Starting phenix.real_space_refine on Tue Sep 15 22:31:18 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/5w5y_8771/09_2026/5w5y_8771.cif Found real_map, /net/cci-nas-00/data/ceres_data/5w5y_8771/09_2026/5w5y_8771.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/5w5y_8771/09_2026/5w5y_8771.map" default_real_map = "/net/cci-nas-00/data/ceres_data/5w5y_8771/09_2026/5w5y_8771.map" model { file = "/net/cci-nas-00/data/ceres_data/5w5y_8771/09_2026/5w5y_8771.cif" } default_model = "/net/cci-nas-00/data/ceres_data/5w5y_8771/09_2026/5w5y_8771.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/5w5y_8771/09_2026/5w5y_8771.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/5w5y_8771/09_2026/5w5y_8771.cif" } resolution = 3.8 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= 0.013 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: 6 Type Number sf(0) Gaussians Zn 6 6.06 5 P 102 5.49 5 S 205 5.16 5 C 29235 2.51 5 N 8048 2.21 5 O 8976 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 34 residue(s): 0.18s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 46572 Number of models: 1 Model: "" Number of chains: 26 Chain: "A" Number of atoms: 11542 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1461, 11542 Classifications: {'peptide': 1461} Link IDs: {'PTRANS': 59, 'TRANS': 1401} Chain breaks: 7 Chain: "B" Number of atoms: 9351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1178, 9351 Classifications: {'peptide': 1178} Link IDs: {'PTRANS': 58, 'TRANS': 1119} Chain breaks: 2 Chain: "C" Number of atoms: 2432 Number of conformers: 1 Conformer: "" Number of residues, atoms: 306, 2432 Classifications: {'peptide': 306} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 286} Chain: "D" Number of atoms: 467 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 467 Classifications: {'peptide': 59} Link IDs: {'PTRANS': 3, 'TRANS': 55} Chain breaks: 1 Chain: "E" Number of atoms: 1760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1760 Classifications: {'peptide': 215} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 202} Chain: "F" Number of atoms: 670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 670 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 6, 'TRANS': 76} Chain: "G" Number of atoms: 1592 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1592 Classifications: {'peptide': 201} Link IDs: {'PTRANS': 11, 'TRANS': 189} Chain breaks: 1 Chain: "H" Number of atoms: 1071 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 1071 Classifications: {'peptide': 133} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 128} Chain breaks: 1 Chain: "I" Number of atoms: 479 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 479 Classifications: {'peptide': 65} Link IDs: {'PTRANS': 3, 'TRANS': 61} 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: 811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 811 Classifications: {'peptide': 103} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 98} Chain: "L" Number of atoms: 359 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 359 Classifications: {'peptide': 45} Modifications used: {'COO': 1} Link IDs: {'TRANS': 44} Chain: "M" Number of atoms: 841 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 841 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 5, 'TRANS': 100} Chain: "N" Number of atoms: 1254 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 1254 Classifications: {'peptide': 158} Link IDs: {'PTRANS': 9, 'TRANS': 148} Chain: "O" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Classifications: {'peptide': 1} Chain: "O" Number of atoms: 5058 Number of conformers: 1 Conformer: "" Number of residues, atoms: 639, 5058 Classifications: {'peptide': 639} Incomplete info: {'truncation_to_alanine': 52} Link IDs: {'PTRANS': 19, 'TRANS': 619} Chain breaks: 4 Unresolved non-hydrogen bonds: 104 Unresolved non-hydrogen angles: 156 Unresolved non-hydrogen dihedrals: 52 Planarities with less than four sites: {'UNK:plan-1': 52} Unresolved non-hydrogen planarities: 52 Chain: "P" Number of atoms: 3238 Number of conformers: 1 Conformer: "" Number of residues, atoms: 387, 3238 Classifications: {'peptide': 387} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 17, 'TRANS': 369} Chain breaks: 4 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 2923 Number of conformers: 1 Conformer: "" Number of residues, atoms: 349, 2923 Classifications: {'peptide': 349} Link IDs: {'PTRANS': 13, 'TRANS': 335} Chain breaks: 2 Chain: "R" Number of atoms: 127 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 127 Classifications: {'RNAv2': 6} Modifications used: {'rna3p_pur': 4, 'rna3p_pyr': 2} Link IDs: {'rna3p': 5} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "S" Number of atoms: 935 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 935 Classifications: {'DNA': 45} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 44} Chain breaks: 1 Chain: "T" Number of atoms: 1082 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 1082 Classifications: {'DNA': 54} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 53} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "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 781 SG CYS A 102 174.503 82.444 82.669 1.00 0.00 S ATOM 806 SG CYS A 105 175.145 79.666 82.755 1.00 0.00 S ATOM 1605 SG CYS A 233 176.147 82.240 85.673 1.00 0.00 S ATOM 1627 SG CYS A 236 177.051 82.001 82.427 1.00 0.00 S ATOM 461 SG CYS A 62 127.549 63.316 83.214 1.00 0.00 S ATOM 480 SG CYS A 65 127.061 60.347 85.435 1.00 0.00 S ATOM 535 SG CYS A 72 126.552 63.217 86.261 1.00 0.00 S ATOM 20196 SG CYS B1104 141.602 55.595 91.699 1.00 0.00 S ATOM 20222 SG CYS B1107 142.904 58.792 91.662 1.00 0.00 S ATOM 20369 SG CYS B1128 140.433 57.247 89.597 1.00 0.00 S ATOM 20397 SG CYS B1131 143.311 55.298 89.657 1.00 0.00 S ATOM 28948 SG CYS I 10 158.831 150.475 89.442 1.00 0.00 S ATOM 28970 SG CYS I 13 156.053 148.623 88.306 1.00 0.00 S ATOM 29090 SG CYS I 30 158.806 146.948 87.457 1.00 0.00 S ATOM 29111 SG CYS I 33 158.424 150.168 86.669 1.00 0.00 S ATOM 29418 SG CYS J 7 88.151 98.304 133.007 1.00 0.00 S ATOM 29441 SG CYS J 10 85.805 96.989 134.821 1.00 0.00 S ATOM 29721 SG CYS J 45 88.250 98.788 136.269 1.00 0.00 S ATOM 29727 SG CYS J 46 84.887 99.800 135.416 1.00 0.00 S ATOM 30794 SG CYS L 31 85.692 103.780 88.997 1.00 0.00 S ATOM 30814 SG CYS L 34 82.537 104.606 89.090 1.00 0.00 S ATOM 30918 SG CYS L 48 83.761 103.264 86.676 1.00 0.00 S ATOM 30941 SG CYS L 51 85.657 105.561 86.730 1.00 0.00 S Residues with excluded nonbonded symmetry interactions: 105 residue: pdb=" N LYS A 991 " occ=0.00 ... (7 atoms not shown) pdb=" NZ LYS A 991 " occ=0.00 residue: pdb=" N PRO A 992 " occ=0.00 ... (5 atoms not shown) pdb=" CD PRO A 992 " occ=0.00 residue: pdb=" N GLN A 993 " occ=0.00 ... (7 atoms not shown) pdb=" NE2 GLN A 993 " occ=0.00 residue: pdb=" N GLU A 994 " occ=0.00 ... (7 atoms not shown) pdb=" OE2 GLU A 994 " occ=0.00 residue: pdb=" N TYR A 995 " occ=0.00 ... (10 atoms not shown) pdb=" OH TYR A 995 " occ=0.00 residue: pdb=" N TYR A 996 " occ=0.00 ... (10 atoms not shown) pdb=" OH TYR A 996 " occ=0.00 residue: pdb=" N PHE A 997 " occ=0.00 ... (9 atoms not shown) pdb=" CZ PHE A 997 " occ=0.00 residue: pdb=" N HIS A 998 " occ=0.00 ... (8 atoms not shown) pdb=" NE2 HIS A 998 " occ=0.00 residue: pdb=" N CYS A 999 " occ=0.00 ... (4 atoms not shown) pdb=" SG CYS A 999 " occ=0.00 residue: pdb=" N MET A1000 " occ=0.00 ... (6 atoms not shown) pdb=" CE MET A1000 " occ=0.00 residue: pdb=" N ALA A1001 " occ=0.00 ... (3 atoms not shown) pdb=" CB ALA A1001 " occ=0.00 residue: pdb=" N GLY A1002 " occ=0.00 ... (2 atoms not shown) pdb=" O GLY A1002 " occ=0.00 ... (remaining 93 not shown) Time building chain proxies: 8.95, per 1000 atoms: 0.19 Number of scatterers: 46572 At special positions: 0 Unit cell: (210.6, 191.1, 200.2, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 6 29.99 S 205 16.00 P 102 15.00 O 8976 8.00 N 8048 7.00 C 29235 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=15, symmetry=0 Links applied TRANS " UNK O 4 " - " ALA O 3 " Number of additional bonds: simple=15, symmetry=0 Coordination: Other bonds: Time building additional restraints: 4.89 Conformation dependent library (CDL) restraints added in 2.0 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1701 " pdb="ZN ZN A1701 " - pdb=" SG CYS A 105 " pdb="ZN ZN A1701 " - pdb=" SG CYS A 102 " pdb="ZN ZN A1701 " - pdb=" SG CYS A 233 " pdb="ZN ZN A1701 " - pdb=" SG CYS A 236 " pdb=" ZN A1702 " pdb="ZN ZN A1702 " - pdb=" NE2 HIS A 75 " pdb="ZN ZN A1702 " - pdb=" SG CYS A 62 " pdb="ZN ZN A1702 " - pdb=" SG CYS A 65 " pdb="ZN ZN A1702 " - pdb=" SG CYS A 72 " pdb=" ZN B1301 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1131 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1107 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1128 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1104 " pdb=" ZN I 201 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 10 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 30 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 13 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 33 " pdb=" ZN J 101 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 7 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 45 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 46 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 10 " pdb=" ZN L 101 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 51 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 34 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 31 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 48 " Number of angles added : 33 10864 Ramachandran restraints generated. 