55352 Sorted by residual: bond pdb=" N MET G 1 " pdb=" CA MET G 1 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.97e+00 bond pdb=" N MET J 1 " pdb=" CA MET J 1 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.94e+00 bond pdb=" N MET K 1 " pdb=" CA MET K 1 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.91e+00 bond pdb=" N MET V 1 " pdb=" CA MET V 1 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.90e+00 bond pdb=" N MET S 1 " pdb=" CA MET S 1 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.86e+00 ... (remaining 55347 not shown) Histogram of bond angle deviations from ideal: 100.27 - 107.01: 1642 107.01 - 113.76: 30678 113.76 - 120.50: 21668 120.50 - 127.24: 20238 127.24 - 133.99: 560 Bond angle restraints: 74786 Sorted by residual: angle pdb=" C ASN N 227 " pdb=" CA ASN N 227 " pdb=" CB ASN N 227 " ideal model delta sigma weight residual 110.42 115.35 -4.93 1.99e+00 2.53e-01 6.14e+00 angle pdb=" C ASN B 227 " pdb=" CA ASN B 227 " pdb=" CB ASN B 227 " ideal model delta sigma weight residual 110.42 115.34 -4.92 1.99e+00 2.53e-01 6.12e+00 angle pdb=" N SER N 229 " pdb=" CA SER N 229 " pdb=" C SER N 229 " ideal model delta sigma weight residual 113.55 110.80 2.75 1.26e+00 6.30e-01 4.75e+00 angle pdb=" N SER B 229 " pdb=" CA SER B 229 " pdb=" C SER B 229 " ideal model delta sigma weight residual 113.55 110.88 2.67 1.26e+00 6.30e-01 4.50e+00 angle pdb=" CA ASP M 370 " pdb=" C ASP M 370 " pdb=" N PRO M 371 " ideal model delta sigma weight residual 117.67 119.50 -1.83 8.80e-01 1.29e+00 4.31e+00 ... (remaining 74781 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.89: 30791 17.89 - 35.79: 2494 35.79 - 53.68: 459 53.68 - 71.58: 96 71.58 - 89.47: 80 Dihedral angle restraints: 33920 sinusoidal: 14154 harmonic: 19766 Sorted by residual: dihedral pdb=" CA GLU N 226 " pdb=" C GLU N 226 " pdb=" N ASN N 227 " pdb=" CA ASN N 227 " ideal model delta harmonic sigma weight residual 180.00 -150.49 -29.51 0 5.00e+00 4.00e-02 3.48e+01 dihedral pdb=" CA GLU B 226 " pdb=" C GLU B 226 " pdb=" N ASN B 227 " pdb=" CA ASN B 227 " ideal model delta harmonic sigma weight residual 180.00 -150.51 -29.49 0 5.00e+00 4.00e-02 3.48e+01 dihedral pdb=" CA CYS C 90 " pdb=" C CYS C 90 " pdb=" N GLU C 91 " pdb=" CA GLU C 91 " ideal model delta harmonic sigma weight residual 180.00 161.10 18.90 0 5.00e+00 4.00e-02 1.43e+01 ... (remaining 33917 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 5785 0.030 - 0.060: 1551 0.060 - 0.090: 457 0.090 - 0.120: 522 0.120 - 0.150: 47 Chirality restraints: 8362 Sorted by residual: chirality pdb=" CA ILE M 596 " pdb=" N ILE M 596 " pdb=" C ILE M 596 " pdb=" CB ILE M 596 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.65e-01 chirality pdb=" CA ILE A 596 " pdb=" N ILE A 596 " pdb=" C ILE A 596 " pdb=" CB ILE A 596 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.46e-01 chirality pdb=" CA ILE A 798 " pdb=" N ILE A 798 " pdb=" C ILE A 798 " pdb=" CB ILE A 798 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.13e-01 ... (remaining 8359 not shown) Planarity restraints: 9702 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR A 395 " -0.038 5.00e-02 4.00e+02 5.82e-02 5.41e+00 pdb=" N PRO A 396 " 0.101 5.00e-02 4.00e+02 pdb=" CA PRO A 396 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO A 396 " -0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR M 395 " 0.038 5.00e-02 4.00e+02 5.75e-02 5.30e+00 pdb=" N PRO M 396 " -0.100 5.00e-02 4.00e+02 pdb=" CA PRO M 396 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO M 396 " 0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP L 32 " 0.026 5.00e-02 4.00e+02 3.99e-02 2.55e+00 pdb=" N PRO L 33 " -0.069 5.00e-02 4.00e+02 pdb=" CA PRO L 33 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO L 33 " 0.022 5.00e-02 4.00e+02 ... (remaining 9699 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.64: 798 2.64 - 3.20: 51757 3.20 - 3.77: 84425 3.77 - 4.33: 120549 4.33 - 4.90: 196827 Nonbonded interactions: 454356 Sorted by model distance: nonbonded pdb=" OG1 THR A1184 " pdb=" OE1 GLN A1190 " model vdw 2.073 2.440 nonbonded pdb=" OG1 THR M1184 " pdb=" OE1 GLN M1190 " model vdw 2.074 2.440 nonbonded pdb=" OD2 ASP D 16 " pdb=" OG SER D 18 " model vdw 2.078 2.440 nonbonded pdb=" OD2 ASP P 16 " pdb=" OG SER P 18 " model vdw 2.079 2.440 nonbonded pdb=" OH TYR M 763 " pdb=" OD2 ASP T 23 " model vdw 2.088 2.440 ... (remaining 454351 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'M' } ncs_group { reference = chain 'B' selection = chain 'N' } ncs_group { reference = chain 'C' selection = chain 'O' } ncs_group { reference = chain 'D' selection = chain 'P' } ncs_group { reference = chain 'E' selection = chain 'Q' } ncs_group { reference = chain 'F' selection = chain 'R' } ncs_group { reference = chain 'G' selection = chain 'S' } ncs_group { reference = chain 'H' selection = chain 'T' } ncs_group { reference = chain 'I' selection = chain 'U' } ncs_group { reference = chain 'J' selection = chain 'V' } ncs_group { reference = chain 'K' selection = chain 'W' } ncs_group { reference = chain 'L' selection = chain 'X' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 4.610 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: 18.760 Check model and map are aligned: 0.720 Set scattering table: 0.380 Process input model: 121.130 Find NCS groups from input model: 2.550 Set up NCS constraints: 0.480 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: 0.010 Load rotamer database and sin/cos tables:2.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 150.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6978 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 : 0.002 0.033 55352 Z= 0.120 Angle : 0.421 5.419 74786 Z= 0.243 Chirality : 0.039 0.150 8362 Planarity : 0.002 0.058 9702 Dihedral : 14.096 89.471 21124 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.30 % 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: 1.13 (0.11), residues: 6690 helix: 1.97 (0.12), residues: 2154 sheet: 0.14 (0.17), residues: 972 loop : 0.27 (0.11), residues: 3564 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP A1192 HIS 0.002 0.000 HIS N 460 PHE 0.007 0.000 PHE A 397 TYR 0.011 0.001 TYR N 648 ARG 0.002 0.000 ARG N 938 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13380 Ramachandran restraints generated. 6690 Oldfield, 0 Emsley, 6690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13380 Ramachandran restraints generated. 6690 Oldfield, 0 Emsley, 6690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1719 residues out of total 6024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1719 time to evaluate : 5.022 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 832 THR cc_start: 0.8015 (p) cc_final: 0.7714 (p) REVERT: A 903 PHE cc_start: 0.7287 (m-80) cc_final: 0.6423 (m-80) REVERT: B 513 GLU cc_start: 0.7919 (mt-10) cc_final: 0.7250 (mt-10) REVERT: B 570 ASN cc_start: 0.8236 (m-40) cc_final: 0.7709 (t0) REVERT: B 739 ASN cc_start: 0.6422 (p0) cc_final: 0.6186 (p0) REVERT: B 967 ILE cc_start: 0.9063 (pt) cc_final: 0.8842 (pt) REVERT: C 48 ASP cc_start: 0.6898 (t0) cc_final: 0.6621 (t0) REVERT: E 64 HIS cc_start: 0.7078 (t-90) cc_final: 0.6866 (t70) REVERT: G 29 LYS cc_start: 0.7818 (tppt) cc_final: 0.7531 (tppt) REVERT: G 141 ASP cc_start: 0.6670 (m-30) cc_final: 0.6438 (m-30) REVERT: G 165 ASP cc_start: 0.6675 (t70) cc_final: 0.6402 (t0) REVERT: K 1 MET cc_start: 0.6078 (tmm) cc_final: 0.5823 (ttt) REVERT: K 96 SER cc_start: 0.7880 (m) cc_final: 0.7534 (t) REVERT: M 418 TYR cc_start: 0.7139 (m-80) cc_final: 0.6887 (m-80) REVERT: M 540 ASP cc_start: 0.7172 (t0) cc_final: 0.6964 (t0) REVERT: M 903 PHE cc_start: 0.7487 (m-80) cc_final: 0.6628 (m-80) REVERT: M 955 GLU cc_start: 0.7195 (tt0) cc_final: 0.6984 (tp30) REVERT: N 504 THR cc_start: 0.8054 (p) cc_final: 0.7844 (p) REVERT: N 513 GLU cc_start: 0.7889 (mt-10) cc_final: 0.7364 (mt-10) REVERT: N 664 TYR cc_start: 0.7220 (m-80) cc_final: 0.6991 (m-10) REVERT: N 683 GLN cc_start: 0.7441 (pp30) cc_final: 0.7103 (pt0) REVERT: Q 74 VAL cc_start: 0.6995 (t) cc_final: 0.6604 (t) REVERT: S 117 MET cc_start: 0.7763 (mmm) cc_final: 0.7542 (mmm) REVERT: S 120 ASP cc_start: 0.8098 (p0) cc_final: 0.7883 (p0) REVERT: S 165 ASP cc_start: 0.6678 (t70) cc_final: 0.6458 (t0) REVERT: T 54 ASP cc_start: 0.5061 (m-30) cc_final: 0.4807 (m-30) REVERT: T 82 PRO cc_start: 0.6904 (Cg_endo) cc_final: 0.6611 (Cg_exo) REVERT: W 1 MET cc_start: 0.6464 (tmm) cc_final: 0.5706 (ttt) REVERT: W 70 LYS cc_start: 0.7939 (pttp) cc_final: 0.7543 (pttp) REVERT: W 111 ASP cc_start: 0.7562 (m-30) cc_final: 0.7234 (m-30) outliers start: 0 outliers final: 0 residues processed: 1719 average time/residue: 0.6094 time to fit residues: 1701.6392 Evaluate side-chains 922 residues out of total 6024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 922 time to evaluate : 4.728 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 664 random chunks: chunk 560 optimal weight: 0.8980 chunk 503 optimal weight: 0.8980 chunk 279 optimal weight: 0.6980 chunk 171 optimal weight: 0.0060 chunk 339 optimal weight: 20.0000 chunk 268 optimal weight: 6.9990 chunk 520 optimal weight: 10.0000 chunk 201 optimal weight: 3.9990 chunk 316 optimal weight: 3.9990 chunk 387 optimal weight: 4.9990 chunk 602 optimal weight: 7.9990 overall best weight: 1.2998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 620 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 673 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 780 ASN A1220 HIS A1397 HIS B 43 GLN B 254 GLN ** B 344 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 370 HIS B 930 GLN C 32 ASN C 108 ASN C 111 GLN ** C 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 43 HIS E 30 GLN E 132 GLN ** E 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 14 HIS H 133 HIS ** I 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 46 GLN I 100 HIS I 121 HIS J 26 GLN J 61 ASN M1397 HIS N 43 GLN ** N 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 265 GLN N 344 GLN N 370 HIS ** N 525 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 930 GLN N 941 GLN O 32 ASN O 66 HIS ** O 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 132 GLN S 4 HIS ** S 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 91 GLN ** U 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 121 HIS V 26 GLN V 61 ASN W 40 HIS Total number of N/Q/H flips: 36 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7288 moved from start: 0.2937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 55352 Z= 0.253 Angle : 0.624 8.501 74786 Z= 0.324 Chirality : 0.046 0.300 8362 Planarity : 0.004 0.070 9702 Dihedral : 3.503 29.322 7396 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 11.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 2.66 % Allowed : 11.49 % Favored : 85.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.30 % 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: 0.52 (0.10), residues: 6690 helix: 1.12 (0.11), residues: 2326 sheet: -0.11 (0.16), residues: 1008 loop : 0.05 (0.11), residues: 3356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP N 573 HIS 0.023 0.001 HIS U 60 PHE 0.030 0.002 PHE S 18 TYR 0.017 0.002 TYR M1308 ARG 0.008 0.001 ARG A 954 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13380 Ramachandran restraints generated. 6690 Oldfield, 0 Emsley, 6690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13380 Ramachandran restraints generated. 6690 Oldfield, 0 Emsley, 6690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1181 residues out of total 6024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 160 poor density : 1021 time to evaluate : 4.809 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 903 PHE cc_start: 0.7641 (m-80) cc_final: 0.7024 (m-80) REVERT: B 513 GLU cc_start: 0.7907 (mt-10) cc_final: 0.7532 (mt-10) REVERT: B 550 MET cc_start: 0.7981 (tmm) cc_final: 0.7601 (tmm) REVERT: B 570 ASN cc_start: 0.8190 (m-40) cc_final: 0.7564 (t0) REVERT: B 766 TYR cc_start: 0.7534 (m-80) cc_final: 0.7217 (m-10) REVERT: C 50 VAL cc_start: 0.7750 (t) cc_final: 0.7506 (m) REVERT: E 73 PHE cc_start: 0.6514 (OUTLIER) cc_final: 0.6233 (t80) REVERT: G 27 LYS cc_start: 0.7031 (ttpt) cc_final: 0.6727 (mtmt) REVERT: G 141 ASP cc_start: 0.6915 (m-30) cc_final: 0.6599 (m-30) REVERT: G 165 ASP cc_start: 0.6765 (t70) cc_final: 0.6507 (t0) REVERT: I 46 GLN cc_start: 0.7169 (OUTLIER) cc_final: 0.6868 (pp30) REVERT: J 46 ARG cc_start: 0.7458 (mtp180) cc_final: 0.7248 (mtp180) REVERT: K 1 MET cc_start: 0.6234 (tmm) cc_final: 0.6002 (ttt) REVERT: K 38 GLU cc_start: 0.6303 (mm-30) cc_final: 0.6062 (mm-30) REVERT: K 96 SER cc_start: 0.7869 (m) cc_final: 0.7495 (t) REVERT: M 540 ASP cc_start: 0.7320 (t0) cc_final: 0.6978 (t0) REVERT: M 903 PHE cc_start: 0.7785 (m-80) cc_final: 0.7096 (m-80) REVERT: N 368 MET cc_start: 0.5169 (mtm) cc_final: 0.4925 (ttm) REVERT: N 505 LEU cc_start: 0.8584 (OUTLIER) cc_final: 0.8205 (mp) REVERT: N 683 GLN cc_start: 0.7320 (pp30) cc_final: 0.6998 (pt0) REVERT: N 733 MET cc_start: 0.7316 (ppp) cc_final: 0.7008 (ptm) REVERT: N 766 TYR cc_start: 0.7238 (m-10) cc_final: 0.6782 (m-80) REVERT: Q 73 PHE cc_start: 0.5263 (OUTLIER) cc_final: 0.4983 (t80) REVERT: S 120 ASP cc_start: 0.8044 (p0) cc_final: 0.7660 (p0) REVERT: S 141 ASP cc_start: 0.6957 (m-30) cc_final: 0.6709 (t0) REVERT: W 1 MET cc_start: 0.6565 (tmm) cc_final: 0.5924 (ttt) outliers start: 160 outliers final: 99 residues processed: 1112 average time/residue: 0.5409 time to fit residues: 1004.8334 Evaluate side-chains 914 residues out of total 6024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 811 time to evaluate : 4.768 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 438 LEU Chi-restraints excluded: chain A residue 457 ILE Chi-restraints excluded: chain A residue 509 LEU Chi-restraints excluded: chain A residue 662 HIS Chi-restraints excluded: chain A residue 736 THR Chi-restraints excluded: chain A residue 947 HIS Chi-restraints excluded: chain A residue 1023 VAL Chi-restraints excluded: chain A residue 1027 ASP Chi-restraints excluded: chain A residue 1095 LEU Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 152 ILE Chi-restraints excluded: chain B residue 215 TYR Chi-restraints excluded: chain B residue 291 ASP Chi-restraints excluded: chain B residue 542 LEU Chi-restraints excluded: chain B residue 657 VAL Chi-restraints excluded: chain B residue 678 THR Chi-restraints excluded: chain B residue 909 VAL Chi-restraints excluded: chain C residue 13 GLU Chi-restraints excluded: chain C residue 41 GLU Chi-restraints excluded: chain C residue 114 HIS Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain C residue 154 ARG Chi-restraints excluded: chain C residue 192 LEU Chi-restraints excluded: chain C residue 235 SER Chi-restraints excluded: chain C residue 246 LEU Chi-restraints excluded: chain D residue 31 THR Chi-restraints excluded: chain D residue 50 SER Chi-restraints excluded: chain D residue 68 THR Chi-restraints excluded: chain D residue 76 ASN Chi-restraints excluded: chain E residue 29 THR Chi-restraints excluded: chain E residue 37 LEU Chi-restraints excluded: chain E residue 73 PHE Chi-restraints excluded: chain E residue 151 MET Chi-restraints excluded: chain F residue 54 THR Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain G residue 39 THR Chi-restraints excluded: chain G residue 90 THR Chi-restraints excluded: chain G residue 115 SER Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain I residue 46 GLN Chi-restraints excluded: chain I residue 53 ILE Chi-restraints excluded: chain J residue 54 ASP Chi-restraints excluded: chain K residue 20 THR Chi-restraints excluded: chain K residue 27 VAL Chi-restraints excluded: chain K residue 71 ILE Chi-restraints excluded: chain K residue 78 THR Chi-restraints excluded: chain K residue 93 ASP Chi-restraints excluded: chain M residue 366 VAL Chi-restraints excluded: chain M residue 420 ILE Chi-restraints excluded: chain M residue 438 LEU Chi-restraints excluded: chain M residue 457 ILE Chi-restraints excluded: chain M residue 509 LEU Chi-restraints excluded: chain M residue 553 VAL Chi-restraints excluded: chain M residue 583 ARG Chi-restraints excluded: chain M residue 662 HIS Chi-restraints excluded: chain M residue 736 THR Chi-restraints