Starting phenix.real_space_refine on Thu Oct 29 20:43:29 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6h67_0146/10_2026/6h67_0146.cif Found real_map, /net/cci-nas-00/data/ceres_data/6h67_0146/10_2026/6h67_0146.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6h67_0146/10_2026/6h67_0146.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6h67_0146/10_2026/6h67_0146.map" model { file = "/net/cci-nas-00/data/ceres_data/6h67_0146/10_2026/6h67_0146.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6h67_0146/10_2026/6h67_0146.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/6h67_0146/10_2026/6h67_0146.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6h67_0146/10_2026/6h67_0146.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= -0.000 sd= 0.004 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: 7 Type Number sf(0) Gaussians Zn 6 6.06 5 P 44 5.49 5 Mg 1 5.21 5 S 166 5.16 5 C 21253 2.51 5 N 5861 2.21 5 O 6472 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.22s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 33803 Number of models: 1 Model: "" Number of chains: 22 Chain: "A" Number of atoms: 11565 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1463, 11565 Classifications: {'peptide': 1463} Link IDs: {'PCIS': 5, 'PTRANS': 54, 'TRANS': 1403} Chain breaks: 6 Chain: "B" Number of atoms: 9329 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1174, 9329 Classifications: {'peptide': 1174} Link IDs: {'PCIS': 1, 'PTRANS': 58, 'TRANS': 1114} Chain breaks: 2 Chain: "C" Number of atoms: 2431 Number of conformers: 1 Conformer: "" Number of residues, atoms: 306, 2431 Classifications: {'peptide': 306} Link IDs: {'PTRANS': 19, 'TRANS': 286} Chain: "D" Number of atoms: 431 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 431 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 2, 'TRANS': 51} Chain breaks: 1 Chain: "E" Number of atoms: 1734 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1734 Classifications: {'peptide': 212} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 199} Chain: "F" Number of atoms: 823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 823 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 6, 'TRANS': 93} Chain: "G" Number of atoms: 1348 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1348 Classifications: {'peptide': 171} Link IDs: {'PTRANS': 10, 'TRANS': 160} Chain breaks: 1 Chain: "H" Number of atoms: 1051 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1051 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 4, 'TRANS': 126} Chain breaks: 1 Chain: "I" Number of atoms: 466 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 466 Classifications: {'peptide': 63} Link IDs: {'PTRANS': 3, 'TRANS': 59} Chain: "J" Number of atoms: 569 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 569 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 2, 'TRANS': 66} Chain: "K" Number of atoms: 792 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 792 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 3, 'TRANS': 97} Chain: "L" Number of atoms: 351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 351 Classifications: {'peptide': 44} Link IDs: {'TRANS': 43} Chain: "M" Number of atoms: 856 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 856 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 5, 'TRANS': 102} Chain: "N" Number of atoms: 1142 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1142 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 9, 'TRANS': 134} Chain breaks: 2 Chain: "R" Number of atoms: 198 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 198 Classifications: {'RNAv2': 9} Modifications used: {'rna3p_pur': 7, 'rna3p_pyr': 2} Link IDs: {'rna3p': 8} Chain: "T" Number of atoms: 435 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 435 Unusual residues: {'TTD': 1} Classifications: {'DNA': 20, 'undetermined': 1} Link IDs: {'rna3p': 18, None: 2} Not linked: pdbres=" DC T 17 " pdbres="TTD T 18 " Not linked: pdbres="TTD T 18 " pdbres=" DT T 19 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Chain: "U" Number of atoms: 275 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 275 Classifications: {'DNA': 13} Link IDs: {'rna3p': 12} Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" 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: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 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} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 461 SG CYS A 62 111.305 109.267 101.171 1.00 57.28 S ATOM 480 SG CYS A 65 111.225 107.909 104.535 1.00 57.22 S ATOM 535 SG CYS A 72 109.230 106.008 102.248 1.00 48.37 S ATOM 781 SG CYS A 102 72.376 142.106 93.649 1.00 81.33 S ATOM 806 SG CYS A 105 73.295 142.998 97.064 1.00 83.28 S ATOM 1589 SG CYS A 233 69.364 143.082 95.375 1.00 78.15 S ATOM 1611 SG CYS A 236 70.945 145.990 93.921 1.00 81.56 S ATOM 20188 SG CYS B1104 100.630 116.325 115.224 1.00 53.66 S ATOM 20214 SG CYS B1107 98.598 117.257 112.233 1.00 57.02 S ATOM 20361 SG CYS B1128 102.400 116.924 112.116 1.00 62.48 S ATOM 20389 SG CYS B1131 100.289 120.490 114.160 1.00 63.66 S ATOM 28797 SG CYS I 13 47.957 111.319 35.727 1.00101.00 S ATOM 28917 SG CYS I 30 47.903 114.925 37.930 1.00107.49 S ATOM 28938 SG CYS I 33 47.800 114.582 33.973 1.00104.04 S ATOM 29232 SG CYS J 7 86.471 40.653 90.468 1.00 20.99 S ATOM 29255 SG CYS J 10 86.656 37.976 92.927 1.00 19.72 S ATOM 29535 SG CYS J 45 83.156 38.324 91.947 1.00 23.88 S ATOM 29541 SG CYS J 46 85.901 36.289 89.911 1.00 24.70 S ATOM 30582 SG CYS L 31 112.904 63.745 62.725 1.00 50.30 S ATOM 30602 SG CYS L 34 113.889 61.524 59.881 1.00 56.50 S ATOM 30706 SG CYS L 48 115.807 64.511 60.636 1.00 74.79 S ATOM 30729 SG CYS L 51 113.118 64.587 57.934 1.00 71.02 S Time building chain proxies: 6.92, per 1000 atoms: 0.20 Number of scatterers: 33803 At special positions: 0 Unit cell: (160.06, 163.24, 163.24, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 6 29.99 S 166 16.00 P 44 15.00 Mg 1 11.99 O 6472 8.00 N 5861 7.00 C 21253 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.74 Conformation dependent library (CDL) restraints added in 1.3 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A3001 " pdb="ZN ZN A3001 " - pdb=" NE2 HIS A 75 " pdb="ZN ZN A3001 " - pdb=" SG CYS A 65 " pdb="ZN ZN A3001 " - pdb=" SG CYS A 62 " pdb="ZN ZN A3001 " - pdb=" SG CYS A 72 " pdb=" ZN A3002 " pdb="ZN ZN A3002 " - pdb=" SG CYS A 105 " pdb="ZN ZN A3002 " - pdb=" SG CYS A 102 " pdb="ZN ZN A3002 " - pdb=" SG CYS A 236 " pdb="ZN ZN A3002 " - pdb=" SG CYS A 233 " pdb=" ZN B3001 " pdb="ZN ZN B3001 " - pdb=" SG CYS B1104 " pdb="ZN ZN B3001 " - pdb=" SG CYS B1107 " pdb="ZN ZN B3001 " - pdb=" SG CYS B1131 " pdb="ZN ZN B3001 " - pdb=" SG CYS B1128 " pdb=" ZN I3001 " pdb="ZN ZN I3001 " - pdb=" SG CYS I 13 " pdb="ZN ZN I3001 " - pdb=" SG CYS I 33 " pdb="ZN ZN I3001 " - pdb=" SG CYS I 30 " pdb=" ZN J3001 " pdb="ZN ZN J3001 " - pdb=" SG CYS J 45 " pdb="ZN ZN J3001 " - pdb=" SG CYS J 46 " pdb="ZN ZN J3001 " - pdb=" SG CYS J 7 " pdb="ZN ZN J3001 " - pdb=" SG CYS J 10 " pdb=" ZN L3001 " pdb="ZN ZN L3001 " - pdb=" SG CYS L 51 " pdb="ZN ZN L3001 " - pdb=" SG CYS L 48 " pdb="ZN ZN L3001 " - pdb=" SG CYS L 31 " pdb="ZN ZN L3001 " - pdb=" SG CYS L 34 " Number of angles added : 27 8172 Ramachandran restraints generated. 4086 Oldfield, 0 Emsley, 4086 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7790 Finding SS restraints... Secondary structure from input PDB file: 141 helices and 50 sheets defined 33.9% alpha, 14.9% beta 20 base pairs and 35 stacking pairs defined. Time for finding SS restraints: 4.26 Creating SS restraints... Processing helix chain 'A' and resid 20 through 28 removed outlier: 3.890A pdb=" N ASN A 26 " --> pdb=" O LYS A 22 " (cutoff:3.500A) Processing helix chain 'A' and resid 90 through 100 Processing helix chain 'A' and resid 111 through 125 Processing helix chain 'A' and resid 135 through 139 Processing helix chain 'A' and resid 176 through 199 Processing helix chain 'A' and resid 209 through 227 Processing helix chain 'A' and resid 257 through 268 Processing helix chain 'A' and resid 317 through 330 removed outlier: 3.702A pdb=" N LYS A 330 " --> pdb=" O THR A 326 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 339 removed outlier: 3.759A pdb=" N LEU A 335 " --> pdb=" O GLU A 331 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N TYR A 337 " --> pdb=" O CYS A 333 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N PHE A 339 " --> pdb=" O LEU A 335 " (cutoff:3.500A) Processing helix chain 'A' and resid 351 through 354 removed outlier: 3.858A pdb=" N SER A 354 " --> pdb=" O LYS A 351 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 351 through 354' Processing helix chain 'A' and resid 364 through 368 removed outlier: 3.746A pdb=" N PHE A 367 " --> pdb=" O PRO A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 380 through 403 removed outlier: 3.782A pdb=" N GLN A 384 " --> pdb=" O ASN A 380 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N LEU A 385 " --> pdb=" O SER A 381 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N ASP A 401 " --> pdb=" O ARG A 397 " (cutoff:3.500A) Processing helix chain 'A' and resid 427 through 439 removed outlier: 4.164A pdb=" N ASP A 433 " --> pdb=" O THR A 429 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N VAL A 434 " --> pdb=" O ILE A 430 " (cutoff:3.500A) Processing helix chain 'A' and resid 466 through 471 Processing helix chain 'A' and resid 498 through 505 Processing helix chain 'A' and resid 512 through 515 Processing helix chain 'A' and resid 516 through 526 Processing helix chain 'A' and resid 556 through 560 removed outlier: 3.592A pdb=" N ASN A 559 " --> pdb=" O ALA A 556 " (cutoff:3.500A) Processing helix chain 'A' and resid 619 through 623 removed outlier: 4.019A pdb=" N GLY A 622 " --> pdb=" O ALA A 619 " (cutoff:3.500A) Processing helix chain 'A' and resid 640 through 647 removed outlier: 3.596A pdb=" N ARG A 644 " --> pdb=" O ASN A 640 " (cutoff:3.500A) Processing helix chain 'A' and resid 652 through 656 Processing helix chain 'A' and resid 670 through 681 removed outlier: 3.783A pdb=" N ILE A 674 " --> pdb=" O ILE A 670 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N SER A 675 " --> pdb=" O GLN A 671 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N TRP A 679 " --> pdb=" O SER A 675 " (cutoff:3.500A) Processing helix chain 'A' and resid 688 through 700 removed outlier: 3.836A pdb=" N TYR A 697 " --> pdb=" O GLN A 693 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N CYS A 699 " --> pdb=" O TYR A 695 " (cutoff:3.500A) Processing helix chain 'A' and resid 727 through 739 removed outlier: 3.669A pdb=" N VAL A 739 " --> pdb=" O VAL A 735 " (cutoff:3.500A) Processing helix chain 'A' and resid 782 through 787 removed outlier: 3.741A pdb=" N TYR A 786 " --> pdb=" O ASP A 782 " (cutoff:3.500A) Processing helix chain 'A' and resid 793 through 801 Processing helix chain 'A' and resid 802 through 824 removed outlier: 4.362A pdb=" N ALA A 806 " --> pdb=" O GLY A 802 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N ALA A 807 " --> pdb=" O PRO A 803 " (cutoff:3.500A) Processing helix chain 'A' and resid 830 through 834 removed outlier: 3.561A pdb=" N LEU A 833 " --> pdb=" O MET A 830 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N ARG A 834 " --> pdb=" O ASP A 831 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 830 through 834' Processing helix chain 'A' and resid 838 through 848 removed outlier: 3.774A pdb=" N TRP A 842 " --> pdb=" O GLU A 838 " (cutoff:3.500A) Processing helix chain 'A' and resid 852 through 862 Processing helix chain 'A' and resid 872 through 885 removed outlier: 3.550A pdb=" N ASP A 885 " --> pdb=" O GLU A 881 " (cutoff:3.500A) Processing helix chain 'A' and resid 887 through 911 removed outlier: 3.830A pdb=" N SER A 897 " --> pdb=" O ASP A 893 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N VAL A 900 " --> pdb=" O THR A 896 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N ALA A 902 " --> pdb=" O SER A 898 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N SER A 905 " --> pdb=" O ASN A 901 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N GLN A 906 " --> pdb=" O ALA A 902 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N VAL A 907 " --> pdb=" O ILE A 903 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N SER A 909 " --> pdb=" O SER A 905 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N CYS A 911 " --> pdb=" O VAL A 907 " (cutoff:3.500A) Processing helix chain 'A' and resid 923 through 930 Processing helix chain 'A' and resid 936 through 945 removed outlier: 3.790A pdb=" N VAL A 940 " --> pdb=" O SER A 936 " (cutoff:3.500A) Processing helix chain 'A' and resid 991 through 1026 removed outlier: 3.829A pdb=" N MET A1000 " --> pdb=" O TYR A 996 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ALA A1001 " --> pdb=" O PHE A 997 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N LYS A1012 " --> pdb=" O ASP A1008 " (cutoff:3.500A) removed outlier: 4.917A pdb=" N THR A1013 " --> pdb=" O THR A1009 " (cutoff:3.500A) removed outlier: 4.893A pdb=" N SER A1014 " --> pdb=" O ALA A1010 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLY A1017 " --> pdb=" O THR A1013 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N TYR A1018 " --> pdb=" O SER A1014 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N LEU A1019 " --> pdb=" O ARG A1015 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N GLN A1026 " --> pdb=" O CYS A1022 " (cutoff:3.500A) Processing helix chain 'A' and resid 1057 through 1061 removed outlier: 3.878A pdb=" N GLU A1060 " --> pdb=" O ILE A1057 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N SER A1061 " --> pdb=" O THR A1058 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1057 through 1061' Processing helix chain 'A' and resid 1065 through 1071 removed outlier: 3.866A pdb=" N ASP A1071 " --> pdb=" O GLU A1067 " (cutoff:3.500A) Processing helix chain 'A' and resid 1072 through 1081 Processing helix chain 'A' and resid 1082 through 1085 Processing helix chain 'A' and resid 1091 through 1108 removed outlier: 4.094A pdb=" N LEU A1095 " --> pdb=" O VAL A1091 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N TYR A1097 " --> pdb=" O SER A1093 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N LYS A1099 " --> pdb=" O LEU A1095 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LYS A1100 " --> pdb=" O LYS A1096 " (cutoff:3.500A) Processing helix chain 'A' and resid 1122 through 1127 removed outlier: 3.725A pdb=" N LYS A1126 " --> pdb=" O PRO A1122 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N TYR A1127 " --> pdb=" O VAL A1123 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1122 through 1127' Processing helix chain 'A' and resid 1137 through 1151 Processing helix chain 'A' and resid 1151 through 1157 removed outlier: 3.531A pdb=" N PHE A1155 " --> pdb=" O ASN A1151 " (cutoff:3.500A) Processing helix chain 'A' and resid 1162 through 1177 removed outlier: 3.925A pdb=" N LEU A1172 " --> pdb=" O ALA A1168 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N MET A1175 " --> pdb=" O GLN A1171 " (cutoff:3.500A) Processing helix chain 'A' and resid 1184 through 1195 removed outlier: 3.611A pdb=" N ILE A1188 " --> pdb=" O ALA A1184 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N VAL A1193 " --> pdb=" O ALA A1189 " (cutoff:3.500A) Processing helix chain 'A' and resid 1196 through 1200 Processing helix chain 'A' and resid 1218 through 1226 removed outlier: 3.709A pdb=" N GLU A1224 " --> pdb=" O PRO A1220 " (cutoff:3.500A) Processing helix chain 'A' and resid 1247 through 1257 Processing helix chain 'A' and resid 1263 through 1265 No H-bonds generated for 'chain 'A' and resid 1263 through 1265' Processing helix chain 'A' and resid 1298 through 1303 removed outlier: 3.620A pdb=" N SER A1303 " --> pdb=" O ASN A1299 " (cutoff:3.500A) Processing helix chain 'A' and resid 1309 through 1318 removed outlier: 3.513A pdb=" N LEU