5432 Oldfield, 0 Emsley, 5432 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10544 Finding SS restraints... Secondary structure from input PDB file: 217 helices and 59 sheets defined 42.5% alpha, 17.0% beta 30 base pairs and 82 stacking pairs defined. Time for finding SS restraints: 6.02 Creating SS restraints... Processing helix chain 'A' and resid 20 through 28 Processing helix chain 'A' and resid 51 through 55 Processing helix chain 'A' and resid 87 through 89 No H-bonds generated for 'chain 'A' and resid 87 through 89' Processing helix chain 'A' and resid 90 through 101 Processing helix chain 'A' and resid 111 through 127 removed outlier: 3.586A pdb=" N TYR A 127 " --> pdb=" O ARG A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 129 through 136 Processing helix chain 'A' and resid 137 through 139 No H-bonds generated for 'chain 'A' and resid 137 through 139' Processing helix chain 'A' and resid 174 through 199 Processing helix chain 'A' and resid 209 through 230 removed outlier: 3.709A pdb=" N ARG A 230 " --> pdb=" O LYS A 226 " (cutoff:3.500A) Processing helix chain 'A' and resid 257 through 267 Processing helix chain 'A' and resid 316 through 331 removed outlier: 3.771A pdb=" N THR A 326 " --> pdb=" O ASN A 322 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 339 removed outlier: 4.583A pdb=" N TYR A 337 " --> pdb=" O CYS A 333 " (cutoff:3.500A) Processing helix chain 'A' and resid 351 through 355 Processing helix chain 'A' and resid 364 through 369 removed outlier: 4.187A pdb=" N LEU A 369 " --> pdb=" O ARG A 366 " (cutoff:3.500A) Processing helix chain 'A' and resid 380 through 406 Processing helix chain 'A' and resid 415 through 439 removed outlier: 4.147A pdb=" N ILE A 419 " --> pdb=" O ASP A 415 " (cutoff:3.500A) Processing helix chain 'A' and resid 440 through 443 Processing helix chain 'A' and resid 455 through 461 Processing helix chain 'A' and resid 466 through 471 Processing helix chain 'A' and resid 498 through 505 Processing helix chain 'A' and resid 515 through 526 Processing helix chain 'A' and resid 550 through 559 Processing helix chain 'A' and resid 596 through 598 No H-bonds generated for 'chain 'A' and resid 596 through 598' Processing helix chain 'A' and resid 620 through 625 Processing helix chain 'A' and resid 640 through 650 Processing helix chain 'A' and resid 652 through 657 Processing helix chain 'A' and resid 670 through 681 removed outlier: 3.512A pdb=" N ILE A 674 " --> pdb=" O ILE A 670 " (cutoff:3.500A) Processing helix chain 'A' and resid 689 through 700 Processing helix chain 'A' and resid 701 through 705 Processing helix chain 'A' and resid 728 through 740 Processing helix chain 'A' and resid 756 through 761 Processing helix chain 'A' and resid 792 through 801 Processing helix chain 'A' and resid 802 through 824 Processing helix chain 'A' and resid 829 through 833 Processing helix chain 'A' and resid 836 through 848 Processing helix chain 'A' and resid 849 through 863 removed outlier: 3.576A pdb=" N THR A 853 " --> pdb=" O THR A 849 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N ARG A 855 " --> pdb=" O VAL A 851 " (cutoff:3.500A) Processing helix chain 'A' and resid 872 through 885 Processing helix chain 'A' and resid 885 through 911 Processing helix chain 'A' and resid 911 through 916 removed outlier: 3.616A pdb=" N GLY A 915 " --> pdb=" O CYS A 911 " (cutoff:3.500A) Processing helix chain 'A' and resid 923 through 931 removed outlier: 3.559A pdb=" N ALA A 929 " --> pdb=" O MET A 925 " (cutoff:3.500A) Processing helix chain 'A' and resid 936 through 945 Processing helix chain 'A' and resid 976 through 979 Processing helix chain 'A' and resid 991 through 1012 removed outlier: 3.799A pdb=" N PHE A 997 " --> pdb=" O GLN A 993 " (cutoff:3.500A) Processing helix chain 'A' and resid 1013 through 1028 removed outlier: 4.339A pdb=" N TYR A1018 " --> pdb=" O SER A1014 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N LEU A1019 " --> pdb=" O ARG A1015 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N LEU A1023 " --> pdb=" O LEU A1019 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N GLN A1026 " --> pdb=" O CYS A1022 " (cutoff:3.500A) Processing helix chain 'A' and resid 1049 through 1053 Processing helix chain 'A' and resid 1056 through 1064 removed outlier: 4.170A pdb=" N SER A1061 " --> pdb=" O ILE A1057 " (cutoff:3.500A) removed outlier: 7.486A pdb=" N HIS A1062 " --> pdb=" O THR A1058 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N MET A1063 " --> pdb=" O LYS A1059 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N THR A1064 " --> pdb=" O GLU A1060 " (cutoff:3.500A) Processing helix chain 'A' and resid 1065 through 1072 Processing helix chain 'A' and resid 1072 through 1080 Processing helix chain 'A' and resid 1081 through 1085 removed outlier: 3.726A pdb=" N ALA A1084 " --> pdb=" O ASN A1081 " (cutoff:3.500A) Processing helix chain 'A' and resid 1092 through 1108 Processing helix chain 'A' and resid 1122 through 1127 removed outlier: 3.627A pdb=" N LYS A1126 " --> pdb=" O PRO A1122 " (cutoff:3.500A) Processing helix chain 'A' and resid 1137 through 1151 Processing helix chain 'A' and resid 1162 through 1176 Processing helix chain 'A' and resid 1184 through 1195 Processing helix chain 'A' and resid 1196 through 1199 Processing helix chain 'A' and resid 1217 through 1226 Processing helix chain 'A' and resid 1247 through 1259 Processing helix chain 'A' and resid 1298 through 1307 Processing helix chain 'A' and resid 1309 through 1320 Processing helix chain 'A' and resid 1320 through 1337 Processing helix chain 'A' and resid 1440 through 1454 Processing helix chain 'A' and resid 1477 through 1481 Processing helix chain 'A' and resid 1484 through 1494 Processing helix chain 'A' and resid 1525 through 1531 removed outlier: 3.849A pdb=" N ASP A1531 " --> pdb=" O GLN A1527 " (cutoff:3.500A) Processing helix chain 'A' and resid 1537 through 1541 Processing helix chain 'A' and resid 1545 through 1554 Processing helix chain 'A' and resid 1554 through 1573 removed outlier: 3.844A pdb=" N TYR A1573 " --> pdb=" O VAL A1569 " (cutoff:3.500A) Processing helix chain 'A' and resid 1578 through 1590 removed outlier: 3.815A pdb=" N LEU A1582 " --> pdb=" O SER A1578 " (cutoff:3.500A) Processing helix chain 'A' and resid 1599 through 1605 removed outlier: 4.296A pdb=" N THR A1605 " --> pdb=" O GLN A1601 " (cutoff:3.500A) Processing helix chain 'A' and resid 1608 through 1614 Processing helix chain 'A' and resid 1617 through 1629 Processing helix chain 'A' and resid 1636 through 1643 Processing helix chain 'A' and resid 1649 through 1652 Processing helix chain 'B' and resid 18 through 27 Processing helix chain 'B' and resid 35 through 42 removed outlier: 3.725A pdb=" N GLN B 39 " --> pdb=" O PHE B 35 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N VAL B 42 " --> pdb=" O LEU B 38 " (cutoff:3.500A) Processing helix chain 'B' and resid 42 through 51 removed outlier: 3.717A pdb=" N SER B 48 " --> pdb=" O PRO B 44 " (cutoff:3.500A) Processing helix chain 'B' and resid 59 through 69 removed outlier: 3.863A 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 147 through 149 No H-bonds generated for 'chain 'B' and resid 147 through 149' Processing helix chain 'B' and resid 170 through 175 removed outlier: 4.171A pdb=" N LYS B 174 " --> pdb=" O HIS B 171 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N MET B 175 " --> pdb=" O LEU B 172 " (cutoff:3.500A) Processing helix chain 'B' and resid 176 through 183 Processing helix chain 'B' and resid 219 through 225 removed outlier: 3.689A pdb=" N ALA B 223 " --> pdb=" O ARG B 219 " (cutoff:3.500A) Processing helix chain 'B' and resid 273 through 281 removed outlier: 3.732A pdb=" N CYS B 281 " --> pdb=" O LEU B 277 " (cutoff:3.500A) Processing helix chain 'B' and resid 284 through 293 Processing helix chain 'B' and resid 299 through 317 Processing helix chain 'B' and resid 322 through 335 Processing helix chain 'B' and resid 345 through 358 Processing helix chain 'B' and resid 359 through 363 Processing helix chain 'B' and resid 366 through 387 Processing helix chain 'B' and resid 396 through 398 No H-bonds generated for 'chain 'B' and resid 396 through 398' Processing helix chain 'B' and resid 404 through 433 Processing helix chain 'B' and resid 442 through 451 Processing helix chain 'B' and resid 456 through 468 removed outlier: 3.630A pdb=" N LYS B 460 " --> pdb=" O ASN B 456 " (cutoff:3.500A) Processing helix chain 'B' and resid 474 through 478 removed outlier: 3.761A pdb=" N ASP B 477 " --> pdb=" O SER B 474 " (cutoff:3.500A) Processing helix chain 'B' and resid 492 through 500 removed outlier: 4.022A pdb=" N PHE B 500 " --> pdb=" O PHE B 496 " (cutoff:3.500A) Processing helix chain 'B' and resid 506 through 512 removed outlier: 3.537A pdb=" N LEU B 512 " --> pdb=" O PHE B 508 " (cutoff:3.500A) Processing helix chain 'B' and resid 521 through 525 Processing helix chain 'B' and resid 560 through 569 Processing helix chain 'B' and resid 573 through 577 removed outlier: 3.997A pdb=" N PHE B 577 " --> pdb=" O ALA B 573 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 573 through 577' Processing helix chain 'B' and resid 597 through 614 Processing helix chain 'B' and resid 665 through 670 removed outlier: 3.924A pdb=" N VAL B 670 " --> pdb=" O PRO B 666 " (cutoff:3.500A) Processing helix chain 'B' and resid 677 through 681 Processing helix chain 'B' and resid 692 through 697 Processing helix chain 'B' and resid 698 through 704 Processing helix chain 'B' and resid 706 through 710 removed outlier: 3.617A pdb=" N ASN B 710 " --> pdb=" O SER B 707 " (cutoff:3.500A) Processing helix chain 'B' and resid 711 through 724 Processing helix chain 'B' and resid 732 through 736 Processing helix chain 'B' and resid 754 through 760 removed outlier: 4.080A pdb=" N ASP B 758 " --> pdb=" O ALA B 754 " (cutoff:3.500A) Processing helix chain 'B' and resid 761 through 765 Processing helix chain 'B' and resid 791 through 796 Processing helix chain 'B' and resid 833 through 839 Processing helix chain 'B' and resid 950 through 952 No H-bonds generated for 'chain 'B' and resid 950 through 952' Processing helix chain 'B' and resid 953 through 958 removed outlier: 3.541A pdb=" N ARG B 957 " --> pdb=" O ALA B 953 " (cutoff:3.500A) Processing helix chain 'B' and resid 959 through 976 removed outlier: 3.753A pdb=" N PHE B 963 " --> pdb=" O THR B 959 " (cutoff:3.500A) Processing helix chain 'B' and resid 991 through 1004 Processing helix chain 'B' and resid 1039 through 1044 Processing helix chain 'B' and resid 1062 through 1066 Processing helix chain 'B' and resid 1072 through 1082 Processing helix chain 'B' and resid 1084 through 1093 Processing helix chain 'B' and resid 1173 through 1185 Proline residue: B1179 - end of helix removed outlier: 3.772A pdb=" N TYR B1184 " --> pdb=" O PHE B1180 " (cutoff:3.500A) Processing helix chain 'C' and resid 32 through 40 Processing helix chain 'C' and resid 60 through 74 Processing helix chain 'C' and resid 93 through 104 Processing helix chain 'C' and resid 109 through 113 removed outlier: 3.514A pdb=" N LEU C 113 " --> pdb=" O PRO C 110 " (cutoff:3.500A) Processing helix chain 'C' and resid 121 through 126 removed outlier: 3.773A pdb=" N PHE C 126 " --> pdb=" O ASP C 122 " (cutoff:3.500A) Processing helix chain 