excluded: chain M residue 1023 VAL Chi-restraints excluded: chain M residue 1095 LEU Chi-restraints excluded: chain M residue 1117 VAL Chi-restraints excluded: chain M residue 1136 THR Chi-restraints excluded: chain M residue 1156 ASP Chi-restraints excluded: chain M residue 1335 ILE Chi-restraints excluded: chain N residue 29 VAL Chi-restraints excluded: chain N residue 215 TYR Chi-restraints excluded: chain N residue 505 LEU Chi-restraints excluded: chain N residue 616 THR Chi-restraints excluded: chain N residue 655 ASP Chi-restraints excluded: chain N residue 657 VAL Chi-restraints excluded: chain N residue 741 HIS Chi-restraints excluded: chain N residue 751 LEU Chi-restraints excluded: chain N residue 909 VAL Chi-restraints excluded: chain O residue 41 GLU Chi-restraints excluded: chain O residue 66 HIS Chi-restraints excluded: chain O residue 115 VAL Chi-restraints excluded: chain O residue 151 VAL Chi-restraints excluded: chain O residue 192 LEU Chi-restraints excluded: chain O residue 235 SER Chi-restraints excluded: chain P residue 31 THR Chi-restraints excluded: chain P residue 62 MET Chi-restraints excluded: chain P residue 68 THR Chi-restraints excluded: chain P residue 76 ASN Chi-restraints excluded: chain P residue 107 THR Chi-restraints excluded: chain Q residue 29 THR Chi-restraints excluded: chain Q residue 64 HIS Chi-restraints excluded: chain Q residue 73 PHE Chi-restraints excluded: chain Q residue 151 MET Chi-restraints excluded: chain S residue 39 THR Chi-restraints excluded: chain S residue 86 ASP Chi-restraints excluded: chain S residue 90 THR Chi-restraints excluded: chain S residue 153 ASP Chi-restraints excluded: chain T residue 110 THR Chi-restraints excluded: chain U residue 53 ILE Chi-restraints excluded: chain U residue 124 THR Chi-restraints excluded: chain V residue 19 GLU Chi-restraints excluded: chain V residue 38 LEU Chi-restraints excluded: chain V residue 54 ASP Chi-restraints excluded: chain W residue 9 SER Chi-restraints excluded: chain W residue 20 THR Chi-restraints excluded: chain W residue 27 VAL Chi-restraints excluded: chain W residue 78 THR Chi-restraints excluded: chain W residue 81 TYR Chi-restraints excluded: chain W residue 93 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 664 random chunks: chunk 335 optimal weight: 6.9990 chunk 187 optimal weight: 0.0270 chunk 501 optimal weight: 8.9990 chunk 410 optimal weight: 3.9990 chunk 166 optimal weight: 6.9990 chunk 604 optimal weight: 6.9990 chunk 652 optimal weight: 6.9990 chunk 537 optimal weight: 8.9990 chunk 599 optimal weight: 3.9990 chunk 205 optimal weight: 9.9990 chunk 484 optimal weight: 0.0970 overall best weight: 3.0242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 673 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1082 HIS B 344 GLN ** B 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 699 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 970 HIS ** B1003 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 111 GLN D 43 HIS D 129 GLN ** E 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 131 ASN K 40 HIS M 576 GLN M 780 ASN M1082 HIS M1220 HIS ** N 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 525 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 699 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 941 GLN O 157 GLN P 43 HIS P 129 GLN ** Q 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 116 GLN ** S 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 155 ASN U 56 ASN V 26 GLN V 61 ASN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7542 moved from start: 0.4035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.083 55352 Z= 0.409 Angle : 0.683 8.825 74786 Z= 0.352 Chirality : 0.048 0.247 8362 Planarity : 0.005 0.076 9702 Dihedral : 4.163 31.246 7396 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 15.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 4.17 % Allowed : 13.86 % Favored : 81.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -0.08 (0.10), residues: 6690 helix: 0.57 (0.11), residues: 2328 sheet: -0.45 (0.15), residues: 1046 loop : -0.24 (0.11), residues: 3316 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP E 11 HIS 0.026 0.002 HIS O 66 PHE 0.030 0.002 PHE N 356 TYR 0.026 0.002 TYR K 81 ARG 0.007 0.001 ARG B 938 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13380 Ramachandran restraints generated. 6690 Oldfield, 0 Emsley, 6690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13380 Ramachandran restraints generated. 6690 Oldfield, 0 Emsley, 6690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1130 residues out of total 6024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 251 poor density : 879 time to evaluate : 4.841 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 540 ASP cc_start: 0.7323 (t0) cc_final: 0.7024 (t0) REVERT: A 1095 LEU cc_start: 0.8722 (OUTLIER) cc_final: 0.8518 (tt) REVERT: B 117 ASN cc_start: 0.8003 (t0) cc_final: 0.7636 (t0) REVERT: B 152 ILE cc_start: 0.7243 (OUTLIER) cc_final: 0.6804 (tt) REVERT: B 169 ARG cc_start: 0.7537 (mmm160) cc_final: 0.7321 (mmm160) REVERT: B 220 GLU cc_start: 0.7845 (tm-30) cc_final: 0.7638 (tt0) REVERT: B 550 MET cc_start: 0.7915 (tmm) cc_final: 0.7590 (tmm) REVERT: B 655 ASP cc_start: 0.5823 (OUTLIER) cc_final: 0.5360 (m-30) REVERT: B 908 MET cc_start: 0.7029 (ppp) cc_final: 0.6726 (ptt) REVERT: G 120 ASP cc_start: 0.8273 (p0) cc_final: 0.7568 (p0) REVERT: G 141 ASP cc_start: 0.7250 (m-30) cc_final: 0.6899 (m-30) REVERT: H 60 ILE cc_start: 0.7742 (OUTLIER) cc_final: 0.7510 (mt) REVERT: K 38 GLU cc_start: 0.6615 (mm-30) cc_final: 0.6345 (mm-30) REVERT: L 27 GLU cc_start: 0.6467 (tp30) cc_final: 0.6255 (tp30) REVERT: M 375 ILE cc_start: 0.8320 (OUTLIER) cc_final: 0.7991 (pt) REVERT: M 540 ASP cc_start: 0.7662 (t0) cc_final: 0.7385 (t0) REVERT: M 903 PHE cc_start: 0.8144 (m-80) cc_final: 0.7404 (m-80) REVERT: N 550 MET cc_start: 0.8155 (tmm) cc_final: 0.7854 (tmm) REVERT: N 665 ILE cc_start: 0.8493 (mp) cc_final: 0.8200 (mm) REVERT: N 683 GLN cc_start: 0.7618 (pp30) cc_final: 0.7116 (pt0) REVERT: N 766 TYR cc_start: 0.7295 (m-10) cc_final: 0.6933 (m-80) REVERT: N 853 LEU cc_start: 0.7216 (mt) cc_final: 0.6962 (mt) REVERT: N 908 MET cc_start: 0.6649 (ppp) cc_final: 0.6387 (ptt) REVERT: N 939 HIS cc_start: 0.8554 (OUTLIER) cc_final: 0.7750 (p-80) REVERT: Q 26 TYR cc_start: 0.6246 (m-80) cc_final: 0.5910 (m-10) REVERT: R 115 TYR cc_start: 0.6791 (p90) cc_final: 0.6447 (p90) REVERT: S 1 MET cc_start: 0.6677 (tpp) cc_final: 0.5761 (tpp) REVERT: S 94 LYS cc_start: 0.7750 (OUTLIER) cc_final: 0.7427 (ptpt) REVERT: S 120 ASP cc_start: 0.8205 (p0) cc_final: 0.7767 (p0) REVERT: S 141 ASP cc_start: 0.7199 (m-30) cc_final: 0.6822 (t0) REVERT: T 7 GLU cc_start: 0.7062 (tp30) cc_final: 0.6844 (tp30) REVERT: T 57 ARG cc_start: 0.7317 (ptt90) cc_final: 0.6986 (ptt90) REVERT: W 1 MET cc_start: 0.6708 (tmm) cc_final: 0.6150 (ttt) outliers start: 251 outliers final: 154 residues processed: 1034 average time/residue: 0.5291 time to fit residues: 921.4966 Evaluate side-chains 921 residues out of total 6024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 161 poor density : 760 time to evaluate : 4.785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 438 LEU Chi-restraints excluded: chain A residue 469 MET Chi-restraints excluded: chain A residue 505 LEU Chi-restraints excluded: chain A residue 605 THR Chi-restraints excluded: chain A residue 662 HIS Chi-restraints excluded: chain A residue 736 THR Chi-restraints excluded: chain A residue 869 GLU Chi-restraints excluded: chain A residue 947 HIS Chi-restraints excluded: chain A residue 1023 VAL Chi-restraints excluded: chain A residue 1027 ASP Chi-restraints excluded: chain A residue 1095 LEU Chi-restraints excluded: chain A residue 1127 LEU Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain A residue 1311 LEU Chi-restraints excluded: chain A residue 1346 VAL Chi-restraints excluded: chain A residue 1347 LEU Chi-restraints excluded: chain A residue 1359 SER Chi-restraints excluded: chain A residue 1484 MET Chi-restraints excluded: chain B residue 26 CYS Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 152 ILE Chi-restraints excluded: chain B residue 195 ILE Chi-restraints excluded: chain B residue 215 TYR Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 309 PHE Chi-restraints excluded: chain B residue 471 ASN Chi-restraints excluded: chain B residue 489 ILE Chi-restraints excluded: chain B residue 542 LEU Chi-restraints excluded: chain B residue 573 TRP Chi-restraints excluded: chain B residue 655 ASP Chi-restraints excluded: chain B residue 657 VAL Chi-restraints excluded: chain B residue 666 ASP Chi-restraints excluded: chain B residue 678 THR Chi-restraints excluded: chain B residue 719 SER Chi-restraints excluded: chain B residue 865 VAL Chi-restraints excluded: chain B residue 909 VAL Chi-restraints excluded: chain B residue 977 THR Chi-restraints excluded: chain B residue 1028 LEU Chi-restraints excluded: chain C residue 9 VAL Chi-restraints excluded: chain C residue 41 GLU Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain C residue 114 HIS Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain C residue 120 LEU Chi-restraints excluded: chain C residue 151 VAL Chi-restraints excluded: chain C residue 154 ARG Chi-restraints excluded: chain C residue 192 LEU Chi-restraints excluded: chain C residue 235 SER Chi-restraints excluded: chain C residue 246 LEU Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 76 ASN Chi-restraints excluded: chain E residue 29 THR Chi-restraints excluded: chain E residue 130 PHE Chi-restraints excluded: chain E residue 151 MET Chi-restraints excluded: chain E residue 159 LEU Chi-restraints excluded: chain F residue 54 THR Chi-restraints excluded: chain F residue 71 LEU Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain G residue 39 THR Chi-restraints excluded: chain G residue 46 ILE Chi-restraints excluded: chain G residue 90 THR Chi-restraints excluded: chain G residue 115 SER Chi-restraints excluded: chain H residue 5 LEU Chi-restraints excluded: chain H residue 15 ILE Chi-restraints excluded: chain H residue 28 LEU Chi-restraints excluded: chain H residue 60 ILE Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain H residue 116 VAL Chi-restraints excluded: chain H residue 141 VAL Chi-restraints excluded: chain I residue 14 ILE Chi-restraints excluded: chain I residue 53 ILE Chi-restraints excluded: chain I residue 115 THR Chi-restraints excluded: chain J residue 30 THR Chi-restraints excluded: chain J residue 36 ASP Chi-restraints excluded: chain J residue 54 ASP Chi-restraints excluded: chain K residue 20 THR Chi-restraints excluded: chain K residue 27 VAL Chi-restraints excluded: chain K residue 71 ILE Chi-restraints excluded: chain K residue 78 THR Chi-restraints excluded: chain K residue 93 ASP Chi-restraints excluded: chain M residue 365 THR Chi-restraints excluded: chain M residue 366 VAL Chi-restraints excluded: chain M residue 375 ILE Chi-restraints excluded: chain M residue 438 LEU Chi-restraints excluded: chain M residue 469 MET Chi-restraints excluded: chain M residue 538 VAL Chi-restraints excluded: chain M residue 553 VAL Chi-restraints excluded: chain M residue 583 ARG Chi-restraints excluded: chain M residue 662 HIS Chi-restraints excluded: chain M residue 736 THR Chi-restraints excluded: chain M residue 869 GLU Chi-restraints excluded: chain M residue 993 ILE Chi-restraints excluded: chain M residue 1023 VAL Chi-restraints excluded: chain M residue 1095 LEU Chi-restraints excluded: chain M residue 1117 VAL Chi-restraints excluded: chain M residue 1127 LEU Chi-restraints excluded: chain M residue 1136 THR Chi-restraints excluded: chain M residue 1156 ASP Chi-restraints excluded: chain M residue 1338 THR Chi-restraints excluded: chain M residue 1346 VAL Chi-restraints excluded: chain N residue 26 CYS Chi-restraints excluded: chain N residue 29 VAL Chi-restraints excluded: chain N residue 195 ILE Chi-restraints excluded: chain N residue 215 TYR Chi-restraints excluded: chain N residue 239 MET Chi-restraints excluded: chain N residue 240 LEU Chi-restraints excluded: chain N residue 416 ARG Chi-restraints excluded: chain N residue 450 THR Chi-restraints excluded: chain N residue 489 ILE Chi-restraints excluded: chain N residue 492 ASP Chi-restraints excluded: chain N residue 573 TRP Chi-restraints excluded: chain N residue 655 ASP Chi-restraints excluded: chain N residue 657 VAL Chi-restraints excluded: chain N residue 666 ASP Chi-restraints excluded: chain N residue 751 LEU Chi-restraints excluded: chain N residue 858 VAL Chi-restraints excluded: chain N residue 865 VAL Chi-restraints excluded: chain N residue 909 VAL Chi-restraints excluded: chain N residue 939 HIS Chi-restraints excluded: chain N residue 977 THR Chi-restraints excluded: chain O residue 9 VAL Chi-restraints excluded: chain O residue 41 GLU Chi-restraints excluded: chain O residue 51 GLN Chi-restraints excluded: chain O residue 66 HIS Chi-restraints excluded: chain O residue 98 SER Chi-restraints excluded: chain O residue 114 HIS Chi-restraints excluded: chain O residue 115 VAL Chi-restraints excluded: chain O residue 120 LEU Chi-restraints excluded: chain O residue 151 VAL Chi-restraints excluded: chain O residue 235 SER Chi-restraints excluded: chain P residue 22 PHE Chi-restraints excluded: chain P residue 37 VAL Chi-restraints excluded: chain P residue 62 MET Chi-restraints excluded: chain P residue 76 ASN Chi-restraints excluded: chain P residue 102 ASN Chi-restraints excluded: chain Q residue 29 THR Chi-restraints excluded: chain Q residue 64 HIS Chi-restraints excluded: chain S residue 39 THR Chi-restraints excluded: chain S residue 46 ILE Chi-restraints excluded: chain S residue 86 ASP Chi-restraints excluded: chain S residue 90 THR Chi-restraints excluded: chain S residue 94 LYS Chi-restraints excluded: chain T residue 28 LEU Chi-restraints excluded: chain T residue 110 THR Chi-restraints excluded: chain T residue 141 VAL Chi-restraints excluded: chain U residue 14 ILE Chi-restraints excluded: chain U residue 53 ILE Chi-restraints excluded: chain U residue 66 THR Chi-restraints excluded: chain U residue 115 THR Chi-restraints excluded: chain U residue 124 THR Chi-restraints excluded: chain V residue 19 GLU Chi-restraints excluded: chain V residue 25 LEU Chi-restraints excluded: chain V residue 36 ASP Chi-restraints excluded: chain V residue 38 LEU Chi-restraints excluded: chain V residue 54 ASP Chi-restraints excluded: chain W residue 19 ILE Chi-restraints excluded: chain W residue 20 THR Chi-restraints excluded: chain W residue 27 VAL Chi-restraints excluded: chain W residue 78 THR Chi-restraints excluded: chain W residue 93 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 664 random chunks: chunk 596 optimal weight: 1.9990 chunk 454 optimal weight: 9.9990 chunk 313 optimal weight: 8.9990 chunk 66 optimal weight: 4.9990 chunk 288 optimal weight: 2.9990 chunk 405 optimal weight: 7.9990 chunk 606 optimal weight: 9.9990 chunk 641 optimal weight: 9.9990 chunk 316 optimal weight: 0.9990 chunk 574 optimal weight: 20.0000 chunk 172 optimal weight: 0.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 620 HIS ** A 673 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 723 ASN ** B 460 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 525 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 699 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 43 HIS E 64 HIS ** E 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 4 HIS H 131 ASN J 26 GLN ** M 576 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 885 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 525 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 699 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 941 GLN P 43 HIS P 102 ASN P 129 GLN Q 22 HIS R 72 GLN ** S 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 26 GLN V 61 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7549 moved from start: 0.4376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.084 55352 Z= 0.331 Angle : 0.611 8.223 74786 Z= 0.315 Chirality : 0.046 0.315 8362 Planarity : 0.004 0.077 9702 Dihedral : 4.161 29.240 7396 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 15.