A1313 " --> pdb=" O SER A1309 " (cutoff:3.500A) Processing helix chain 'A' and resid 1320 through 1334 removed outlier: 3.637A pdb=" N LEU A1324 " --> pdb=" O GLN A1320 " (cutoff:3.500A) Processing helix chain 'A' and resid 1442 through 1454 removed outlier: 3.509A pdb=" N HIS A1454 " --> pdb=" O ILE A1450 " (cutoff:3.500A) Processing helix chain 'A' and resid 1484 through 1496 removed outlier: 3.839A pdb=" N ILE A1488 " --> pdb=" O LEU A1484 " (cutoff:3.500A) Processing helix chain 'A' and resid 1529 through 1533 removed outlier: 3.563A pdb=" N GLN A1532 " --> pdb=" O MET A1529 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N GLU A1533 " --> pdb=" O TRP A1530 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1529 through 1533' Processing helix chain 'A' and resid 1546 through 1553 Processing helix chain 'A' and resid 1553 through 1571 removed outlier: 4.236A pdb=" N ALA A1557 " --> pdb=" O TYR A1553 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N ALA A1558 " --> pdb=" O GLY A1554 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ASN A1568 " --> pdb=" O ASN A1564 " (cutoff:3.500A) Processing helix chain 'A' and resid 1578 through 1590 removed outlier: 4.083A pdb=" N LEU A1582 " --> pdb=" O SER A1578 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N LEU A1584 " --> pdb=" O ARG A1580 " (cutoff:3.500A) Processing helix chain 'A' and resid 1599 through 1603 removed outlier: 3.503A pdb=" N MET A1603 " --> pdb=" O ARG A1600 " (cutoff:3.500A) Processing helix chain 'A' and resid 1608 through 1614 removed outlier: 3.872A pdb=" N LYS A1612 " --> pdb=" O SER A1608 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N SER A1614 " --> pdb=" O PHE A1610 " (cutoff:3.500A) Processing helix chain 'A' and resid 1618 through 1627 Processing helix chain 'A' and resid 1636 through 1643 Processing helix chain 'A' and resid 1649 through 1652 removed outlier: 3.639A pdb=" N GLY A1652 " --> pdb=" O VAL A1649 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1649 through 1652' Processing helix chain 'B' and resid 17 through 27 Processing helix chain 'B' and resid 37 through 41 Processing helix chain 'B' and resid 42 through 51 Processing helix chain 'B' and resid 60 through 69 removed outlier: 4.367A pdb=" N LYS B 66 " --> pdb=" O ASN B 62 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N GLY B 69 " --> pdb=" O VAL B 65 " (cutoff:3.500A) Processing helix chain 'B' and resid 122 through 130 Processing helix chain 'B' and resid 176 through 183 Processing helix chain 'B' and resid 219 through 226 removed outlier: 3.699A pdb=" N ARG B 225 " --> pdb=" O PHE B 222 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLY B 226 " --> pdb=" O ALA B 223 " (cutoff:3.500A) Processing helix chain 'B' and resid 273 through 281 removed outlier: 4.052A pdb=" N CYS B 281 " --> pdb=" O LEU B 277 " (cutoff:3.500A) Processing helix chain 'B' and resid 284 through 294 removed outlier: 3.823A pdb=" N ILE B 288 " --> pdb=" O SER B 284 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ILE B 293 " --> pdb=" O PHE B 289 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLY B 294 " --> pdb=" O ASP B 290 " (cutoff:3.500A) Processing helix chain 'B' and resid 299 through 306 removed outlier: 3.666A pdb=" N THR B 303 " --> pdb=" O ASP B 299 " (cutoff:3.500A) Processing helix chain 'B' and resid 306 through 314 removed outlier: 4.167A pdb=" N GLY B 312 " --> pdb=" O LEU B 308 " (cutoff:3.500A) Processing helix chain 'B' and resid 322 through 334 Processing helix chain 'B' and resid 334 through 339 removed outlier: 3.919A pdb=" N PHE B 338 " --> pdb=" O PHE B 334 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLN B 339 " --> pdb=" O ARG B 335 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 334 through 339' Processing helix chain 'B' and resid 345 through 357 removed outlier: 3.581A pdb=" N GLN B 351 " --> pdb=" O LEU B 347 " (cutoff:3.500A) Processing helix chain 'B' and resid 359 through 363 removed outlier: 3.689A pdb=" N GLY B 363 " --> pdb=" O VAL B 360 " (cutoff:3.500A) Processing helix chain 'B' and resid 366 through 382 removed outlier: 3.806A pdb=" N ARG B 372 " --> pdb=" O GLN B 368 " (cutoff:3.500A) Processing helix chain 'B' and resid 396 through 400 removed outlier: 3.727A pdb=" N GLN B 400 " --> pdb=" O THR B 397 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 435 Processing helix chain 'B' and resid 442 through 450 Processing helix chain 'B' and resid 456 through 468 removed outlier: 3.678A pdb=" N LYS B 460 " --> pdb=" O ASN B 456 " (cutoff:3.500A) Processing helix chain 'B' and resid 474 through 478 removed outlier: 4.290A pdb=" N ASP B 477 " --> pdb=" O SER B 474 " (cutoff:3.500A) Processing helix chain 'B' and resid 492 through 499 Processing helix chain 'B' and resid 521 through 525 removed outlier: 3.533A pdb=" N SER B 524 " --> pdb=" O LEU B 521 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N TRP B 525 " --> pdb=" O PRO B 522 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 521 through 525' Processing helix chain 'B' and resid 560 through 568 Processing helix chain 'B' and resid 597 through 615 removed outlier: 3.619A pdb=" N ILE B 603 " --> pdb=" O GLU B 599 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ARG B 609 " --> pdb=" O ALA B 605 " (cutoff:3.500A) Processing helix chain 'B' and resid 706 through 710 Processing helix chain 'B' and resid 711 through 719 Processing helix chain 'B' and resid 754 through 758 removed outlier: 4.049A pdb=" N ASP B 758 " --> pdb=" O ASN B 755 " (cutoff:3.500A) Processing helix chain 'B' and resid 761 through 765 removed outlier: 3.730A pdb=" N ASN B 764 " --> pdb=" O GLY B 761 " (cutoff:3.500A) Processing helix chain 'B' and resid 791 through 795 Processing helix chain 'B' and resid 834 through 839 removed outlier: 4.018A pdb=" N LEU B 837 " --> pdb=" O LYS B 834 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LYS B 839 " --> pdb=" O TRP B 836 " (cutoff:3.500A) Processing helix chain 'B' and resid 951 through 954 Processing helix chain 'B' and resid 960 through 976 removed outlier: 3.863A pdb=" N LEU B 967 " --> pdb=" O PHE B 963 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N HIS B 975 " --> pdb=" O ALA B 971 " (cutoff:3.500A) Processing helix chain 'B' and resid 991 through 1001 removed outlier: 3.971A pdb=" N GLN B 999 " --> pdb=" O TYR B 995 " (cutoff:3.500A) Processing helix chain 'B' and resid 1002 through 1004 No H-bonds generated for 'chain 'B' and resid 1002 through 1004' Processing helix chain 'B' and resid 1073 through 1082 removed outlier: 3.893A pdb=" N ASP B1077 " --> pdb=" O GLU B1073 " (cutoff:3.500A) Processing helix chain 'B' and resid 1088 through 1093 Processing helix chain 'B' and resid 1180 through 1190 Processing helix chain 'C' and resid 32 through 39 removed outlier: 4.207A pdb=" N ASP C 39 " --> pdb=" O LYS C 35 " (cutoff:3.500A) Processing helix chain 'C' and resid 60 through 73 removed outlier: 3.519A pdb=" N ALA C 64 " --> pdb=" O ASP C 60 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N SER C 73 " --> pdb=" O ARG C 69 " (cutoff:3.500A) Processing helix chain 'C' and resid 93 through 103 Processing helix chain 'C' and resid 152 through 156 removed outlier: 3.515A pdb=" N LEU C 156 " --> pdb=" O ASP C 152 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 152 through 156' Processing helix chain 'C' and resid 174 through 179 Processing helix chain 'C' and resid 216 through 220 Processing helix chain 'C' and resid 242 through 251 removed outlier: 3.848A pdb=" N ARG C 246 " --> pdb=" O GLU C 242 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N PHE C 247 " --> pdb=" O SER C 243 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N GLN C 248 " --> pdb=" O ALA C 244 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N PHE C 251 " --> pdb=" O PHE C 247 " (cutoff:3.500A) Processing helix chain 'C' and resid 278 through 281 Processing helix chain 'C' and resid 282 through 287 removed outlier: 3.676A pdb=" N ASP C 287 " --> pdb=" O GLU C 283 " (cutoff:3.500A) Processing helix chain 'C' and resid 309 through 330 Processing helix chain 'D' and resid 41 through 47 Processing helix chain 'D' and resid 82 through 90 removed outlier: 3.586A pdb=" N ILE D 86 " --> pdb=" O LEU D 82 " (cutoff:3.500A) Processing helix chain 'E' and resid 5 through 27 Processing helix chain 'E' and resid 31 through 36 removed outlier: 4.113A pdb=" N VAL E 35 " --> pdb=" O THR E 31 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N GLU E 36 " --> pdb=" O GLN E 32 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 31 through 36' Processing helix chain 'E' and resid 38 through 46 removed outlier: 3.572A pdb=" N PHE E 42 " --> pdb=" O PRO E 38 " (cutoff:3.500A) Processing helix chain 'E' and resid 65 through 72 Processing helix chain 'E' and resid 89 through 104 removed outlier: 3.525A pdb=" N MET E 93 " --> pdb=" O GLY E 89 " (cutoff:3.500A) Processing helix chain 'E' and resid 117 through 122 Processing helix chain 'E' and resid 143 through 147 removed outlier: 3.520A pdb=" N HIS E 147 " --> pdb=" O ILE E 144 " (cutoff:3.500A) Processing helix chain 'E' and resid 157 through 168 removed outlier: 3.555A pdb=" N LYS E 161 " --> pdb=" O SER E 157 " (cutoff:3.500A) Processing helix chain 'E' and resid 184 through 189 Processing helix chain 'F' and resid 56 through 71 Processing helix chain 'F' and resid 86 through 103 Processing helix chain 'F' and resid 116 through 125 Processing helix chain 'F' and resid 126 through 128 No H-bonds generated for 'chain 'F' and resid 126 through 128' Processing helix chain 'F' and resid 149 through 151 No H-bonds generated for 'chain 'F' and resid 149 through 151' Processing helix chain 'G' and resid 50 through 54 removed outlier: 3.662A pdb=" N LEU G 54 " --> pdb=" O PRO G 51 " (cutoff:3.500A) Processing helix chain 'G' and resid 56 through 65 Processing helix chain 'G' and resid 66 through 70 Processing helix chain 'I' and resid 58 through 64 Processing helix chain 'J' and resid 14 through 17 Processing helix chain 'J' and resid 18 through 29 removed outlier: 3.678A pdb=" N ASP J 28 " --> pdb=" O LEU J 24 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLU J 29 " --> pdb=" O LEU J 25 " (cutoff:3.500A) Processing helix chain 'J' and resid 31 through 39 Processing helix chain 'J' and resid 43 through 52 removed outlier: 4.216A pdb=" N MET J 49 " --> pdb=" O CYS J 45 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N ILE J 50 " --> pdb=" O CYS J 46 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N THR J 52 " --> pdb=" O ARG J 48 " (cutoff:3.500A) Processing helix chain 'J' and resid 56 through 62 removed outlier: 3.789A pdb=" N ARG J 62 " --> pdb=" O GLU J 58 " (cutoff:3.500A) Processing helix chain 'K' and resid 51 through 54 removed outlier: 3.611A pdb=" N THR K 54 " --> pdb=" O THR K 51 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 51 through 54' Processing helix chain 'K' and resid 69 through 81 removed outlier: 3.634A pdb=" N GLY K 73 " --> pdb=" O ASP K 69 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ALA K 75 " --> pdb=" O THR K 71 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N TYR K 78 " --> pdb=" O ASN K 74 " (cutoff:3.500A) Processing helix chain 'K' and resid 112 through 140 removed outlier: 4.188A pdb=" N ALA K 116 " --> pdb=" O THR K 112 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N LEU K 124 " --> pdb=" O GLY K 120 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N THR K 136 " --> pdb=" O GLU K 132 " (cutoff:3.500A) Processing helix chain 'M' and resid 68 through 74 removed outlier: 4.425A pdb=" N ALA M 72 " --> pdb=" O SER M 68 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N SER M 73 " --> pdb=" O SER M 69 " (cutoff:3.500A) Processing helix chain 'N' and resid 149 through 154 Processing sheet with id=AA1, first strand: chain 'A' and resid 10 through 17 removed outlier: 5.018A pdb=" N ILE A 11 " --> pdb=" O GLU B1201 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N GLU B1201 " --> pdb=" O ILE A 11 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 77 through 86 removed outlier: 11.219A pdb=" N LEU A 81 " --> pdb=" O VAL A 361 " (cutoff:3.500A) removed outlier: 11.157A pdb=" N VAL A 361 " --> pdb=" O LEU A 81 " (cutoff:3.500A) removed outlier: 10.714A pdb=" N VAL A 83 " --> pdb=" O VAL A 359 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N VAL A 359 " --> pdb=" O VAL A 83 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 243 through 246 removed outlier: 3.864A pdb=" N LYS A 250 " --> pdb=" O ASP A 246 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 474 through 476 removed outlier: 3.504A pdb=" N ILE B1069 " --> pdb=" O VAL A 476 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 614 through 616 removed outlier: 6.984A pdb=" N LEU A 614 " --> pdb=" O ARG A 481 " (cutoff:3.500A) removed outlier: 5.826A pdb=" N VAL A 483 " --> pdb=" O LEU A 614 " (cutoff:3.500A) removed outlier: 7.766A pdb=" N LEU A 616 " --> pdb=" O VAL A 483 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N SER A 485 " --> pdb=" O LEU A 616 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N SER A 482 " --> pdb=" O MET A 633 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N MET A 633 " --> pdb=" O SER A 482 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 494 through 497 Processing sheet with id=AA7, first strand: chain 'A' and resid 506 through 510 removed outlier: 3.999A pdb=" N GLN A 535 " --> pdb=" O TYR A 578 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N HIS A 580 " --> pdb=" O ALA A 533 " (cutoff:3.500A) removed outlier: 7.157A pdb=" N ALA A 533 " --> pdb=" O HIS A 580 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 719 through 721 removed outlier: 6.359A pdb=" N VAL H 96 " --> pdb=" O PHE A 720 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N LEU H 55 " --> pdb=" O ILE H 9 " (cutoff:3.500A) removed outlier: 5.280A pdb=" N ILE H 9 " --> pdb=" O LEU H 55 " (cutoff:3.500A) removed outlier: 7.076A pdb=" N VAL H 57 " --> pdb=" O ASP H 7 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N ASP H 7 " --> pdb=" O VAL H 57 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N ILE H 59 " --> pdb=" O LEU H 5 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N GLU H 27 " --> pdb=" O SER H 13 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N VAL H 15 " --> pdb=" O ARG H 25 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N ARG H 25 " --> pdb=" O VAL H 15 " (cutoff:3.500A) removed outlier: 4.979A pdb=" N LEU H 122 " --> pdb=" O ASP H 41 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N LYS H 103 " --> pdb=" O TYR H 115 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N SER H 117 " --> pdb=" O ALA H 101 " (cutoff:3.500A) removed outlier: 5.594A pdb=" N ALA H 101 " --> pdb=" O SER H 117 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 749 through 751 Processing sheet with id=AB1, first strand: chain 'A' and resid 826 through 827 removed outlier: 4.276A pdb=" N TYR B1027 " --> pdb=" O VAL B 775 " (cutoff:3.500A) removed outlier: 7.411A pdb=" N MET B 787 " --> pdb=" O SER B 928 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N LYS B 930 " --> pdb=" O MET B 787 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N ILE B 789 " --> pdb=" O LYS B 930 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ALA B 774 " --> pdb=" O ILE B 947 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 1031 through 1032 removed outlier: 6.741A pdb=" N ILE A1038 " --> pdb=" O VAL A1046 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 1507 through 1508 Processing sheet with id=AB4, first strand: chain 'A' and resid 1267 through 1272 removed outlier: 6.752A pdb=" N ARG A1295 " --> pdb=" O ASP A1268 " (cutoff:3.500A) removed outlier: 4.856A pdb=" N VAL A1270 " --> pdb=" O HIS A1293 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N HIS A1293 " --> pdb=" O VAL A1270 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N VAL A1272 " --> pdb=" O VAL A1291 " (cutoff:3.500A) removed