'C' and resid 165 through 167 No H-bonds generated for 'chain 'C' and resid 165 through 167' Processing helix chain 'C' and resid 173 through 179 Processing helix chain 'C' and resid 216 through 220 Processing helix chain 'C' and resid 240 through 249 Processing helix chain 'C' and resid 269 through 273 Processing helix chain 'C' and resid 277 through 281 Processing helix chain 'C' and resid 282 through 287 removed outlier: 4.374A pdb=" N ASP C 287 " --> pdb=" O GLU C 283 " (cutoff:3.500A) Processing helix chain 'C' and resid 309 through 331 Processing helix chain 'D' and resid 32 through 49 Processing helix chain 'D' and resid 81 through 96 removed outlier: 3.824A pdb=" N SER D 85 " --> pdb=" O ASN D 81 " (cutoff:3.500A) Processing helix chain 'E' and resid 2 through 27 Processing helix chain 'E' and resid 31 through 36 Processing helix chain 'E' and resid 38 through 47 Processing helix chain 'E' and resid 54 through 59 Processing helix chain 'E' and resid 65 through 72 Processing helix chain 'E' and resid 89 through 104 Processing helix chain 'E' and resid 117 through 124 Processing helix chain 'E' and resid 138 through 142 removed outlier: 4.171A pdb=" N VAL E 142 " --> pdb=" O ALA E 139 " (cutoff:3.500A) Processing helix chain 'E' and resid 143 through 147 Processing helix chain 'E' and resid 157 through 168 Processing helix chain 'E' and resid 171 through 175 Processing helix chain 'E' and resid 182 through 189 Processing helix chain 'F' and resid 75 through 79 Processing helix chain 'F' and resid 86 through 103 Processing helix chain 'F' and resid 116 through 127 Processing helix chain 'G' and resid 10 through 20 Processing helix chain 'G' and resid 28 through 32 Processing helix chain 'G' and resid 50 through 54 removed outlier: 3.597A pdb=" N TYR G 53 " --> pdb=" O ALA G 50 " (cutoff:3.500A) Processing helix chain 'G' and resid 56 through 65 Processing helix chain 'G' and resid 150 through 152 No H-bonds generated for 'chain 'G' and resid 150 through 152' Processing helix chain 'G' and resid 160 through 162 No H-bonds generated for 'chain 'G' and resid 160 through 162' Processing helix chain 'H' and resid 88 through 92 Processing helix chain 'H' and resid 129 through 134 Processing helix chain 'I' and resid 58 through 64 Processing helix chain 'J' and resid 17 through 27 Processing helix chain 'J' and resid 31 through 40 Processing helix chain 'J' and resid 43 through 52 removed outlier: 3.503A pdb=" N ILE J 50 " --> pdb=" O CYS J 46 " (cutoff:3.500A) Processing helix chain 'J' and resid 56 through 62 removed outlier: 3.872A pdb=" N ARG J 62 " --> pdb=" O GLU J 58 " (cutoff:3.500A) Processing helix chain 'K' and resid 51 through 54 Processing helix chain 'K' and resid 69 through 82 removed outlier: 4.408A pdb=" N ALA K 75 " --> pdb=" O THR K 71 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LYS K 82 " --> pdb=" O TYR K 78 " (cutoff:3.500A) Processing helix chain 'K' and resid 95 through 98 Processing helix chain 'K' and resid 112 through 142 removed outlier: 3.517A pdb=" N MET K 142 " --> pdb=" O LYS K 138 " (cutoff:3.500A) Processing helix chain 'M' and resid 67 through 72 Processing helix chain 'M' and resid 104 through 107 removed outlier: 3.635A pdb=" N ASN M 107 " --> pdb=" O SER M 104 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 104 through 107' Processing helix chain 'N' and resid 63 through 67 Processing helix chain 'N' and resid 71 through 75 Processing helix chain 'N' and resid 93 through 97 removed outlier: 3.556A pdb=" N GLU N 96 " --> pdb=" O THR N 93 " (cutoff:3.500A) Processing helix chain 'N' and resid 149 through 154 Processing helix chain 'N' and resid 176 through 180 removed outlier: 3.505A pdb=" N ASP N 179 " --> pdb=" O ASP N 176 " (cutoff:3.500A) Processing helix chain 'O' and resid 294 through 298 removed outlier: 3.569A pdb=" N ASP O 298 " --> pdb=" O VAL O 295 " (cutoff:3.500A) Processing helix chain 'O' and resid 574 through 579 removed outlier: 3.517A pdb=" N ASN O 579 " --> pdb=" O SER O 576 " (cutoff:3.500A) Processing helix chain 'O' and resid 583 through 614 Processing helix chain 'O' and resid 619 through 644 removed outlier: 3.532A pdb=" N ASP O 625 " --> pdb=" O LYS O 621 " (cutoff:3.500A) Processing helix chain 'O' and resid 671 through 686 Processing helix chain 'O' and resid 695 through 704 removed outlier: 4.047A pdb=" N LEU O 699 " --> pdb=" O GLY O 695 " (cutoff:3.500A) Processing helix chain 'O' and resid 711 through 723 removed outlier: 3.834A pdb=" N TYR O 715 " --> pdb=" O LEU O 711 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ASN O 716 " --> pdb=" O ASP O 712 " (cutoff:3.500A) Processing helix chain 'O' and resid 730 through 744 removed outlier: 3.634A pdb=" N VAL O 737 " --> pdb=" O THR O 733 " (cutoff:3.500A) Processing helix chain 'O' and resid 752 through 764 Processing helix chain 'O' and resid 765 through 777 Processing helix chain 'P' and resid 97 through 124 Processing helix chain 'P' and resid 125 through 147 removed outlier: 3.692A pdb=" N GLU P 130 " --> pdb=" O PRO P 126 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N THR P 143 " --> pdb=" O LYS P 139 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ILE P 144 " --> pdb=" O ILE P 140 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ASP P 146 " --> pdb=" O LYS P 142 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLN P 147 " --> pdb=" O THR P 143 " (cutoff:3.500A) Processing helix chain 'P' and resid 157 through 173 removed outlier: 4.039A pdb=" N THR P 161 " --> pdb=" O HIS P 157 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N ILE P 162 " --> pdb=" O MET P 158 " (cutoff:3.500A) Processing helix chain 'P' and resid 177 through 188 Processing helix chain 'P' and resid 201 through 206 Processing helix chain 'P' and resid 223 through 227 removed outlier: 3.542A pdb=" N LEU P 226 " --> pdb=" O ASN P 223 " (cutoff:3.500A) Processing helix chain 'P' and resid 229 through 238 Processing helix chain 'P' and resid 238 through 243 Processing helix chain 'P' and resid 249 through 260 removed outlier: 4.152A pdb=" N LEU P 253 " --> pdb=" O CYS P 249 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N CYS P 260 " --> pdb=" O LEU P 256 " (cutoff:3.500A) Processing helix chain 'P' and resid 264 through 278 removed outlier: 4.411A pdb=" N PHE P 268 " --> pdb=" O PRO P 264 " (cutoff:3.500A) Processing helix chain 'P' and resid 301 through 320 Processing helix chain 'P' and resid 327 through 339 removed outlier: 4.146A pdb=" N LEU P 332 " --> pdb=" O LEU P 328 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N SER P 333 " --> pdb=" O LYS P 329 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LEU P 338 " --> pdb=" O LEU P 334 " (cutoff:3.500A) Processing helix chain 'P' and resid 345 through 355 Processing helix chain 'P' and resid 362 through 369 Processing helix chain 'P' and resid 371 through 385 Processing helix chain 'P' and resid 404 through 417 Processing helix chain 'P' and resid 437 through 449 Processing helix chain 'P' and resid 470 through 491 removed outlier: 3.616A pdb=" N HIS P 482 " --> pdb=" O ARG P 478 " (cutoff:3.500A) Processing helix chain 'P' and resid 496 through 510 removed outlier: 3.593A pdb=" N LEU P 510 " --> pdb=" O LYS P 506 " (cutoff:3.500A) Processing helix chain 'Q' and resid 12 through 35 Processing helix chain 'Q' and resid 122 through 130 Processing helix chain 'Q' and resid 159 through 167 Processing helix chain 'Q' and resid 168 through 179 removed outlier: 3.988A pdb=" N ILE Q 175 " --> pdb=" O ARG Q 171 " (cutoff:3.500A) Proline residue: Q 176 - end of helix removed outlier: 3.726A pdb=" N HIS Q 179 " --> pdb=" O ILE Q 175 " (cutoff:3.500A) Processing helix chain 'Q' and resid 181 through 192 Processing helix chain 'Q' and resid 207 through 225 removed outlier: 3.624A pdb=" N HIS Q 221 " --> pdb=" O THR Q 217 " (cutoff:3.500A) Processing helix chain 'Q' and resid 228 through 242 removed outlier: 4.341A pdb=" N LYS Q 234 " --> pdb=" O SER Q 230 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ARG Q 241 " --> pdb=" O ALA Q 237 " (cutoff:3.500A) Processing helix chain 'Q' and resid 247 through 261 removed outlier: 4.085A pdb=" N VAL Q 255 " --> pdb=" O TRP Q 251 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N GLU Q 256 " --> pdb=" O GLY Q 252 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N LEU Q 258 " --> pdb=" O GLY Q 254 " (cutoff:3.500A) Processing helix chain 'Q' and resid 267 through 277 Processing helix chain 'Q' and resid 306 through 322 removed outlier: 3.502A pdb=" N LYS Q 322 " --> pdb=" O ILE Q 318 " (cutoff:3.500A) Processing helix chain 'Q' and resid 340 through 351 Processing helix chain 'Q' and resid 362 through 382 removed outlier: 3.803A pdb=" N LEU Q 379 " --> pdb=" O LYS Q 375 " (cutoff:3.500A) Processing helix chain 'Q' and resid 398 through 421 removed outlier: 3.794A pdb=" N ASN Q 402 " --> pdb=" O ASP Q 398 " (cutoff:3.500A) Processing helix chain 'Q' and resid 427 through 443 removed outlier: 3.798A pdb=" N ILE Q 431 " --> pdb=" O PRO Q 427 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ARG Q 441 " --> pdb=" O SER Q 437 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LEU Q 442 " --> pdb=" O PHE Q 438 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 1631 through 1632 removed outlier: 4.396A pdb=" N SER A 13 " --> pdb=" O MET B1192 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 38 through 39 Processing sheet with id=AA3, first strand: chain 'A' and resid 77 through 79 Processing sheet with id=AA4, first strand: chain 'A' and resid 243 through 245 removed outlier: 4.396A pdb=" N ILE A 251 " --> pdb=" O ILE A 315 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 371 through 373 Processing sheet with id=AA6, first strand: chain 'A' and resid 474 through 475 Processing sheet with id=AA7, first strand: chain 'B' and resid 1045 through 1047 removed outlier: 5.653A pdb=" N ILE A 495 " --> pdb=" O ARG A 606 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 506 through 510 removed outlier: 3.826A pdb=" N GLN A 535 " --> pdb=" O TYR A 578 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 686 through 688 Processing sheet with id=AB1, first strand: chain 'A' and resid 749 through 752 removed outlier: 6.275A pdb=" N LEU A 770 " --> pdb=" O LEU A 777 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 826 through 827 removed outlier: 7.833A pdb=" N ILE B 789 " --> pdb=" O SER B 928 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N LYS B 930 " --> pdb=" O ILE B 789 