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 4.22 % Allowed : 16.38 % Favored : 79.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.30 % 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: -0.15 (0.10), residues: 6690 helix: 0.58 (0.11), residues: 2326 sheet: -0.65 (0.15), residues: 1036 loop : -0.29 (0.11), residues: 3328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP E 11 HIS 0.017 0.001 HIS U 60 PHE 0.020 0.002 PHE N 769 TYR 0.023 0.002 TYR N1047 ARG 0.009 0.001 ARG S 63 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13380 Ramachandran restraints generated. 6690 Oldfield, 0 Emsley, 6690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13380 Ramachandran restraints generated. 6690 Oldfield, 0 Emsley, 6690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1056 residues out of total 6024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 254 poor density : 802 time to evaluate : 4.860 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 540 ASP cc_start: 0.7288 (t0) cc_final: 0.7036 (t0) REVERT: A 903 PHE cc_start: 0.7996 (m-80) cc_final: 0.7468 (m-80) REVERT: A 1095 LEU cc_start: 0.8723 (OUTLIER) cc_final: 0.8431 (tt) REVERT: B 117 ASN cc_start: 0.7956 (t0) cc_final: 0.7543 (t0) REVERT: B 152 ILE cc_start: 0.7241 (OUTLIER) cc_final: 0.6809 (tt) REVERT: B 169 ARG cc_start: 0.7578 (mmm160) cc_final: 0.7368 (mmm160) REVERT: B 655 ASP cc_start: 0.5896 (OUTLIER) cc_final: 0.5432 (m-30) REVERT: B 766 TYR cc_start: 0.7447 (m-80) cc_final: 0.7126 (m-80) REVERT: B 908 MET cc_start: 0.7050 (ppp) cc_final: 0.6793 (ptt) REVERT: B 939 HIS cc_start: 0.8283 (OUTLIER) cc_final: 0.7919 (p-80) REVERT: G 120 ASP cc_start: 0.8209 (p0) cc_final: 0.7680 (p0) REVERT: G 141 ASP cc_start: 0.7291 (m-30) cc_final: 0.6922 (m-30) REVERT: H 140 ARG cc_start: 0.7960 (mmm-85) cc_final: 0.7648 (mmm160) REVERT: J 26 GLN cc_start: 0.5894 (OUTLIER) cc_final: 0.5615 (mt0) REVERT: M 375 ILE cc_start: 0.8316 (OUTLIER) cc_final: 0.8033 (pt) REVERT: M 540 ASP cc_start: 0.7556 (t0) cc_final: 0.7341 (t0) REVERT: M 545 VAL cc_start: 0.8603 (OUTLIER) cc_final: 0.8343 (t) REVERT: M 824 GLU cc_start: 0.7781 (OUTLIER) cc_final: 0.7055 (pm20) REVERT: M 903 PHE cc_start: 0.8057 (m-80) cc_final: 0.7619 (m-80) REVERT: M 1348 SER cc_start: 0.8195 (m) cc_final: 0.7759 (p) REVERT: N 287 HIS cc_start: 0.6775 (m90) cc_final: 0.6250 (m90) REVERT: N 550 MET cc_start: 0.8174 (tmm) cc_final: 0.7905 (tmm) REVERT: N 683 GLN cc_start: 0.7605 (pp30) cc_final: 0.7142 (pt0) REVERT: N 766 TYR cc_start: 0.7224 (m-10) cc_final: 0.6859 (m-80) REVERT: N 908 MET cc_start: 0.6701 (ppp) cc_final: 0.6381 (ptt) REVERT: R 115 TYR cc_start: 0.6860 (p90) cc_final: 0.6640 (p90) REVERT: S 1 MET cc_start: 0.6618 (tpp) cc_final: 0.5931 (tpp) REVERT: S 94 LYS cc_start: 0.7674 (pttm) cc_final: 0.7380 (ptpt) REVERT: T 92 MET cc_start: 0.7155 (ttm) cc_final: 0.6935 (ttm) REVERT: W 1 MET cc_start: 0.6593 (tmm) cc_final: 0.6059 (ttt) outliers start: 254 outliers final: 166 residues processed: 968 average time/residue: 0.5239 time to fit residues: 858.0461 Evaluate side-chains 915 residues out of total 6024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 174 poor density : 741 time to evaluate : 4.841 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 375 ILE Chi-restraints excluded: chain A residue 420 ILE Chi-restraints excluded: chain A residue 438 LEU Chi-restraints excluded: chain A residue 452 ASP Chi-restraints excluded: chain A residue 505 LEU Chi-restraints excluded: chain A residue 538 VAL Chi-restraints excluded: chain A residue 662 HIS Chi-restraints excluded: chain A residue 674 THR Chi-restraints excluded: chain A residue 736 THR Chi-restraints excluded: chain A residue 869 GLU Chi-restraints excluded: chain A residue 909 LEU Chi-restraints excluded: chain A residue 947 HIS Chi-restraints excluded: chain A residue 1023 VAL Chi-restraints excluded: chain A residue 1027 ASP Chi-restraints excluded: chain A residue 1040 LEU Chi-restraints excluded: chain A residue 1095 LEU Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain A residue 1311 LEU Chi-restraints excluded: chain A residue 1359 SER Chi-restraints excluded: chain A residue 1374 VAL Chi-restraints excluded: chain A residue 1385 VAL Chi-restraints excluded: chain B residue 152 ILE Chi-restraints excluded: chain B residue 215 TYR Chi-restraints excluded: chain B residue 309 PHE Chi-restraints excluded: chain B residue 460 HIS Chi-restraints excluded: chain B residue 471 ASN Chi-restraints excluded: chain B residue 492 ASP Chi-restraints excluded: chain B residue 542 LEU Chi-restraints excluded: chain B residue 573 TRP Chi-restraints excluded: chain B residue 655 ASP Chi-restraints excluded: chain B residue 657 VAL Chi-restraints excluded: chain B residue 666 ASP Chi-restraints excluded: chain B residue 678 THR Chi-restraints excluded: chain B residue 865 VAL Chi-restraints excluded: chain B residue 866 ILE Chi-restraints excluded: chain B residue 909 VAL Chi-restraints excluded: chain B residue 939 HIS Chi-restraints excluded: chain B residue 944 THR Chi-restraints excluded: chain B residue 977 THR Chi-restraints excluded: chain B residue 1000 THR Chi-restraints excluded: chain B residue 1028 LEU Chi-restraints excluded: chain C residue 41 GLU Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain C residue 112 THR Chi-restraints excluded: chain C residue 114 HIS Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain C residue 146 ASP Chi-restraints excluded: chain C residue 151 VAL Chi-restraints excluded: chain C residue 235 SER Chi-restraints excluded: chain C residue 246 LEU Chi-restraints excluded: chain D residue 76 ASN Chi-restraints excluded: chain E residue 29 THR Chi-restraints excluded: chain E residue 64 HIS Chi-restraints excluded: chain E residue 130 PHE Chi-restraints excluded: chain E residue 159 LEU Chi-restraints excluded: chain E residue 185 ILE Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain G residue 39 THR Chi-restraints excluded: chain G residue 46 ILE Chi-restraints excluded: chain G residue 90 THR Chi-restraints excluded: chain H residue 5 LEU Chi-restraints excluded: chain H residue 15 ILE Chi-restraints excluded: chain H residue 28 LEU Chi-restraints excluded: chain H residue 80 ASP Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain H residue 116 VAL Chi-restraints excluded: chain H residue 141 VAL Chi-restraints excluded: chain H residue 145 MET Chi-restraints excluded: chain I residue 14 ILE Chi-restraints excluded: chain I residue 95 VAL Chi-restraints excluded: chain J residue 26 GLN Chi-restraints excluded: chain J residue 30 THR Chi-restraints excluded: chain J residue 36 ASP Chi-restraints excluded: chain J residue 54 ASP Chi-restraints excluded: chain K residue 19 ILE Chi-restraints excluded: chain K residue 20 THR Chi-restraints excluded: chain K residue 27 VAL Chi-restraints excluded: chain K residue 71 ILE Chi-restraints excluded: chain K residue 78 THR Chi-restraints excluded: chain K residue 93 ASP Chi-restraints excluded: chain K residue 101 LEU Chi-restraints excluded: chain M residue 366 VAL Chi-restraints excluded: chain M residue 375 ILE Chi-restraints excluded: chain M residue 420 ILE Chi-restraints excluded: chain M residue 438 LEU Chi-restraints excluded: chain M residue 543 THR Chi-restraints excluded: chain M residue 545 VAL Chi-restraints excluded: chain M residue 583 ARG Chi-restraints excluded: chain M residue 674 THR Chi-restraints excluded: chain M residue 736 THR Chi-restraints excluded: chain M residue 824 GLU Chi-restraints excluded: chain M residue 849 ASP Chi-restraints excluded: chain M residue 869 GLU Chi-restraints excluded: chain M residue 909 LEU Chi-restraints excluded: chain M residue 938 LEU Chi-restraints excluded: chain M residue 1023 VAL Chi-restraints excluded: chain M residue 1040 LEU Chi-restraints excluded: chain M residue 1095 LEU Chi-restraints excluded: chain M residue 1117 VAL Chi-restraints excluded: chain M residue 1136 THR Chi-restraints excluded: chain M residue 1156 ASP Chi-restraints excluded: chain M residue 1338 THR Chi-restraints excluded: chain M residue 1358 THR Chi-restraints excluded: chain M residue 1359 SER Chi-restraints excluded: chain M residue 1374 VAL Chi-restraints excluded: chain N residue 29 VAL Chi-restraints excluded: chain N residue 160 TYR Chi-restraints excluded: chain N residue 215 TYR Chi-restraints excluded: chain N residue 239 MET Chi-restraints excluded: chain N residue 240 LEU Chi-restraints excluded: chain N residue 276 LEU Chi-restraints excluded: chain N residue 309 PHE Chi-restraints excluded: chain N residue 416 ARG Chi-restraints excluded: chain N residue 431 LEU Chi-restraints excluded: chain N residue 460 HIS Chi-restraints excluded: chain N residue 489 ILE Chi-restraints excluded: chain N residue 492 ASP Chi-restraints excluded: chain N residue 573 TRP Chi-restraints excluded: chain N residue 655 ASP Chi-restraints excluded: chain N residue 657 VAL Chi-restraints excluded: chain N residue 662 VAL Chi-restraints excluded: chain N residue 666 ASP Chi-restraints excluded: chain N residue 675 LEU Chi-restraints excluded: chain N residue 751 LEU Chi-restraints excluded: chain N residue 865 VAL Chi-restraints excluded: chain N residue 909 VAL Chi-restraints excluded: chain N residue 944 THR Chi-restraints excluded: chain N residue 977 THR Chi-restraints excluded: chain O residue 9 VAL Chi-restraints excluded: chain O residue 51 GLN Chi-restraints excluded: chain O residue 66 HIS Chi-restraints excluded: chain O residue 75 SER Chi-restraints excluded: chain O residue 98 SER Chi-restraints excluded: chain O residue 114 HIS Chi-restraints excluded: chain O residue 115 VAL Chi-restraints excluded: chain O residue 151 VAL Chi-restraints excluded: chain O residue 235 SER Chi-restraints excluded: chain P residue 22 PHE Chi-restraints excluded: chain P residue 62 MET Chi-restraints excluded: chain P residue 76 ASN Chi-restraints excluded: chain P residue 102 ASN Chi-restraints excluded: chain P residue 129 GLN Chi-restraints excluded: chain Q residue 22 HIS Chi-restraints excluded: chain Q residue 29 THR Chi-restraints excluded: chain Q residue 64 HIS Chi-restraints excluded: chain Q residue 151 MET Chi-restraints excluded: chain R residue 71 LEU Chi-restraints excluded: chain R residue 125 ILE Chi-restraints excluded: chain S residue 39 THR Chi-restraints excluded: chain S residue 46 ILE Chi-restraints excluded: chain S residue 86 ASP Chi-restraints excluded: chain S residue 90 THR Chi-restraints excluded: chain S residue 153 ASP Chi-restraints excluded: chain T residue 5 LEU Chi-restraints excluded: chain T residue 28 LEU Chi-restraints excluded: chain T residue 80 ASP Chi-restraints excluded: chain T residue 110 THR Chi-restraints excluded: chain T residue 141 VAL Chi-restraints excluded: chain T residue 145 MET Chi-restraints excluded: chain U residue 53 ILE Chi-restraints excluded: chain U residue 95 VAL Chi-restraints excluded: chain U residue 115 THR Chi-restraints excluded: chain V residue 19 GLU Chi-restraints excluded: chain V residue 30 THR Chi-restraints excluded: chain V residue 36 ASP Chi-restraints excluded: chain V residue 54 ASP Chi-restraints excluded: chain W residue 20 THR Chi-restraints excluded: chain W residue 22 ASN Chi-restraints excluded: chain W residue 27 VAL Chi-restraints excluded: chain W residue 71 ILE Chi-restraints excluded: chain W residue 78 THR Chi-restraints excluded: chain W residue 93 ASP Chi-restraints excluded: chain W residue 101 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 664 random chunks: chunk 534 optimal weight: 0.9990 chunk 364 optimal weight: 5.9990 chunk 9 optimal weight: 6.9990 chunk 477 optimal weight: 0.9980 chunk 264 optimal weight: 1.9990 chunk 547 optimal weight: 10.0000 chunk 443 optimal weight: 0.8980 chunk 0 optimal weight: 5.9990 chunk 327 optimal weight: 0.9980 chunk 576 optimal weight: 8.9990 chunk 161 optimal weight: 0.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 576 GLN ** A 673 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 982 ASN ** B 460 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 525 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 699 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 43 HIS ** E 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 131 ASN I 74 GLN J 26 GLN ** M 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 576 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 620 HIS ** M 673 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M1291 ASN ** N 525 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 699 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 913 GLN ** N 941 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 265 HIS P 43 HIS P 102 ASN P 129 GLN ** S 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 26 GLN W 89 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7492 moved from start: 0.4481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 55352 Z= 0.205 Angle : 0.559 7.922 74786 Z= 0.285 Chirality : 0.044 0.249 8362 Planarity : 0.004 0.077 9702 Dihedral : 4.011 29.620 7396 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 13.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 3.70 % Allowed : 17.76 % Favored : 78.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.30 % 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 (0.10), residues: 6690 helix: 0.74 (0.11), residues: 2326 sheet: -0.61 (0.15), residues: 1032 loop : -0.27 (0.11), residues: 3332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP E 11 HIS 0.015 0.001 HIS U 60 PHE 0.017 0.002 PHE Q 75 TYR 0.022 0.001 TYR N1047 ARG 0.008 0.000 ARG B 938 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13380 Ramachandran restraints generated. 6690 Oldfield, 0 Emsley, 6690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13380 Ramachandran restraints generated. 