outlier: 6.238A pdb=" N VAL A1291 " --> pdb=" O VAL A1272 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N LYS A1459 " --> pdb=" O LYS A1473 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N GLU A1475 " --> pdb=" O ILE A1457 " (cutoff:3.500A) removed outlier: 5.965A pdb=" N ILE A1457 " --> pdb=" O GLU A1475 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 143 through 147 Processing sheet with id=AB6, first strand: chain 'B' and resid 71 through 73 removed outlier: 7.055A pdb=" N LYS B 140 " --> pdb=" O GLU B 100 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N VAL B 102 " --> pdb=" O LEU B 138 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N LEU B 138 " --> pdb=" O VAL B 102 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N ILE B 104 " --> pdb=" O LYS B 136 " (cutoff:3.500A) removed outlier: 5.734A pdb=" N LYS B 136 " --> pdb=" O ILE B 104 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N LEU B 137 " --> pdb=" O CYS B 158 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N CYS B 158 " --> pdb=" O LEU B 137 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 108 through 109 removed outlier: 3.591A pdb=" N ARG B 119 " --> pdb=" O SER B 109 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 194 through 196 Processing sheet with id=AB9, first strand: chain 'B' and resid 215 through 216 removed outlier: 6.254A pdb=" N THR B 247 " --> pdb=" O SER B 263 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N SER B 263 " --> pdb=" O THR B 247 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 502 through 503 removed outlier: 3.847A pdb=" N VAL B 503 " --> pdb=" O ASN B 543 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 550 through 551 removed outlier: 3.515A pdb=" N ARG B 550 " --> pdb=" O LEU B 650 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 591 through 596 removed outlier: 6.775A pdb=" N VAL B 586 " --> pdb=" O ILE B 593 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N TRP B 595 " --> pdb=" O CYS B 584 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N CYS B 584 " --> pdb=" O TRP B 595 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LEU B 640 " --> pdb=" O CYS B 585 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N VAL B 629 " --> pdb=" O GLY B 639 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 660 through 663 removed outlier: 3.620A pdb=" N LYS B 660 " --> pdb=" O TYR B 655 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 740 through 744 removed outlier: 7.115A pdb=" N THR B 900 " --> pdb=" O LEU B 887 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N LEU B 887 " --> pdb=" O THR B 900 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N SER B 902 " --> pdb=" O VAL B 885 " (cutoff:3.500A) removed outlier: 5.051A pdb=" N VAL B 885 " --> pdb=" O SER B 902 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N LYS B 904 " --> pdb=" O GLU B 883 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 752 through 753 Processing sheet with id=AC7, first strand: chain 'B' and resid 823 through 825 removed outlier: 3.678A pdb=" N CYS B 859 " --> pdb=" O LYS B 872 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 938 through 939 removed outlier: 3.666A pdb=" N PHE B 938 " --> pdb=" O TYR B1014 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 1098 through 1099 Processing sheet with id=AD1, first strand: chain 'B' and resid 1102 through 1104 Processing sheet with id=AD2, first strand: chain 'B' and resid 1133 through 1134 Processing sheet with id=AD3, first strand: chain 'C' and resid 46 through 47 removed outlier: 4.371A pdb=" N LEU C 230 " --> pdb=" O VAL C 294 " (cutoff:3.500A) removed outlier: 8.463A pdb=" N ASN C 296 " --> pdb=" O ARG C 228 " (cutoff:3.500A) removed outlier: 9.935A pdb=" N ARG C 228 " --> pdb=" O ASN C 296 " (cutoff:3.500A) removed outlier: 9.402A pdb=" N PHE C 298 " --> pdb=" O SER C 226 " (cutoff:3.500A) removed outlier: 10.725A pdb=" N SER C 226 " --> pdb=" O PHE C 298 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 168 through 170 removed outlier: 4.494A pdb=" N VAL C 133 " --> pdb=" O GLU C 170 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N SER C 203 " --> pdb=" O PHE C 86 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N TYR C 82 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N ILE C 209 " --> pdb=" O ALA C 80 " (cutoff:3.500A) removed outlier: 5.274A pdb=" N ALA C 80 " --> pdb=" O ILE C 209 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N GLY C 211 " --> pdb=" O VAL C 78 " (cutoff:3.500A) removed outlier: 5.356A pdb=" N VAL C 78 " --> pdb=" O GLY C 211 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N VAL C 83 " --> pdb=" O PHE L 67 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 141 through 142 Processing sheet with id=AD6, first strand: chain 'C' and resid 161 through 163 removed outlier: 6.623A pdb=" N VAL C 162 " --> pdb=" O LEU C 193 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 256 through 259 Processing sheet with id=AD8, first strand: chain 'D' and resid 22 through 24 removed outlier: 3.762A pdb=" N HIS D 23 " --> pdb=" O ALA G 44 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ALA G 44 " --> pdb=" O HIS D 23 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'D' and resid 22 through 24 removed outlier: 3.762A pdb=" N HIS D 23 " --> pdb=" O ALA G 44 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ALA G 44 " --> pdb=" O HIS D 23 " (cutoff:3.500A) removed outlier: 7.672A pdb=" N TRP G 117 " --> pdb=" O LYS G 88 " (cutoff:3.500A) removed outlier: 7.313A pdb=" N LYS G 88 " --> pdb=" O TRP G 117 " (cutoff:3.500A) removed outlier: 5.586A pdb=" N HIS G 119 " --> pdb=" O GLY G 86 " (cutoff:3.500A) removed outlier: 6.153A pdb=" N GLY G 86 " --> pdb=" O HIS G 119 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N ASN G 121 " --> pdb=" O TYR G 84 " (cutoff:3.500A) removed outlier: 4.710A pdb=" N TYR G 84 " --> pdb=" O ASN G 121 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N TYR G 123 " --> pdb=" O LEU G 82 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'E' and resid 60 through 62 removed outlier: 3.604A pdb=" N GLU E 133 " --> pdb=" O GLY E 108 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'E' and resid 152 through 155 removed outlier: 4.042A pdb=" N LYS E 152 " --> pdb=" O ILE E 199 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ILE E 199 " --> pdb=" O LYS E 152 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'E' and resid 177 through 178 Processing sheet with id=AE4, first strand: chain 'G' and resid 136 through 137 removed outlier: 4.097A pdb=" N LEU G 147 " --> pdb=" O ALA G 155 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N PHE G 153 " --> pdb=" O ILE G 149 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'G' and resid 168 through 169 removed outlier: 4.193A pdb=" N VAL G 169 " --> pdb=" O HIS G 216 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N HIS G 216 " --> pdb=" O VAL G 169 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE5 Processing sheet with id=AE6, first strand: chain 'G' and resid 236 through 237 Processing sheet with id=AE7, first strand: chain 'I' and resid 3 through 4 Processing sheet with id=AE8, first strand: chain 'K' and resid 47 through 49 removed outlier: 6.528A pdb=" N GLN K 106 " --> pdb=" O GLU K 87 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'K' and resid 47 through 49 Processing sheet with id=AF1, first strand: chain 'L' and resid 29 through 30 Processing sheet with id=AF2, first strand: chain 'M' and resid 11 through 15 removed outlier: 6.594A pdb=" N LEU M 90 " --> pdb=" O GLU M 13 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N VAL M 15 " --> pdb=" O LEU M 90 " (cutoff:3.500A) removed outlier: 7.054A pdb=" N LYS M 92 " --> pdb=" O VAL M 15 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N GLN M 89 " --> pdb=" O LEU M 80 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N LEU M 80 " --> pdb=" O GLN M 89 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N GLN N 52 " --> pdb=" O PHE M 81 " (cutoff:3.500A) removed outlier: 7.333A pdb=" N VAL N 53 " --> pdb=" O LYS N 135 " (cutoff:3.500A) removed outlier: 7.904A pdb=" N PHE N 137 " --> pdb=" O VAL N 53 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N LEU N 55 " --> pdb=" O PHE N 137 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N SER N 138 " --> pdb=" O MET N 90 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'M' and resid 22 through 25 Processing sheet with id=AF4, first strand: chain 'M' and resid 97 through 102 Processing sheet with id=AF5, first strand: chain 'N' and resid 86 through 87 removed outlier: 4.054A pdb=" N ASP N 86 " --> pdb=" O THR N 142 " (cutoff:3.500A) 1081 hydrogen bonds defined for protein. 2967 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 52 hydrogen bonds 104 hydrogen bond angles 0 basepair planarities 20 basepair parallelities 35 stacking parallelities Total time for adding SS restraints: 8.41 Time building geometry restraints manager: 3.75 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 5586 1.31 - 1.44: 9050 1.44 - 1.57: 19565 1.57 - 1.69: 85 1.69 - 1.82: 263 Bond restraints: 34549 Sorted by residual: bond pdb=" N1 TTD T 18 " pdb=" C2 TTD T 18 " ideal model delta sigma weight residual 1.353 1.518 -0.165 2.00e-02 2.50e+03 6.77e+01 bond pdb=" C2' TTD T 18 " pdb=" C3R TTD T 18 " ideal model delta sigma weight residual 1.520 1.393 0.127 2.00e-02 2.50e+03 4.04e+01 bond pdb=" C2T TTD T 18 " pdb=" N1T TTD T 18 " ideal model delta sigma weight residual 1.360 1.482 -0.122 2.00e-02 2.50e+03 3.74e+01 bond pdb=" C2T TTD T 18 " pdb=" N3T TTD T 18 " ideal model delta sigma weight residual 1.386 1.486 -0.100 2.00e-02 2.50e+03 2.49e+01 bond pdb=" C2 TTD T 18 " pdb=" N3 TTD T 18 " ideal model delta sigma weight residual 1.396 1.491 -0.095 2.00e-02 2.50e+03 2.25e+01 ... (remaining 34544 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.23: 46392 3.23 - 6.47: 416 6.47 - 9.70: 51 9.70 - 12.93: 6 12.93 - 16.16: 3 Bond angle restraints: 46868 Sorted by residual: angle pdb=" O4P TTD T 18 " pdb=" PB TTD T 18 " pdb=" O5P TTD T 18 " ideal model delta sigma weight residual 122.50 106.34 16.16 3.00e+00 1.11e-01 2.90e+01 angle pdb=" C ILE B 588 " pdb=" N ASP B 589 " pdb=" CA ASP B 589 " ideal model delta sigma weight residual 121.54 130.57 -9.03 1.91e+00 2.74e-01 2.23e+01 angle pdb=" C4 TTD T 18 " pdb=" C5 TTD T 18 " pdb=" C6 TTD T 18 " ideal model delta sigma weight residual 111.34 124.65 -13.31 3.00e+00 1.11e-01 1.97e+01 angle pdb=" N3 DT T 19 " pdb=" C4 DT T 19 " pdb=" O4 DT T 19 " ideal model delta sigma weight residual 119.90 122.50 -2.60 6.00e-01 2.78e+00 1.88e+01 angle pdb=" N3 DT T 12 " pdb=" C4 DT T 12 " pdb=" O4 DT T 12 " ideal model delta sigma weight residual 119.90 122.46 -2.56 6.00e-01 2.78e+00 1.82e+01 ... (remaining 46863 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.76: 20707 33.76 - 67.53: 254 67.53 - 101.29: 35 101.29 - 135.05: 5 135.05 - 168.81: 3 Dihedral angle restraints: 21004 sinusoidal: 8951 harmonic: 12053 Sorted by residual: dihedral pdb=" CA MET B 783 " pdb=" C MET B 783 " pdb=" N ASP B 784 " pdb=" CA ASP B 784 " ideal model delta harmonic sigma weight residual -180.00 -132.47 -47.53 0 5.00e+00 4.00e-02 9.03e+01 dihedral pdb=" CA ILE A 670 " pdb=" C ILE A 670 " pdb=" N GLN A 671 " pdb=" CA GLN A 671 " ideal model delta harmonic sigma weight residual 180.00 -146.11 -33.89 0 5.00e+00 4.00e-02 4.60e+01 dihedral pdb=" CA GLN A1500 " pdb=" C GLN A1500 " pdb=" N ILE A1501 " pdb=" CA ILE A1501 " ideal model delta harmonic sigma weight residual 180.00 146.59 33.41 0 5.00e+00 4.00e-02 4.47e+01 ... (remaining 21001 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.095: 4767 0.095 - 0.190: 450 0.190 - 0.285: 23 0.285 - 0.380: 2 0.380 - 0.475: 3 Chirality restraints: 5245 Sorted by residual: chirality pdb=" C5T TTD T 18 " pdb=" C5 TTD T 18 " pdb=" C4T TTD T 18 " pdb=" C6T TTD T 18 " both_signs ideal model delta sigma weight residual False 2.95 2.47 0.48 2.00e-01 2.50e+01 5.64e+00 chirality pdb=" C5 TTD T 18 " pdb=" C4 TTD T 18 " pdb=" C6 TTD T 18 " pdb=" C5T TTD T 18 " both_signs ideal model delta sigma weight residual False -3.16 -2.69 -0.47 2.00e-01 2.50e+01 5.50e+00 chirality pdb=" C1R TTD T 18 " pdb=" C2R TTD T 18 " pdb=" N1T TTD T 18 " pdb=" O4R TTD T 18 " both_signs ideal model delta sigma weight residual False 2.39 1.96 0.42 2.00e-01 2.50e+01 4.50e+00 ... (remaining 5242 not shown) Planarity restraints: 5899 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1R TTD T 18 " -0.034 2.00e-02 2.50e+03 3.66e-02 3.01e+01 pdb=" C2T TTD T 18 " -0.001 2.00e-02 2.50e+03 pdb=" C4T TTD T 18 " 0.028 2.00e-02 2.50e+03 pdb=" C5T TTD T 18 " -0.072 2.00e-02 2.50e+03 pdb=" C6T TTD T 18 " 0.067 2.00e-02 2.50e+03 pdb=" N1T TTD T 18 " 0.019 2.00e-02 2.50e+03 pdb=" N3T TTD T 18 " 0.001 2.00e-02 2.50e+03 pdb=" O2T TTD T 18 " -0.002 2.00e-02 2.50e+03 pdb=" O4T TTD T 18 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET B 783 " 0.013 2.00e-02 2.50e+03 2.64e-02 6.97e+00 pdb=" C MET B 783 " -0.046 2.00e-02 2.50e+03 pdb=" O MET B 783 " 0.017 2.00e-02 2.50e+03 pdb=" N ASP B 784 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL G 41 " 0.040 5.00e-02 4.00e+02 6.14e-02 6.02e+00 pdb=" N PRO G 42 " -0.106 5.00e-02 4.00e+02 pdb=" CA PRO G 42 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO G 42 " 0.034 5.00e-02 4.00e+02 ... (remaining 5896 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 333 2.62 - 3.19: 27619 3.19 - 3.76: 49725 3.76 - 4.33: 70762 4.33 - 4.90: 114954 Nonbonded interactions: 263393 Sorted by model distance: nonbonded pdb=" O3' A R 10 " pdb="MG MG A3003 " model vdw 2.050 2.170 nonbonded pdb=" OD1 ASP A 627 " pdb="MG MG A3003 " model vdw 2.114 2.170 nonbonded pdb=" OD2 ASP A 631 " pdb="MG MG A3003 " model vdw 2.131 2.170 nonbonded pdb=" OD1 ASP A 631 " pdb="MG MG A3003 " model vdw 2.136 2.170 nonbonded pdb=" N CYS J 46 " pdb="ZN ZN J3001 " model vdw 2.214 2.310 ... (remaining 263388 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 1.780 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: 0.060 Extract box with map and model: 0.520 Check model and map are aligned: 0.100 Set scattering table: 0.070 Process input model: 38.830 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.060 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:1.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7228 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 : 0.010 0.633 34574 Z= 0.398 Angle : 1.030 48.589 46895 Z= 0.502 Chirality : 0.057 0.475 5245 Planarity : 0.007 0.061 5899 Dihedral : 11.693 168.814 13214 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.02 % Allowed : 7.49 % Favored : 92.49 % Rotamer: Outliers : 0.05 % Allowed : 1.03 % Favored : 98.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.14 (0.10), residues: 4086 helix: -2.98 (0.10), residues: 1223 sheet: -2.44 (0.18), residues: 595 loop : -2.74 (0.11), residues: 2268 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 305 TYR 0.038 0.003 TYR B 409 PHE 0.032 0.003 PHE B 954 TRP 0.038 0.003 TRP B 143 HIS 0.017 0.002 HIS A 603 Details of bonding type rmsd/Z covalent geometry : bond 0.00637 / 0.30 (34549) covalent geometry : angle 0.89649 / 0.49 (46868) hydrogen bonds : bond 0.17393 / 11.76 ( 1125) hydrogen bonds : angle 7.60025 / 5.15 ( 3071) metal coordination : bond 0.29174 / 17.37 ( 23) metal coordination : angle 21.13212 / 12.67 ( 27) Misc. bond : bond 0.05796 / 3.02 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8172 Ramachandran restraints generated. 4086 Oldfield, 0 Emsley, 4086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8172 Ramachandran restraints generated. 