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 826 through 827 removed outlier: 4.595A pdb=" N TYR B1027 " --> pdb=" O VAL B 775 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 948 through 949 Processing sheet with id=AB5, first strand: chain 'A' and resid 1030 through 1032 removed outlier: 6.279A pdb=" N ASP A1040 " --> pdb=" O LEU A1045 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N LEU A1045 " --> pdb=" O ASP A1040 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 1504 through 1508 removed outlier: 3.870A pdb=" N ARG A1506 " --> pdb=" O GLU A1522 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 1261 through 1262 removed outlier: 6.499A pdb=" N VAL A1261 " --> pdb=" O ILE A1498 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 1461 through 1462 Processing sheet with id=AB9, first strand: chain 'D' and resid 21 through 24 removed outlier: 3.768A pdb=" N VAL D 21 " --> pdb=" O TYR G 46 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N LYS G 106 " --> pdb=" O PHE G 115 " (cutoff:3.500A) removed outlier: 7.574A pdb=" N TRP G 117 " --> pdb=" O LEU G 104 " (cutoff:3.500A) removed outlier: 9.667A pdb=" N LEU G 104 " --> pdb=" O TRP G 117 " (cutoff:3.500A) removed outlier: 15.236A pdb=" N HIS G 119 " --> pdb=" O GLU G 102 " (cutoff:3.500A) removed outlier: 16.797A pdb=" N GLU G 102 " --> pdb=" O HIS G 119 " (cutoff:3.500A) removed outlier: 5.267A pdb=" N VAL A1656 " --> pdb=" O ILE G 107 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 21 through 24 removed outlier: 3.768A pdb=" N VAL D 21 " --> pdb=" O TYR G 46 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N TRP G 117 " --> pdb=" O LYS G 88 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N LYS G 88 " --> pdb=" O TRP G 117 " (cutoff:3.500A) removed outlier: 5.889A pdb=" N HIS G 119 " --> pdb=" O GLY G 86 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N GLY G 86 " --> pdb=" O HIS G 119 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N ASN G 121 " --> pdb=" O TYR G 84 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N TYR G 84 " --> pdb=" O ASN G 121 " (cutoff:3.500A) removed outlier: 6.051A pdb=" N TYR G 123 " --> pdb=" O LEU G 82 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N VAL G 80 " --> pdb=" O TRP G 125 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 70 through 74 removed outlier: 6.557A pdb=" N LYS B 140 " --> pdb=" O GLU B 100 " (cutoff:3.500A) removed outlier: 4.770A pdb=" N VAL B 102 " --> pdb=" O LEU B 138 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N LEU B 138 " --> pdb=" O VAL B 102 " (cutoff:3.500A) removed outlier: 4.848A pdb=" N ILE B 104 " --> pdb=" O LYS B 136 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N LYS B 136 " --> pdb=" O ILE B 104 " (cutoff:3.500A) removed outlier: 5.135A pdb=" N GLY B 135 " --> pdb=" O GLY B 160 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N GLY B 160 " --> pdb=" O GLY B 135 " (cutoff:3.500A) removed outlier: 5.419A pdb=" N LEU B 137 " --> pdb=" O CYS B 158 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 108 through 109 removed outlier: 3.789A pdb=" N ARG B 119 " --> pdb=" O SER B 109 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 194 through 196 Processing sheet with id=AC5, first strand: chain 'B' and resid 400 through 403 removed outlier: 6.615A pdb=" N MET B 205 " --> pdb=" O HIS B 504 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 215 through 218 removed outlier: 5.652A pdb=" N TYR B 232 " --> pdb=" O TYR B 252 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N TYR B 252 " --> pdb=" O TYR B 232 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N THR B 247 " --> pdb=" O SER B 263 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N SER B 263 " --> pdb=" O THR B 247 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 550 through 551 Processing sheet with id=AC8, first strand: chain 'B' and resid 550 through 551 Processing sheet with id=AC9, first strand: chain 'B' and resid 571 through 572 removed outlier: 5.479A pdb=" N ILE B 592 " --> pdb=" O ILE B 588 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N ILE B 588 " --> pdb=" O ILE B 592 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N CYS B 585 " --> pdb=" O LEU B 640 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N LEU B 642 " --> pdb=" O CYS B 585 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N GLN B 587 " --> pdb=" O LEU B 642 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 740 through 744 removed outlier: 7.572A pdb=" N THR B 900 " --> pdb=" O LEU B 887 " (cutoff:3.500A) removed outlier: 5.100A pdb=" N LEU B 887 " --> pdb=" O THR B 900 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N SER B 902 " --> pdb=" O VAL B 885 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N VAL B 885 " --> pdb=" O SER B 902 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N LYS B 904 " --> pdb=" O GLU B 883 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 740 through 744 removed outlier: 7.572A pdb=" N THR B 900 " --> pdb=" O LEU B 887 " (cutoff:3.500A) removed outlier: 5.100A pdb=" N LEU B 887 " --> pdb=" O THR B 900 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N SER B 902 " --> pdb=" O VAL B 885 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N VAL B 885 " --> pdb=" O SER B 902 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N LYS B 904 " --> pdb=" O GLU B 883 " (cutoff:3.500A) removed outlier: 5.116A pdb=" N VAL B 885 " --> pdb=" O LYS L 58 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 752 through 753 Processing sheet with id=AD4, first strand: chain 'B' and resid 824 through 825 removed outlier: 3.666A pdb=" N CYS B 859 " --> pdb=" O LYS B 872 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 938 through 939 Processing sheet with id=AD6, first strand: chain 'B' and resid 1098 through 1104 Processing sheet with id=AD7, first strand: chain 'B' and resid 1113 through 1115 Processing sheet with id=AD8, first strand: chain 'B' and resid 1132 through 1134 Processing sheet with id=AD9, first strand: chain 'C' and resid 41 through 47 removed outlier: 5.380A pdb=" N VAL C 42 " --> pdb=" O ILE C 57 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N ILE C 57 " --> pdb=" O VAL C 42 " (cutoff:3.500A) removed outlier: 5.276A pdb=" N ILE C 44 " --> pdb=" O ASP C 55 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N ASP C 55 " --> pdb=" O ILE C 44 " (cutoff:3.500A) removed outlier: 10.013A pdb=" N ARG C 293 " --> pdb=" O ASN C 234 " (cutoff:3.500A) removed outlier: 8.939A pdb=" N ASN C 234 " --> pdb=" O ARG C 293 " (cutoff:3.500A) removed outlier: 9.845A pdb=" N ARG C 295 " --> pdb=" O GLN C 232 " (cutoff:3.500A) removed outlier: 11.139A pdb=" N GLN C 232 " --> pdb=" O ARG C 295 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N HIS C 297 " --> pdb=" O LEU C 230 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N THR C 224 " --> pdb=" O GLU C 303 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 168 through 170 removed outlier: 4.044A pdb=" N VAL C 133 " --> pdb=" O GLU C 170 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N GLU C 201 " --> pdb=" O ASN C 87 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N ASN C 87 " --> pdb=" O GLU C 201 " (cutoff:3.500A) removed outlier: 7.555A pdb=" N SER C 203 " --> pdb=" O PHE C 85 " (cutoff:3.500A) removed outlier: 4.813A pdb=" N PHE C 85 " --> pdb=" O SER C 203 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N LYS C 205 " --> pdb=" O VAL C 83 " (cutoff:3.500A) removed outlier: 4.672A pdb=" N VAL C 83 " --> pdb=" O LYS C 205 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N HIS C 207 " --> pdb=" O GLU C 81 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 141 through 142 Processing sheet with id=AE3, first strand: chain 'C' and resid 161 through 163 removed outlier: 6.875A pdb=" N VAL C 162 " --> pdb=" O LEU C 193 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 256 through 257 Processing sheet with id=AE5, first strand: chain 'E' and resid 60 through 62 removed outlier: 6.368A pdb=" N TRP E 79 " --> pdb=" O ILE E 109 " (cutoff:3.500A) removed outlier: 7.456A pdb=" N VAL E 111 " --> pdb=" O TRP E 79 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N GLU E 81 " --> pdb=" O VAL E 111 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'E' and resid 87 through 88 Processing sheet with id=AE7, first strand: chain 'E' and resid 152 through 155 Processing sheet with id=AE8, first strand: chain 'G' and resid 132 through 141 removed outlier: 3.629A pdb=" N TYR G 136 " --> pdb=" O LEU G 148 " (cutoff:3.500A) removed outlier: 6.017A pdb=" N GLY G 146 " --> pdb=" O PHE G 138 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N GLN G 140 " --> pdb=" O HIS G 144 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N HIS G 144 " --> pdb=" O GLN G 140 " (cutoff:3.500A) removed outlier: 7.099A pdb=" N ASN G 154 " --> pdb=" O VAL G 245 " (cutoff:3.500A) removed outlier: 7.610A pdb=" N GLY G 247 " --> pdb=" O ASN G 154 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N SER G 156 " --> pdb=" O GLY G 247 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N THR G 248 " --> pdb=" O VAL G 233 " (cutoff:3.500A) removed outlier: 5.517A pdb=" N VAL G 233 " --> pdb=" O THR G 248 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'G' and resid 167 through 169 Processing sheet with id=AF1, first strand: chain 'H' and resid 4 through 16 removed outlier: 6.363A pdb=" N GLU H 27 " --> pdb=" O SER H 13 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N VAL H 15 " --> pdb=" O ARG H 25 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N ARG H 25 " --> pdb=" O VAL H 15 " (cutoff:3.500A) removed outlier: 4.933A pdb=" N LEU H 122 " --> pdb=" O ASP H 41 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N LYS H 103 " --> pdb=" O TYR H 115 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N SER H 117 " --> pdb=" O ALA H 101 " (cutoff:3.500A) removed outlier: 5.662A pdb=" N ALA H 101 " --> pdb=" O SER H 117 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'I' and resid 3 through 4 Processing sheet with id=AF3, first strand: chain 'K' and resid 47 through 49 Processing sheet with id=AF4, first strand: chain 'M' and resid 10 through 11 Processing sheet with id=AF5, first strand: chain 'M' and resid 14 through 16 removed outlier: 3.608A pdb=" N LYS M 92 " --> pdb=" O GLN M 16 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N SER M 87 " --> pdb=" O ASN M 82 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N VAL N 53 " --> pdb=" O LYS N 135 " (cutoff:3.500A) removed outlier: 7.934A pdb=" N PHE N 137 " --> pdb=" O VAL N 53 " (cutoff:3.500A) removed outlier: 5.771A pdb=" N LEU N 55 " --> pdb=" O PHE N 137 " (cutoff:3.500A) removed outlier: 7.419A pdb=" N VAL N 139 " --> pdb=" O LEU N 55 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N LYS N 57 " --> pdb=" O VAL N 139 " (cutoff:3.500A) removed outlier: 7.992A pdb=" N GLU N 141 " --> pdb=" O LYS N 57 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N VAL N 136 " --> pdb=" O ASP N 92 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'M' and resid 39 through 45 removed outlier: 3.730A pdb=" N VAL M 52 " --> pdb=" O TYR M 41 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N GLU M 50 " --> pdb=" O LYS M 43 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'O' and resid 57 through 60 removed outlier: 3.549A pdb=" N TYR O 548 " --> pdb=" O VAL O 539 " (cutoff:3.500A) removed outlier: 7.836A pdb=" N ASP O 536 " --> pdb=" O THR O 510 " (cutoff:3.500A) removed outlier: 5.313A pdb=" N THR O 510 " --> pdb=" O ASP O 536 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N LEU O 538 " --> pdb=" O ILE O 508 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N ILE O 508 " --> pdb=" O LEU O 538 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N LYS O 540 " --> pdb=" O THR O 506 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'O' and resid 201 through 205 removed outlier: 4.268A pdb=" N GLU O 201 " --> pdb=" O LEU O 219 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'O' and resid 242 through 245 removed outlier: 6.629A pdb=" N ILE O 264 " --> pdb=" O LYS O 243 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'O' and resid 305 through 306 Processing sheet with id=AG2, first strand: chain 'O' and resid 361 through 365 removed outlier: 3.635A pdb=" N ARG O 362 " --> pdb=" O PHE O 375 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N GLU O 382 " --> pdb=" O THR O 391 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'O' and resid 402 through 405 removed outlier: 6.878A pdb=" N THR O 417 " --> pdb=" O ARG O 403 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'O' and resid 452 through 457 Processing sheet with id=AG5, first strand: chain 'O' and resid 452 through 457 2000 hydrogen bonds defined for protein. 5475 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 65 hydrogen bonds 106 hydrogen bond angles 0 basepair planarities 30 basepair parallelities 82 stacking parallelities Total time for adding SS restraints: 13.71 Time building geometry restraints manager: 6.22 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 7676 1.32 - 1.44: 12903 1.44 - 1.57: 26566 1.57 - 1.69: 241 1.69 - 1.82: 326 Bond restraints: 47712 Sorted by residual: bond pdb=" CA ASP O 353 " pdb=" C ASP O 353 " ideal model delta sigma weight residual 1.524 1.661 -0.137 1.26e-02 6.30e+03 1.18e+02 bond pdb=" CA LYS A1115 " pdb=" C LYS A1115 " ideal model delta sigma weight residual 1.523 1.635 -0.112 1.34e-02 5.57e+03 6.99e+01 bond pdb=" CA ARG O 584 " pdb=" C ARG O 584 " ideal model delta sigma weight residual 1.523 1.630 -0.107 1.34e-02 5.57e+03 6.37e+01 bond pdb=" CA ILE O 297 " pdb=" C ILE O 297 " ideal model delta sigma weight residual 1.523 1.621 -0.098 1.27e-02 6.20e+03 5.96e+01 bond pdb=" CA HIS P 511 " pdb=" C HIS P 511 " ideal model delta sigma weight residual 1.524 1.629 -0.105 1.40e-02 5.10e+03 5.61e+01 ... (remaining 47707 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.01: 64079 5.01 - 10.02: 686 10.02 - 15.03: 130 15.03 - 20.04: 28 20.04 - 25.05: 7 Bond angle restraints: 64930 Sorted by residual: angle pdb=" N VAL P 356 " pdb=" CA VAL P 356 " pdb=" C VAL P 356 " ideal model delta sigma weight residual 112.17 91.23 20.94 9.50e-01 1.11e+00 4.86e+02 angle pdb=" N HIS O 705 " pdb=" CA HIS O 705 " pdb=" C HIS O 705 " ideal model delta sigma weight residual 113.21 91.02 22.19 1.15e+00 7.56e-01 3.72e+02 angle pdb=" N LYS O 749 " pdb=" CA LYS O 749 " pdb=" C LYS O 749 " ideal model delta sigma weight residual 109.30 132.03 -22.73 1.49e+00 4.50e-01 2.33e+02 angle pdb=" C PHE P 125 " pdb=" N PRO P 126 " pdb=" CA PRO P 126 " ideal model delta sigma weight residual 119.84 138.50 -18.66 1.25e+00 6.40e-01 2.23e+02 angle pdb=" C LYS B 77 " pdb=" N PRO B 78 " pdb=" CA PRO B 78 " ideal model delta sigma weight residual 119.84 102.09 17.75 1.25e+00 6.40e-01 2.02e+02 ... (remaining 64925 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.89: 27941 34.89 - 69.78: 772 69.78 - 104.67: 42 104.67 - 139.56: 0 139.56 - 174.46: 1 Dihedral angle restraints: 28756 sinusoidal: 12499 harmonic: 16257 Sorted by residual: dihedral pdb=" C LYS A 410 " pdb=" N LYS A 410 " pdb=" CA LYS A 410 " pdb=" CB LYS A 410 " ideal model delta harmonic sigma weight residual -122.60 -157.53 34.93 0 2.50e+00 1.60e-01 1.95e+02 dihedral pdb=" N LYS A 410 " pdb=" C LYS A 410 " pdb=" CA LYS A 410 " pdb=" CB LYS A 410 " ideal model delta harmonic sigma weight residual 122.80 157.15 -34.35 0 2.50e+00 1.60e-01 1.89e+02 dihedral pdb=" O4' C R 4 " pdb=" C2' C R 4 " pdb=" C1' C R 4 " pdb=" C3' C R 4 " ideal model delta sinusoidal sigma weight residual 25.59 -4.26 29.85 3 3.80e+00 6.93e-02 7.33e+01 ... (remaining 28753 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.296: 7156 0.296 - 0.592: 96 0.592 - 0.889: 9 0.889 - 1.185: 2 1.185 - 1.481: 1 Chirality restraints: 7264 Sorted by residual: chirality pdb=" CA LYS A 410 " pdb=" N LYS A 410 " pdb=" C LYS A 410 " pdb=" CB LYS A 410 " both_signs ideal model delta sigma weight residual False 2.51 1.03 1.48 2.00e-01 2.50e+01 5.48e+01 chirality pdb=" CA GLN Q 147 " pdb=" N GLN Q 147 " pdb=" C GLN Q 147 " pdb=" CB GLN Q 147 " both_signs ideal model delta sigma weight residual False 2.51 1.59 0.92 2.00e-01 2.50e+01 2.13e+01 chirality pdb=" CA GLU P 246 " pdb=" N GLU P 246 " pdb=" C GLU P 246 " pdb=" CB GLU P 246 " both_signs ideal model delta sigma weight residual False 2.51 1.62 0.89 2.00e-01 2.50e+01 1.99e+01 ... (remaining 7261 not shown) Planarity restraints: 7979 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE Q 188 " 0.100 2.00e-02 2.50e+03 6.14e-02 6.59e+01 pdb=" CG PHE Q 188 " -0.074 2.00e-02 2.50e+03 pdb=" CD1 PHE Q 188 " -0.058 2.00e-02 2.50e+03 pdb=" CD2 PHE Q 188 " -0.054 2.00e-02 2.50e+03 pdb=" CE1 PHE Q 188 " 0.012 2.00e-02 2.50e+03 pdb=" CE2 PHE Q 188 " 0.009 2.00e-02 2.50e+03 pdb=" CZ PHE Q 188 " 0.066 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE Q 270 " 0.083 2.00e-02 2.50e+03 5.20e-02 4.74e+01 pdb=" CG PHE Q 270 " -0.056 2.00e-02 2.50e+03 pdb=" CD1 PHE Q 270 " -0.063 2.00e-02 2.50e+03 pdb=" CD2 PHE Q 270 " -0.040 2.00e-02 2.50e+03 pdb=" CE1 PHE Q 270 " 0.021 2.00e-02 2.50e+03 pdb=" CE2 PHE Q 270 " -0.000 2.00e-02 2.50e+03 pdb=" CZ PHE Q 270 " 0.055 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR Q 443 " 0.049 2.00e-02 2.50e+03 4.73e-02 4.48e+01 pdb=" CG TYR Q 443 " -0.004 2.00e-02 2.50e+03 pdb=" CD1 TYR Q 443 " -0.002 2.00e-02 2.50e+03 pdb=" CD2 TYR Q 443 " -0.006 2.00e-02 2.50e+03 pdb=" CE1 TYR Q 443 " -0.038 2.00e-02 2.50e+03 pdb=" CE2 TYR Q 443 " -0.042 2.00e-02 2.50e+03 pdb=" CZ TYR Q 443 " -0.054 2.00e-02 2.50e+03 pdb=" OH TYR Q 443 " 0.097 2.00e-02 2.50e+03 ... (remaining 7976 not shown) Histogram of nonbonded interaction distances: 1.01 - 1.78: 168 1.78 - 2.56: 1950 2.56 - 3.34: 64616 3.34 - 4.12: 120434 4.12 - 4.90: 211079 Nonbonded interactions: 398247 Sorted by model distance: nonbonded pdb=" NZ LYS M 45 " pdb=" OE2 GLU M 50 " model vdw 1.006 3.120 nonbonded pdb=" CB ALA P 195 " pdb=" CB GLU P 216 " model vdw 1.043 3.860 nonbonded pdb=" OE1 GLU O 614 " pdb=" CB ALA O 670 " model vdw 1.053 3.460 nonbonded pdb=" O ALA P 261 " pdb=" CD PRO P 263 " model vdw 1.087 3.440 nonbonded pdb=" CG2 ILE O 351 " pdb=" CE MET Q 157 " model vdw 1.088 3.880 ... (remaining 398242 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=0.00 max=1.00 mean=0.96 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: 0.490 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: 0.040 Extract box with map and model: 0.630 Check model and map are aligned: 0.100 Set scattering table: 0.080 Process input model: 55.500 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.090 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:1.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 58.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6399 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 0.452 47752 Z= 0.715 Angle : 1.521 54.363 64966 Z= 0.931 Chirality : 0.087 1.481 7264 Planarity : 0.011 0.147 7978 Dihedral : 15.191 174.456 18209 Min Nonbonded Distance : 1.006 Molprobity Statistics. All-atom Clashscore : 83.39 Ramachandran Plot: Outliers : 4.05 % Allowed : 9.02 % Favored : 86.93 % Rotamer: Outliers : 5.40 % Allowed : 5.27 % Favored : 89.33 % Cbeta Deviations : 0.85 % Peptide Plane: Cis-proline : 0.00 % 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: -3.51 (0.10), residues: 5432 helix: -1.98 (0.09), residues: 1911 sheet: -1.66 (0.16), residues: 767 loop : -2.82 (0.10), residues: 2754 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.095 0.011 ARG A 59 TYR 0.097 0.007 TYR Q 443 PHE 0.100 0.003 PHE Q 188 TRP 0.061 0.004 TRP Q 273 HIS 0.028 0.002 HIS B 875 Details of bonding type rmsd/Z covalent geometry : bond 0.00661 / 0.43 (47712) covalent geometry : angle 1.41858 / 0.93 (64930) hydrogen bonds : bond 0.20761 / 13.75 ( 2015) hydrogen bonds : angle 9.60275 / 6.70 ( 5581) metal coordination : bond 0.20313 / 12.13 ( 24) metal coordination : angle 24.43198 / 15.54 ( 33) Misc. bond : bond 0.31070 / 17.88 ( 15) link_TRANS : bond 0.00801 / 0.42 ( 1) link_TRANS : angle 0.55168 / 0.28 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10864 Ramachandran restraints generated. 5432 Oldfield, 0 Emsley, 5432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10864 Ramachandran restraints generated. 