6690 Oldfield, 0 Emsley, 6690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1040 residues out of total 6024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 223 poor density : 817 time to evaluate : 4.810 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 540 ASP cc_start: 0.7216 (t0) cc_final: 0.6981 (t0) REVERT: A 986 MET cc_start: 0.6363 (mtm) cc_final: 0.5789 (mmt) REVERT: A 1095 LEU cc_start: 0.8686 (OUTLIER) cc_final: 0.8411 (tt) REVERT: B 152 ILE cc_start: 0.7170 (OUTLIER) cc_final: 0.6754 (tt) REVERT: B 550 MET cc_start: 0.7779 (tmm) cc_final: 0.7156 (tmm) REVERT: B 576 ILE cc_start: 0.8313 (pt) cc_final: 0.8072 (tt) REVERT: B 584 MET cc_start: 0.7168 (OUTLIER) cc_final: 0.6824 (mmm) REVERT: B 655 ASP cc_start: 0.5868 (OUTLIER) cc_final: 0.5397 (m-30) REVERT: B 766 TYR cc_start: 0.7364 (m-80) cc_final: 0.7000 (m-80) REVERT: B 908 MET cc_start: 0.6976 (ppp) cc_final: 0.6700 (ptt) REVERT: B 939 HIS cc_start: 0.8113 (OUTLIER) cc_final: 0.7894 (p-80) REVERT: D 39 MET cc_start: 0.8159 (mtm) cc_final: 0.7951 (mtp) REVERT: G 10 GLU cc_start: 0.6729 (mm-30) cc_final: 0.6420 (mm-30) REVERT: G 117 MET cc_start: 0.7616 (tpp) cc_final: 0.7277 (mmm) REVERT: G 120 ASP cc_start: 0.8198 (p0) cc_final: 0.7605 (p0) REVERT: G 141 ASP cc_start: 0.7288 (m-30) cc_final: 0.6932 (m-30) REVERT: I 32 ASN cc_start: 0.7694 (t0) cc_final: 0.7476 (t0) REVERT: L 27 GLU cc_start: 0.6328 (tp30) cc_final: 0.6095 (tp30) REVERT: M 540 ASP cc_start: 0.7462 (t0) cc_final: 0.7211 (t0) REVERT: M 903 PHE cc_start: 0.8080 (m-80) cc_final: 0.7679 (m-80) REVERT: M 986 MET cc_start: 0.6078 (mtm) cc_final: 0.5527 (mmt) REVERT: M 1321 ILE cc_start: 0.7621 (tp) cc_final: 0.7409 (tp) REVERT: M 1348 SER cc_start: 0.8210 (m) cc_final: 0.7833 (p) REVERT: N 287 HIS cc_start: 0.6687 (m90) cc_final: 0.6169 (m90) REVERT: N 550 MET cc_start: 0.8162 (tmm) cc_final: 0.7956 (tmm) REVERT: N 683 GLN cc_start: 0.7550 (pp30) cc_final: 0.7090 (pt0) REVERT: N 739 ASN cc_start: 0.7020 (p0) cc_final: 0.6694 (p0) REVERT: N 766 TYR cc_start: 0.7155 (m-10) cc_final: 0.6815 (m-80) REVERT: N 853 LEU cc_start: 0.7169 (mt) cc_final: 0.6958 (mt) REVERT: N 854 ILE cc_start: 0.7829 (tp) cc_final: 0.7587 (tt) REVERT: N 908 MET cc_start: 0.6591 (ppp) cc_final: 0.6281 (ptt) REVERT: O 60 HIS cc_start: 0.5906 (OUTLIER) cc_final: 0.5054 (m-70) REVERT: R 115 TYR cc_start: 0.6681 (p90) cc_final: 0.6457 (p90) REVERT: S 94 LYS cc_start: 0.7729 (OUTLIER) cc_final: 0.7413 (ptpt) REVERT: S 120 ASP cc_start: 0.8332 (p0) cc_final: 0.7889 (p0) REVERT: W 1 MET cc_start: 0.6564 (tmm) cc_final: 0.6044 (ttt) outliers start: 223 outliers final: 145 residues processed: 958 average time/residue: 0.5126 time to fit residues: 834.6225 Evaluate side-chains 899 residues out of total 6024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 152 poor density : 747 time to evaluate : 4.800 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 420 ILE Chi-restraints excluded: chain A residue 509 LEU Chi-restraints excluded: chain A residue 662 HIS Chi-restraints excluded: chain A residue 869 GLU Chi-restraints excluded: chain A residue 905 ASN Chi-restraints excluded: chain A residue 909 LEU Chi-restraints excluded: chain A residue 1023 VAL Chi-restraints excluded: chain A residue 1027 ASP Chi-restraints excluded: chain A residue 1040 LEU Chi-restraints excluded: chain A residue 1095 LEU Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain A residue 1311 LEU Chi-restraints excluded: chain A residue 1359 SER Chi-restraints excluded: chain A residue 1374 VAL Chi-restraints excluded: chain B residue 152 ILE Chi-restraints excluded: chain B residue 215 TYR Chi-restraints excluded: chain B residue 232 THR Chi-restraints excluded: chain B residue 309 PHE Chi-restraints excluded: chain B residue 460 HIS Chi-restraints excluded: chain B residue 471 ASN Chi-restraints excluded: chain B residue 492 ASP Chi-restraints excluded: chain B residue 542 LEU Chi-restraints excluded: chain B residue 573 TRP Chi-restraints excluded: chain B residue 584 MET Chi-restraints excluded: chain B residue 655 ASP Chi-restraints excluded: chain B residue 657 VAL Chi-restraints excluded: chain B residue 666 ASP Chi-restraints excluded: chain B residue 678 THR Chi-restraints excluded: chain B residue 865 VAL Chi-restraints excluded: chain B residue 939 HIS Chi-restraints excluded: chain B residue 944 THR Chi-restraints excluded: chain B residue 1028 LEU Chi-restraints excluded: chain C residue 9 VAL Chi-restraints excluded: chain C residue 41 GLU Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain C residue 112 THR Chi-restraints excluded: chain C residue 114 HIS Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain C residue 146 ASP Chi-restraints excluded: chain C residue 151 VAL Chi-restraints excluded: chain C residue 246 LEU Chi-restraints excluded: chain D residue 18 SER Chi-restraints excluded: chain D residue 76 ASN Chi-restraints excluded: chain E residue 29 THR Chi-restraints excluded: chain E residue 130 PHE Chi-restraints excluded: chain E residue 151 MET Chi-restraints excluded: chain E residue 159 LEU Chi-restraints excluded: chain E residue 185 ILE Chi-restraints excluded: chain F residue 71 LEU Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain G residue 39 THR Chi-restraints excluded: chain G residue 115 SER Chi-restraints excluded: chain H residue 5 LEU Chi-restraints excluded: chain H residue 15 ILE Chi-restraints excluded: chain H residue 28 LEU Chi-restraints excluded: chain H residue 80 ASP Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain H residue 116 VAL Chi-restraints excluded: chain H residue 141 VAL Chi-restraints excluded: chain I residue 14 ILE Chi-restraints excluded: chain I residue 23 MET Chi-restraints excluded: chain J residue 36 ASP Chi-restraints excluded: chain J residue 54 ASP Chi-restraints excluded: chain K residue 19 ILE Chi-restraints excluded: chain K residue 20 THR Chi-restraints excluded: chain K residue 27 VAL Chi-restraints excluded: chain K residue 71 ILE Chi-restraints excluded: chain K residue 78 THR Chi-restraints excluded: chain K residue 82 SER Chi-restraints excluded: chain K residue 101 LEU Chi-restraints excluded: chain M residue 538 VAL Chi-restraints excluded: chain M residue 583 ARG Chi-restraints excluded: chain M residue 662 HIS Chi-restraints excluded: chain M residue 674 THR Chi-restraints excluded: chain M residue 771 VAL Chi-restraints excluded: chain M residue 849 ASP Chi-restraints excluded: chain M residue 869 GLU Chi-restraints excluded: chain M residue 870 SER Chi-restraints excluded: chain M residue 909 LEU Chi-restraints excluded: chain M residue 938 LEU Chi-restraints excluded: chain M residue 1023 VAL Chi-restraints excluded: chain M residue 1040 LEU Chi-restraints excluded: chain M residue 1095 LEU Chi-restraints excluded: chain M residue 1117 VAL Chi-restraints excluded: chain M residue 1127 LEU Chi-restraints excluded: chain M residue 1136 THR Chi-restraints excluded: chain M residue 1156 ASP Chi-restraints excluded: chain M residue 1338 THR Chi-restraints excluded: chain M residue 1374 VAL Chi-restraints excluded: chain M residue 1484 MET Chi-restraints excluded: chain N residue 160 TYR Chi-restraints excluded: chain N residue 215 TYR Chi-restraints excluded: chain N residue 232 THR Chi-restraints excluded: chain N residue 276 LEU Chi-restraints excluded: chain N residue 416 ARG Chi-restraints excluded: chain N residue 460 HIS Chi-restraints excluded: chain N residue 573 TRP Chi-restraints excluded: chain N residue 655 ASP Chi-restraints excluded: chain N residue 657 VAL Chi-restraints excluded: chain N residue 666 ASP Chi-restraints excluded: chain N residue 741 HIS Chi-restraints excluded: chain N residue 751 LEU Chi-restraints excluded: chain N residue 865 VAL Chi-restraints excluded: chain N residue 909 VAL Chi-restraints excluded: chain N residue 944 THR Chi-restraints excluded: chain N residue 977 THR Chi-restraints excluded: chain O residue 51 GLN Chi-restraints excluded: chain O residue 60 HIS Chi-restraints excluded: chain O residue 66 HIS Chi-restraints excluded: chain O residue 75 SER Chi-restraints excluded: chain O residue 114 HIS Chi-restraints excluded: chain O residue 115 VAL Chi-restraints excluded: chain O residue 235 SER Chi-restraints excluded: chain P residue 22 PHE Chi-restraints excluded: chain P residue 62 MET Chi-restraints excluded: chain P residue 76 ASN Chi-restraints excluded: chain P residue 129 GLN Chi-restraints excluded: chain P residue 131 LEU Chi-restraints excluded: chain Q residue 29 THR Chi-restraints excluded: chain Q residue 64 HIS Chi-restraints excluded: chain Q residue 151 MET Chi-restraints excluded: chain Q residue 185 ILE Chi-restraints excluded: chain R residue 71 LEU Chi-restraints excluded: chain R residue 90 LEU Chi-restraints excluded: chain R residue 125 ILE Chi-restraints excluded: chain S residue 6 SER Chi-restraints excluded: chain S residue 22 LEU Chi-restraints excluded: chain S residue 39 THR Chi-restraints excluded: chain S residue 86 ASP Chi-restraints excluded: chain S residue 94 LYS Chi-restraints excluded: chain S residue 153 ASP Chi-restraints excluded: chain T residue 5 LEU Chi-restraints excluded: chain T residue 28 LEU Chi-restraints excluded: chain T residue 110 THR Chi-restraints excluded: chain T residue 141 VAL Chi-restraints excluded: chain U residue 14 ILE Chi-restraints excluded: chain U residue 95 VAL Chi-restraints excluded: chain U residue 115 THR Chi-restraints excluded: chain V residue 19 GLU Chi-restraints excluded: chain V residue 25 LEU Chi-restraints excluded: chain V residue 30 THR Chi-restraints excluded: chain V residue 36 ASP Chi-restraints excluded: chain V residue 38 LEU Chi-restraints excluded: chain V residue 54 ASP Chi-restraints excluded: chain W residue 19 ILE Chi-restraints excluded: chain W residue 20 THR Chi-restraints excluded: chain W residue 22 ASN Chi-restraints excluded: chain W residue 27 VAL Chi-restraints excluded: chain W residue 78 THR Chi-restraints excluded: chain W residue 93 ASP Chi-restraints excluded: chain W residue 101 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 664 random chunks: chunk 215 optimal weight: 6.9990 chunk 577 optimal weight: 1.9990 chunk 126 optimal weight: 2.9990 chunk 376 optimal weight: 0.5980 chunk 158 optimal weight: 7.9990 chunk 642 optimal weight: 2.9990 chunk 533 optimal weight: 4.9990 chunk 297 optimal weight: 0.6980 chunk 53 optimal weight: 7.9990 chunk 212 optimal weight: 3.9990 chunk 337 optimal weight: 4.9990 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 576 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 673 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 780 ASN ** A 982 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 287 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 460 HIS ** B 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 525 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 699 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 43 HIS E 64 HIS ** E 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 72 GLN H 131 ASN M 485 ASN ** M 576 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 673 GLN M 780 ASN ** N 525 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 699 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 755 GLN N 777 ASN P 43 HIS P 129 GLN ** S 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 26 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7536 moved from start: 0.4685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 55352 Z= 0.278 Angle : 0.586 9.453 74786 Z= 0.298 Chirality : 0.045 0.287 8362 Planarity : 0.004 0.077 9702 Dihedral : 4.082 31.195 7396 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 15.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 4.33 % Allowed : 18.44 % Favored : 77.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.30 % 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: -0.12 (0.10), residues: 6690 helix: 0.66 (0.11), residues: 2354 sheet: -0.66 (0.15), residues: 1034 loop : -0.31 (0.11), residues: 3302 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP E 11 HIS 0.011 0.001 HIS N 577 PHE 0.040 0.002 PHE S 18 TYR 0.022 0.002 TYR N1047 ARG 0.007 0.000 ARG B 938 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13380 Ramachandran restraints generated. 6690 Oldfield, 0 Emsley, 6690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13380 Ramachandran restraints generated. 6690 Oldfield, 0 Emsley, 6690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1038 residues out of total 6024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 261 poor density : 777 time to evaluate : 4.903 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 986 MET cc_start: 0.6486 (mtm) cc_final: 0.5844 (mmt) REVERT: A 1095 LEU cc_start: 0.8712 (OUTLIER) cc_final: 0.8407 (tt) REVERT: B 152 ILE cc_start: 0.7183 (OUTLIER) cc_final: 0.6751 (tt) REVERT: B 302 LYS cc_start: 0.7675 (mttt) cc_final: 0.7459 (mmmt) REVERT: B 655 ASP cc_start: 0.5926 (OUTLIER) cc_final: 0.5406 (m-30) REVERT: B 766 TYR cc_start: 0.7519 (m-80) cc_final: 0.7205 (m-80) REVERT: B 908 MET cc_start: 0.7029 (ppp) cc_final: 0.6797 (ptt) REVERT: C 60 HIS cc_start: 0.5420 (OUTLIER) cc_final: 0.4898 (m-70) REVERT: D 39 MET cc_start: 0.8198 (mtm) cc_final: 0.7991 (mtp) REVERT: G 120 ASP cc_start: 0.8160 (p0) cc_final: 0.7612 (p0) REVERT: G 141 ASP cc_start: 0.7321 (m-30) cc_final: 0.6939 (m-30) REVERT: H 140 ARG cc_start: 0.8129 (mmm-85) cc_final: 0.7663 (mmm160) REVERT: I 32 ASN cc_start: 0.7742 (t0) cc_final: 0.7542 (t0) REVERT: I 81 THR cc_start: 0.8321 (OUTLIER) cc_final: 0.8037 (t) REVERT: M 375 ILE cc_start: 0.8308 (OUTLIER) cc_final: 0.8008 (pt) REVERT: M 540 ASP cc_start: 0.7517 (t0) cc_final: 0.7292 (t0) REVERT: M 824 GLU cc_start: 0.7762 (OUTLIER) cc_final: 0.7060 (pm20) REVERT: M 903 PHE cc_start: 0.8090 (m-80) cc_final: 0.7730 (m-80) REVERT: M 986 MET cc_start: 0.6055 (mtm) cc_final: 0.5426 (mmt) REVERT: M 1348 SER cc_start: 0.8049 (m) cc_final: 0.7755 (p) REVERT: N 47 PHE cc_start: 0.7737 (t80) cc_final: 0.7448 (t80) REVERT: N 287 HIS cc_start: 0.6780 (m90) cc_final: 0.6272 (m90) REVERT: N 683 GLN cc_start: 0.7588 (pp30) cc_final: 0.7106 (pt0) REVERT: N 766 TYR cc_start: 0.7253 (m-80) cc_final: 0.6910 (m-80) REVERT: N 853 LEU cc_start: 0.7262 (mt) cc_final: 0.7034 (mt) REVERT: N 854 ILE cc_start: 0.7909 (tp) cc_final: 0.7660 (tt) REVERT: N 908 MET cc_start: 0.6667 (ppp) cc_final: 0.6389 (ptt) REVERT: O 60 HIS cc_start: 0.6055 (OUTLIER) cc_final: 0.5222 (m-70) REVERT: S 1 MET cc_start: 0.6166 (tpp) cc_final: 0.5735 (tpp) REVERT: S 10 GLU cc_start: 0.6698 (mm-30) cc_final: 0.6476 (mm-30) REVERT: S 94 LYS cc_start: 0.7717 (OUTLIER) cc_final: 0.7427 (ptpt) REVERT: S 120 ASP cc_start: 0.8201 (p0) cc_final: 0.7798 (p0) REVERT: U 37 TYR cc_start: 0.5625 (m-10) cc_final: 0.5417 (m-10) REVERT: W 1 MET cc_start: 0.6587 (tmm) cc_final: 0.6074 (ttt) outliers start: 261 outliers final: 184 residues processed: 948 average time/residue: 0.5219 time to fit residues: 840.9197 Evaluate side-chains 926 residues out of total 6024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 193 poor density : 733 time to evaluate : 4.825 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 375 ILE Chi-restraints excluded: chain A residue 438 LEU Chi-restraints excluded: chain A residue 452 ASP Chi-restraints excluded: chain A residue 505 LEU Chi-restraints excluded: chain A residue 520 MET Chi-restraints excluded: chain A residue 538 VAL Chi-restraints excluded: chain A residue 611 ASP Chi-restraints excluded: chain A residue 662 HIS Chi-restraints excluded: chain A residue 674 THR Chi-restraints excluded: chain A residue 736 THR Chi-restraints excluded: chain A residue 771 VAL Chi-restraints excluded: chain A residue 905 ASN Chi-restraints excluded: chain A residue 909 LEU Chi-restraints excluded: chain A residue 1023 VAL Chi-restraints excluded: chain A residue 1027 ASP Chi-restraints excluded: chain A residue 1040 LEU Chi-restraints excluded: chain A residue 1095 LEU Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain A residue 1298 LEU Chi-restraints excluded: chain A residue 1311 LEU Chi-restraints excluded: chain A residue 1359 SER Chi-restraints excluded: chain A residue 1374 VAL Chi-restraints excluded: chain A residue 1385 VAL Chi-restraints excluded: chain B residue 152 ILE Chi-restraints excluded: chain B residue 174 LEU Chi-restraints excluded: chain B residue 215 TYR Chi-restraints excluded: chain B residue 232 THR Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 309 PHE Chi-restraints excluded: chain B residue 460 HIS Chi-restraints excluded: chain B residue 471 ASN Chi-restraints excluded: chain B residue 542 LEU Chi-restraints excluded: chain B residue 573 TRP Chi-restraints excluded: chain B residue 652 SER Chi-restraints excluded: chain B residue 655 ASP Chi-restraints excluded: chain B residue 657 VAL Chi-restraints excluded: chain B residue 662 VAL Chi-restraints excluded: chain B residue 666 ASP Chi-restraints excluded: chain B residue 678 THR Chi-restraints excluded: chain B residue 865 VAL Chi-restraints excluded: chain B residue 866 ILE Chi-restraints excluded: chain B residue 909 VAL Chi-restraints excluded: chain B residue 911 LEU Chi-restraints excluded: chain B residue 944 THR Chi-restraints excluded: chain B residue 977 THR Chi-restraints excluded: chain B residue 1000 THR Chi-restraints excluded: chain B residue 1028 LEU Chi-restraints excluded: chain C residue 9 VAL Chi-restraints excluded: chain C residue 41 GLU Chi-restraints excluded: chain C residue 60 HIS Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain C residue 112 THR Chi-restraints excluded: chain C residue 114 HIS Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain C residue 146 ASP Chi-restraints excluded: chain C residue 151 VAL Chi-restraints excluded: chain C residue 235 SER Chi-restraints excluded: chain C residue 246 LEU Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 76 ASN Chi-restraints excluded: chain D residue 102 ASN Chi-restraints excluded: chain E residue 130 PHE Chi-restraints excluded: chain E residue 185 ILE Chi-restraints excluded: chain F residue 71 LEU Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain G residue 39 THR Chi-restraints excluded: chain G residue 90 THR Chi-restraints excluded: chain G residue 91 GLN Chi-restraints excluded: chain G residue 115 SER Chi-restraints excluded: chain H residue 5 LEU Chi-restraints excluded: chain H residue 15 ILE Chi-restraints excluded: chain H residue 28 LEU Chi-restraints excluded: chain H residue 80 ASP Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain H residue 116 VAL Chi-restraints excluded: chain H residue 141 VAL Chi-restraints excluded: chain H residue 144 LEU Chi-restraints excluded: chain H residue 145 MET Chi-restraints excluded: chain I residue 23 MET Chi-restraints excluded: chain I residue 81 THR Chi-restraints excluded: chain I residue 95 VAL Chi-restraints excluded: chain J residue 30 THR Chi-restraints excluded: chain J residue 36 ASP Chi-restraints excluded: chain J residue 54 ASP Chi-restraints excluded: chain K residue 13 PHE Chi-restraints excluded: chain K residue 20 THR Chi-restraints excluded: chain K residue 27 VAL Chi-restraints excluded: chain K residue 71 ILE Chi-restraints excluded: chain K residue 78 THR Chi-restraints excluded: chain K residue 82 SER Chi-restraints excluded: chain K residue 93 ASP Chi-restraints excluded: chain K residue 101 LEU Chi-restraints excluded: chain K residue 111 ASP Chi-restraints excluded: chain M residue 365 THR Chi-restraints excluded: chain M residue 366 VAL Chi-restraints excluded: chain M residue 375 ILE Chi-restraints excluded: chain M residue 438 LEU Chi-restraints excluded: chain M residue 485 ASN Chi-restraints excluded: chain M residue 520 MET Chi-restraints excluded: chain M residue 538 VAL Chi-restraints excluded: chain M residue 583 ARG Chi-restraints excluded: chain M residue 611 ASP Chi-restraints excluded: chain M residue 662 HIS Chi-restraints excluded: chain M residue 674 THR Chi-restraints excluded: chain M residue 736 THR Chi-restraints excluded: chain M residue 771 VAL Chi-restraints excluded: chain M residue 824 GLU Chi-restraints excluded: chain M residue 849 ASP Chi-restraints excluded: chain M residue 869 GLU Chi-restraints excluded: chain M residue 870 SER Chi-restraints excluded: chain M residue 905 ASN Chi-restraints excluded: chain M residue 909 LEU Chi-restraints excluded: chain M residue 938 LEU Chi-restraints excluded: chain M residue 1023 VAL Chi-restraints excluded: chain M residue 1040 LEU Chi-restraints excluded: chain M residue 1095 LEU Chi-restraints excluded: chain M residue 1117 VAL Chi-restraints excluded: chain M residue 1127 LEU Chi-restraints excluded: chain M residue 1136 THR Chi-restraints excluded: chain M residue 1156 ASP Chi-restraints excluded: chain M residue 1293 LEU Chi-restraints excluded: chain M residue 1338 THR Chi-restraints excluded: chain M residue 1374 VAL Chi-restraints excluded: chain N residue 26 CYS Chi-restraints excluded: chain N residue 160 TYR Chi-restraints excluded: chain N residue 195 ILE Chi-restraints excluded: chain N residue 215 TYR Chi-restraints excluded: chain N residue 232 THR Chi-restraints excluded: chain N residue 276 LEU Chi-restraints excluded: chain N residue 416 ARG Chi-restraints excluded: chain N residue 431 LEU Chi-restraints excluded: chain N residue 460 HIS Chi-restraints excluded: chain N residue 492 ASP Chi-restraints excluded: chain N residue 573 TRP Chi-restraints excluded: chain N residue 655 ASP Chi-restraints excluded: chain N residue 657 VAL Chi-restraints excluded: chain N residue 662 VAL Chi-restraints excluded: chain N residue 666 ASP Chi-restraints excluded: chain N residue 741 HIS Chi-restraints excluded: chain N residue 751 LEU Chi-restraints excluded: chain N residue 865 VAL Chi-restraints excluded: chain N residue 909 VAL Chi-restraints excluded: chain N residue 944 THR Chi-restraints excluded: chain N residue 977 THR Chi-restraints excluded: chain O residue 9 VAL Chi-restraints excluded: chain O residue 45 ILE Chi-restraints excluded: chain O residue 51 GLN Chi-restraints excluded: chain O residue 60 HIS Chi-restraints excluded: chain O residue 66 HIS Chi-restraints excluded: chain O residue 75 SER Chi-restraints excluded: chain O residue 98 SER Chi-restraints excluded: chain O residue 114 HIS Chi-restraints excluded: chain O residue 115 VAL Chi-restraints excluded: chain O residue 120 LEU Chi-restraints excluded: chain O residue 235 SER Chi-restraints excluded: chain P residue 22 PHE Chi-restraints excluded: chain P residue 37 VAL Chi-restraints excluded: chain P residue 62 MET Chi-restraints excluded: chain P residue 129 GLN Chi-restraints excluded: chain P residue 131 LEU Chi-restraints excluded: chain Q residue 29 THR Chi-restraints excluded: chain Q residue 64 HIS Chi-restraints excluded: chain Q residue 151 MET Chi-restraints excluded: chain R residue 71 LEU Chi-restraints excluded: chain R residue 90 LEU Chi-restraints excluded: chain R residue 125 ILE Chi-restraints excluded: chain S residue 6 SER Chi-restraints excluded: chain S residue 39 THR Chi-restraints excluded: chain S residue 86 ASP Chi-restraints excluded: chain S residue 94 LYS Chi-restraints excluded: chain S residue 153 ASP Chi-restraints excluded: chain T residue 5 LEU Chi-restraints excluded: chain T residue 28 LEU Chi-restraints excluded: chain T residue 80 ASP Chi-restraints excluded: chain T residue 110 THR Chi-restraints excluded: chain T residue 141 VAL Chi-restraints excluded: chain T residue 145 MET Chi-restraints excluded: chain U residue 14 ILE Chi-restraints excluded: chain U residue 95 VAL Chi-restraints excluded: chain U residue 115 THR Chi-restraints excluded: chain V residue 19 GLU Chi-restraints excluded: chain V residue 25 LEU Chi-restraints excluded: chain V residue 29 TYR Chi-restraints excluded: chain V residue 30 THR Chi-restraints excluded: chain V residue 36 ASP Chi-restraints excluded: chain V residue 54 ASP Chi-restraints excluded: chain W residue 20 THR Chi-restraints excluded: chain W residue 22 ASN Chi-restraints excluded: chain W residue 27 VAL Chi-restraints excluded: chain W residue 78 THR Chi-restraints excluded: chain W residue 93 ASP Chi-restraints excluded: chain W residue 101 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 664 random chunks: chunk 619 optimal weight: 6.9990 chunk 72 optimal weight: 2.9990 chunk 366 optimal weight: 0.9990 chunk 469 optimal weight: 0.7980 chunk 363 optimal weight: 3.9990 chunk 540 optimal weight: 1.9990 chunk 358 optimal weight: 1.9990 chunk 639 optimal weight: 0.0870 chunk 400 optimal weight: 2.9990 chunk 390 optimal weight: 6.9990 chunk 295 optimal weight: 2.9990 overall best weight: 1.1764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 673 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 780 ASN ** A 982 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 287 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 460 HIS ** B 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 525 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 699 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 755 GLN B 777 ASN B 913 GLN B 968 ASN ** C 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 157 GLN D 43 HIS E 64 HIS ** E 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 131 ASN ** J 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 485 ASN ** M 576 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 780 ASN ** N 525 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 699 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 913 GLN P 43 HIS ** S 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 26 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7506 moved from start: 0.4767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 55352 Z= 0.218 Angle : 0.573 9.310 74786 Z= 0.289 Chirality : 0.044 0.285 8362 Planarity : 0.004 0.077 9702 Dihedral : 4.038 30.813 7396 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 14.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 3.95 % Allowed : 19.46 % Favored : 76.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.30 % 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: -0.06 (0.10), residues: 6690 helix: 0.74 (0.11), residues: 2342 sheet: -0.68 (0.15), residues: 1036 loop : -0.29 (0.11), residues: 3312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP E 11 HIS 0.016 0.001 HIS B 460 PHE 0.031 0.002 PHE G 18 TYR 0.023 0.001 TYR N1047 ARG 0.007 0.000 ARG B 938 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13380 Ramachandran restraints generated. 6690 Oldfield, 0 Emsley, 6690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13380 Ramachandran restraints generated. 6690 Oldfield, 0 Emsley, 6690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1033 residues out of total 6024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 238 poor density : 795 time to evaluate : 4.950 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 986 MET cc_start: 0.6361 (mtm) cc_final: 0.5757 (mmt) REVERT: A 1095 LEU cc_start: 0.8678 (OUTLIER) cc_final: 0.8387 (tt) REVERT: B 513 GLU cc_start: 0.8188 (mt-10) cc_final: 0.7766 (mt-10) REVERT: B 550 MET cc_start: 0.7756 (tmm) cc_final: 0.7498 (tmm) REVERT: B 655 ASP cc_start: 0.5859 (OUTLIER) cc_final: 0.5368 (m-30) REVERT: B 766 TYR cc_start: 0.7457 (m-80) cc_final: 0.7156 (m-80) REVERT: B 840 MET cc_start: 0.5930 (mtt) cc_final: 0.5387 (mtt) REVERT: B 908 MET cc_start: 0.6999 (ppp) cc_final: 0.6765 (ptp) REVERT: C 60 HIS cc_start: 0.5165 (OUTLIER) cc_final: 0.4639 (m-70) REVERT: D 39 MET cc_start: 0.8180 (mtm) cc_final: 0.7966 (mtp) REVERT: G 141 ASP cc_start: 0.7313 (m-30) cc_final: 0.6907 (m-30) REVERT: I 32 ASN cc_start: 0.7771 (t0) cc_final: 0.7566 (t0) REVERT: I 81 THR cc_start: 0.8303 (OUTLIER) cc_final: 0.8022 (t) REVERT: M 375 ILE cc_start: 0.8217 (OUTLIER) cc_final: 0.7984 (pt) REVERT: M 540 ASP cc_start: 0.7462 (t0) cc_final: 0.7215 (t0) REVERT: M 824 GLU cc_start: 0.7770 (OUTLIER) cc_final: 0.7050 (pm20) REVERT: M 964 GLU cc_start: 0.6025 (OUTLIER) cc_final: 0.5742 (pm20) REVERT: M 986 MET cc_start: 0.5979 (mtm) cc_final: 0.5365 (mmt) REVERT: M 1321 ILE cc_start: 0.7659 (tp) cc_final: 0.7442 (tp) REVERT: M 1348 SER cc_start: 0.8024 (m) cc_final: 0.7696 (p) REVERT: N 287 HIS cc_start: 0.6772 (m90) cc_final: 0.6255 (m90) REVERT: N 550 MET cc_start: 0.7933 (tmm) cc_final: 0.7507 (tmm) REVERT: N 683 GLN cc_start: 0.7616 (pp30) cc_final: 0.7114 (pt0) REVERT: N 739 ASN cc_start: 0.7019 (p0) cc_final: 0.6702 (p0) REVERT: N 766 TYR cc_start: 0.7236 (m-80) cc_final: 0.6892 (m-80) REVERT: N 853 LEU cc_start: 0.7135 (mt) cc_final: 0.6924 (mt) REVERT: N 854 ILE cc_start: 0.7877 (tp) cc_final: 0.7643 (tt) REVERT: N 908 MET cc_start: 0.6694 (ppp) cc_final: 0.6411 (ptt) REVERT: O 60 HIS cc_start: 0.5900 (OUTLIER) cc_final: 0.5078 (m-70) REVERT: S 1 MET cc_start: 0.6161 (tpp) cc_final: 0.5802 (tpp) REVERT: S 94 LYS cc_start: 0.7702 (OUTLIER) cc_final: 0.7398 (ptpt) REVERT: S 141 ASP cc_start: 0.7298 (m-30) cc_final: 0.7073 (t0) REVERT: W 1 MET cc_start: 0.6645 (tmm) cc_final: 0.6171 (ttt) outliers start: 238 outliers final: 182 residues processed: 945 average time/residue: 0.5224 time to fit residues: 840.6631 Evaluate side-chains 935 residues out of total 6024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 191 poor density : 744 time to evaluate : 4.840 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 452 ASP Chi-restraints excluded: chain A residue 520 MET Chi-restraints excluded: chain A residue 538 VAL Chi-restraints excluded: chain A residue 611 ASP Chi-restraints excluded: chain A residue 662 HIS Chi-restraints excluded: chain A residue 674 THR Chi-restraints excluded: chain A residue 771 VAL Chi-restraints excluded: chain A residue 869 GLU Chi-restraints excluded: chain A residue 905 ASN Chi-restraints excluded: chain A residue 909 LEU Chi-restraints excluded: chain A residue 1023 VAL Chi-restraints excluded: chain A residue 1027 ASP Chi-restraints excluded: chain A residue 1040 LEU Chi-restraints excluded: chain A residue 1095 LEU Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain A residue 1298 LEU Chi-restraints excluded: chain A residue 1311 LEU Chi-restraints excluded: chain A residue 1331 LEU Chi-restraints excluded: chain A residue 1348 SER Chi-restraints excluded: chain A residue 1359 SER Chi-restraints excluded: chain A residue 1374 VAL Chi-restraints excluded: chain B residue 152 ILE Chi-restraints excluded: chain B residue 215 TYR Chi-restraints excluded: chain B residue 232 THR Chi-restraints excluded: chain B residue 309 PHE Chi-restraints excluded: chain B residue 353 VAL Chi-restraints excluded: chain B residue 460 HIS Chi-restraints excluded: chain B residue 471 ASN Chi-restraints excluded: chain B residue 489 ILE Chi-restraints excluded: chain B residue 542 LEU Chi-restraints excluded: chain B residue 573 TRP Chi-restraints excluded: chain B residue 598 VAL Chi-restraints excluded: chain B residue 652 SER Chi-restraints excluded: chain B residue 655 ASP Chi-restraints excluded: chain B residue 657 VAL Chi-restraints excluded: chain B residue 662 VAL Chi-restraints excluded: chain B residue 666 ASP Chi-restraints excluded: chain B residue 678 THR Chi-restraints excluded: chain B residue 733 MET Chi-restraints excluded: chain B residue 865 VAL Chi-restraints excluded: chain B residue 866 ILE Chi-restraints excluded: chain B residue 909 VAL Chi-restraints excluded: chain B residue 911 LEU Chi-restraints excluded: chain B residue 939 HIS Chi-restraints excluded: chain B residue 944 THR Chi-restraints excluded: chain B residue 1028 LEU Chi-restraints excluded: chain C residue 9 VAL Chi-restraints excluded: chain C residue 60 HIS Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain C residue 112 THR Chi-restraints excluded: chain C residue 114 HIS Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain C residue 146 ASP Chi-restraints excluded: chain C residue 151 VAL Chi-restraints excluded: chain C residue 235 SER Chi-restraints excluded: chain C residue 246 LEU Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 76 ASN Chi-restraints excluded: chain D residue 102 ASN Chi-restraints excluded: chain E residue 64 HIS Chi-restraints excluded: chain E residue 185 ILE Chi-restraints excluded: chain F residue 71 LEU Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain G residue 39 THR Chi-restraints excluded: chain G residue 86 ASP Chi-restraints excluded: chain G residue 90 THR Chi-restraints excluded: chain G residue 91 GLN Chi-restraints excluded: chain G residue 92 VAL Chi-restraints excluded: chain G residue 115 SER Chi-restraints excluded: chain H residue 15 ILE Chi-restraints excluded: chain H residue 28 LEU Chi-restraints excluded: chain H residue 80 ASP Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain H residue 116 VAL Chi-restraints excluded: chain H residue 141 VAL Chi-restraints excluded: chain H residue 144 LEU Chi-restraints excluded: chain H residue 145 MET Chi-restraints excluded: chain I residue 23 MET Chi-restraints excluded: chain I residue 81 THR Chi-restraints excluded: chain J residue 30 THR Chi-restraints excluded: chain J residue 36 ASP Chi-restraints excluded: chain J residue 54 ASP Chi-restraints excluded: chain K residue 13 PHE Chi-restraints excluded: chain K residue 20 THR Chi-restraints excluded: chain K residue 27 VAL Chi-restraints excluded: chain K residue 71 ILE Chi-restraints excluded: chain K residue 78 THR Chi-restraints excluded: chain K residue 82 SER Chi-restraints excluded: chain K residue 93 ASP Chi-restraints excluded: chain K residue 101 LEU Chi-restraints excluded: chain K residue 111 ASP Chi-restraints excluded: chain M residue 365 THR Chi-restraints excluded: chain M residue 366 VAL Chi-restraints excluded: chain M residue 375 ILE Chi-restraints excluded: chain M residue 438 LEU Chi-restraints excluded: chain M residue 538 VAL Chi-restraints excluded: chain M residue 583 ARG Chi-restraints excluded: chain M residue 611 ASP Chi-restraints excluded: chain M residue 662 HIS Chi-restraints excluded: chain M residue 674 THR Chi-restraints excluded: chain M residue 771 VAL Chi-restraints excluded: chain M residue 824 GLU Chi-restraints excluded: chain M residue 849 ASP Chi-restraints excluded: chain M residue 869 GLU Chi-restraints excluded: chain M residue 870 SER Chi-restraints excluded: chain M residue 905 ASN Chi-restraints excluded: chain M residue 909 LEU Chi-restraints excluded: chain M residue 938 LEU Chi-restraints excluded: chain M residue 964 GLU Chi-restraints excluded: chain M residue 1023 VAL Chi-restraints excluded: chain M residue 1040 LEU Chi-restraints excluded: chain M residue 1095 LEU Chi-restraints excluded: chain M residue 1117 VAL Chi-restraints excluded: chain M residue 1127 LEU Chi-restraints excluded: chain M residue 1136 THR Chi-restraints excluded: chain M residue 1156 ASP Chi-restraints excluded: chain M residue 1293 LEU Chi-restraints excluded: chain M residue 1338 THR Chi-restraints excluded: chain M residue 1374 VAL Chi-restraints excluded: chain N residue 160 TYR Chi-restraints excluded: chain N residue 215 TYR Chi-restraints excluded: chain N residue 232 THR Chi-restraints excluded: chain N residue 276 LEU Chi-restraints excluded: chain N residue 416 ARG Chi-restraints excluded: chain N residue 460 HIS Chi-restraints excluded: chain N residue 573 TRP Chi-restraints excluded: chain N residue 657 VAL Chi-restraints excluded: chain N residue 662 VAL Chi-restraints excluded: chain N residue 666 ASP Chi-restraints excluded: chain N residue 741 HIS Chi-restraints excluded: chain N residue 751 LEU Chi-restraints excluded: chain N residue 858 VAL Chi-restraints excluded: chain N residue 865 VAL Chi-restraints excluded: chain N residue 909 VAL Chi-restraints excluded: chain N residue 944 THR Chi-restraints excluded: chain N residue 977 THR Chi-restraints excluded: chain O residue 9 VAL Chi-restraints excluded: chain O residue 51 GLN Chi-restraints excluded: chain O residue 60 HIS Chi-restraints excluded: chain O residue 66 HIS Chi-restraints excluded: chain O residue 68 LEU Chi-restraints excluded: chain O residue 75 SER Chi-restraints excluded: chain O residue 114 HIS Chi-restraints excluded: chain O residue 115 VAL Chi-restraints excluded: chain O residue 120 LEU Chi-restraints excluded: chain O residue 235 SER Chi-restraints excluded: chain P residue 22 PHE Chi-restraints excluded: chain P residue 37 VAL Chi-restraints excluded: chain P residue 62 MET Chi-restraints excluded: chain P residue 76 ASN Chi-restraints excluded: chain P residue 131 LEU Chi-restraints excluded: chain Q residue 29 THR Chi-restraints excluded: chain Q residue 64 HIS Chi-restraints excluded: chain Q residue 87 ILE Chi-restraints excluded: chain Q residue 151 MET Chi-restraints excluded: chain R residue 71 LEU Chi-restraints excluded: chain R residue 90 LEU Chi-restraints excluded: chain R residue 125 ILE Chi-restraints excluded: chain S residue 6 SER Chi-restraints excluded: chain S residue 22 LEU Chi-restraints excluded: chain S residue 32 THR Chi-restraints excluded: chain S residue 39 THR Chi-restraints excluded: chain S residue 86 ASP Chi-restraints excluded: chain S residue 94 LYS Chi-restraints excluded: chain S residue 153 ASP Chi-restraints excluded: chain T residue 5 LEU Chi-restraints excluded: chain T residue 28 LEU Chi-restraints excluded: chain T residue 80 ASP Chi-restraints excluded: chain T residue 110 THR Chi-restraints excluded: chain T residue 141 VAL Chi-restraints excluded: chain T residue 144 LEU Chi-restraints excluded: chain T residue 145 MET Chi-restraints excluded: chain U residue 14 ILE Chi-restraints excluded: chain U residue 23 MET Chi-restraints excluded: chain U residue 95 VAL Chi-restraints excluded: chain U residue 115 THR Chi-restraints excluded: chain V residue 19 GLU Chi-restraints excluded: chain V residue 25 LEU Chi-restraints excluded: chain V residue 29 TYR Chi-restraints excluded: chain V residue 30 THR Chi-restraints excluded: chain V residue 54 ASP Chi-restraints excluded: chain W residue 20 THR Chi-restraints excluded: chain W residue 22 ASN Chi-restraints excluded: chain W residue 27 VAL Chi-restraints excluded: chain W residue 71 ILE Chi-restraints excluded: chain W residue 78 THR Chi-restraints excluded: chain W residue 93 ASP Chi-restraints excluded: chain W residue 101 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 664 random chunks: chunk 395 optimal weight: 10.0000 chunk 255 optimal weight: 5.9990 chunk 382 optimal weight: 4.9990 chunk 192 optimal weight: 3.9990 chunk 125 optimal weight: 0.6980 chunk 123 optimal weight: 20.0000 chunk 406 optimal weight: 9.9990 chunk 436 optimal weight: 3.9990 chunk 316 optimal weight: 2.9990 chunk 59 optimal weight: 0.9980 chunk 503 optimal weight: 2.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 485 ASN A 673 GLN ** A 764 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 780 ASN A 982 ASN ** B 287 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 460 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 500 GLN ** B 525 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 699 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 66 HIS C 265 HIS D 43 HIS ** E 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 131 ASN ** J 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 576 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 780 ASN M1244 ASN N 144 HIS ** N 525 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 699 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 60 HIS P 43 HIS P 129 GLN ** S 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 26 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7569 moved from start: 0.4972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 55352 Z= 0.326 Angle : 0.624 9.293 74786 Z= 0.317 Chirality : 0.046 0.306 8362 Planarity : 0.004 0.077 9702 Dihedral : 4.211 30.612 7396 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 15.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 4.17 % Allowed : 19.85 % Favored : 75.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.30 % 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: -0.22 (0.10), residues: 6690 helix: 0.60 (0.11), residues: 2352 sheet: -0.73 (0.15), residues: 1054 loop : -0.38 (0.11), residues: 3284 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.056 0.002 TRP E 11 HIS 0.018 0.001 HIS B 460 PHE 0.023 0.002 PHE G 18 TYR 0.025 0.002 TYR N1047 ARG 0.008 0.000 ARG M1408 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13380 Ramachandran restraints generated. 6690 Oldfield, 0 Emsley, 6690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13380 Ramachandran restraints generated. 6690 Oldfield, 0 Emsley, 6690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 997 residues out of total 6024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 251 poor density : 746 time to evaluate : 4.773 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 986 MET cc_start: 0.6346 (mtm) cc_final: 0.5706 (mmt) REVERT: A 1095 LEU cc_start: 0.8729 (OUTLIER) cc_final: 0.8418 (tt) REVERT: B 152 ILE cc_start: 0.7209 (OUTLIER) cc_final: 0.6783 (tt) REVERT: B 550 MET cc_start: 0.7815 (tmm) cc_final: 0.7529 (tmm) REVERT: B 655 ASP cc_start: 0.5958 (OUTLIER) cc_final: 0.5391 (m-30) REVERT: C 60 HIS cc_start: 0.5412 (OUTLIER) cc_final: 0.4857 (m-70) REVERT: C 94 CYS cc_start: 0.6388 (OUTLIER) cc_final: 0.5939 (p) REVERT: C 111 GLN cc_start: 0.7698 (pm20) cc_final: 0.7458 (pm20) REVERT: D 39 MET cc_start: 0.8226 (mtm) cc_final: 0.7982 (mtp) REVERT: E 73 PHE cc_start: 0.7107 (OUTLIER) cc_final: 0.6754 (t80) REVERT: G 141 ASP cc_start: 0.7321 (m-30) cc_final: 0.6917 (m-30) REVERT: I 81 THR cc_start: 0.8324 (OUTLIER) cc_final: 0.8024 (t) REVERT: M 375 ILE cc_start: 0.8351 (OUTLIER) cc_final: 0.8055 (pt) REVERT: M 540 ASP cc_start: 0.7546 (t0) cc_final: 0.7317 (t0) REVERT: M 824 GLU cc_start: 0.7812 (OUTLIER) cc_final: 0.7099 (pm20) REVERT: M 986 MET cc_start: 0.6000 (mtm) cc_final: 0.5332 (mmt) REVERT: M 1348 SER cc_start: 0.8083 (m) cc_final: 0.7748 (p) REVERT: N 287 HIS cc_start: 0.6927 (m90) cc_final: 0.6440 (m90) REVERT: N 550 MET cc_start: 0.8005 (tmm) cc_final: 0.7304 (tmm) REVERT: N 674 MET cc_start: 0.8207 (tpt) cc_final: 0.7995 (tpt) REVERT: N 683 GLN cc_start: 0.7670 (pp30) cc_final: 0.7146 (pt0) REVERT: N 853 LEU cc_start: 0.7309 (mt) cc_final: 0.7077 (mt) REVERT: N 854 ILE cc_start: 0.7999 (tp) cc_final: 0.7786 (tt) REVERT: N 908 MET cc_start: 0.6805 (ppp) cc_final: 0.6538 (ptt) REVERT: O 60 HIS cc_start: 0.6243 (OUTLIER) cc_final: 0.5381 (m90) REVERT: S 94 LYS cc_start: 0.7679 (pttm) cc_final: 0.7398 (ptpt) REVERT: S 141 ASP cc_start: 0.7339 (m-30) cc_final: 0.7113 (t0) REVERT: W 1 MET cc_start: 0.6701 (tmm) cc_final: 0.6261 (ttt) outliers start: 251 outliers final: 193 residues processed: 917 average time/residue: 0.5096 time to fit residues: 795.6638 Evaluate side-chains 921 residues out of total 6024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 203 poor density : 718 time to evaluate : 4.745 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 375 ILE Chi-restraints excluded: chain A residue 438 LEU Chi-restraints excluded: chain A residue 452 ASP Chi-restraints excluded: chain A residue 485 ASN Chi-restraints excluded: chain A residue 505 LEU Chi-restraints excluded: chain A residue 520 MET Chi-restraints excluded: chain A residue 538 VAL Chi-restraints excluded: chain A residue 587 THR Chi-restraints excluded: chain A residue 611 ASP Chi-restraints excluded: chain A residue 662 HIS Chi-restraints excluded: chain A residue 674 THR Chi-restraints excluded: chain A residue 771 VAL Chi-restraints excluded: chain A residue 905 ASN Chi-restraints excluded: chain A residue 909 LEU Chi-restraints excluded: chain A residue 1023 VAL Chi-restraints excluded: chain A residue 1027 ASP Chi-restraints excluded: chain A residue 1040 LEU Chi-restraints excluded: chain A residue 1095 LEU Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain A residue 1311 LEU Chi-restraints excluded: chain A residue 1348 SER Chi-restraints excluded: chain A residue 1358 THR Chi-restraints excluded: chain A residue 1374 VAL Chi-restraints excluded: chain A residue 1385 VAL Chi-restraints excluded: chain B residue 152 ILE Chi-restraints excluded: chain B residue 215 TYR Chi-restraints excluded: chain B residue 232 THR Chi-restraints excluded: chain B residue 309 PHE Chi-restraints excluded: chain B residue 353 VAL Chi-restraints excluded: chain B residue 460 HIS Chi-restraints excluded: chain B residue 471 ASN Chi-restraints excluded: chain B residue 489 ILE Chi-restraints excluded: chain B residue 542 LEU Chi-restraints excluded: chain B residue 573 TRP Chi-restraints excluded: chain B residue 598 VAL Chi-restraints excluded: chain B residue 652 SER Chi-restraints excluded: chain B residue 655 ASP Chi-restraints excluded: chain B residue 657 VAL Chi-restraints excluded: chain B residue 662 VAL Chi-restraints excluded: chain B residue 666 ASP Chi-restraints excluded: chain B residue 678 THR Chi-restraints excluded: chain B residue 733 MET Chi-restraints excluded: chain B residue 865 VAL Chi-restraints excluded: chain B residue 866 ILE Chi-restraints excluded: chain B residue 909 VAL Chi-restraints excluded: chain B residue 939 HIS Chi-restraints excluded: chain B residue 944 THR Chi-restraints excluded: chain B residue 976 MET Chi-restraints excluded: chain B residue 1000 THR Chi-restraints excluded: chain B residue 1028 LEU Chi-restraints excluded: chain C residue 9 VAL Chi-restraints excluded: chain C residue 41 GLU Chi-restraints excluded: chain C residue 60 HIS Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 94 CYS Chi-restraints excluded: chain C residue 112 THR Chi-restraints excluded: chain C residue 114 HIS Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain C residue 146 ASP Chi-restraints excluded: chain C residue 151 VAL Chi-restraints excluded: chain C residue 235 SER Chi-restraints excluded: chain C residue 246 LEU Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 102 ASN Chi-restraints excluded: chain E residue 73 PHE Chi-restraints excluded: chain E residue 185 ILE Chi-restraints excluded: chain F residue 71 LEU Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain G residue 22 LEU Chi-restraints excluded: chain G residue 39 THR Chi-restraints excluded: chain G residue 90 THR Chi-restraints excluded: chain G residue 115 SER Chi-restraints excluded: chain H residue 15 ILE Chi-restraints excluded: chain H residue 28 LEU Chi-restraints excluded: chain H residue 80 ASP Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain H residue 116 VAL Chi-restraints excluded: chain H residue 141 VAL Chi-restraints excluded: chain H residue 144 LEU Chi-restraints excluded: chain H residue 145 MET Chi-restraints excluded: chain I residue 15 ARG Chi-restraints excluded: chain I residue 23 MET Chi-restraints excluded: chain I residue 81 THR Chi-restraints excluded: chain I residue 95 VAL Chi-restraints excluded: chain J residue 30 THR Chi-restraints excluded: chain J residue 36 ASP Chi-restraints excluded: chain J residue 54 ASP Chi-restraints excluded: chain K residue 13 PHE Chi-restraints excluded: chain K residue 20 THR Chi-restraints excluded: chain K residue 27 VAL Chi-restraints excluded: chain K residue 71 ILE Chi-restraints excluded: chain K residue 78 THR Chi-restraints excluded: chain K residue 82 SER Chi-restraints excluded: chain K residue 93 ASP Chi-restraints excluded: chain K residue 101 LEU Chi-restraints excluded: chain K residue 111 ASP Chi-restraints excluded: chain M residue 365 THR Chi-restraints excluded: chain M residue 366 VAL Chi-restraints excluded: chain M residue 375 ILE Chi-restraints excluded: chain M residue 438 LEU Chi-restraints excluded: chain M residue 457 ILE Chi-restraints excluded: chain M residue 520 MET Chi-restraints excluded: chain M residue 538 VAL Chi-restraints excluded: chain M residue 583 ARG Chi-restraints excluded: chain M residue 611 ASP Chi-restraints excluded: chain M residue 674 THR Chi-restraints excluded: chain M residue 736 THR Chi-restraints excluded: chain M residue 771 VAL Chi-restraints excluded: chain M residue 824 GLU Chi-restraints excluded: chain M residue 869 GLU Chi-restraints excluded: chain M residue 870 SER Chi-restraints excluded: chain M residue 905 ASN Chi-restraints excluded: chain M residue 909 LEU Chi-restraints excluded: chain M residue 938 LEU Chi-restraints excluded: chain M residue 1023 VAL Chi-restraints excluded: chain M residue 1040 LEU Chi-restraints excluded: chain M residue 1095 LEU Chi-restraints excluded: chain M residue 1117 VAL Chi-restraints excluded: chain M residue 1127 LEU Chi-restraints excluded: chain M residue 1136 THR Chi-restraints excluded: chain M residue 1156 ASP Chi-restraints excluded: chain M residue 1293 LEU Chi-restraints excluded: chain M residue 1338 THR Chi-restraints excluded: chain M residue 1374 VAL Chi-restraints excluded: chain N residue 26 CYS Chi-restraints excluded: chain N residue 160 TYR Chi-restraints excluded: chain N residue 195 ILE Chi-restraints excluded: chain N residue 215 TYR Chi-restraints excluded: chain N residue 232 THR Chi-restraints excluded: chain N residue 276 LEU Chi-restraints excluded: chain N residue 416 ARG Chi-restraints excluded: chain N residue 460 HIS Chi-restraints excluded: chain N residue 492 ASP Chi-restraints excluded: chain N residue 573 TRP Chi-restraints excluded: chain N residue 655 ASP Chi-restraints excluded: chain N residue 657 VAL Chi-restraints excluded: chain N residue 662 VAL Chi-restraints excluded: chain N residue 666 ASP Chi-restraints excluded: chain N residue 751 LEU Chi-restraints excluded: chain N residue 858 VAL Chi-restraints excluded: chain N residue 865 VAL Chi-restraints excluded: chain N residue 909 VAL Chi-restraints excluded: chain N residue 944 THR Chi-restraints excluded: chain N residue 977 THR Chi-restraints excluded: chain O residue 9 VAL Chi-restraints excluded: chain O residue 45 ILE Chi-restraints excluded: chain O residue 51 GLN Chi-restraints excluded: chain O residue 60 HIS Chi-restraints excluded: chain O residue 66 HIS Chi-restraints excluded: chain O residue 68 LEU Chi-restraints excluded: chain O residue 75 SER Chi-restraints excluded: chain O residue 98 SER Chi-restraints excluded: chain O residue 114 HIS Chi-restraints excluded: chain O residue 115 VAL Chi-restraints excluded: chain O residue 120 LEU Chi-restraints excluded: chain O residue 235 SER Chi-restraints excluded: chain P residue 22 PHE Chi-restraints excluded: chain P residue 37 VAL Chi-restraints excluded: chain P residue 62 MET Chi-restraints excluded: chain P residue 68 THR Chi-restraints excluded: chain P residue 76 ASN Chi-restraints excluded: chain P residue 107 THR Chi-restraints excluded: chain P residue 129 GLN Chi-restraints excluded: chain P residue 131 LEU Chi-restraints excluded: chain Q residue 29 THR