4086 Oldfield, 0 Emsley, 4086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1017 residues out of total 3673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 1015 time to evaluate : 1.427 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 253 GLU cc_start: 0.6073 (tt0) cc_final: 0.5685 (mt-10) REVERT: A 315 ILE cc_start: 0.8043 (tt) cc_final: 0.6873 (tp) REVERT: A 634 ASN cc_start: 0.8480 (m110) cc_final: 0.8246 (m110) REVERT: A 646 GLU cc_start: 0.7293 (mt-10) cc_final: 0.6966 (mt-10) REVERT: A 961 VAL cc_start: 0.8449 (p) cc_final: 0.8230 (m) REVERT: A 1268 ASP cc_start: 0.6986 (t70) cc_final: 0.6644 (t0) REVERT: A 1553 TYR cc_start: 0.8154 (m-10) cc_final: 0.7916 (m-80) REVERT: A 1576 SER cc_start: 0.8301 (t) cc_final: 0.8050 (p) REVERT: A 1588 MET cc_start: 0.7780 (tpt) cc_final: 0.7469 (tpp) REVERT: B 190 ILE cc_start: 0.7923 (pt) cc_final: 0.7655 (pt) REVERT: B 461 MET cc_start: 0.8446 (mmm) cc_final: 0.7600 (mmt) REVERT: B 839 LYS cc_start: 0.7430 (mptt) cc_final: 0.7214 (mmtp) REVERT: B 975 HIS cc_start: 0.7456 (m-70) cc_final: 0.7136 (m-70) REVERT: B 1090 ASP cc_start: 0.7556 (t0) cc_final: 0.7253 (t0) REVERT: C 289 VAL cc_start: 0.7934 (t) cc_final: 0.7734 (m) REVERT: E 50 MET cc_start: 0.5458 (mmm) cc_final: 0.5185 (tpt) REVERT: E 83 CYS cc_start: 0.5631 (t) cc_final: 0.4883 (p) REVERT: E 134 THR cc_start: 0.7570 (p) cc_final: 0.6687 (p) REVERT: F 86 THR cc_start: 0.6175 (p) cc_final: 0.5811 (p) REVERT: J 17 LYS cc_start: 0.7960 (mttp) cc_final: 0.7693 (mttt) REVERT: J 31 ASP cc_start: 0.4515 (t0) cc_final: 0.4301 (m-30) REVERT: K 68 GLU cc_start: 0.7819 (mm-30) cc_final: 0.7112 (mm-30) REVERT: M 23 VAL cc_start: 0.6306 (t) cc_final: 0.5839 (t) REVERT: N 36 LYS cc_start: 0.6528 (mmtm) cc_final: 0.5243 (mppt) REVERT: N 90 MET cc_start: 0.5909 (mtm) cc_final: 0.5555 (ttm) outliers start: 2 outliers final: 0 residues processed: 1017 average time/residue: 0.2334 time to fit residues: 369.2122 Evaluate side-chains 521 residues out of total 3673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 521 time to evaluate : 1.064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: [197, 388, 215, 20, 132, 261, 248, 207, 401, 155, 244] chunk 197 optimal weight: 0.9990 chunk 388 optimal weight: 8.9990 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 20.0000 chunk 132 optimal weight: 8.9990 chunk 261 optimal weight: 1.9990 chunk 248 optimal weight: 0.4980 chunk 207 optimal weight: 5.9990 chunk 401 optimal weight: 0.0370 chunk 155 optimal weight: 2.9990 chunk 244 optimal weight: 6.9990 overall best weight: 1.1064 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 470 HIS A 489 ASN A 537 GLN ** A 590 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 620 ASN A 639 GLN A 649 ASN A 656 GLN A 673 HIS A 880 GLN A 886 ASN ** A1072 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1180 ASN A1250 GLN A1447 GLN B 182 GLN B 197 ASN B 243 GLN B 398 GLN B 646 HIS ** B 695 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 702 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 715 ASN ** B 745 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 764 ASN B 770 ASN B 923 GLN B1157 GLN ** C 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 237 GLN E 99 HIS E 153 HIS E 179 GLN H 33 GLN ** H 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 21 ASN J 53 HIS K 64 GLN K 106 GLN M 71 GLN M 74 ASN Total number of N/Q/H flips: 34 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4212 r_free = 0.4212 target = 0.159761 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.133966 restraints weight = 63305.230| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.135474 restraints weight = 38312.819| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.137521 restraints weight = 26627.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.137424 restraints weight = 22422.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.137491 restraints weight = 19902.109| |-----------------------------------------------------------------------------| r_work (final): 0.3909 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7297 moved from start: 0.2398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.091 34574 Z= 0.141 Angle : 0.684 17.069 46895 Z= 0.348 Chirality : 0.046 0.355 5245 Planarity : 0.006 0.054 5899 Dihedral : 12.839 163.204 5016 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 2.07 % Allowed : 9.09 % Favored : 88.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.07 (0.12), residues: 4086 helix: -1.51 (0.13), residues: 1219 sheet: -2.13 (0.19), residues: 597 loop : -2.35 (0.12), residues: 2270 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 55 TYR 0.031 0.002 TYR G 73 PHE 0.033 0.002 PHE A 223 TRP 0.030 0.001 TRP B 143 HIS 0.013 0.001 HIS A1293 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.14 (34549) covalent geometry : angle 0.66180 / 0.35 (46868) hydrogen bonds : bond 0.04652 / 3.17 ( 1125) hydrogen bonds : angle 5.88983 / 4.04 ( 3071) metal coordination : bond 0.01855 / 1.08 ( 23) metal coordination : angle 7.31452 / 5.01 ( 27) Misc. bond : bond 0.00149 / 0.08 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8172 Ramachandran restraints generated. 4086 Oldfield, 0 Emsley, 4086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8172 Ramachandran restraints generated. 4086 Oldfield, 0 Emsley, 4086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 683 residues out of total 3673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 607 time to evaluate : 1.272 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 253 GLU cc_start: 0.6240 (tt0) cc_final: 0.6031 (mt-10) REVERT: A 322 ASN cc_start: 0.7075 (m110) cc_final: 0.6761 (m-40) REVERT: A 646 GLU cc_start: 0.7356 (mt-10) cc_final: 0.6981 (mt-10) REVERT: A 1142 ASP cc_start: 0.7488 (m-30) cc_final: 0.7247 (m-30) REVERT: A 1553 TYR cc_start: 0.8362 (m-10) cc_final: 0.8090 (m-80) REVERT: A 1576 SER cc_start: 0.8575 (t) cc_final: 0.8303 (p) REVERT: B 215 MET cc_start: 0.6744 (OUTLIER) cc_final: 0.6511 (mtp) REVERT: B 446 MET cc_start: 0.7966 (ttp) cc_final: 0.7531 (ttp) REVERT: B 461 MET cc_start: 0.8162 (mmm) cc_final: 0.7925 (mmt) REVERT: B 496 PHE cc_start: 0.8685 (t80) cc_final: 0.8382 (t80) REVERT: B 519 LYS cc_start: 0.8273 (mmtp) cc_final: 0.8011 (ptmt) REVERT: B 839 LYS cc_start: 0.7598 (mptt) cc_final: 0.7313 (mmtp) REVERT: B 875 HIS cc_start: 0.5673 (t-90) cc_final: 0.5396 (t70) REVERT: B 975 HIS cc_start: 0.7735 (m-70) cc_final: 0.7385 (m-70) REVERT: B 1090 ASP cc_start: 0.7559 (t0) cc_final: 0.7215 (t0) REVERT: C 131 THR cc_start: 0.8703 (m) cc_final: 0.8362 (p) REVERT: C 289 VAL cc_start: 0.7914 (t) cc_final: 0.7655 (m) REVERT: C 308 MET cc_start: 0.7265 (mpp) cc_final: 0.7032 (mpp) REVERT: E 50 MET cc_start: 0.5478 (mmm) cc_final: 0.5136 (tpt) REVERT: E 52 ARG cc_start: 0.7967 (mtt180) cc_final: 0.7548 (tpm170) REVERT: E 133 GLU cc_start: 0.7001 (mp0) cc_final: 0.6773 (mp0) REVERT: E 134 THR cc_start: 0.8103 (p) cc_final: 0.7402 (p) REVERT: F 89 GLU cc_start: 0.6246 (mt-10) cc_final: 0.5886 (mp0) REVERT: F 100 GLN cc_start: 0.7332 (mm-40) cc_final: 0.6732 (mm110) REVERT: F 135 ARG cc_start: 0.7631 (ttm170) cc_final: 0.6556 (ttt-90) REVERT: J 17 LYS cc_start: 0.7959 (mttp) cc_final: 0.7645 (mttt) REVERT: J 31 ASP cc_start: 0.5055 (t0) cc_final: 0.4551 (m-30) REVERT: J 49 MET cc_start: 0.8395 (mmm) cc_final: 0.7449 (mmm) REVERT: L 28 LYS cc_start: 0.6750 (mttp) cc_final: 0.6147 (mttp) REVERT: N 36 LYS cc_start: 0.6297 (mmtm) cc_final: 0.5022 (mppt) REVERT: N 58 PHE cc_start: 0.5865 (m-80) cc_final: 0.5660 (m-80) outliers start: 76 outliers final: 41 residues processed: 650 average time/residue: 0.2142 time to fit residues: 228.2583 Evaluate side-chains 531 residues out of total 3673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 489 time to evaluate : 1.127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 ILE Chi-restraints excluded: chain A residue 354 SER Chi-restraints excluded: chain A residue 357 MET Chi-restraints excluded: chain A residue 586 VAL Chi-restraints excluded: chain A residue 1330 VAL Chi-restraints excluded: chain A residue 1516 LYS Chi-restraints excluded: chain A residue 1594 THR Chi-restraints excluded: chain A residue 1632 GLU Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 179 GLU Chi-restraints excluded: chain B residue 215 MET Chi-restraints excluded: chain B residue 303 THR Chi-restraints excluded: chain B residue 498 SER Chi-restraints excluded: chain B residue 684 ASN Chi-restraints excluded: chain B residue 700 LEU Chi-restraints excluded: chain B residue 752 VAL Chi-restraints excluded: chain B residue 777 SER Chi-restraints excluded: chain B residue 913 ILE Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1018 THR Chi-restraints excluded: chain B residue 1110 ILE Chi-restraints excluded: chain C residue 290 LYS Chi-restraints excluded: chain C residue 309 THR Chi-restraints excluded: chain E residue 36 GLU Chi-restraints excluded: chain E residue 91 LYS Chi-restraints excluded: chain E residue 117 THR Chi-restraints excluded: chain E residue 204 THR Chi-restraints excluded: chain F residue 99 LEU Chi-restraints excluded: chain F residue 107 VAL Chi-restraints excluded: chain F residue 115 THR Chi-restraints excluded: chain F residue 118 LEU Chi-restraints excluded: chain G residue 75 ASN Chi-restraints excluded: chain G residue 111 THR Chi-restraints excluded: chain G residue 118 CYS Chi-restraints excluded: chain H residue 11 GLN Chi-restraints excluded: chain H residue 144 ILE Chi-restraints excluded: chain I residue 49 THR Chi-restraints excluded: chain J residue 34 THR Chi-restraints excluded: chain K residue 81 MET Chi-restraints excluded: chain L residue 37 LYS Chi-restraints excluded: chain N residue 55 LEU Chi-restraints excluded: chain N residue 60 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: [27, 52, 398, 93, 336, 225, 246, 239, 203, 327, 160] chunk 27 optimal weight: 20.0000 chunk 52 optimal weight: 8.9990 chunk 398 optimal weight: 0.0170 chunk 93 optimal weight: 20.0000 chunk 336 optimal weight: 7.9990 chunk 225 optimal weight: 8.9990 chunk 246 optimal weight: 0.0570 chunk 239 optimal weight: 8.9990 chunk 203 optimal weight: 9.9990 chunk 327 optimal weight: 5.9990 chunk 160 optimal weight: 0.8980 overall best weight: 2.9940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 590 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 634 ASN A 656 GLN ** A 706 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 886 ASN A 998 HIS ** A1108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 27 ASN B 197 ASN B 587 GLN ** B 695 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 702 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 724 GLN B 745 GLN B1058 GLN B1089 GLN ** C 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 93 GLN ** C 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 146 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4177 r_free = 0.4177 target = 0.156938 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.131258 restraints weight = 63766.638| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.132409 restraints weight = 38891.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.134320 restraints weight = 28095.696| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.134438 restraints weight = 24322.068| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.134402 restraints weight = 20891.530| |-----------------------------------------------------------------------------| r_work (final): 0.3862 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7373 moved from start: 0.2858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 34574 Z= 0.180 Angle : 0.667 15.024 46895 Z= 0.342 Chirality : 0.047 0.355 5245 Planarity : 0.005 0.085 5899 Dihedral : 12.651 162.258 5016 Min Nonbonded Distance : 1.869 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.07 % Favored : 93.93 % Rotamer: Outliers : 2.70 % Allowed : 10.84 % Favored : 86.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.63 (0.12), residues: 4086 helix: -0.93 (0.14), residues: 1228 sheet: -2.00 (0.20), residues: 562 loop : -2.19 (0.12), residues: 2296 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 609 TYR 0.032 0.002 TYR G 73 PHE 0.034 0.002 PHE A 223 TRP 0.021 0.002 TRP B 143 HIS 0.008 0.001 HIS B 361 Details of bonding type rmsd/Z covalent geometry : bond 0.00412 / 0.18 (34549) covalent geometry : angle 0.65368 / 0.34 (46868) hydrogen bonds : bond 0.04236 / 2.87 ( 1125) hydrogen bonds : angle 5.50854 / 3.79 ( 3071) metal coordination : bond 0.00946 / 0.61 ( 23) metal coordination : angle 5.63154 / 3.84 ( 27) Misc. bond : bond 0.00190 / 0.10 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8172 Ramachandran restraints generated. 4086 Oldfield, 0 Emsley, 4086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8172 Ramachandran restraints generated. 4086 Oldfield, 0 Emsley, 4086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 612 residues out of total 3673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 513 time to evaluate : 1.523 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: A 322 ASN cc_start: 0.7287 (m110) cc_final: 0.7068 (m-40) REVERT: A 493 ASN cc_start: 0.7815 (p0) cc_final: 0.7355 (p0) REVERT: A 646 GLU cc_start: 0.7335 (mt-10) cc_final: 0.7131 (mt-10) REVERT: A 772 LYS cc_start: 0.8120 (OUTLIER) cc_final: 0.7664 (ttmm) REVERT: A 1167 ARG cc_start: 0.8341 (ttm170) cc_final: 0.8000 (mtt180) REVERT: A 1553 TYR cc_start: 0.8486 (m-10) cc_final: 0.8286 (m-80) REVERT: A 1588 MET cc_start: 0.7848 (tpt) cc_final: 0.7442 (tpp) REVERT: A 1615 TYR cc_start: 0.7130 (t80) cc_final: 0.6882 (t80) REVERT: B 197 ASN cc_start: 0.8088 (OUTLIER) cc_final: 0.7733 (t0) REVERT: B 461 MET cc_start: 0.8144 (mmm) cc_final: 0.7415 (mmt) REVERT: B 494 TYR cc_start: 0.8295 (m-80) cc_final: 0.7904 (m-80) REVERT: B 496 PHE cc_start: 0.8665 (t80) cc_final: 0.8354 (t80) REVERT: B 519 LYS cc_start: 0.8281 (mmtp) cc_final: 0.8027 (ptmt) REVERT: B 649 MET cc_start: 0.8307 (mtm) cc_final: 0.7984 (mtm) REVERT: B 839 LYS cc_start: 0.7662 (mptt) cc_final: 0.7405 (mmtp) REVERT: B 875 HIS cc_start: 0.5641 (t-90) cc_final: 0.5356 (t70) REVERT: B 975 HIS cc_start: 0.7792 (m-70) cc_final: 0.7463 (m-70) REVERT: B 1090 ASP cc_start: 0.7619 (t0) cc_final: 0.7307 (t0) REVERT: C 97 LEU cc_start: 0.8439 (OUTLIER) cc_final: 0.8171 (tp) REVERT: C 131 THR cc_start: 0.8703 (m) cc_final: 0.8364 (p) REVERT: C 289 VAL cc_start: 0.7942 (t) cc_final: 0.7688 (m) REVERT: C 308 MET cc_start: 0.7263 (mpp) cc_final: 0.6964 (mpp) REVERT: E 50 MET cc_start: 0.5509 (mmm) cc_final: 0.5090 (tpt) REVERT: H 35 GLN cc_start: 0.5783 (tm-30) cc_final: 0.4816 (pp30) REVERT: J 17 LYS cc_start: 0.8062 (mttp) cc_final: 0.7786 (mttt) REVERT: J 31 ASP cc_start: 0.5052 (t0) cc_final: 0.4623 (m-30) REVERT: J 49 MET cc_start: 0.8393 (mmm) cc_final: 0.7382 (mmm) REVERT: K 71 THR cc_start: 0.8262 (m) cc_final: 0.8031 (p) REVERT: L 28 LYS cc_start: 0.6696 (mttp) cc_final: 0.6228 (mttp) REVERT: M 54 HIS cc_start: 0.7607 (m90) cc_final: 0.7340 (m-70) REVERT: M 114 LYS cc_start: 0.7589 (mtpt) cc_final: 0.7383 (mptt) REVERT: N 36 LYS cc_start: 0.6282 (mmtm) cc_final: 0.5014 (mppt) REVERT: N 58 PHE cc_start: 0.6147 (m-80) cc_final: 0.5905 (m-80) REVERT: N 90 MET cc_start: 0.4763 (ttm) cc_final: 0.4559 (ttm) outliers start: 99 outliers final: 63 residues processed: 575 average time/residue: 0.2016 time to fit residues: 192.5768 Evaluate side-chains 529 residues out of total 3673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 463 time to evaluate : 1.128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 ILE Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 357 MET Chi-restraints excluded: chain A residue 581 ILE Chi-restraints excluded: chain A residue 586 VAL Chi-restraints excluded: chain A residue 700 ILE Chi-restraints excluded: chain A residue 747 ILE Chi-restraints excluded: chain A residue 772 LYS Chi-restraints excluded: chain A residue 780 ILE Chi-restraints excluded: chain A residue 926 GLN Chi-restraints excluded: chain A residue 946 LEU Chi-restraints excluded: chain A residue 990 ILE Chi-restraints excluded: chain A residue 1071 ASP Chi-restraints excluded: chain A residue 1330 VAL Chi-restraints excluded: chain A residue 1550 LEU Chi-restraints excluded: chain A residue 1594 THR Chi-restraints excluded: chain A