5432 Oldfield, 0 Emsley, 5432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1854 residues out of total 4950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 267 poor density : 1587 time to evaluate : 1.856 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 450 LYS cc_start: 0.5508 (OUTLIER) cc_final: 0.4083 (mttm) REVERT: A 589 MET cc_start: 0.7919 (mmm) cc_final: 0.7514 (mmm) REVERT: A 635 MET cc_start: 0.7844 (ttp) cc_final: 0.7602 (ttp) REVERT: A 640 ASN cc_start: 0.7834 (t0) cc_final: 0.7575 (m-40) REVERT: A 732 ILE cc_start: 0.9115 (mm) cc_final: 0.8899 (mt) REVERT: A 994 GLU cc_start: 0.2470 (mt-10) cc_final: 0.1969 (mt-10) REVERT: A 1006 LEU cc_start: 0.1244 (mt) cc_final: 0.0680 (mt) REVERT: A 1013 THR cc_start: 0.0730 (OUTLIER) cc_final: -0.0003 (t) REVERT: A 1015 ARG cc_start: 0.1997 (mtm180) cc_final: 0.1489 (mmm-85) REVERT: A 1016 SER cc_start: 0.1841 (p) cc_final: 0.1329 (t) REVERT: A 1118 VAL cc_start: 0.5309 (OUTLIER) cc_final: 0.5064 (p) REVERT: A 1576 SER cc_start: 0.8013 (m) cc_final: 0.7731 (p) REVERT: A 1627 LEU cc_start: 0.7878 (mt) cc_final: 0.7435 (mt) REVERT: B 77 LYS cc_start: 0.5602 (OUTLIER) cc_final: 0.5394 (tptt) REVERT: B 158 CYS cc_start: 0.5829 (m) cc_final: 0.5392 (m) REVERT: B 217 ILE cc_start: 0.8898 (pt) cc_final: 0.8684 (pt) REVERT: B 450 LEU cc_start: 0.6860 (mt) cc_final: 0.6310 (mp) REVERT: B 821 ILE cc_start: 0.7177 (OUTLIER) cc_final: 0.6973 (tp) REVERT: B 900 THR cc_start: 0.8456 (m) cc_final: 0.8019 (p) REVERT: B 1055 LEU cc_start: 0.7794 (mt) cc_final: 0.7539 (mt) REVERT: B 1113 THR cc_start: 0.8440 (p) cc_final: 0.8067 (p) REVERT: B 1189 LEU cc_start: 0.7614 (mt) cc_final: 0.7237 (tt) REVERT: C 115 TRP cc_start: 0.8413 (m100) cc_final: 0.8198 (m100) REVERT: D 25 THR cc_start: 0.6313 (p) cc_final: 0.5603 (p) REVERT: E 211 TYR cc_start: 0.8225 (m-80) cc_final: 0.7770 (m-10) REVERT: F 90 ARG cc_start: 0.8317 (ttt-90) cc_final: 0.7995 (ttt-90) REVERT: F 144 GLU cc_start: 0.7149 (mt-10) cc_final: 0.6775 (mt-10) REVERT: G 53 TYR cc_start: 0.6549 (m-80) cc_final: 0.6178 (m-80) REVERT: G 100 THR cc_start: 0.6594 (OUTLIER) cc_final: 0.6244 (p) REVERT: H 25 ARG cc_start: 0.7444 (ttp80) cc_final: 0.7002 (ttp80) REVERT: I 41 GLN cc_start: 0.6762 (OUTLIER) cc_final: 0.6344 (tp-100) REVERT: K 66 VAL cc_start: 0.8732 (m) cc_final: 0.8488 (t) REVERT: K 125 MET cc_start: 0.5862 (mtp) cc_final: 0.5543 (mtp) REVERT: O 197 ARG cc_start: 0.3792 (OUTLIER) cc_final: 0.2788 (tpm170) REVERT: O 485 LYS cc_start: 0.8779 (OUTLIER) cc_final: 0.8418 (mppt) REVERT: P 312 LEU cc_start: 0.8130 (OUTLIER) cc_final: 0.7548 (mt) REVERT: P 512 ARG cc_start: 0.2231 (OUTLIER) cc_final: -0.0240 (mtm180) REVERT: Q 166 GLU cc_start: 0.7362 (tt0) cc_final: 0.7161 (pt0) REVERT: Q 214 VAL cc_start: 0.8296 (t) cc_final: 0.7475 (t) REVERT: Q 271 LEU cc_start: 0.8601 (mt) cc_final: 0.8303 (mt) outliers start: 267 outliers final: 108 residues processed: 1806 average time/residue: 0.2961 time to fit residues: 874.2178 Evaluate side-chains 1041 residues out of total 4950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 922 time to evaluate : 1.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 450 LYS Chi-restraints excluded: chain A residue 721 LYS Chi-restraints excluded: chain A residue 789 SER Chi-restraints excluded: chain A residue 790 LYS Chi-restraints excluded: chain A residue 1013 THR Chi-restraints excluded: chain A residue 1114 TYR Chi-restraints excluded: chain A residue 1116 GLN Chi-restraints excluded: chain A residue 1117 SER Chi-restraints excluded: chain A residue 1118 VAL Chi-restraints excluded: chain A residue 1119 LYS Chi-restraints excluded: chain B residue 77 LYS Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 813 LEU Chi-restraints excluded: chain B residue 819 ASP Chi-restraints excluded: chain B residue 821 ILE Chi-restraints excluded: chain B residue 1117 VAL Chi-restraints excluded: chain B residue 1194 ILE Chi-restraints excluded: chain G residue 95 LEU Chi-restraints excluded: chain G residue 96 SER Chi-restraints excluded: chain G residue 97 LYS Chi-restraints excluded: chain G residue 100 THR Chi-restraints excluded: chain I residue 40 SER Chi-restraints excluded: chain I residue 41 GLN Chi-restraints excluded: chain M residue 47 GLU Chi-restraints excluded: chain M residue 51 PHE Chi-restraints excluded: chain M residue 113 ILE Chi-restraints excluded: chain N residue 25 ILE Chi-restraints excluded: chain N residue 128 ASN Chi-restraints excluded: chain N residue 131 LEU Chi-restraints excluded: chain O residue 197 ARG Chi-restraints excluded: chain O residue 200 THR Chi-restraints excluded: chain O residue 202 ILE Chi-restraints excluded: chain O residue 203 ILE Chi-restraints excluded: chain O residue 216 ILE Chi-restraints excluded: chain O residue 221 ARG Chi-restraints excluded: chain O residue 222 GLN Chi-restraints excluded: chain O residue 224 THR Chi-restraints excluded: chain O residue 237 GLU Chi-restraints excluded: chain O residue 260 LEU Chi-restraints excluded: chain O residue 292 LEU Chi-restraints excluded: chain O residue 350 THR Chi-restraints excluded: chain O residue 439 LYS Chi-restraints excluded: chain O residue 485 LYS Chi-restraints excluded: chain O residue 574 TRP Chi-restraints excluded: chain O residue 583 GLU Chi-restraints excluded: chain O residue 585 GLU Chi-restraints excluded: chain O residue 586 LYS Chi-restraints excluded: chain O residue 615 ASN Chi-restraints excluded: chain O residue 616 SER Chi-restraints excluded: chain O residue 617 HIS Chi-restraints excluded: chain O residue 626 LEU Chi-restraints excluded: chain O residue 637 LEU Chi-restraints excluded: chain O residue 649 ILE Chi-restraints excluded: chain O residue 650 LEU Chi-restraints excluded: chain O residue 655 SER Chi-restraints excluded: chain O residue 659 LEU Chi-restraints excluded: chain O residue 662 LEU Chi-restraints excluded: chain O residue 665 ASN Chi-restraints excluded: chain O residue 702 LEU Chi-restraints excluded: chain O residue 712 ASP Chi-restraints excluded: chain O residue 726 SER Chi-restraints excluded: chain O residue 744 LEU Chi-restraints excluded: chain O residue 772 ILE Chi-restraints excluded: chain P residue 95 LEU Chi-restraints excluded: chain P residue 147 GLN Chi-restraints excluded: chain P residue 150 GLU Chi-restraints excluded: chain P residue 151 GLU Chi-restraints excluded: chain P residue 152 LEU Chi-restraints excluded: chain P residue 154 LEU Chi-restraints excluded: chain P residue 170 THR Chi-restraints excluded: chain P residue 172 LEU Chi-restraints excluded: chain P residue 193 PHE Chi-restraints excluded: chain P residue 215 LEU Chi-restraints excluded: chain P residue 225 GLN Chi-restraints excluded: chain P residue 236 MET Chi-restraints excluded: chain P residue 279 THR Chi-restraints excluded: chain P residue 281 ILE Chi-restraints excluded: chain P residue 284 LEU Chi-restraints excluded: chain P residue 291 ASP Chi-restraints excluded: chain P residue 301 HIS Chi-restraints excluded: chain P residue 312 LEU Chi-restraints excluded: chain P residue 341 ARG Chi-restraints excluded: chain P residue 355 VAL Chi-restraints excluded: chain P residue 365 ASP Chi-restraints excluded: chain P residue 385 PHE Chi-restraints excluded: chain P residue 388 THR Chi-restraints excluded: chain P residue 422 GLU Chi-restraints excluded: chain P residue 444 GLU Chi-restraints excluded: chain P residue 453 PHE Chi-restraints excluded: chain P residue 493 ILE Chi-restraints excluded: chain P residue 495 LYS Chi-restraints excluded: chain P residue 497 GLN Chi-restraints excluded: chain P residue 512 ARG Chi-restraints excluded: chain Q residue 4 VAL Chi-restraints excluded: chain Q residue 27 ILE Chi-restraints excluded: chain Q residue 138 PHE Chi-restraints excluded: chain Q residue 147 GLN Chi-restraints excluded: chain Q residue 152 ILE Chi-restraints excluded: chain Q residue 155 GLN Chi-restraints excluded: chain Q residue 168 ILE Chi-restraints excluded: chain Q residue 180 CYS Chi-restraints excluded: chain Q residue 200 THR Chi-restraints excluded: chain Q residue 203 SER Chi-restraints excluded: chain Q residue 204 GLU Chi-restraints excluded: chain Q residue 206 ARG Chi-restraints excluded: chain Q residue 208 TYR Chi-restraints excluded: chain Q residue 246 GLN Chi-restraints excluded: chain Q residue 247 ILE Chi-restraints excluded: chain Q residue 248 LYS Chi-restraints excluded: chain Q residue 272 GLN Chi-restraints excluded: chain Q residue 298 GLN Chi-restraints excluded: chain Q residue 317 LEU Chi-restraints excluded: chain Q residue 364 VAL Chi-restraints excluded: chain Q residue 367 ILE Chi-restraints excluded: chain Q residue 384 VAL Chi-restraints excluded: chain Q residue 390 ASN Chi-restraints excluded: chain Q residue 393 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 555 random chunks: chunk 394 optimal weight: 9.9990 chunk 430 optimal weight: 30.0000 chunk 41 optimal weight: 0.3980 chunk 265 optimal weight: 6.9990 chunk 523 optimal weight: 2.9990 chunk 497 optimal weight: 0.0270 chunk 414 optimal weight: 30.0000 chunk 310 optimal weight: 5.9990 chunk 488 optimal weight: 40.0000 chunk 366 optimal weight: 8.9990 chunk 223 optimal weight: 6.9990 overall best weight: 3.2844 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 43 HIS A 60 ASN ** A 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 384 GLN A 525 ASN ** A 580 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 656 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 738 ASN A 785 GLN A 798 HIS A 926 GLN A1113 HIS A1314 GLN A1647 ASN B 27 ASN B 147 ASN B 254 ASN ** B 504 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 555 GLN B 575 HIS B 683 ASN B 710 ASN ** B 720 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 824 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 886 ASN ** B 899 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1010 ASN ** B1163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 88 GLN ** E 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 99 HIS E 113 GLN ** E 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 36 ASN G 64 GLN ** G 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 237 HIS H 139 ASN L 66 GLN ** M 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 54 HIS ** M 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 145 ASN P 147 GLN ** P 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 157 HIS ** P 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 482 HIS P 486 GLN P 497 GLN P 511 HIS ** Q 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 221 HIS ** Q 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 276 GLN ** Q 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 304 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 372 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 387 ASN ** Q 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 39 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.119230 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.085842 restraints weight = 143470.096| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.088567 restraints weight = 66481.521| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.089672 restraints weight = 39535.347| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.089650 restraints weight = 27140.