Chi-restraints excluded: chain Q residue 64 HIS Chi-restraints excluded: chain Q residue 151 MET Chi-restraints excluded: chain R residue 71 LEU Chi-restraints excluded: chain R residue 90 LEU Chi-restraints excluded: chain R residue 125 ILE Chi-restraints excluded: chain S residue 6 SER Chi-restraints excluded: chain S residue 32 THR Chi-restraints excluded: chain S residue 39 THR Chi-restraints excluded: chain S residue 86 ASP Chi-restraints excluded: chain S residue 91 GLN Chi-restraints excluded: chain S residue 122 ASN Chi-restraints excluded: chain S residue 153 ASP Chi-restraints excluded: chain T residue 5 LEU Chi-restraints excluded: chain T residue 28 LEU Chi-restraints excluded: chain T residue 80 ASP Chi-restraints excluded: chain T residue 110 THR Chi-restraints excluded: chain T residue 141 VAL Chi-restraints excluded: chain T residue 144 LEU Chi-restraints excluded: chain T residue 145 MET Chi-restraints excluded: chain U residue 14 ILE Chi-restraints excluded: chain U residue 23 MET Chi-restraints excluded: chain U residue 95 VAL Chi-restraints excluded: chain U residue 115 THR Chi-restraints excluded: chain U residue 124 THR Chi-restraints excluded: chain V residue 19 GLU Chi-restraints excluded: chain V residue 25 LEU Chi-restraints excluded: chain V residue 29 TYR Chi-restraints excluded: chain V residue 30 THR Chi-restraints excluded: chain V residue 54 ASP Chi-restraints excluded: chain W residue 20 THR Chi-restraints excluded: chain W residue 27 VAL Chi-restraints excluded: chain W residue 71 ILE Chi-restraints excluded: chain W residue 78 THR Chi-restraints excluded: chain W residue 81 TYR Chi-restraints excluded: chain W residue 93 ASP Chi-restraints excluded: chain W residue 101 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 664 random chunks: chunk 582 optimal weight: 5.9990 chunk 613 optimal weight: 0.7980 chunk 559 optimal weight: 5.9990 chunk 596 optimal weight: 4.9990 chunk 612 optimal weight: 0.8980 chunk 358 optimal weight: 0.6980 chunk 259 optimal weight: 0.9990 chunk 468 optimal weight: 5.9990 chunk 183 optimal weight: 9.9990 chunk 538 optimal weight: 1.9990 chunk 564 optimal weight: 0.9980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 576 GLN A 780 ASN ** A 982 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1244 ASN ** A1267 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 460 HIS ** B 525 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 699 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1003 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 51 GLN D 43 HIS E 64 HIS ** E 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 72 GLN H 131 ASN ** J 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 576 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 780 ASN M 989 ASN ** M1036 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 525 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 699 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 43 HIS P 129 GLN ** S 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7505 moved from start: 0.5001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 55352 Z= 0.206 Angle : 0.596 10.534 74786 Z= 0.301 Chirality : 0.044 0.292 8362 Planarity : 0.004 0.076 9702 Dihedral : 4.130 29.638 7396 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 14.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 3.64 % Allowed : 20.80 % Favored : 75.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.30 % 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: -0.10 (0.10), residues: 6690 helix: 0.73 (0.11), residues: 2330 sheet: -0.72 (0.15), residues: 1054 loop : -0.31 (0.11), residues: 3306 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.002 TRP E 11 HIS 0.012 0.001 HIS B 577 PHE 0.036 0.002 PHE G 18 TYR 0.024 0.001 TYR N1047 ARG 0.008 0.000 ARG N 169 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13380 Ramachandran restraints generated. 6690 Oldfield, 0 Emsley, 6690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13380 Ramachandran restraints generated. 6690 Oldfield, 0 Emsley, 6690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 981 residues out of total 6024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 219 poor density : 762 time to evaluate : 4.937 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 986 MET cc_start: 0.6367 (mtm) cc_final: 0.5766 (mmt) REVERT: A 1095 LEU cc_start: 0.8678 (OUTLIER) cc_final: 0.8380 (tt) REVERT: B 513 GLU cc_start: 0.8150 (mt-10) cc_final: 0.7736 (mt-10) REVERT: B 550 MET cc_start: 0.7749 (tmm) cc_final: 0.7546 (tmm) REVERT: B 655 ASP cc_start: 0.5839 (OUTLIER) cc_final: 0.5350 (m-30) REVERT: B 908 MET cc_start: 0.6467 (ppp) cc_final: 0.6227 (ptt) REVERT: C 60 HIS cc_start: 0.5363 (OUTLIER) cc_final: 0.4853 (m-70) REVERT: C 94 CYS cc_start: 0.6385 (OUTLIER) cc_final: 0.5939 (p) REVERT: D 39 MET cc_start: 0.8179 (mtm) cc_final: 0.7932 (mtp) REVERT: D 90 LYS cc_start: 0.8349 (mttp) cc_final: 0.8034 (ptpp) REVERT: G 141 ASP cc_start: 0.7313 (m-30) cc_final: 0.6908 (m-30) REVERT: I 81 THR cc_start: 0.8311 (OUTLIER) cc_final: 0.8070 (t) REVERT: M 375 ILE cc_start: 0.8237 (OUTLIER) cc_final: 0.7996 (pt) REVERT: M 540 ASP cc_start: 0.7473 (t0) cc_final: 0.7195 (t0) REVERT: M 824 GLU cc_start: 0.7780 (OUTLIER) cc_final: 0.7066 (pm20) REVERT: M 909 LEU cc_start: 0.7185 (OUTLIER) cc_final: 0.6863 (pt) REVERT: M 986 MET cc_start: 0.6016 (mtm) cc_final: 0.5333 (mmt) REVERT: M 1321 ILE cc_start: 0.7658 (tp) cc_final: 0.7408 (tp) REVERT: M 1348 SER cc_start: 0.8020 (m) cc_final: 0.7647 (p) REVERT: N 287 HIS cc_start: 0.6754 (m90) cc_final: 0.6291 (m90) REVERT: N 529 MET cc_start: 0.8659 (tpp) cc_final: 0.8420 (tpp) REVERT: N 550 MET cc_start: 0.8007 (tmm) cc_final: 0.7580 (tmm) REVERT: N 674 MET cc_start: 0.8116 (tpt) cc_final: 0.7859 (tpt) REVERT: N 683 GLN cc_start: 0.7613 (pp30) cc_final: 0.7096 (pt0) REVERT: N 739 ASN cc_start: 0.6948 (p0) cc_final: 0.6584 (p0) REVERT: N 766 TYR cc_start: 0.6970 (m-10) cc_final: 0.6666 (m-80) REVERT: N 853 LEU cc_start: 0.7172 (mt) cc_final: 0.6957 (mt) REVERT: N 854 ILE cc_start: 0.7962 (tp) cc_final: 0.7741 (tt) REVERT: N 908 MET cc_start: 0.6692 (ppp) cc_final: 0.6415 (ptt) REVERT: P 90 LYS cc_start: 0.8144 (OUTLIER) cc_final: 0.7856 (mttp) REVERT: S 10 GLU cc_start: 0.6777 (mm-30) cc_final: 0.6508 (mm-30) REVERT: S 94 LYS cc_start: 0.7654 (pttm) cc_final: 0.7377 (ptpt) REVERT: S 117 MET cc_start: 0.7627 (mmm) cc_final: 0.7154 (tpp) REVERT: S 141 ASP cc_start: 0.7327 (m-30) cc_final: 0.7104 (t0) REVERT: W 1 MET cc_start: 0.6752 (tmm) cc_final: 0.6291 (ttt) outliers start: 219 outliers final: 173 residues processed: 905 average time/residue: 0.5208 time to fit residues: 800.7476 Evaluate side-chains 913 residues out of total 6024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 182 poor density : 731 time to evaluate : 4.797 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 375 ILE Chi-restraints excluded: chain A residue 452 ASP Chi-restraints excluded: chain A residue 538 VAL Chi-restraints excluded: chain A residue 576 GLN Chi-restraints excluded: chain A residue 611 ASP Chi-restraints excluded: chain A residue 662 HIS Chi-restraints excluded: chain A residue 699 TYR Chi-restraints excluded: chain A residue 905 ASN Chi-restraints excluded: chain A residue 909 LEU Chi-restraints excluded: chain A residue 947 HIS Chi-restraints excluded: chain A residue 1023 VAL Chi-restraints excluded: chain A residue 1027 ASP Chi-restraints excluded: chain A residue 1040 LEU Chi-restraints excluded: chain A residue 1095 LEU Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain A residue 1298 LEU Chi-restraints excluded: chain A residue 1309 MET Chi-restraints excluded: chain A residue 1311 LEU Chi-restraints excluded: chain A residue 1348 SER Chi-restraints excluded: chain A residue 1374 VAL Chi-restraints excluded: chain B residue 152 ILE Chi-restraints excluded: chain B residue 215 TYR Chi-restraints excluded: chain B residue 232 THR Chi-restraints excluded: chain B residue 309 PHE Chi-restraints excluded: chain B residue 353 VAL Chi-restraints excluded: chain B residue 460 HIS Chi-restraints excluded: chain B residue 471 ASN Chi-restraints excluded: chain B residue 489 ILE Chi-restraints excluded: chain B residue 573 TRP Chi-restraints excluded: chain B residue 598 VAL Chi-restraints excluded: chain B residue 652 SER Chi-restraints excluded: chain B residue 655 ASP Chi-restraints excluded: chain B residue 657 VAL Chi-restraints excluded: chain B residue 662 VAL Chi-restraints excluded: chain B residue 666 ASP Chi-restraints excluded: chain B residue 678 THR Chi-restraints excluded: chain B residue 733 MET Chi-restraints excluded: chain B residue 865 VAL Chi-restraints excluded: chain B residue 866 ILE Chi-restraints excluded: chain B residue 909 VAL Chi-restraints excluded: chain B residue 939 HIS Chi-restraints excluded: chain B residue 944 THR Chi-restraints excluded: chain B residue 976 MET Chi-restraints excluded: chain B residue 1000 THR Chi-restraints excluded: chain B residue 1028 LEU Chi-restraints excluded: chain C residue 9 VAL Chi-restraints excluded: chain C residue 60 HIS Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 94 CYS Chi-restraints excluded: chain C residue 112 THR Chi-restraints excluded: chain C residue 114 HIS Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain C residue 146 ASP Chi-restraints excluded: chain C residue 151 VAL Chi-restraints excluded: chain C residue 235 SER Chi-restraints excluded: chain C residue 246 LEU Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain E residue 185 ILE Chi-restraints excluded: chain F residue 71 LEU Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain G residue 22 LEU Chi-restraints excluded: chain G residue 39 THR Chi-restraints excluded: chain G residue 86 ASP Chi-restraints excluded: chain G residue 90 THR Chi-restraints excluded: chain G residue 91 GLN Chi-restraints excluded: chain G residue 115 SER Chi-restraints excluded: chain H residue 5 LEU Chi-restraints excluded: chain H residue 15 ILE Chi-restraints excluded: chain H residue 28 LEU Chi-restraints excluded: chain H residue 80 ASP Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain H residue 116 VAL Chi-restraints excluded: chain H residue 141 VAL Chi-restraints excluded: chain H residue 144 LEU Chi-restraints excluded: chain H residue 145 MET Chi-restraints excluded: chain I residue 23 MET Chi-restraints excluded: chain I residue 81 THR Chi-restraints excluded: chain I residue 95 VAL Chi-restraints excluded: chain J residue 30 THR Chi-restraints excluded: chain J residue 36 ASP Chi-restraints excluded: chain J residue 54 ASP Chi-restraints excluded: chain K residue 13 PHE Chi-restraints excluded: chain K residue 20 THR Chi-restraints excluded: chain K residue 27 VAL Chi-restraints excluded: chain K residue 71 ILE Chi-restraints excluded: chain K residue 78 THR Chi-restraints excluded: chain K residue 82 SER Chi-restraints excluded: chain K residue 93 ASP Chi-restraints excluded: chain K residue 101 LEU Chi-restraints excluded: chain M residue 365 THR Chi-restraints excluded: chain M residue 375 ILE Chi-restraints excluded: chain M residue 520 MET Chi-restraints excluded: chain M residue 538 VAL Chi-restraints excluded: chain M residue 611 ASP Chi-restraints excluded: chain M residue 662 HIS Chi-restraints excluded: chain M residue 674 THR Chi-restraints excluded: chain M residue 824 GLU Chi-restraints excluded: chain M residue 869 GLU Chi-restraints excluded: chain M residue 870 SER Chi-restraints excluded: chain M residue 905 ASN Chi-restraints excluded: chain M residue 909 LEU Chi-restraints excluded: chain M residue 938 LEU Chi-restraints excluded: chain M residue 989 ASN Chi-restraints excluded: chain M residue 1023 VAL Chi-restraints excluded: chain M residue 1040 LEU Chi-restraints excluded: chain M residue 1095 LEU Chi-restraints excluded: chain M residue 1117 VAL Chi-restraints excluded: chain M residue 1127 LEU Chi-restraints excluded: chain M residue 1136 THR Chi-restraints excluded: chain M residue 1156 ASP Chi-restraints excluded: chain M residue 1293 LEU Chi-restraints excluded: chain M residue 1338 THR Chi-restraints excluded: chain M residue 1374 VAL Chi-restraints excluded: chain N residue 160 TYR Chi-restraints excluded: chain N residue 215 TYR Chi-restraints excluded: chain N residue 232 THR Chi-restraints excluded: chain N residue 276 LEU Chi-restraints excluded: chain N residue 416 ARG Chi-restraints excluded: chain N residue 460 HIS Chi-restraints excluded: chain N residue 573 TRP Chi-restraints excluded: chain N residue 657 VAL Chi-restraints excluded: chain N residue 662 VAL Chi-restraints excluded: chain N residue 666 ASP Chi-restraints excluded: chain N residue 751 LEU Chi-restraints excluded: chain N residue 858 VAL Chi-restraints excluded: chain N residue 865 VAL Chi-restraints excluded: chain N residue 909 VAL Chi-restraints excluded: chain N residue 944 THR Chi-restraints excluded: chain N residue 977 THR Chi-restraints excluded: chain O residue 16 ASP Chi-restraints excluded: chain O residue 51 GLN Chi-restraints excluded: chain O residue 66 HIS Chi-restraints excluded: chain O residue 68 LEU Chi-restraints excluded: chain O residue 75 SER Chi-restraints excluded: chain O residue 114 HIS Chi-restraints excluded: chain O residue 115 VAL Chi-restraints excluded: chain O residue 120 LEU Chi-restraints excluded: chain O residue 235 SER Chi-restraints excluded: chain P residue 22 PHE Chi-restraints excluded: chain P residue 37 VAL Chi-restraints excluded: chain P residue 62 MET Chi-restraints excluded: chain P residue 68 THR Chi-restraints excluded: chain P residue 76 ASN Chi-restraints excluded: chain P residue 90 LYS Chi-restraints excluded: chain P residue 107 THR Chi-restraints excluded: chain P residue 124 ASP Chi-restraints excluded: chain P residue 131 LEU Chi-restraints excluded: chain Q residue 64 HIS Chi-restraints excluded: chain Q residue 151 MET Chi-restraints excluded: chain R residue 71 LEU Chi-restraints excluded: chain R residue 90 LEU Chi-restraints excluded: chain R residue 125 ILE Chi-restraints excluded: chain S residue 6 SER Chi-restraints excluded: chain S residue 22 LEU Chi-restraints excluded: chain S residue 32 THR Chi-restraints excluded: chain S residue 39 THR Chi-restraints excluded: chain S residue 86 ASP Chi-restraints excluded: chain S residue 153 ASP Chi-restraints excluded: chain T residue 5 LEU Chi-restraints excluded: chain T residue 28 LEU Chi-restraints excluded: chain T residue 80 ASP Chi-restraints excluded: chain T residue 110 THR Chi-restraints excluded: chain T residue 141 VAL Chi-restraints excluded: chain T residue 144 LEU Chi-restraints excluded: chain T residue 145 MET Chi-restraints excluded: chain U residue 14 ILE Chi-restraints excluded: chain U residue 23 MET Chi-restraints excluded: chain U residue 95 VAL Chi-restraints excluded: chain U residue 115 THR Chi-restraints excluded: chain U residue 124 THR Chi-restraints excluded: chain V residue 19 GLU Chi-restraints excluded: chain V residue 25 LEU Chi-restraints excluded: chain V residue 29 TYR Chi-restraints excluded: chain V residue 30 THR Chi-restraints excluded: chain V residue 54 ASP Chi-restraints excluded: chain W residue 20 THR Chi-restraints excluded: chain W residue 27 VAL Chi-restraints excluded: chain W residue 71 ILE Chi-restraints excluded: chain W residue 78 THR Chi-restraints excluded: chain W residue 101 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 664 random chunks: chunk 594 optimal weight: 0.9980 chunk 391 optimal weight: 3.9990 chunk 630 optimal weight: 6.9990 chunk 384 optimal weight: 1.9990 chunk 299 optimal weight: 0.7980 chunk 438 optimal weight: 0.9980 chunk 661 optimal weight: 7.9990 chunk 608 optimal weight: 5.9990 chunk 526 optimal weight: 0.3980 chunk 54 optimal weight: 8.9990 chunk 406 optimal weight: 10.0000 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 576 GLN ** A 678 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 780 ASN A 982 ASN ** A1267 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 370 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 525 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 699 HIS ** B 906 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1003 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 43 HIS ** E 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 133 GLN F 72 GLN H 131 ASN ** J 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 576 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 678 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 780 ASN M 989 ASN ** M1036 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M1267 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 525 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 699 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 43 HIS P 129 GLN ** S 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 26 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7500 moved from start: 0.5057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 55352 Z= 0.216 Angle : 0.605 12.497 74786 Z= 0.305 Chirality : 0.045 0.321 8362 Planarity : 0.004 0.076 9702 Dihedral : 4.136 28.666 7396 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 14.