residue 1632 GLU Chi-restraints excluded: chain B residue 124 SER Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 179 GLU Chi-restraints excluded: chain B residue 197 ASN Chi-restraints excluded: chain B residue 303 THR Chi-restraints excluded: chain B residue 441 LYS Chi-restraints excluded: chain B residue 485 THR Chi-restraints excluded: chain B residue 486 VAL Chi-restraints excluded: chain B residue 498 SER Chi-restraints excluded: chain B residue 647 SER Chi-restraints excluded: chain B residue 656 LEU Chi-restraints excluded: chain B residue 684 ASN Chi-restraints excluded: chain B residue 752 VAL Chi-restraints excluded: chain B residue 802 THR Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1018 THR Chi-restraints excluded: chain B residue 1110 ILE Chi-restraints excluded: chain B residue 1111 LEU Chi-restraints excluded: chain B residue 1200 VAL Chi-restraints excluded: chain C residue 94 ASP Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain C residue 99 HIS Chi-restraints excluded: chain C residue 309 THR Chi-restraints excluded: chain E residue 91 LYS Chi-restraints excluded: chain E residue 117 THR Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain E residue 150 VAL Chi-restraints excluded: chain E residue 204 THR Chi-restraints excluded: chain F residue 99 LEU Chi-restraints excluded: chain F residue 101 ILE Chi-restraints excluded: chain F residue 107 VAL Chi-restraints excluded: chain F residue 115 THR Chi-restraints excluded: chain F residue 120 ILE Chi-restraints excluded: chain G residue 45 LEU Chi-restraints excluded: chain G residue 48 SER Chi-restraints excluded: chain G residue 75 ASN Chi-restraints excluded: chain G residue 108 THR Chi-restraints excluded: chain G residue 111 THR Chi-restraints excluded: chain G residue 118 CYS Chi-restraints excluded: chain G residue 243 VAL Chi-restraints excluded: chain H residue 144 ILE Chi-restraints excluded: chain J residue 34 THR Chi-restraints excluded: chain K residue 81 MET Chi-restraints excluded: chain K residue 107 THR Chi-restraints excluded: chain L residue 37 LYS Chi-restraints excluded: chain L residue 61 THR Chi-restraints excluded: chain M residue 23 VAL Chi-restraints excluded: chain N residue 60 SER Chi-restraints excluded: chain N residue 64 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: [101, 314, 240, 272, 160, 253, 5, 227, 326, 16, 355] chunk 101 optimal weight: 4.9990 chunk 314 optimal weight: 3.9990 chunk 240 optimal weight: 4.9990 chunk 272 optimal weight: 10.0000 chunk 160 optimal weight: 0.9990 chunk 253 optimal weight: 9.9990 chunk 5 optimal weight: 8.9990 chunk 227 optimal weight: 0.8980 chunk 326 optimal weight: 0.0770 chunk 16 optimal weight: 7.9990 chunk 355 optimal weight: 0.2980 overall best weight: 1.2542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 590 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 656 GLN ** A 706 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 886 ASN A 998 HIS ** A1072 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1108 HIS A1141 GLN ** B 695 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1165 ASN ** C 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 232 GLN D 30 HIS K 64 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4201 r_free = 0.4201 target = 0.158929 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.133375 restraints weight = 63067.477| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.134668 restraints weight = 39385.988| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.135419 restraints weight = 27457.539| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.135929 restraints weight = 26060.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.135978 restraints weight = 22620.018| |-----------------------------------------------------------------------------| r_work (final): 0.3885 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7337 moved from start: 0.3102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 34574 Z= 0.122 Angle : 0.600 12.453 46895 Z= 0.308 Chirality : 0.045 0.341 5245 Planarity : 0.004 0.065 5899 Dihedral : 12.486 162.567 5016 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer: Outliers : 2.29 % Allowed : 11.98 % Favored : 85.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.23 (0.12), residues: 4086 helix: -0.46 (0.14), residues: 1226 sheet: -1.88 (0.20), residues: 572 loop : -1.98 (0.12), residues: 2288 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 609 TYR 0.027 0.002 TYR A 618 PHE 0.033 0.001 PHE A 223 TRP 0.026 0.001 TRP B 143 HIS 0.005 0.001 HIS B 361 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.12 (34549) covalent geometry : angle 0.59088 / 0.31 (46868) hydrogen bonds : bond 0.03645 / 2.48 ( 1125) hydrogen bonds : angle 5.21680 / 3.60 ( 3071) metal coordination : bond 0.00867 / 0.52 ( 23) metal coordination : angle 4.32636 / 2.98 ( 27) Misc. bond : bond 0.00025 / 0.01 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8172 Ramachandran restraints generated. 4086 Oldfield, 0 Emsley, 4086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8172 Ramachandran restraints generated. 4086 Oldfield, 0 Emsley, 4086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 600 residues out of total 3673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 516 time to evaluate : 1.513 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 493 ASN cc_start: 0.7925 (p0) cc_final: 0.7512 (p0) REVERT: A 926 GLN cc_start: 0.8004 (OUTLIER) cc_final: 0.7657 (mt0) REVERT: A 1142 ASP cc_start: 0.7405 (m-30) cc_final: 0.7176 (m-30) REVERT: B 22 GLU cc_start: 0.7514 (mm-30) cc_final: 0.6994 (mm-30) REVERT: B 461 MET cc_start: 0.8156 (mmm) cc_final: 0.7489 (mmt) REVERT: B 494 TYR cc_start: 0.8244 (m-80) cc_final: 0.7957 (m-80) REVERT: B 649 MET cc_start: 0.8293 (mtm) cc_final: 0.8048 (mtm) REVERT: B 717 TYR cc_start: 0.7803 (t80) cc_final: 0.7591 (t80) REVERT: B 762 MET cc_start: 0.7933 (mmm) cc_final: 0.7649 (tpp) REVERT: B 848 ILE cc_start: 0.8811 (mm) cc_final: 0.8479 (mm) REVERT: B 975 HIS cc_start: 0.7736 (m-70) cc_final: 0.7413 (m-70) REVERT: C 131 THR cc_start: 0.8673 (m) cc_final: 0.8372 (p) REVERT: C 308 MET cc_start: 0.7033 (mpp) cc_final: 0.6659 (mpp) REVERT: E 50 MET cc_start: 0.5495 (mmm) cc_final: 0.5081 (tpt) REVERT: E 106 GLN cc_start: 0.6309 (tp40) cc_final: 0.6044 (tp40) REVERT: E 133 GLU cc_start: 0.6488 (mp0) cc_final: 0.6197 (mp0) REVERT: H 35 GLN cc_start: 0.5624 (tm-30) cc_final: 0.4827 (pp30) REVERT: J 17 LYS cc_start: 0.8037 (mttp) cc_final: 0.7817 (mtpp) REVERT: J 31 ASP cc_start: 0.4841 (t0) cc_final: 0.4458 (m-30) REVERT: J 49 MET cc_start: 0.8287 (mmm) cc_final: 0.7347 (mmm) REVERT: N 36 LYS cc_start: 0.6353 (mmtm) cc_final: 0.5098 (mppt) REVERT: N 58 PHE cc_start: 0.5922 (m-80) cc_final: 0.5699 (m-80) REVERT: N 90 MET cc_start: 0.4953 (ttm) cc_final: 0.4717 (ttm) REVERT: N 107 MET cc_start: 0.6045 (mmm) cc_final: 0.5309 (ptt) outliers start: 84 outliers final: 52 residues processed: 560 average time/residue: 0.2075 time to fit residues: 192.9187 Evaluate side-chains 516 residues out of total 3673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 463 time to evaluate : 1.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 SER Chi-restraints excluded: chain A residue 9 SER Chi-restraints excluded: chain A residue 18 ILE Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 586 VAL Chi-restraints excluded: chain A residue 700 ILE Chi-restraints excluded: chain A residue 747 ILE Chi-restraints excluded: chain A residue 886 ASN Chi-restraints excluded: chain A residue 926 GLN Chi-restraints excluded: chain A residue 946 LEU Chi-restraints excluded: chain A residue 952 LEU Chi-restraints excluded: chain A residue 1594 THR Chi-restraints excluded: chain B residue 179 GLU Chi-restraints excluded: chain B residue 190 ILE Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 441 LYS Chi-restraints excluded: chain B residue 485 THR Chi-restraints excluded: chain B residue 498 SER Chi-restraints excluded: chain B residue 656 LEU Chi-restraints excluded: chain B residue 684 ASN Chi-restraints excluded: chain B residue 752 VAL Chi-restraints excluded: chain B residue 802 THR Chi-restraints excluded: chain B residue 947 ILE Chi-restraints excluded: chain B residue 977 ILE Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1018 THR Chi-restraints excluded: chain B residue 1110 ILE Chi-restraints excluded: chain B residue 1111 LEU Chi-restraints excluded: chain C residue 99 HIS Chi-restraints excluded: chain C residue 309 THR Chi-restraints excluded: chain E residue 91 LYS Chi-restraints excluded: chain E residue 117 THR Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain E residue 204 THR Chi-restraints excluded: chain F residue 101 ILE Chi-restraints excluded: chain F residue 107 VAL Chi-restraints excluded: chain F residue 152 ILE Chi-restraints excluded: chain G residue 45 LEU Chi-restraints excluded: chain G residue 75 ASN Chi-restraints excluded: chain G residue 108 THR Chi-restraints excluded: chain G residue 111 THR Chi-restraints excluded: chain G residue 118 CYS Chi-restraints excluded: chain H residue 144 ILE Chi-restraints excluded: chain I residue 49 THR Chi-restraints excluded: chain K residue 81 MET Chi-restraints excluded: chain L residue 37 LYS Chi-restraints excluded: chain L residue 61 THR Chi-restraints excluded: chain M residue 23 VAL Chi-restraints excluded: chain M residue 66 THR Chi-restraints excluded: chain N residue 60 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: [349, 328, 192, 12, 188, 195, 340, 113, 194, 309, 146] chunk 349 optimal weight: 10.0000 chunk 328 optimal weight: 10.0000 chunk 192 optimal weight: 0.0370 chunk 12 optimal weight: 6.9990 chunk 188 optimal weight: 10.0000 chunk 195 optimal weight: 0.0020 chunk 340 optimal weight: 20.0000 chunk 113 optimal weight: 1.9990 chunk 194 optimal weight: 0.0970 chunk 309 optimal weight: 10.0000 chunk 146 optimal weight: 9.9990 overall best weight: 1.8268 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 590 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 656 GLN ** A 706 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 998 HIS A1072 ASN ** B 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 636 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 695 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 30 HIS G 64 GLN K 64 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4192 r_free = 0.4192 target = 0.158041 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.132390 restraints weight = 63509.196| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.133873 restraints weight = 38792.493| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.134364 restraints weight = 27754.362| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.134954 restraints weight = 26571.401| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.134985 restraints weight = 23144.698| |-----------------------------------------------------------------------------| r_work (final): 0.3870 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7364 moved from start: 0.3287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 34574 Z= 0.135 Angle : 0.596 11.496 46895 Z= 0.304 Chirality : 0.045 0.344 5245 Planarity : 0.004 0.056 5899 Dihedral : 12.392 161.952 5016 Min Nonbonded Distance : 1.877 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.75 % Favored : 94.25 % Rotamer: Outliers : 2.37 % Allowed : 12.71 % Favored : 84.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.05 (0.13), residues: 4086 helix: -0.26 (0.15), residues: 1226 sheet: -1.76 (0.20), residues: 566 loop : -1.91 (0.12), residues: 2294 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 244 TYR 0.021 0.002 TYR A 478 PHE 0.033 0.001 PHE A 223 TRP 0.034 0.001 TRP B 143 HIS 0.004 0.001 HIS B 361 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.13 (34549) covalent geometry : angle 0.58915 / 0.30 (46868) hydrogen bonds : bond 0.03576 / 2.43 ( 1125) hydrogen bonds : angle 5.08298 / 3.51 ( 3071) metal coordination : bond 0.00738 / 0.46 ( 23) metal coordination : angle 3.92098 / 2.75 ( 27) Misc. bond : bond 0.00038 / 0.02 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8172 Ramachandran restraints generated. 4086 Oldfield, 0 Emsley, 4086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8172 Ramachandran restraints generated. 4086 Oldfield, 0 Emsley, 4086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 582 residues out of total 3673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 495 time to evaluate : 1.299 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: A 322 ASN cc_start: 0.7228 (m110) cc_final: 0.7018 (m-40) REVERT: A 493 ASN cc_start: 0.7939 (p0) cc_final: 0.7536 (p0) REVERT: A 519 LEU cc_start: 0.7049 (OUTLIER) cc_final: 0.6770 (mm) REVERT: A 911 CYS cc_start: 0.7048 (m) cc_final: 0.6829 (m) REVERT: A 926 GLN cc_start: 0.7904 (OUTLIER) cc_final: 0.7532 (mt0) REVERT: A 930 LEU cc_start: 0.7838 (OUTLIER) cc_final: 0.7468 (mp) REVERT: A 1000 MET cc_start: 0.7664 (mtt) cc_final: 0.7354 (mtt) REVERT: A 1615 TYR cc_start: 0.7083 (t80) cc_final: 0.6781 (t80) REVERT: B 22 GLU cc_start: 0.7533 (mm-30) cc_final: 0.6994 (mm-30) REVERT: B 494 TYR cc_start: 0.8228 (m-80) cc_final: 0.7914 (m-80) REVERT: B 649 MET cc_start: 0.8315 (mtm) cc_final: 0.7995 (mtm) REVERT: B 753 LYS cc_start: 0.7620 (OUTLIER) cc_final: 0.6910 (ttmm) REVERT: B 762 MET cc_start: 0.7929 (mmm) cc_final: 0.7629 (tpp) REVERT: B 875 HIS cc_start: 0.5675 (t-90) cc_final: 0.5262 (t-90) REVERT: B 975 HIS cc_start: 0.7731 (m-70) cc_final: 0.7409 (m-70) REVERT: C 97 LEU cc_start: 0.8435 (OUTLIER) cc_final: 0.8126 (tp) REVERT: C 131 THR cc_start: 0.8691 (m) cc_final: 0.8396 (p) REVERT: E 50 MET cc_start: 0.5533 (mmm) cc_final: 0.5113 (tpt) REVERT: E 52 ARG cc_start: 0.8026 (mtt180) cc_final: 0.7550 (mmm-85) REVERT: E 54 GLN cc_start: 0.6156 (mp10) cc_final: 0.5777 (mp-120) REVERT: E 57 MET cc_start: 0.6075 (ptt) cc_final: 0.5838 (ptt) REVERT: E 106 GLN cc_start: 0.6431 (tp40) cc_final: 0.6216 (tp40) REVERT: E 133 GLU cc_start: 0.6456 (mp0) cc_final: 0.6091 (mp0) REVERT: H 35 GLN cc_start: 0.5602 (tm-30) cc_final: 0.4729 (pp30) REVERT: J 17 LYS cc_start: 0.8025 (mttp) cc_final: 0.7756 (mttt) REVERT: J 31 ASP cc_start: 0.5051 (t0) cc_final: 0.4609 (m-30) REVERT: J 49 MET cc_start: 0.8269 (mmm) cc_final: 0.6995 (mmm) REVERT: L 28 LYS cc_start: 0.7118 (mtmt) cc_final: 0.6447 (mtpp) REVERT: N 36 LYS cc_start: 0.6310 (mmtm) cc_final: 0.5047 (mppt) REVERT: N 90 MET cc_start: 0.4628 (ttm) cc_final: 0.4408 (ttm) outliers start: 87 outliers final: 61 residues processed: 540 average time/residue: 0.2037 time to fit residues: 182.3296 Evaluate side-chains 520 residues out of total 3673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 454 time to evaluate : 1.