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.089973 restraints weight = 27891.138| |-----------------------------------------------------------------------------| r_work (final): 0.3296 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7631 moved from start: 0.3938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.199 47752 Z= 0.282 Angle : 1.125 31.838 64966 Z= 0.571 Chirality : 0.057 0.414 7264 Planarity : 0.008 0.117 7978 Dihedral : 15.483 176.102 7423 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 25.43 Ramachandran Plot: Outliers : 1.47 % Allowed : 7.58 % Favored : 90.94 % Rotamer: Outliers : 5.64 % Allowed : 14.65 % Favored : 79.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.65 % Twisted General : 0.19 % 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: -2.09 (0.10), residues: 5432 helix: -0.59 (0.11), residues: 1963 sheet: -1.27 (0.17), residues: 739 loop : -2.03 (0.11), residues: 2730 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG Q 29 TYR 0.045 0.003 TYR O 196 PHE 0.087 0.004 PHE Q 358 TRP 0.076 0.004 TRP O 310 HIS 0.019 0.002 HIS Q 212 Details of bonding type rmsd/Z covalent geometry : bond 0.00630 / 0.28 (47712) covalent geometry : angle 1.09707 / 0.57 (64930) hydrogen bonds : bond 0.07112 / 4.85 ( 2015) hydrogen bonds : angle 6.82054 / 4.78 ( 5581) metal coordination : bond 0.01912 / 1.07 ( 24) metal coordination : angle 11.03470 / 8.21 ( 33) Misc. bond : bond 0.01273 / 0.76 ( 15) link_TRANS : bond 0.00048 / 0.03 ( 1) link_TRANS : angle 0.64014 / 0.35 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10864 Ramachandran restraints generated. 5432 Oldfield, 0 Emsley, 5432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10864 Ramachandran restraints generated. 5432 Oldfield, 0 Emsley, 5432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1277 residues out of total 4950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 279 poor density : 998 time to evaluate : 1.874 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.8450 (tpp) cc_final: 0.7909 (tpp) REVERT: A 108 PHE cc_start: 0.9229 (m-80) cc_final: 0.8474 (m-80) REVERT: A 243 PHE cc_start: 0.8503 (m-80) cc_final: 0.8047 (m-80) REVERT: A 357 MET cc_start: 0.8725 (mpp) cc_final: 0.8386 (mpp) REVERT: A 435 ASN cc_start: 0.8173 (m-40) cc_final: 0.7924 (m110) REVERT: A 450 LYS cc_start: 0.4736 (OUTLIER) cc_final: 0.3275 (mttm) REVERT: A 453 ILE cc_start: 0.8960 (pt) cc_final: 0.8727 (pt) REVERT: A 723 TYR cc_start: 0.7525 (m-80) cc_final: 0.7261 (m-80) REVERT: A 819 ASN cc_start: 0.9129 (m-40) cc_final: 0.8635 (m-40) REVERT: A 881 GLU cc_start: 0.8616 (tt0) cc_final: 0.8007 (tp30) REVERT: A 882 ILE cc_start: 0.9507 (mm) cc_final: 0.9305 (mt) REVERT: A 1015 ARG cc_start: -0.0820 (mtm180) cc_final: -0.1244 (mmm-85) REVERT: A 1040 ASP cc_start: 0.9026 (t0) cc_final: 0.8681 (t70) REVERT: A 1071 ASP cc_start: 0.8557 (t0) cc_final: 0.8353 (t0) REVERT: A 1115 LYS cc_start: 0.8691 (tptt) cc_final: 0.8468 (mmmm) REVERT: A 1183 GLU cc_start: 0.8271 (tp30) cc_final: 0.8036 (tp30) REVERT: A 1191 GLN cc_start: 0.8777 (mt0) cc_final: 0.8469 (mt0) REVERT: A 1294 MET cc_start: 0.8967 (mtm) cc_final: 0.8344 (ptp) REVERT: A 1334 LYS cc_start: 0.9129 (OUTLIER) cc_final: 0.8874 (pttp) REVERT: A 1497 ILE cc_start: 0.9381 (pp) cc_final: 0.9181 (pt) REVERT: A 1545 ASP cc_start: 0.9150 (t0) cc_final: 0.8933 (t0) REVERT: A 1576 SER cc_start: 0.8916 (m) cc_final: 0.8374 (p) REVERT: A 1611 MET cc_start: 0.8617 (tmm) cc_final: 0.8329 (tmm) REVERT: A 1616 GLU cc_start: 0.8270 (tt0) cc_final: 0.7887 (tt0) REVERT: A 1620 GLN cc_start: 0.8792 (mp10) cc_final: 0.8587 (mp10) REVERT: B 108 MET cc_start: 0.8955 (mmm) cc_final: 0.8543 (mmp) REVERT: B 125 GLU cc_start: 0.8013 (mp0) cc_final: 0.7725 (mp0) REVERT: B 149 GLU cc_start: 0.8583 (tt0) cc_final: 0.8208 (tm-30) REVERT: B 175 MET cc_start: 0.8890 (mtp) cc_final: 0.8644 (mtp) REVERT: B 388 GLU cc_start: 0.7896 (pt0) cc_final: 0.7683 (pt0) REVERT: B 419 GLU cc_start: 0.8069 (tp30) cc_final: 0.7293 (tp30) REVERT: B 422 GLN cc_start: 0.8740 (mt0) cc_final: 0.8533 (mt0) REVERT: B 512 LEU cc_start: 0.8793 (mt) cc_final: 0.8516 (mp) REVERT: B 555 GLN cc_start: 0.7860 (tt0) cc_final: 0.7648 (tt0) REVERT: B 589 ASP cc_start: 0.8812 (m-30) cc_final: 0.8587 (m-30) REVERT: B 759 ASP cc_start: 0.8355 (t0) cc_final: 0.7975 (t0) REVERT: B 778 TYR cc_start: 0.8855 (t80) cc_final: 0.8138 (t80) REVERT: B 783 MET cc_start: 0.7289 (mtt) cc_final: 0.7060 (mtt) REVERT: B 807 GLU cc_start: 0.7994 (tt0) cc_final: 0.7477 (tt0) REVERT: B 816 ASN cc_start: 0.6455 (OUTLIER) cc_final: 0.5770 (m110) REVERT: B 900 THR cc_start: 0.9493 (m) cc_final: 0.8946 (p) REVERT: B 905 TYR cc_start: 0.8864 (m-80) cc_final: 0.8617 (m-80) REVERT: C 188 ASP cc_start: 0.8499 (m-30) cc_final: 0.8277 (m-30) REVERT: C 232 GLN cc_start: 0.7656 (tm-30) cc_final: 0.6706 (tm-30) REVERT: D 37 LEU cc_start: 0.9646 (pp) cc_final: 0.9311 (pp) REVERT: E 22 MET cc_start: 0.8723 (ttp) cc_final: 0.8346 (ttp) REVERT: E 32 GLN cc_start: 0.9068 (pm20) cc_final: 0.8781 (pp30) REVERT: E 78 LEU cc_start: 0.9430 (tt) cc_final: 0.9140 (tt) REVERT: E 83 CYS cc_start: 0.6432 (t) cc_final: 0.5950 (t) REVERT: E 112 TYR cc_start: 0.9165 (p90) cc_final: 0.8131 (p90) REVERT: E 114 ASN cc_start: 0.9533 (t0) cc_final: 0.9203 (t0) REVERT: E 187 TYR cc_start: 0.8483 (t80) cc_final: 0.8109 (t80) REVERT: E 211 TYR cc_start: 0.9261 (m-80) cc_final: 0.8801 (m-10) REVERT: E 215 MET cc_start: 0.8756 (mmt) cc_final: 0.8249 (mmm) REVERT: F 77 ASP cc_start: 0.8444 (p0) cc_final: 0.7620 (p0) REVERT: F 137 TYR cc_start: 0.9312 (m-80) cc_final: 0.9104 (m-10) REVERT: F 140 ASP cc_start: 0.9046 (p0) cc_final: 0.8359 (p0) REVERT: F 142 SER cc_start: 0.9280 (m) cc_final: 0.8633 (p) REVERT: F 144 GLU cc_start: 0.7847 (mt-10) cc_final: 0.7595 (mt-10) REVERT: G 53 TYR cc_start: 0.8505 (m-80) cc_final: 0.7909 (m-80) REVERT: G 64 GLN cc_start: 0.8573 (OUTLIER) cc_final: 0.8129 (mt0) REVERT: G 99 ASP cc_start: 0.8884 (p0) cc_final: 0.8668 (p0) REVERT: G 126 GLN cc_start: 0.8111 (tm-30) cc_final: 0.7880 (tm-30) REVERT: G 229 LEU cc_start: 0.9465 (tt) cc_final: 0.9038 (mt) REVERT: H 27 GLU cc_start: 0.8200 (mt-10) cc_final: 0.7954 (mt-10) REVERT: I 56 PHE cc_start: 0.7864 (m-80) cc_final: 0.7465 (m-80) REVERT: J 27 GLU cc_start: 0.8590 (tm-30) cc_final: 0.7583 (tm-30) REVERT: J 28 ASP cc_start: 0.9028 (t0) cc_final: 0.8683 (m-30) REVERT: K 43 ASP cc_start: 0.7927 (t70) cc_final: 0.7688 (t0) REVERT: K 80 ILE cc_start: 0.9614 (mt) cc_final: 0.9405 (tt) REVERT: K 81 MET cc_start: 0.8391 (mmm) cc_final: 0.8165 (mmm) REVERT: K 86 VAL cc_start: 0.9275 (t) cc_final: 0.9057 (m) REVERT: L 50 ASP cc_start: 0.8595 (m-30) cc_final: 0.8362 (m-30) REVERT: M 19 PRO cc_start: 0.7776 (Cg_exo) cc_final: 0.7552 (Cg_endo) REVERT: M 27 PHE cc_start: 0.7025 (p90) cc_final: 0.6730 (p90) REVERT: M 61 GLU cc_start: 0.8570 (mp0) cc_final: 0.8364 (mp0) REVERT: M 62 TYR cc_start: 0.5546 (p90) cc_final: 0.4931 (p90) REVERT: N 87 TYR cc_start: 0.9211 (m-80) cc_final: 0.8934 (m-80) REVERT: N 108 THR cc_start: 0.8476 (m) cc_final: 0.8171 (p) REVERT: O 221 ARG cc_start: 0.7926 (OUTLIER) cc_final: 0.6954 (mmm160) REVERT: O 350 THR cc_start: 0.7865 (OUTLIER) cc_final: 0.7560 (m) REVERT: O 383 ILE cc_start: 0.8470 (OUTLIER) cc_final: 0.8236 (tt) REVERT: O 401 ASN cc_start: 0.8587 (m110) cc_final: 0.8252 (p0) REVERT: O 415 LEU cc_start: 0.9380 (tt) cc_final: 0.9072 (tt) REVERT: O 420 GLU cc_start: 0.8312 (tt0) cc_final: 0.7882 (mp0) REVERT: O 439 LYS cc_start: 0.7998 (OUTLIER) cc_final: 0.7792 (pttm) REVERT: O 471 MET cc_start: 0.9161 (mtt) cc_final: 0.8848 (mmt) REVERT: O 574 TRP cc_start: 0.8562 (OUTLIER) cc_final: 0.8284 (m-90) REVERT: P 127 LYS cc_start: 0.8973 (mtpt) cc_final: 0.8751 (mmmt) REVERT: P 131 HIS cc_start: 0.9071 (m90) cc_final: 0.8101 (m90) REVERT: P 152 LEU cc_start: 0.6566 (OUTLIER) cc_final: 0.6206 (mm) REVERT: P 192 TYR cc_start: 0.7534 (t80) cc_final: 0.7137 (t80) REVERT: P 312 LEU cc_start: 0.9295 (OUTLIER) cc_final: 0.8977 (mt) REVERT: P 434 HIS cc_start: 0.8995 (m90) cc_final: 0.8731 (m-70) REVERT: P 497 GLN cc_start: 0.8936 (OUTLIER) cc_final: 0.8041 (tp-100) REVERT: P 512 ARG cc_start: 0.6788 (OUTLIER) cc_final: 0.5348 (mpp-170) REVERT: Q 204 GLU cc_start: 0.8398 (OUTLIER) cc_final: 0.8012 (pm20) REVERT: Q 229 TRP cc_start: 0.7202 (p-90) cc_final: 0.6850 (p-90) REVERT: Q 307 LYS cc_start: 0.9302 (OUTLIER) cc_final: 0.8926 (tppp) outliers start: 279 outliers final: 130 residues processed: 1190 average time/residue: 0.2809 time to fit residues: 560.4273 Evaluate side-chains 960 residues out of total 4950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 145 poor density : 815 time to evaluate : 1.896 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 ASN Chi-restraints excluded: chain A residue 85 CYS Chi-restraints excluded: chain A residue 94 LEU Chi-restraints excluded: chain A residue 222 GLU Chi-restraints excluded: chain A residue 323 ILE Chi-restraints excluded: chain A residue 339 PHE Chi-restraints excluded: chain A residue 346 SER Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 419 ILE Chi-restraints excluded: chain A residue 450 LYS Chi-restraints excluded: chain A residue 484 ILE Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 565 SER Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 678 VAL Chi-restraints excluded: chain A residue 685 SER Chi-restraints excluded: chain A residue 721 LYS Chi-restraints excluded: chain A residue 952 LEU Chi-restraints excluded: chain A residue 957 VAL Chi-restraints excluded: chain A residue 1033 SER Chi-restraints excluded: chain A residue 1114 TYR Chi-restraints excluded: chain A residue 1118 VAL Chi-restraints excluded: chain A residue 1119 LYS Chi-restraints excluded: chain A residue 1216 THR Chi-restraints excluded: chain A residue 1323 HIS Chi-restraints excluded: chain A residue 1334 LYS Chi-restraints excluded: chain A residue 1491 GLU Chi-restraints excluded: chain A residue 1543 SER Chi-restraints excluded: chain A residue 1634 LEU Chi-restraints excluded: chain A residue 1649 VAL Chi-restraints excluded: chain A residue 1655 ASP Chi-restraints excluded: chain B residue 35 PHE Chi-restraints excluded: chain B residue 75 ASP Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 190 ILE Chi-restraints excluded: chain B residue 218 ILE Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 255 ASP Chi-restraints excluded: chain B residue 