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 3.37 % Allowed : 21.22 % Favored : 75.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.30 % 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: -0.09 (0.10), residues: 6690 helix: 0.73 (0.11), residues: 2338 sheet: -0.73 (0.15), residues: 1054 loop : -0.29 (0.11), residues: 3298 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP E 11 HIS 0.014 0.001 HIS B 460 PHE 0.029 0.001 PHE G 18 TYR 0.046 0.001 TYR E 125 ARG 0.010 0.000 ARG L 31 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13380 Ramachandran restraints generated. 6690 Oldfield, 0 Emsley, 6690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13380 Ramachandran restraints generated. 6690 Oldfield, 0 Emsley, 6690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 958 residues out of total 6024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 203 poor density : 755 time to evaluate : 5.090 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 539 GLN cc_start: 0.7580 (pm20) cc_final: 0.6905 (pt0) REVERT: A 986 MET cc_start: 0.6373 (mtm) cc_final: 0.5753 (mmt) REVERT: A 1095 LEU cc_start: 0.8676 (OUTLIER) cc_final: 0.8360 (tt) REVERT: B 513 GLU cc_start: 0.8150 (mt-10) cc_final: 0.7732 (mt-10) REVERT: B 655 ASP cc_start: 0.5933 (OUTLIER) cc_final: 0.5455 (m-30) REVERT: B 766 TYR cc_start: 0.7378 (m-80) cc_final: 0.7150 (m-80) REVERT: B 908 MET cc_start: 0.6483 (ppp) cc_final: 0.6199 (ptt) REVERT: C 60 HIS cc_start: 0.5331 (OUTLIER) cc_final: 0.4829 (m-70) REVERT: C 94 CYS cc_start: 0.6424 (OUTLIER) cc_final: 0.5970 (p) REVERT: D 39 MET cc_start: 0.8188 (mtm) cc_final: 0.7965 (mtp) REVERT: G 27 LYS cc_start: 0.7292 (ttpt) cc_final: 0.6954 (mtmt) REVERT: G 141 ASP cc_start: 0.7328 (m-30) cc_final: 0.6918 (m-30) REVERT: I 81 THR cc_start: 0.8304 (OUTLIER) cc_final: 0.8009 (t) REVERT: M 375 ILE cc_start: 0.8217 (OUTLIER) cc_final: 0.7971 (pt) REVERT: M 540 ASP cc_start: 0.7467 (t0) cc_final: 0.7159 (t0) REVERT: M 824 GLU cc_start: 0.7786 (OUTLIER) cc_final: 0.7077 (pm20) REVERT: M 909 LEU cc_start: 0.7203 (OUTLIER) cc_final: 0.6829 (pt) REVERT: M 986 MET cc_start: 0.6030 (mtm) cc_final: 0.5389 (mmt) REVERT: M 1054 MET cc_start: 0.7136 (mmm) cc_final: 0.6015 (mmm) REVERT: M 1321 ILE cc_start: 0.7687 (tp) cc_final: 0.7441 (tp) REVERT: M 1348 SER cc_start: 0.7990 (m) cc_final: 0.7585 (p) REVERT: N 169 ARG cc_start: 0.7517 (mmm160) cc_final: 0.6816 (mmm160) REVERT: N 287 HIS cc_start: 0.6708 (m90) cc_final: 0.6275 (m90) REVERT: N 529 MET cc_start: 0.8648 (tpp) cc_final: 0.8373 (tpp) REVERT: N 531 TYR cc_start: 0.7353 (OUTLIER) cc_final: 0.6269 (p90) REVERT: N 550 MET cc_start: 0.8025 (tmm) cc_final: 0.7640 (tmm) REVERT: N 674 MET cc_start: 0.8124 (tpt) cc_final: 0.7922 (tpt) REVERT: N 683 GLN cc_start: 0.7619 (pp30) cc_final: 0.7098 (pt0) REVERT: N 739 ASN cc_start: 0.7031 (p0) cc_final: 0.6666 (p0) REVERT: N 766 TYR cc_start: 0.6986 (m-10) cc_final: 0.6646 (m-80) REVERT: N 854 ILE cc_start: 0.7950 (tp) cc_final: 0.7750 (tt) REVERT: N 908 MET cc_start: 0.6691 (ppp) cc_final: 0.6365 (ptt) REVERT: S 10 GLU cc_start: 0.6748 (mm-30) cc_final: 0.6513 (mm-30) REVERT: S 94 LYS cc_start: 0.7657 (pttm) cc_final: 0.7376 (ptpt) REVERT: S 117 MET cc_start: 0.7534 (mmm) cc_final: 0.7097 (tpp) REVERT: S 141 ASP cc_start: 0.7333 (m-30) cc_final: 0.7080 (t0) REVERT: W 1 MET cc_start: 0.6711 (tmm) cc_final: 0.6269 (ttt) outliers start: 203 outliers final: 170 residues processed: 887 average time/residue: 0.5201 time to fit residues: 785.6339 Evaluate side-chains 903 residues out of total 6024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 179 poor density : 724 time to evaluate : 4.808 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 375 ILE Chi-restraints excluded: chain A residue 452 ASP Chi-restraints excluded: chain A residue 520 MET Chi-restraints excluded: chain A residue 538 VAL Chi-restraints excluded: chain A residue 611 ASP Chi-restraints excluded: chain A residue 662 HIS Chi-restraints excluded: chain A residue 674 THR Chi-restraints excluded: chain A residue 699 TYR Chi-restraints excluded: chain A residue 909 LEU Chi-restraints excluded: chain A residue 947 HIS Chi-restraints excluded: chain A residue 1023 VAL Chi-restraints excluded: chain A residue 1027 ASP Chi-restraints excluded: chain A residue 1040 LEU Chi-restraints excluded: chain A residue 1095 LEU Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain A residue 1309 MET Chi-restraints excluded: chain A residue 1311 LEU Chi-restraints excluded: chain A residue 1348 SER Chi-restraints excluded: chain A residue 1374 VAL Chi-restraints excluded: chain B residue 152 ILE Chi-restraints excluded: chain B residue 215 TYR Chi-restraints excluded: chain B residue 232 THR Chi-restraints excluded: chain B residue 309 PHE Chi-restraints excluded: chain B residue 353 VAL Chi-restraints excluded: chain B residue 471 ASN Chi-restraints excluded: chain B residue 489 ILE Chi-restraints excluded: chain B residue 492 ASP Chi-restraints excluded: chain B residue 573 TRP Chi-restraints excluded: chain B residue 598 VAL Chi-restraints excluded: chain B residue 652 SER Chi-restraints excluded: chain B residue 655 ASP Chi-restraints excluded: chain B residue 657 VAL Chi-restraints excluded: chain B residue 662 VAL Chi-restraints excluded: chain B residue 666 ASP Chi-restraints excluded: chain B residue 678 THR Chi-restraints excluded: chain B residue 733 MET Chi-restraints excluded: chain B residue 865 VAL Chi-restraints excluded: chain B residue 866 ILE Chi-restraints excluded: chain B residue 909 VAL Chi-restraints excluded: chain B residue 939 HIS Chi-restraints excluded: chain B residue 944 THR Chi-restraints excluded: chain B residue 976 MET Chi-restraints excluded: chain B residue 1000 THR Chi-restraints excluded: chain B residue 1028 LEU Chi-restraints excluded: chain C residue 9 VAL Chi-restraints excluded: chain C residue 60 HIS Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 94 CYS Chi-restraints excluded: chain C residue 112 THR Chi-restraints excluded: chain C residue 114 HIS Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain C residue 146 ASP Chi-restraints excluded: chain C residue 151 VAL Chi-restraints excluded: chain C residue 235 SER Chi-restraints excluded: chain C residue 246 LEU Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 76 ASN Chi-restraints excluded: chain E residue 185 ILE Chi-restraints excluded: chain F residue 71 LEU Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain G residue 22 LEU Chi-restraints excluded: chain G residue 39 THR Chi-restraints excluded: chain G residue 86 ASP Chi-restraints excluded: chain G residue 90 THR Chi-restraints excluded: chain G residue 91 GLN Chi-restraints excluded: chain G residue 115 SER Chi-restraints excluded: chain H residue 5 LEU Chi-restraints excluded: chain H residue 15 ILE Chi-restraints excluded: chain H residue 28 LEU Chi-restraints excluded: chain H residue 80 ASP Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain H residue 116 VAL Chi-restraints excluded: chain H residue 141 VAL Chi-restraints excluded: chain H residue 144 LEU Chi-restraints excluded: chain I residue 23 MET Chi-restraints excluded: chain I residue 81 THR Chi-restraints excluded: chain I residue 95 VAL Chi-restraints excluded: chain J residue 30 THR Chi-restraints excluded: chain J residue 36 ASP Chi-restraints excluded: chain J residue 54 ASP Chi-restraints excluded: chain K residue 13 PHE Chi-restraints excluded: chain K residue 20 THR Chi-restraints excluded: chain K residue 27 VAL Chi-restraints excluded: chain K residue 71 ILE Chi-restraints excluded: chain K residue 78 THR Chi-restraints excluded: chain K residue 82 SER Chi-restraints excluded: chain K residue 93 ASP Chi-restraints excluded: chain K residue 101 LEU Chi-restraints excluded: chain M residue 365 THR Chi-restraints excluded: chain M residue 375 ILE Chi-restraints excluded: chain M residue 438 LEU Chi-restraints excluded: chain M residue 520 MET Chi-restraints excluded: chain M residue 538 VAL Chi-restraints excluded: chain M residue 611 ASP Chi-restraints excluded: chain M residue 662 HIS Chi-restraints excluded: chain M residue 674 THR Chi-restraints excluded: chain M residue 824 GLU Chi-restraints excluded: chain M residue 869 GLU Chi-restraints excluded: chain M residue 870 SER Chi-restraints excluded: chain M residue 905 ASN Chi-restraints excluded: chain M residue 909 LEU Chi-restraints excluded: chain M residue 938 LEU Chi-restraints excluded: chain M residue 1023 VAL Chi-restraints excluded: chain M residue 1040 LEU Chi-restraints excluded: chain M residue 1095 LEU Chi-restraints excluded: chain M residue 1117 VAL Chi-restraints excluded: chain M residue 1127 LEU Chi-restraints excluded: chain M residue 1136 THR Chi-restraints excluded: chain M residue 1293 LEU Chi-restraints excluded: chain M residue 1338 THR Chi-restraints excluded: chain M residue 1374 VAL Chi-restraints excluded: chain N residue 160 TYR Chi-restraints excluded: chain N residue 215 TYR Chi-restraints excluded: chain N residue 232 THR Chi-restraints excluded: chain N residue 276 LEU Chi-restraints excluded: chain N residue 460 HIS Chi-restraints excluded: chain N residue 531 TYR Chi-restraints excluded: chain N residue 573 TRP Chi-restraints excluded: chain N residue 657 VAL Chi-restraints excluded: chain N residue 662 VAL Chi-restraints excluded: chain N residue 666 ASP Chi-restraints excluded: chain N residue 751 LEU Chi-restraints excluded: chain N residue 858 VAL Chi-restraints excluded: chain N residue 865 VAL Chi-restraints excluded: chain N residue 909 VAL Chi-restraints excluded: chain N residue 944 THR Chi-restraints excluded: chain N residue 977 THR Chi-restraints excluded: chain O residue 9 VAL Chi-restraints excluded: chain O residue 16 ASP Chi-restraints excluded: chain O residue 51 GLN Chi-restraints excluded: chain O residue 66 HIS Chi-restraints excluded: chain O residue 68 LEU Chi-restraints excluded: chain O residue 75 SER Chi-restraints excluded: chain O residue 114 HIS Chi-restraints excluded: chain O residue 120 LEU Chi-restraints excluded: chain O residue 235 SER Chi-restraints excluded: chain P residue 22 PHE Chi-restraints excluded: chain P residue 37 VAL Chi-restraints excluded: chain P residue 62 MET Chi-restraints excluded: chain P residue 68 THR Chi-restraints excluded: chain P residue 76 ASN Chi-restraints excluded: chain P residue 107 THR Chi-restraints excluded: chain P residue 124 ASP Chi-restraints excluded: chain P residue 129 GLN Chi-restraints excluded: chain P residue 131 LEU Chi-restraints excluded: chain Q residue 64 HIS Chi-restraints excluded: chain R residue 71 LEU Chi-restraints excluded: chain R residue 90 LEU Chi-restraints excluded: chain R residue 125 ILE Chi-restraints excluded: chain S residue 6 SER Chi-restraints excluded: chain S residue 32 THR Chi-restraints excluded: chain S residue 39 THR Chi-restraints excluded: chain S residue 86 ASP Chi-restraints excluded: chain S residue 153 ASP Chi-restraints excluded: chain T residue 28 LEU Chi-restraints excluded: chain T residue 80 ASP Chi-restraints excluded: chain T residue 110 THR Chi-restraints excluded: chain T residue 141 VAL Chi-restraints excluded: chain T residue 144 LEU Chi-restraints excluded: chain T residue 145 MET Chi-restraints excluded: chain U residue 14 ILE Chi-restraints excluded: chain U residue 23 MET Chi-restraints excluded: chain U residue 95 VAL Chi-restraints excluded: chain U residue 115 THR Chi-restraints excluded: chain U residue 124 THR Chi-restraints excluded: chain V residue 19 GLU Chi-restraints excluded: chain V residue 25 LEU Chi-restraints excluded: chain V residue 29 TYR Chi-restraints excluded: chain V residue 30 THR Chi-restraints excluded: chain V residue 54 ASP Chi-restraints excluded: chain W residue 20 THR Chi-restraints excluded: chain W residue 22 ASN Chi-restraints excluded: chain W residue 27 VAL Chi-restraints excluded: chain W residue 71 ILE Chi-restraints excluded: chain W residue 78 THR Chi-restraints excluded: chain W residue 81 TYR Chi-restraints excluded: chain W residue 101 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 664 random chunks: chunk 322 optimal weight: 5.9990 chunk 418 optimal weight: 3.9990 chunk 561 optimal weight: 8.9990 chunk 161 optimal weight: 0.6980 chunk 485 optimal weight: 0.1980 chunk 77 optimal weight: 5.9990 chunk 146 optimal weight: 10.0000 chunk 527 optimal weight: 0.4980 chunk 220 optimal weight: 0.9980 chunk 541 optimal weight: 0.2980 chunk 66 optimal weight: 8.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 576 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 780 ASN ** A1036 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1267 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 460 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 525 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 906 GLN ** B1003 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 83 GLN ** C 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 43 HIS ** E 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 116 GLN ** E 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 133 GLN F 72 GLN H 131 ASN ** J 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 576 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 780 ASN ** M1036 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M1267 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 52 GLN ** N 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 525 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 699 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 906 GLN O 60 HIS P 43 HIS P 129 GLN ** Q 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 60 GLN ** U 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 118 HIS Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4363 r_free = 0.4363 target = 0.167428 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.135755 restraints weight = 95481.221| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.137291 restraints weight = 72435.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.138058 restraints weight = 55523.683| |-----------------------------------------------------------------------------| r_work (final): 0.3986 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7583 moved from start: 0.5106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.081 55352 Z= 0.183 Angle : 0.599 12.570 74786 Z= 0.299 Chirality : 0.044 0.384 8362 Planarity : 0.004 0.076 9702 Dihedral : 4.074 28.090 7396 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 14.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 2.99 % Allowed : 21.76 % Favored : 75.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.30 % 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 (0.10), residues: 6690 helix: 0.82 (0.11), residues: 2334 sheet: -0.63 (0.16), residues: 1002 loop : -0.23 (0.11), residues: 3354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP E 11 HIS 0.012 0.001 HIS B 577 PHE 0.030 0.001 PHE E 73 TYR 0.037 0.001 TYR E 125 ARG 0.009 0.000 ARG L 31 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14163.53 seconds wall clock time: 249 minutes 36.22 seconds (14976.22 seconds total)