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 SER Chi-restraints excluded: chain A residue 18 ILE Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 357 MET Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 519 LEU Chi-restraints excluded: chain A residue 581 ILE Chi-restraints excluded: chain A residue 586 VAL Chi-restraints excluded: chain A residue 700 ILE Chi-restraints excluded: chain A residue 747 ILE Chi-restraints excluded: chain A residue 780 ILE Chi-restraints excluded: chain A residue 926 GLN Chi-restraints excluded: chain A residue 930 LEU Chi-restraints excluded: chain A residue 946 LEU Chi-restraints excluded: chain A residue 952 LEU Chi-restraints excluded: chain A residue 990 ILE Chi-restraints excluded: chain A residue 1072 ASN Chi-restraints excluded: chain A residue 1102 LEU Chi-restraints excluded: chain A residue 1330 VAL Chi-restraints excluded: chain A residue 1516 LYS Chi-restraints excluded: chain A residue 1594 THR Chi-restraints excluded: chain B residue 179 GLU Chi-restraints excluded: chain B residue 190 ILE Chi-restraints excluded: chain B residue 441 LYS Chi-restraints excluded: chain B residue 485 THR Chi-restraints excluded: chain B residue 498 SER Chi-restraints excluded: chain B residue 684 ASN Chi-restraints excluded: chain B residue 752 VAL Chi-restraints excluded: chain B residue 753 LYS Chi-restraints excluded: chain B residue 802 THR Chi-restraints excluded: chain B residue 977 ILE Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1018 THR Chi-restraints excluded: chain B residue 1099 THR Chi-restraints excluded: chain B residue 1110 ILE Chi-restraints excluded: chain B residue 1111 LEU Chi-restraints excluded: chain B residue 1200 VAL Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain C residue 99 HIS Chi-restraints excluded: chain C residue 290 LYS Chi-restraints excluded: chain C residue 309 THR Chi-restraints excluded: chain E residue 91 LYS Chi-restraints excluded: chain E residue 117 THR Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain E residue 134 THR Chi-restraints excluded: chain E residue 204 THR Chi-restraints excluded: chain F residue 101 ILE Chi-restraints excluded: chain F residue 107 VAL Chi-restraints excluded: chain G residue 45 LEU Chi-restraints excluded: chain G residue 75 ASN Chi-restraints excluded: chain G residue 108 THR Chi-restraints excluded: chain G residue 111 THR Chi-restraints excluded: chain G residue 118 CYS Chi-restraints excluded: chain G residue 243 VAL Chi-restraints excluded: chain H residue 144 ILE Chi-restraints excluded: chain J residue 34 THR Chi-restraints excluded: chain J residue 67 GLU Chi-restraints excluded: chain K residue 81 MET Chi-restraints excluded: chain K residue 107 THR Chi-restraints excluded: chain L residue 37 LYS Chi-restraints excluded: chain L residue 61 THR Chi-restraints excluded: chain M residue 23 VAL Chi-restraints excluded: chain M residue 66 THR Chi-restraints excluded: chain N residue 60 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: [321, 284, 340, 78, 296, 118, 233, 209, 282, 141, 19] chunk 321 optimal weight: 0.1980 chunk 284 optimal weight: 6.9990 chunk 340 optimal weight: 30.0000 chunk 78 optimal weight: 0.0870 chunk 296 optimal weight: 30.0000 chunk 118 optimal weight: 9.9990 chunk 233 optimal weight: 6.9990 chunk 209 optimal weight: 0.8980 chunk 282 optimal weight: 7.9990 chunk 141 optimal weight: 6.9990 chunk 19 optimal weight: 10.0000 overall best weight: 3.0362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 656 GLN ** A 706 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 939 ASN A 998 HIS A1072 ASN B 243 GLN ** B 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 636 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 695 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 987 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 30 HIS G 119 HIS K 64 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4172 r_free = 0.4172 target = 0.156468 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.131270 restraints weight = 63900.353| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.132521 restraints weight = 40684.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.132975 restraints weight = 30349.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.133591 restraints weight = 27579.196| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.133571 restraints weight = 23918.598| |-----------------------------------------------------------------------------| r_work (final): 0.3855 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7387 moved from start: 0.3442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 34574 Z= 0.175 Angle : 0.633 12.288 46895 Z= 0.322 Chirality : 0.046 0.347 5245 Planarity : 0.004 0.059 5899 Dihedral : 12.375 161.315 5016 Min Nonbonded Distance : 1.859 Molprobity Statistics. All-atom Clashscore : 9.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.44 % Favored : 93.56 % Rotamer: Outliers : 3.10 % Allowed : 12.77 % Favored : 84.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.01 (0.13), residues: 4086 helix: -0.23 (0.15), residues: 1231 sheet: -1.73 (0.20), residues: 580 loop : -1.89 (0.13), residues: 2275 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 244 TYR 0.020 0.002 TYR C 227 PHE 0.034 0.002 PHE A 223 TRP 0.046 0.002 TRP B 143 HIS 0.005 0.001 HIS C 99 Details of bonding type rmsd/Z covalent geometry : bond 0.00409 / 0.17 (34549) covalent geometry : angle 0.62571 / 0.32 (46868) hydrogen bonds : bond 0.03723 / 2.53 ( 1125) hydrogen bonds : angle 5.10003 / 3.54 ( 3071) metal coordination : bond 0.00767 / 0.53 ( 23) metal coordination : angle 3.94433 / 2.74 ( 27) Misc. bond : bond 0.00019 / 0.01 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8172 Ramachandran restraints generated. 4086 Oldfield, 0 Emsley, 4086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8172 Ramachandran restraints generated. 4086 Oldfield, 0 Emsley, 4086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 570 residues out of total 3673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 456 time to evaluate : 1.382 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: A 493 ASN cc_start: 0.7824 (p0) cc_final: 0.7441 (p0) REVERT: A 519 LEU cc_start: 0.7063 (OUTLIER) cc_final: 0.6762 (mm) REVERT: A 632 GLU cc_start: 0.7090 (OUTLIER) cc_final: 0.6736 (mp0) REVERT: A 926 GLN cc_start: 0.7949 (OUTLIER) cc_final: 0.7621 (mt0) REVERT: A 930 LEU cc_start: 0.7881 (OUTLIER) cc_final: 0.7512 (mp) REVERT: A 1000 MET cc_start: 0.7766 (mtt) cc_final: 0.7471 (mtt) REVERT: A 1485 MET cc_start: 0.5587 (mmt) cc_final: 0.5280 (tpp) REVERT: B 149 GLU cc_start: 0.7445 (tp30) cc_final: 0.7100 (mm-30) REVERT: B 202 LEU cc_start: 0.8816 (OUTLIER) cc_final: 0.8602 (pp) REVERT: B 494 TYR cc_start: 0.8235 (m-80) cc_final: 0.7907 (m-80) REVERT: B 649 MET cc_start: 0.8317 (mtm) cc_final: 0.7919 (mtm) REVERT: B 753 LYS cc_start: 0.7670 (OUTLIER) cc_final: 0.6987 (ttmm) REVERT: B 762 MET cc_start: 0.7991 (mmm) cc_final: 0.7680 (tpp) REVERT: B 875 HIS cc_start: 0.5630 (t-90) cc_final: 0.5260 (t-90) REVERT: C 91 VAL cc_start: 0.7883 (OUTLIER) cc_final: 0.7612 (p) REVERT: C 97 LEU cc_start: 0.8386 (OUTLIER) cc_final: 0.8072 (tp) REVERT: C 131 THR cc_start: 0.8711 (m) cc_final: 0.8387 (p) REVERT: E 50 MET cc_start: 0.5576 (mmm) cc_final: 0.5172 (tpt) REVERT: E 52 ARG cc_start: 0.7925 (mtt180) cc_final: 0.7610 (mmm-85) REVERT: E 133 GLU cc_start: 0.6338 (mp0) cc_final: 0.5941 (mp0) REVERT: J 17 LYS cc_start: 0.8099 (mttp) cc_final: 0.7857 (mttm) REVERT: J 31 ASP cc_start: 0.5139 (t0) cc_final: 0.4710 (m-30) REVERT: J 49 MET cc_start: 0.8271 (mmm) cc_final: 0.6968 (mmm) REVERT: L 28 LYS cc_start: 0.7165 (mtmt) cc_final: 0.6374 (mtpp) REVERT: M 61 GLU cc_start: 0.6999 (tp30) cc_final: 0.6454 (pm20) REVERT: N 36 LYS cc_start: 0.6452 (mmtm) cc_final: 0.5196 (mppt) REVERT: N 90 MET cc_start: 0.5155 (ttm) cc_final: 0.4866 (ttm) REVERT: N 107 MET cc_start: 0.5774 (mmm) cc_final: 0.5109 (ptt) outliers start: 114 outliers final: 76 residues processed: 520 average time/residue: 0.2002 time to fit residues: 171.9119 Evaluate side-chains 512 residues out of total 3673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 428 time to evaluate : 1.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 SER Chi-restraints excluded: chain A residue 18 ILE Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 120 CYS Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 357 MET Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 519 LEU Chi-restraints excluded: chain A residue 581 ILE Chi-restraints excluded: chain A residue 586 VAL Chi-restraints excluded: chain A residue 632 GLU Chi-restraints excluded: chain A residue 700 ILE Chi-restraints excluded: chain A residue 747 ILE Chi-restraints excluded: chain A residue 780 ILE Chi-restraints excluded: chain A residue 926 GLN Chi-restraints excluded: chain A residue 930 LEU Chi-restraints excluded: chain A residue 946 LEU Chi-restraints excluded: chain A residue 952 LEU Chi-restraints excluded: chain A residue 961 VAL Chi-restraints excluded: chain A residue 985 ARG Chi-restraints excluded: chain A residue 990 ILE Chi-restraints excluded: chain A residue 1049 MET Chi-restraints excluded: chain A residue 1102 LEU Chi-restraints excluded: chain A residue 1124 LEU Chi-restraints excluded: chain A residue 1330 VAL Chi-restraints excluded: chain A residue 1516 LYS Chi-restraints excluded: chain A residue 1594 THR Chi-restraints excluded: chain B residue 124 SER Chi-restraints excluded: chain B residue 179 GLU Chi-restraints excluded: chain B residue 190 ILE Chi-restraints excluded: chain B residue 202 LEU Chi-restraints excluded: chain B residue 212 ASN Chi-restraints excluded: chain B residue 441 LYS Chi-restraints excluded: chain B residue 485 THR Chi-restraints excluded: chain B residue 498 SER Chi-restraints excluded: chain B residue 587 GLN Chi-restraints excluded: chain B residue 684 ASN Chi-restraints excluded: chain B residue 752 VAL Chi-restraints excluded: chain B residue 753 LYS Chi-restraints excluded: chain B residue 792 SER Chi-restraints excluded: chain B residue 802 THR Chi-restraints excluded: chain B residue 977 ILE Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1018 THR Chi-restraints excluded: chain B residue 1099 THR Chi-restraints excluded: chain B residue 1110 ILE Chi-restraints excluded: chain B residue 1173 THR Chi-restraints excluded: chain B residue 1200 VAL Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain C residue 94 ASP Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain C residue 99 HIS Chi-restraints excluded: chain C residue 224 THR Chi-restraints excluded: chain C residue 290 LYS Chi-restraints excluded: chain C residue 309 THR Chi-restraints excluded: chain E residue 91 LYS Chi-restraints excluded: chain E residue 117 THR Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain E residue 134 THR Chi-restraints excluded: chain E residue 190 LEU Chi-restraints excluded: chain E residue 204 THR Chi-restraints excluded: chain F residue 101 ILE Chi-restraints excluded: chain G residue 45 LEU Chi-restraints excluded: chain G residue 71 MET Chi-restraints excluded: chain G residue 108 THR Chi-restraints excluded: chain G residue 111 THR Chi-restraints excluded: chain G residue 118 CYS Chi-restraints excluded: chain G residue 243 VAL Chi-restraints excluded: chain H residue 54 SER Chi-restraints excluded: chain H residue 144 ILE Chi-restraints excluded: chain I residue 12 ASP Chi-restraints excluded: chain I residue 49 THR Chi-restraints excluded: chain J residue 34 THR Chi-restraints excluded: chain K residue 81 MET Chi-restraints excluded: chain K residue 107 THR Chi-restraints excluded: chain L residue 37 LYS Chi-restraints excluded: chain L residue 61 THR Chi-restraints excluded: chain M residue 23 VAL Chi-restraints excluded: chain M residue 66 THR Chi-restraints excluded: chain M residue 96 LEU Chi-restraints excluded: chain N residue 55 LEU Chi-restraints excluded: chain N residue 60 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: [27, 122, 113, 82, 265, 317, 276, 79, 400, 315, 250] chunk 27 optimal weight: 10.0000 chunk 122 optimal weight: 0.9980 chunk 113 optimal weight: 0.9990 chunk 82 optimal weight: 6.9990 chunk 265 optimal weight: 10.0000 chunk 317 optimal weight: 10.0000 chunk 276 optimal weight: 9.9990 chunk 79 optimal weight: 2.9990 chunk 400 optimal weight: 20.0000 chunk 315 optimal weight: 0.9990 chunk 250 optimal weight: 0.8980 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 322 ASN A 656 GLN ** A 706 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 886 ASN A 998 HIS A1072 ASN B 243 GLN ** B 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 636 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 695 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 987 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1114 GLN ** C 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 30 HIS E 32 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4193 r_free = 0.4193 target = 0.158151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.132232 restraints weight = 63844.547| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.134233 restraints weight = 37334.066| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.134930 restraints weight = 26095.041| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.135416 restraints weight = 24886.324| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.135518 restraints weight = 21846.542| |-----------------------------------------------------------------------------| r_work (final): 0.3878 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7358 moved from start: 0.3568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 34574 Z= 0.122 Angle : 0.600 10.789 46895 Z= 0.305 Chirality : 0.044 0.334 5245 Planarity : 0.004 0.065 5899 Dihedral : 12.280 161.791 5016 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 2.34 % Allowed : 14.10 % Favored : 83.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.83 (0.13), residues: 4086 helix: -0.05 (0.15), residues: 1226 sheet: -1.72 (0.20), residues: 587 loop : -1.75 (0.13), residues: 2273 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 55 TYR 0.024 0.002 TYR J 21 PHE 0.035 0.001 PHE A 223 TRP 0.019 0.001 TRP B 143 HIS 0.004 0.001 HIS B 361 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.12 (34549) covalent geometry : angle 0.59486 / 0.30 (46868) hydrogen bonds : bond 0.03433 / 2.32 ( 1125) hydrogen bonds : angle 4.94652 / 3.44 ( 3071) metal coordination : bond 0.00706 / 0.43 ( 23) metal coordination : angle 3.45977 / 2.40 ( 27) Misc. bond : bond 0.00018 / 0.01 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8172 Ramachandran restraints generated. 4086 Oldfield, 0 Emsley, 4086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8172 Ramachandran restraints generated. 4086 Oldfield, 0 Emsley, 4086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 552 residues out of total 3673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 466 time to evaluate : 1.252 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 493 ASN cc_start: 0.7800 (p0) cc_final: 0.7445 (p0) REVERT: A 519 LEU cc_start: 0.7112 (OUTLIER) cc_final: 0.6807 (mm) REVERT: A 930 LEU cc_start: 0.7877 (OUTLIER) cc_final: 0.7526 (mp) REVERT: A 1000 MET cc_start: 0.7749 (mtt) cc_final: 0.7484 (mtt) REVERT: A 1105 ARG cc_start: 0.7695 (ttm-80) cc_final: 0.7326 (ttm-80) REVERT: A 1485 MET cc_start: 0.5658 (mmt) cc_final: 0.5335 (tpp) REVERT: B 22 GLU cc_start: 0.7715 (mm-30) cc_final: 0.7210 (mm-30) REVERT: B 149 GLU cc_start: 0.7466 (tp30) cc_final: 0.6983 (mm-30) REVERT: B 494 TYR cc_start: 0.8195 (m-80) cc_final: 0.7921 (m-80) REVERT: B 649 MET cc_start: 0.8249 (mtm) cc_final: 0.7815 (mtm) REVERT: B 762 MET cc_start: 0.7933 (mmm) cc_final: 0.7635 (tpp) REVERT: B 875 HIS cc_start: 0.5682 (t-90) cc_final: 0.5310 (t-90) REVERT: B 975 HIS cc_start: 0.7743 (m-70) cc_final: 0.7391 (m-70) REVERT: B 1013 MET cc_start: 0.8151 (ptm) cc_final: 0.7945 (ptm) REVERT: C 91 VAL cc_start: 0.7844 (OUTLIER) cc_final: 0.7577 (p) REVERT: C 97 LEU cc_start: 0.8427 (OUTLIER) cc_final: 0.8101 (tp) REVERT: C 131 THR cc_start: 0.8688 (m) cc_final: 0.8407 (p) REVERT: E 50 MET cc_start: 0.5534 (mmm) cc_final: 0.5104 (tpt) REVERT: E 52 ARG cc_start: 0.8003 (mtt180) cc_final: 0.7618 (mmm-85) REVERT: E 133 GLU cc_start: 0.6358 (mp0) cc_final: 0.5730 (mp0) REVERT: J 17 LYS cc_start: 0.8076 (mttp) cc_final: 0.7670 (mttt) REVERT: J 31 ASP cc_start: 0.5001 (t0) cc_final: 0.4613 (m-30) REVERT: J 49 MET cc_start: 0.8234 (mmm) cc_final: 0.6973 (mmm) REVERT: K 110 GLU cc_start: 0.8141 (pm20) cc_final: 0.7524 (pm20) REVERT: L 28 LYS cc_start: 0.7123 (mtmt) cc_final: 0.6312 (mtpp) REVERT: N 36 LYS cc_start: 0.6316 (mmtm) cc_final: 0.5092 (mppt) REVERT: N 90 MET cc_start: 0.4812 (ttm) cc_final: 0.4552 (ttm) REVERT: N 107 MET cc_start: 0.6155 (mmm) cc_final: 0.5278 (ptt) outliers start: 86 outliers final: 63 residues processed: 514 average time/residue: 0.1931 time to fit residues: 165.7603 Evaluate side-chains 508 residues out of total 3673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 441 time to evaluate : 1.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 ILE Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 188 TYR Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 357 MET Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 519 LEU Chi-restraints excluded: chain A residue 581 ILE Chi-restraints excluded: chain A residue 586 VAL Chi-restraints excluded: chain A residue 700 ILE Chi-restraints excluded: chain A residue 744 MET Chi-restraints excluded: chain A residue 747 ILE Chi-restraints excluded: chain A residue 780 ILE Chi-restraints excluded: chain A residue 930 LEU Chi-restraints excluded: chain A residue 952 LEU Chi-restraints excluded: chain A residue 985 ARG Chi-restraints excluded: chain A residue 1071 ASP Chi-restraints excluded: chain A residue 1072 ASN Chi-restraints excluded: chain A residue 1102 LEU Chi-restraints excluded: chain A residue 1124 LEU Chi-restraints excluded: chain A residue 1516 LYS Chi-restraints excluded: chain A residue 1594 THR Chi-restraints excluded: chain B residue 179 GLU Chi-restraints excluded: chain B residue 190 ILE Chi-restraints excluded: chain B residue 441 LYS Chi-restraints excluded: chain B residue 485 THR Chi-restraints excluded: chain B residue 498 SER Chi-restraints excluded: chain B residue 587 GLN Chi-restraints excluded: chain B residue 684 ASN Chi-restraints excluded: chain B residue 752 VAL Chi-restraints excluded: chain B residue 792 SER Chi-restraints excluded: chain B residue 802 THR Chi-restraints excluded: chain B residue 834 LYS Chi-restraints excluded: chain B residue 977 ILE Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1018 THR Chi-restraints excluded: chain B residue 1110 ILE Chi-restraints excluded: chain B residue 1111 LEU Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain C residue 99 HIS Chi-restraints excluded: chain C residue 290 LYS Chi-restraints excluded: chain C residue 309 THR Chi-restraints excluded: chain E residue 91 LYS Chi-restraints excluded: chain E residue 117 THR Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain E residue 134 THR Chi-restraints excluded: chain E residue 204 THR Chi-restraints excluded: chain F residue 101 ILE Chi-restraints excluded: chain F residue 107 VAL Chi-restraints excluded: chain G residue 45 LEU Chi-restraints excluded: chain G residue 108 THR Chi-restraints excluded: chain G residue 111 THR Chi-restraints excluded: chain G residue 118 CYS Chi-restraints excluded: chain G residue 243 VAL Chi-restraints excluded: chain H residue 54 SER Chi-restraints excluded: chain H residue 144 ILE Chi-restraints excluded: chain I residue 12 ASP Chi-restraints excluded: chain J residue 34 THR Chi-restraints excluded: chain K residue 81 MET Chi-restraints excluded: chain K residue 107 THR Chi-restraints excluded: chain L residue 61 THR Chi-restraints excluded: chain M residue 66 THR Chi-restraints excluded: chain N residue 55 LEU Chi-restraints excluded: chain N residue 60 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: [234, 24, 134, 153, 189, 170, 74, 320, 102, 152, 329] chunk 234 optimal weight: 4.9990 chunk 24 optimal weight: 0.9990 chunk 134 optimal weight: 20.0000 chunk 153 optimal weight: 20.0000 chunk 189 optimal weight: 3.9990 chunk 170 optimal weight: 6.9990 chunk 74 optimal weight: 4.9990 chunk 320 optimal weight: 2.9990 chunk 102 optimal weight: 7.9990 chunk 152 optimal weight: 5.9990 chunk 329 optimal weight: 8.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 264 ASN A 656 GLN ** A 706 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 886 ASN ** A 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 950 GLN A 998 HIS A1500 GLN B 243 GLN ** B 695 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 987 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 161 HIS ** C 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 30 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4159 r_free = 0.4159 target = 0.155545 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.130445 restraints weight = 63790.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.131798 restraints weight = 39195.026| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.132276 restraints weight = 28233.038| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.132649 restraints weight = 27177.211| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.132726 restraints weight = 23789.256| |-----------------------------------------------------------------------------| r_work (final): 0.3841 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7406 moved from start: 0.3653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 34574 Z= 0.195 Angle : 0.651 11.532 46895 Z= 0.331 Chirality : 0.046 0.345 5245 Planarity : 0.005 0.065 5899 Dihedral : 12.293 160.663 5016 Min Nonbonded Distance : 1.852 Molprobity Statistics. All-atom Clashscore : 10.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.10 % Favored : 92.90 % Rotamer: Outliers : 2.89 % Allowed : 13.75 % Favored : 83.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.89 (0.13), residues: 4086 helix: -0.09 (0.15), residues: 1216 sheet: -1.74 (0.20), residues: 574 loop : -1.81 (0.13), residues: 2296 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 55 TYR 0.031 0.002 TYR J 21 PHE 0.036 0.002 PHE A 223 TRP 0.015 0.002 TRP A1469 HIS 0.007 0.001 HIS C 99 Details of bonding type rmsd/Z covalent geometry : bond 0.00457 / 0.19 (34549) covalent geometry : angle 0.64417 / 0.33 (46868) hydrogen bonds : bond 0.03807 / 2.58 ( 1125) hydrogen bonds : angle 5.08385 / 3.54 ( 3071) metal coordination : bond 0.00800 / 0.56 ( 23) metal coordination : angle 3.92223 / 2.71 ( 27) Misc. bond : bond 0.00036 / 0.02 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8172 Ramachandran restraints generated. 4086 Oldfield, 0 Emsley, 4086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8172 Ramachandran restraints generated. 4086 Oldfield, 0 Emsley, 4086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 555 residues out of total 3673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 449 time to evaluate : 1.277 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: A 493 ASN cc_start: 0.7894 (p0) cc_final: 0.7519 (p0) REVERT: A 519 LEU cc_start: 0.7110 (OUTLIER) cc_final: 0.6777 (mm) REVERT: A 1000 MET cc_start: 0.7867 (mtt) cc_final: 0.7597 (mtt) REVERT: A 1105 ARG cc_start: 0.7685 (ttm-80) cc_final: 0.7370 (ttm-80) REVERT: A 1485 MET cc_start: 0.5712 (mmt) cc_final: 0.5402 (tpp) REVERT: A 1615 TYR cc_start: 0.6940 (t80) cc_final: 0.6717 (t80) REVERT: B 22 GLU cc_start: 0.7746 (mm-30) cc_final: 0.7182 (mm-30) REVERT: B 494 TYR cc_start: 0.8228 (m-80) cc_final: 0.7924 (m-80) REVERT: B 496 PHE cc_start: 0.8565 (t80) cc_final: 0.8141 (t80) REVERT: B 649 MET cc_start: 0.8291 (mtm) cc_final: 0.7866 (mtm) REVERT: B 753 LYS cc_start: 0.7730 (OUTLIER) cc_final: 0.6991 (ttmm) REVERT: B 762 MET cc_start: 0.8024 (mmm) cc_final: 0.7745 (tpp) REVERT: C 91 VAL cc_start: 0.7909 (OUTLIER) cc_final: 0.7641 (p) REVERT: C 131 THR cc_start: 0.8789 (m) cc_final: 0.8459 (p) REVERT: E 50 MET cc_start: 0.5540 (mmm) cc_final: 0.5082 (tpt) REVERT: E 52 ARG cc_start: 0.7921 (mtt180) cc_final: 0.7636 (mmm-85) REVERT: E 133 GLU cc_start: 0.6388 (mp0) cc_final: 0.5757 (mp0) REVERT: G 71 MET cc_start: 0.8378 (OUTLIER) cc_final: 0.7817 (mtp) REVERT: H 93 TYR cc_start: 0.6274 (m-10) cc_final: 0.5415 (m-80) REVERT: J 17 LYS cc_start: 0.8049 (mttp) cc_final: 0.7683 (mttt) REVERT: J 31 ASP cc_start: 0.5007 (t0) cc_final: 0.4603 (m-30) REVERT: J 49 MET cc_start: 0.8316 (mmm) cc_final: 0.7023 (mmm) REVERT: L 28 LYS cc_start: 0.7066 (mtmt) cc_final: 0.6468 (mtpp) REVERT: N 36 LYS cc_start: 0.6417 (mmtm) cc_final: 0.5176 (mppt) REVERT: N 90 MET cc_start: 0.5226 (ttm) cc_final: 0.4930 (ttm) REVERT: N 107 MET cc_start: 0.6219 (mmm) cc_final: 0.5360 (ptt) outliers start: 106 outliers final: 76 residues processed: 513 average time/residue: 0.1929 time to fit residues: 164.5679 Evaluate side-chains 509 residues out of total 3673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 429 time to evaluate : 1.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 ILE Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 120 CYS Chi-restraints excluded: chain A residue 188 TYR Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 357 MET Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 519 LEU Chi-restraints excluded: chain A residue 581 ILE Chi-restraints excluded: chain A residue 586 VAL Chi-restraints excluded: chain A residue 700 ILE Chi-restraints excluded: chain A residue 744 MET Chi-restraints excluded: chain A residue 747 ILE Chi-restraints excluded: chain A residue 780 ILE Chi-restraints excluded: chain A residue 886 ASN Chi-restraints excluded: chain A residue 952 LEU Chi-restraints excluded: chain A residue 985 ARG Chi-restraints excluded: chain A residue 990 ILE Chi-restraints excluded: chain A residue 1049 MET Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain A residue 1102 LEU Chi-restraints excluded: chain A residue 1124 LEU Chi-restraints excluded: chain A residue 1330 VAL Chi-restraints excluded: chain A residue 1594 THR Chi-restraints excluded: chain B residue 19 LEU Chi-restraints excluded: chain B residue 124 SER Chi-restraints excluded: chain B residue 179 GLU Chi-restraints excluded: chain B residue 190 ILE Chi-restraints excluded: chain B residue 212 ASN Chi-restraints excluded: chain B residue 430 MET Chi-restraints excluded: chain B residue 441 LYS Chi-restraints excluded: chain B residue 485 THR Chi-restraints excluded: chain B residue 498 SER Chi-restraints excluded: chain B residue 587 GLN Chi-restraints excluded: chain B residue 684 ASN Chi-restraints excluded: chain B residue 752 VAL Chi-restraints excluded: chain B residue 753 LYS Chi-restraints excluded: chain B residue 792 SER Chi-restraints excluded: chain B residue 802 THR Chi-restraints excluded: chain B residue 977 ILE Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1018 THR Chi-restraints excluded: chain B residue 1099 THR Chi-restraints excluded: chain B residue 1110 ILE Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain C residue 94 ASP Chi-restraints excluded: chain C residue 99 HIS Chi-restraints excluded: chain C residue 224 THR Chi-restraints excluded: chain C residue 290 LYS Chi-restraints excluded: chain C residue 309 THR Chi-restraints excluded: chain E residue 91 LYS Chi-restraints excluded: chain E residue 117 THR Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain E residue 134 THR Chi-restraints excluded: chain E residue 190 LEU Chi-restraints excluded: chain E residue 204 THR Chi-restraints excluded: chain F residue 101 ILE Chi-restraints excluded: chain F residue 107 VAL Chi-restraints excluded: chain F residue 152 ILE Chi-restraints excluded: chain G residue 45 LEU Chi-restraints excluded: chain G residue 48 SER Chi-restraints excluded: chain G residue 71 MET Chi-restraints excluded: chain G residue 108 THR Chi-restraints excluded: chain G residue 111 THR Chi-restraints excluded: chain G residue 118 CYS Chi-restraints excluded: chain G residue 243 VAL Chi-restraints excluded: chain H residue 144 ILE Chi-restraints excluded: chain I residue 12 ASP Chi-restraints excluded: chain I residue 49 THR Chi-restraints excluded: chain J residue 24 LEU Chi-restraints excluded: chain J residue 28 ASP Chi-restraints excluded: chain J residue 34 THR Chi-restraints excluded: chain K residue 81 MET Chi-restraints excluded: chain K residue 107 THR Chi-restraints excluded: chain L residue 61 THR Chi-restraints excluded: chain M residue 66 THR Chi-restraints excluded: chain N residue 55 LEU Chi-restraints excluded: chain N residue 60 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: [146, 89, 405, 278, 362, 15, 42, 197, 316, 139, 358] chunk 146 optimal weight: 10.0000 chunk 89 optimal weight: 2.9990 chunk 405 optimal weight: 9.9990 chunk 278 optimal weight: 7.9990 chunk 362 optimal weight: 20.0000 chunk 15 optimal weight: 3.9990 chunk 42 optimal weight: 7.9990 chunk 197 optimal weight: 0.9980 chunk 316 optimal weight: 1.9990 chunk 139 optimal weight: 7.9990 chunk 358 optimal weight: 9.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 656 GLN ** A 706 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 886 ASN A 926 GLN A 998 HIS B 243 GLN ** B 695 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 952 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 987 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 30 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4151 r_free = 0.4151 target = 0.154998 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.129196 restraints weight = 63969.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.130683 restraints weight = 40787.547| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.131494 restraints weight = 30096.162| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.131941 restraints weight = 27192.993| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.131988 restraints weight = 23037.704| |-----------------------------------------------------------------------------| r_work (final): 0.3826 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7437 moved from start: 0.3763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 34574 Z= 0.196 Angle : 0.664 11.684 46895 Z= 0.338 Chirality : 0.046 0.338 5245 Planarity : 0.005 0.065 5899 Dihedral : 12.305 160.661 5016 Min Nonbonded Distance : 1.863 Molprobity Statistics. All-atom Clashscore : 10.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.85 % Favored : 93.15 % Rotamer: Outliers : 2.70 % Allowed : 14.54 % Favored : 82.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.91 (0.13), residues: 4086 helix: -0.14 (0.15), residues: 1224 sheet: -1.77 (0.21), residues: 567 loop : -1.80 (0.12), residues: 2295 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.033 0.001 ARG H 145 TYR 0.024 0.002 TYR J 21 PHE 0.037 0.002 PHE A 223 TRP 0.018 0.002 TRP A1469 HIS 0.006 0.001 HIS C 99 Details of bonding type rmsd/Z covalent geometry : bond 0.00461 / 0.20 (34549) covalent geometry : angle 0.65787 / 0.34 (46868) hydrogen bonds : bond 0.03861 / 2.61 ( 1125) hydrogen bonds : angle 5.11644 / 3.57 ( 3071) metal coordination : bond 0.00831 / 0.57 ( 23) metal coordination : angle 3.93504 / 2.64 ( 27) Misc. bond : bond 0.00022 / 0.01 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8172 Ramachandran restraints generated. 4086 Oldfield, 0 Emsley, 4086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8172 Ramachandran restraints generated. 4086 Oldfield, 0 Emsley, 4086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 539 residues out of total 3673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 440 time to evaluate : 1.416 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: A 471 MET cc_start: 0.7284 (mtp) cc_final: 0.6981 (mtp) REVERT: A 493 ASN cc_start: 0.7884 (p0) cc_final: 0.7525 (p0) REVERT: A 519 LEU cc_start: 0.7150 (OUTLIER) cc_final: 0.6798 (mm) REVERT: A 1000 MET cc_start: 0.7876 (mtt) cc_final: 0.7567 (mtt) REVERT: A 1073 TYR cc_start: 0.6676 (t80) cc_final: 0.6457 (t80) REVERT: A 1105 ARG cc_start: 0.7669 (ttm-80) cc_final: 0.7356 (ttm-80) REVERT: A 1485 MET cc_start: 0.5745 (mmt) cc_final: 0.5420 (tpp) REVERT: B 22 GLU cc_start: 0.7693 (mm-30) cc_final: 0.7179 (mm-30) REVERT: B 143 TRP cc_start: 0.6927 (OUTLIER) cc_final: 0.6723 (t60) REVERT: B 494 TYR cc_start: 0.8219 (m-80) cc_final: 0.7857 (m-80) REVERT: B 496 PHE cc_start: 0.8593 (t80) cc_final: 0.8180 (t80) REVERT: B 649 MET cc_start: 0.8301 (mtm) cc_final: 0.7875 (mtm) REVERT: B 753 LYS cc_start: 0.7782 (OUTLIER) cc_final: 0.7038 (ttmm) REVERT: B 762 MET cc_start: 0.8087 (mmm) cc_final: 0.7782 (tpp) REVERT: B 875 HIS cc_start: 0.5840 (t-90) cc_final: 0.5562 (t-90) REVERT: C 91 VAL cc_start: 0.7966 (OUTLIER) cc_final: 0.7713 (p) REVERT: C 131 THR cc_start: 0.8826 (m) cc_final: 0.8490 (p) REVERT: E 50 MET cc_start: 0.5439 (mmm) cc_final: 0.4861 (tpt) REVERT: E 114 ASN cc_start: 0.5594 (p0) cc_final: 0.5359 (m110) REVERT: E 133 GLU cc_start: 0.6414 (mp0) cc_final: 0.5725 (mp0) REVERT: G 71 MET cc_start: 0.8231 (OUTLIER) cc_final: 0.7666 (mtp) REVERT: J 31 ASP cc_start: 0.5156 (t0) cc_final: 0.4798 (m-30) REVERT: J 49 MET cc_start: 0.8275 (mmm) cc_final: 0.7002 (mmm) REVERT: N 36 LYS cc_start: 0.6257 (mmtm) cc_final: 0.5224 (mppt) REVERT: N 107 MET cc_start: 0.6324 (mmm) cc_final: 0.5448 (ptt) outliers start: 99 outliers final: 80 residues processed: 497 average time/residue: 0.1912 time to fit residues: 157.6210 Evaluate side-chains 511 residues out of total 3673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 426 time to evaluate : 1.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 SER Chi-restraints excluded: chain A residue 18 ILE Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 120 CYS Chi-restraints excluded: chain A residue 188 TYR Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 357 MET Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 519 LEU Chi-restraints excluded: chain A residue 571 HIS Chi-restraints excluded: chain A residue 581 ILE Chi-restraints excluded: chain A residue 586 VAL Chi-restraints excluded: chain A residue 700 ILE Chi-restraints excluded: chain A residue 744 MET Chi-restraints excluded: chain A residue 780 ILE Chi-restraints excluded: chain A residue 926 GLN Chi-restraints excluded: chain A residue 946 LEU Chi-restraints excluded: chain A residue 952 LEU Chi-restraints excluded: chain A residue 961 VAL Chi-restraints excluded: chain A residue 985 ARG Chi-restraints excluded: chain A residue 990 ILE Chi-restraints excluded: chain A residue 1049 MET Chi-restraints excluded: chain A residue 1071 ASP Chi-restraints excluded: chain A residue 1086 ILE Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain A residue 1102 LEU Chi-restraints excluded: chain A residue 1124 LEU Chi-restraints excluded: chain A residue 1330 VAL Chi-restraints excluded: chain A residue 1569 VAL Chi-restraints excluded: chain A residue 1594 THR Chi-restraints excluded: chain B residue 19 LEU Chi-restraints excluded: chain B residue 124 SER Chi-restraints excluded: chain B residue 143 TRP Chi-restraints excluded: chain B residue 179 GLU Chi-restraints excluded: chain B residue 190 ILE Chi-restraints excluded: chain B residue 212 ASN Chi-restraints excluded: chain B residue 332 ASP Chi-restraints excluded: chain B residue 441 LYS Chi-restraints excluded: chain B residue 485 THR Chi-restraints excluded: chain B residue 498 SER Chi-restraints excluded: chain B residue 587 GLN Chi-restraints excluded: chain B residue 684 ASN Chi-restraints excluded: chain B residue 752 VAL Chi-restraints excluded: chain B residue 753 LYS Chi-restraints excluded: chain B residue 792 SER Chi-restraints excluded: chain B residue 802 THR Chi-restraints excluded: chain B residue 977 ILE Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1018 THR Chi-restraints excluded: chain B residue 1099 THR Chi-restraints excluded: chain B residue 1110 ILE Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain C residue 94 ASP Chi-restraints excluded: chain C residue 99 HIS Chi-restraints excluded: chain C residue 224 THR Chi-restraints excluded: chain C residue 290 LYS Chi-restraints excluded: chain C residue 309 THR Chi-restraints excluded: chain E residue 91 LYS Chi-restraints excluded: chain E residue 117 THR Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain E residue 134 THR Chi-restraints excluded: chain E residue 149 LEU Chi-restraints excluded: chain E residue 190 LEU Chi-restraints excluded: chain E residue 204 THR Chi-restraints excluded: chain F residue 101 ILE Chi-restraints excluded: chain F residue 107 VAL Chi-restraints excluded: chain F residue 118 LEU Chi-restraints excluded: chain G residue 45 LEU Chi-restraints excluded: chain G residue 48 SER Chi-restraints excluded: chain G residue 71 MET Chi-restraints excluded: chain G residue 108 THR Chi-restraints excluded: chain G residue 111 THR Chi-restraints excluded: chain G residue 118 CYS Chi-restraints excluded: chain G residue 243 VAL Chi-restraints excluded: chain I residue 12 ASP Chi-restraints excluded: chain I residue 49 THR Chi-restraints excluded: chain J residue 34 THR Chi-restraints excluded: chain K residue 81 MET Chi-restraints excluded: chain K residue 107 THR Chi-restraints excluded: chain L residue 61 THR Chi-restraints excluded: chain M residue 66 THR Chi-restraints excluded: chain N residue 55 LEU Chi-restraints excluded: chain N residue 60 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: [44, 137, 382, 72, 325, 225, 57, 185, 321, 355, 53] chunk 44 optimal weight: 0.8980 chunk 137 optimal weight: 7.9990 chunk 382 optimal weight: 10.0000 chunk 72 optimal weight: 0.6980 chunk 325 optimal weight: 5.9990 chunk 225 optimal weight: 10.0000 chunk 57 optimal weight: 1.9990 chunk 185 optimal weight: 0.9990 chunk 321 optimal weight: 6.9990 chunk 355 optimal weight: 1.9990 chunk 53 optimal weight: 4.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 656 GLN ** A 706 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 886 ASN A 926 GLN A 998 HIS A1072 ASN ** B 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 243 GLN ** B 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 636 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 695 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 952 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 987 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 30 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4181 r_free = 0.4181 target = 0.157270 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.132103 restraints weight = 64013.206| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.133024 restraints weight = 40205.203| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.133735 restraints weight = 28943.803| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.134484 restraints weight = 27240.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.134396 restraints weight = 24347.622| |-----------------------------------------------------------------------------| r_work (final): 0.3863 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7378 moved from start: 0.3843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 34574 Z= 0.127 Angle : 0.614 10.825 46895 Z= 0.311 Chirality : 0.045 0.325 5245 Planarity : 0.004 0.070 5899 Dihedral : 12.202 161.396 5016 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 2.23 % Allowed : 15.30 % Favored : 82.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.69 (0.13), residues: 4086 helix: 0.10 (0.15), residues: 1215 sheet: -1.69 (0.21), residues: 570 loop : -1.68 (0.13), residues: 2301 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG H 145 TYR 0.025 0.002 TYR A1034 PHE 0.037 0.002 PHE A 223 TRP 0.013 0.001 TRP A1469 HIS 0.004 0.001 HIS B 361 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.13 (34549) covalent geometry : angle 0.60932 / 0.31 (46868) hydrogen bonds : bond 0.03469 / 2.35 ( 1125) hydrogen bonds : angle 4.91705 / 3.43 ( 3071) metal coordination : bond 0.00740 / 0.44 ( 23) metal coordination : angle 3.36859 / 2.29 ( 27) Misc. bond : bond 0.00016 / 0.01 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8172 Ramachandran restraints generated. 4086 Oldfield, 0 Emsley, 4086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8172 Ramachandran restraints generated. 4086 Oldfield, 0 Emsley, 4086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 533 residues out of total 3673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 451 time to evaluate : 1.257 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 471 MET cc_start: 0.7156 (mtp) cc_final: 0.6883 (mtp) REVERT: A 493 ASN cc_start: 0.7922 (p0) cc_final: 0.7563 (p0) REVERT: A 519 LEU cc_start: 0.7105 (OUTLIER) cc_final: 0.6761 (mm) REVERT: A 926 GLN cc_start: 0.8231 (OUTLIER) cc_final: 0.7821 (mm-40) REVERT: A 1000 MET cc_start: 0.7827 (mtt) cc_final: 0.7581 (mtt) REVERT: A 1105 ARG cc_start: 0.7621 (ttm-80) cc_final: 0.7297 (ttm-80) REVERT: A 1485 MET cc_start: 0.5705 (mmt) cc_final: 0.5409 (tpp) REVERT: B 22 GLU cc_start: 0.7676 (mm-30) cc_final: 0.7124 (mm-30) REVERT: B 143 TRP cc_start: 0.6962 (OUTLIER) cc_final: 0.6745 (t60) REVERT: B 411 MET cc_start: 0.6523 (mtt) cc_final: 0.6164 (mtp) REVERT: B 494 TYR cc_start: 0.8156 (m-80) cc_final: 0.7802 (m-80) REVERT: B 649 MET cc_start: 0.8251 (mtm) cc_final: 0.7887 (mtm) REVERT: B 753 LYS cc_start: 0.7695 (OUTLIER) cc_final: 0.6950 (ttmm) REVERT: B 762 MET cc_start: 0.8035 (mmm) cc_final: 0.7693 (tpp) REVERT: B 875 HIS cc_start: 0.5800 (t-90) cc_final: 0.5557 (t-90) REVERT: B 975 HIS cc_start: 0.7668 (m-70) cc_final: 0.7341 (m-70) REVERT: C 91 VAL cc_start: 0.7932 (OUTLIER) cc_final: 0.7659 (p) REVERT: C 131 THR cc_start: 0.8761 (m) cc_final: 0.8481 (p) REVERT: E 50 MET cc_start: 0.5404 (mmm) cc_final: 0.4872 (tpt) REVERT: E 52 ARG cc_start: 0.7931 (mtt180) cc_final: 0.7631 (mmm-85) REVERT: E 114 ASN cc_start: 0.5661 (p0) cc_final: 0.5323 (m110) REVERT: E 133 GLU cc_start: 0.6209 (mp0) cc_final: 0.5514 (mp0) REVERT: G 71 MET cc_start: 0.8270 (OUTLIER) cc_final: 0.7768 (mtp) REVERT: J 17 LYS cc_start: 0.8201 (OUTLIER) cc_final: 0.7895 (mttm) REVERT: J 31 ASP cc_start: 0.4986 (t0) cc_final: 0.4534 (m-30) REVERT: J 49 MET cc_start: 0.8220 (mmm) cc_final: 0.6974 (mmm) REVERT: K 67 GLU cc_start: 0.7137 (tp30) cc_final: 0.6766 (tp30) REVERT: K 68 GLU cc_start: 0.7419 (mm-30) cc_final: 0.7077 (mm-30) REVERT: K 110 GLU cc_start: 0.8066 (pm20) cc_final: 0.7536 (pm20) REVERT: L 28 LYS cc_start: 0.6339 (mtmm) cc_final: 0.6100 (mtpp) REVERT: N 36 LYS cc_start: 0.6284 (mmtm) cc_final: 0.5289 (mppt) REVERT: N 107 MET cc_start: 0.6254 (mmm) cc_final: 0.5635 (ptt) outliers start: 82 outliers final: 60 residues processed: 499 average time/residue: 0.1896 time to fit residues: 157.0033 Evaluate side-chains 494 residues out of total 3673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 427 time to evaluate : 0.940 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 SER Chi-restraints excluded: chain A residue 18 ILE Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 188 TYR Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 519 LEU Chi-restraints excluded: chain A residue 581 ILE Chi-restraints excluded: chain A residue 586 VAL Chi-restraints excluded: chain A residue 700 ILE Chi-restraints excluded: chain A residue 744 MET Chi-restraints excluded: chain A residue 886 ASN Chi-restraints excluded: chain A residue 926 GLN Chi-restraints excluded: chain A residue 946 LEU Chi-restraints excluded: chain A residue 952 LEU Chi-restraints excluded: chain A residue 990 ILE Chi-restraints excluded: chain A residue 1072 ASN Chi-restraints excluded: chain A residue 1102 LEU Chi-restraints excluded: chain A residue 1124 LEU Chi-restraints excluded: chain A residue 1330 VAL Chi-restraints excluded: chain A residue 1569 VAL Chi-restraints excluded: chain A residue 1594 THR Chi-restraints excluded: chain B residue 19 LEU Chi-restraints excluded: chain B residue 143 TRP Chi-restraints excluded: chain B residue 179 GLU Chi-restraints excluded: chain B residue 190 ILE Chi-restraints excluded: chain B residue 441 LYS Chi-restraints excluded: chain B residue 485 THR Chi-restraints excluded: chain B residue 587 GLN Chi-restraints excluded: chain B residue 684 ASN Chi-restraints excluded: chain B residue 752 VAL Chi-restraints excluded: chain B residue 753 LYS Chi-restraints excluded: chain B residue 802 THR Chi-restraints excluded: chain B residue 977 ILE Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1018 THR Chi-restraints excluded: chain B residue 1099 THR Chi-restraints excluded: chain B residue 1110 ILE Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain C residue 99 HIS Chi-restraints excluded: chain C residue 224 THR Chi-restraints excluded: chain C residue 309 THR Chi-restraints excluded: chain E residue 91 LYS Chi-restraints excluded: chain E residue 117 THR Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain E residue 134 THR Chi-restraints excluded: chain E residue 204 THR Chi-restraints excluded: chain F residue 101 ILE Chi-restraints excluded: chain F residue 107 VAL Chi-restraints excluded: chain G residue 45 LEU Chi-restraints excluded: chain G residue 48 SER Chi-restraints excluded: chain G residue 71 MET Chi-restraints excluded: chain G residue 108 THR Chi-restraints excluded: chain G residue 111 THR Chi-restraints excluded: chain G residue 118 CYS Chi-restraints excluded: chain G residue 243 VAL Chi-restraints excluded: chain H residue 104 PHE Chi-restraints excluded: chain I residue 12 ASP Chi-restraints excluded: chain I residue 49 THR Chi-restraints excluded: chain J residue 17 LYS Chi-restraints excluded: chain J residue 34 THR Chi-restraints excluded: chain K residue 81 MET Chi-restraints excluded: chain K residue 107 THR Chi-restraints excluded: chain L residue 61 THR Chi-restraints excluded: chain M residue 66 THR Chi-restraints excluded: chain N residue 55 LEU Chi-restraints excluded: chain N residue 60 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: [46, 253, 17, 318, 218, 92, 233, 292, 368, 302, 212] chunk 46 optimal weight: 9.9990 chunk 253 optimal weight: 0.8980 chunk 17 optimal weight: 9.9990 chunk 318 optimal weight: 9.9990 chunk 218 optimal weight: 5.9990 chunk 92 optimal weight: 5.9990 chunk 233 optimal weight: 10.0000 chunk 292 optimal weight: 7.9990 chunk 368 optimal weight: 1.9990 chunk 302 optimal weight: 0.7980 chunk 212 optimal weight: 7.9990 overall best weight: 3.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 656 GLN ** A 706 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 886 ASN A 998 HIS ** A1072 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 243 GLN ** B 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 636 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 695 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 987 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 23 HIS D 30 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4177 r_free = 0.4177 target = 0.157009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.131463 restraints weight = 63686.825| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.133026 restraints weight = 40076.606| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.133369 restraints weight = 27709.549| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.133947 restraints weight = 27784.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.134004 restraints weight = 24053.585| |-----------------------------------------------------------------------------| r_work (final): 0.3851 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7400 moved from start: 0.3866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.366 34574 Z= 0.256 Angle : 0.831 59.200 46895 Z= 0.492 Chirality : 0.045 0.325 5245 Planarity : 0.005 0.142 5899 Dihedral : 12.207 161.360 5016 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 11.01 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.56 % Favored : 94.42 % Rotamer: Outliers : 1.99 % Allowed : 15.65 % Favored : 82.36 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 3.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.70 (0.13), residues: 4086 helix: 0.09 (0.15), residues: 1214 sheet: -1.68 (0.21), residues: 564 loop : -1.69 (0.13), residues: 2308 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG H 145 TYR 0.044 0.002 TYR A 578 PHE 0.035 0.002 PHE A 223 TRP 0.013 0.001 TRP A1469 HIS 0.005 0.001 HIS D 23 Details of bonding type rmsd/Z covalent geometry : bond 0.00526 / 0.26 (34549) covalent geometry : angle 0.82780 / 0.49 (46868) hydrogen bonds : bond 0.03508 / 2.38 ( 1125) hydrogen bonds : angle 4.91779 / 3.43 ( 3071) metal coordination : bond 0.00771 / 0.48 ( 23) metal coordination : angle 3.35835 / 2.29 ( 27) Misc. bond : bond 0.00010 / 0.00 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5672.67 seconds wall clock time: 98 minutes 53.43 seconds (5933.43 seconds total)