288 ILE Chi-restraints excluded: chain B residue 455 GLU Chi-restraints excluded: chain B residue 472 SER Chi-restraints excluded: chain B residue 564 ILE Chi-restraints excluded: chain B residue 592 ILE Chi-restraints excluded: chain B residue 620 LEU Chi-restraints excluded: chain B residue 725 THR Chi-restraints excluded: chain B residue 816 ASN Chi-restraints excluded: chain B residue 918 SER Chi-restraints excluded: chain B residue 985 ILE Chi-restraints excluded: chain B residue 1049 THR Chi-restraints excluded: chain C residue 73 SER Chi-restraints excluded: chain C residue 328 LEU Chi-restraints excluded: chain D residue 46 GLU Chi-restraints excluded: chain D residue 85 SER Chi-restraints excluded: chain D residue 99 LEU Chi-restraints excluded: chain E residue 93 MET Chi-restraints excluded: chain F residue 93 ILE Chi-restraints excluded: chain G residue 61 VAL Chi-restraints excluded: chain G residue 64 GLN Chi-restraints excluded: chain G residue 95 LEU Chi-restraints excluded: chain G residue 97 LYS Chi-restraints excluded: chain G residue 105 ILE Chi-restraints excluded: chain G residue 110 ASP Chi-restraints excluded: chain G residue 226 ASP Chi-restraints excluded: chain G residue 245 VAL Chi-restraints excluded: chain H residue 57 VAL Chi-restraints excluded: chain H residue 61 SER Chi-restraints excluded: chain I residue 6 SER Chi-restraints excluded: chain I residue 39 LYS Chi-restraints excluded: chain J residue 50 ILE Chi-restraints excluded: chain J residue 57 ILE Chi-restraints excluded: chain L residue 46 VAL Chi-restraints excluded: chain L residue 66 GLN Chi-restraints excluded: chain M residue 66 THR Chi-restraints excluded: chain M residue 69 SER Chi-restraints excluded: chain N residue 25 ILE Chi-restraints excluded: chain N residue 32 CYS Chi-restraints excluded: chain N residue 111 VAL Chi-restraints excluded: chain N residue 128 ASN Chi-restraints excluded: chain N residue 131 LEU Chi-restraints excluded: chain N residue 160 VAL Chi-restraints excluded: chain N residue 173 THR Chi-restraints excluded: chain O residue 200 THR Chi-restraints excluded: chain O residue 203 ILE Chi-restraints excluded: chain O residue 210 THR Chi-restraints excluded: chain O residue 221 ARG Chi-restraints excluded: chain O residue 224 THR Chi-restraints excluded: chain O residue 260 LEU Chi-restraints excluded: chain O residue 274 ILE Chi-restraints excluded: chain O residue 292 LEU Chi-restraints excluded: chain O residue 329 ILE Chi-restraints excluded: chain O residue 344 ILE Chi-restraints excluded: chain O residue 350 THR Chi-restraints excluded: chain O residue 353 ASP Chi-restraints excluded: chain O residue 383 ILE Chi-restraints excluded: chain O residue 439 LYS Chi-restraints excluded: chain O residue 480 VAL Chi-restraints excluded: chain O residue 574 TRP Chi-restraints excluded: chain O residue 583 GLU Chi-restraints excluded: chain O residue 617 HIS Chi-restraints excluded: chain O residue 622 TYR Chi-restraints excluded: chain O residue 626 LEU Chi-restraints excluded: chain O residue 629 ARG Chi-restraints excluded: chain O residue 659 LEU Chi-restraints excluded: chain O residue 661 ASN Chi-restraints excluded: chain O residue 665 ASN Chi-restraints excluded: chain O residue 668 SER Chi-restraints excluded: chain O residue 707 ASP Chi-restraints excluded: chain O residue 726 SER Chi-restraints excluded: chain P residue 95 LEU Chi-restraints excluded: chain P residue 147 GLN Chi-restraints excluded: chain P residue 150 GLU Chi-restraints excluded: chain P residue 152 LEU Chi-restraints excluded: chain P residue 154 LEU Chi-restraints excluded: chain P residue 172 LEU Chi-restraints excluded: chain P residue 215 LEU Chi-restraints excluded: chain P residue 259 GLN Chi-restraints excluded: chain P residue 304 LEU Chi-restraints excluded: chain P residue 312 LEU Chi-restraints excluded: chain P residue 370 SER Chi-restraints excluded: chain P residue 388 THR Chi-restraints excluded: chain P residue 437 THR Chi-restraints excluded: chain P residue 453 PHE Chi-restraints excluded: chain P residue 493 ILE Chi-restraints excluded: chain P residue 497 GLN Chi-restraints excluded: chain P residue 512 ARG Chi-restraints excluded: chain Q residue 1 MET Chi-restraints excluded: chain Q residue 4 VAL Chi-restraints excluded: chain Q residue 27 ILE Chi-restraints excluded: chain Q residue 128 TRP Chi-restraints excluded: chain Q residue 138 PHE Chi-restraints excluded: chain Q residue 155 GLN Chi-restraints excluded: chain Q residue 168 ILE Chi-restraints excluded: chain Q residue 180 CYS Chi-restraints excluded: chain Q residue 204 GLU Chi-restraints excluded: chain Q residue 218 ASP Chi-restraints excluded: chain Q residue 247 ILE Chi-restraints excluded: chain Q residue 248 LYS Chi-restraints excluded: chain Q residue 298 GLN Chi-restraints excluded: chain Q residue 307 LYS Chi-restraints excluded: chain Q residue 317 LEU Chi-restraints excluded: chain Q residue 352 TRP Chi-restraints excluded: chain Q residue 384 VAL Chi-restraints excluded: chain Q residue 390 ASN Chi-restraints excluded: chain Q residue 393 ILE Chi-restraints excluded: chain Q residue 426 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 555 random chunks: chunk 522 optimal weight: 10.0000 chunk 450 optimal weight: 30.0000 chunk 501 optimal weight: 10.0000 chunk 194 optimal weight: 8.9990 chunk 445 optimal weight: 20.0000 chunk 133 optimal weight: 7.9990 chunk 179 optimal weight: 9.9990 chunk 408 optimal weight: 8.9990 chunk 250 optimal weight: 2.9990 chunk 507 optimal weight: 9.9990 chunk 183 optimal weight: 9.9990 overall best weight: 7.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 40 ASN A 93 GLN ** A 431 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 432 ASN ** A 580 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 656 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 926 GLN A1438 ASN ** B 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 197 ASN ** B 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 499 HIS ** B 504 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 720 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 824 HIS B1034 GLN ** B1163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 93 GLN C 175 GLN ** C 297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 36 ASN ** G 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 237 HIS H 133 ASN H 137 GLN I 41 GLN ** M 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 22 GLN Q 246 GLN Q 289 ASN ** Q 372 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 387 ASN Q 402 ASN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.114693 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.081368 restraints weight = 143747.561| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.083848 restraints weight = 69753.999| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.084803 restraints weight = 37367.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.085020 restraints weight = 30318.673| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.085091 restraints weight = 27862.467| |-----------------------------------------------------------------------------| r_work (final): 0.3201 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7767 moved from start: 0.4847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.102 47752 Z= 0.355 Angle : 0.996 26.089 64966 Z= 0.510 Chirality : 0.054 0.480 7264 Planarity : 0.007 0.139 7978 Dihedral : 14.819 168.069 7274 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 23.42 Ramachandran Plot: Outliers : 1.05 % Allowed : 8.08 % Favored : 90.87 % Rotamer: Outliers : 5.84 % Allowed : 16.23 % Favored : 77.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.65 % 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: -1.60 (0.11), residues: 5432 helix: -0.04 (0.11), residues: 1993 sheet: -1.25 (0.17), residues: 758 loop : -1.81 (0.12), residues: 2681 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG P 445 TYR 0.052 0.003 TYR P 211 PHE 0.104 0.003 PHE Q 358 TRP 0.075 0.003 TRP O 310 HIS 0.012 0.002 HIS P 482 Details of bonding type rmsd/Z covalent geometry : bond 0.00777 / 0.35 (47712) covalent geometry : angle 0.97696 / 0.51 (64930) hydrogen bonds : bond 0.06253 / 4.22 ( 2015) hydrogen bonds : angle 6.36814 / 4.47 ( 5581) metal coordination : bond 0.02546 / 1.46 ( 24) metal coordination : angle 8.63819 / 6.49 ( 33) Misc. bond : bond 0.01606 / 0.73 ( 15) link_TRANS : bond 0.00193 / 0.10 ( 1) link_TRANS : angle 0.36267 / 0.20 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10864 Ramachandran restraints generated. 5432 Oldfield, 0 Emsley, 5432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10864 Ramachandran restraints generated. 5432 Oldfield, 0 Emsley, 5432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1114 residues out of total 4950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 289 poor density : 825 time to evaluate : 1.866 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.8602 (tpp) cc_final: 0.8052 (tpp) REVERT: A 342 ARG cc_start: 0.8096 (ptp-110) cc_final: 0.7363 (ttm-80) REVERT: A 435 ASN cc_start: 0.8577 (m-40) cc_final: 0.8288 (m-40) REVERT: A 442 LYS cc_start: 0.8917 (OUTLIER) cc_final: 0.8484 (mmtp) REVERT: A 450 LYS cc_start: 0.4782 (OUTLIER) cc_final: 0.3270 (mttm) REVERT: A 553 GLN cc_start: 0.8673 (OUTLIER) cc_final: 0.8461 (pt0) REVERT: A 589 MET cc_start: 0.8503 (mmm) cc_final: 0.8238 (mmm) REVERT: A 635 MET cc_start: 0.8949 (ttp) cc_final: 0.8667 (ttp) REVERT: A 721 LYS cc_start: 0.8456 (OUTLIER) cc_final: 0.7982 (tptt) REVERT: A 723 TYR cc_start: 0.7636 (m-80) cc_final: 0.7419 (m-10) REVERT: A 881 GLU cc_start: 0.8668 (tt0) cc_final: 0.8311 (tp30) REVERT: A 882 ILE cc_start: 0.9547 (mm) cc_final: 0.9342 (mt) REVERT: A 1004 GLU cc_start: 0.1411 (tm-30) cc_final: 0.0979 (tp30) REVERT: A 1015 ARG cc_start: -0.1191 (mtm180) cc_final: -0.1472 (mmm-85) REVERT: A 1071 ASP cc_start: 0.8582 (t0) cc_final: 0.8364 (t0) REVERT: A 1294 MET cc_start: 0.8989 (mtm) cc_final: 0.8572 (ptp) REVERT: A 1575 ILE cc_start: 0.9325 (mm) cc_final: 0.9061 (tp) REVERT: A 1576 SER cc_start: 0.9127 (m) cc_final: 0.8635 (p) REVERT: A 1611 MET cc_start: 0.8698 (tmm) cc_final: 0.8354 (tmm) REVERT: A 1620 GLN cc_start: 0.8983 (mp10) cc_final: 0.8537 (mp10) REVERT: B 97 VAL cc_start: 0.9513 (t) cc_final: 0.9213 (m) REVERT: B 175 MET cc_start: 0.8974 (mtt) cc_final: 0.8646 (mtp) REVERT: B 377 MET cc_start: 0.8768 (mtm) cc_final: 0.8516 (mtm) REVERT: B 419 GLU cc_start: 0.8220 (tp30) cc_final: 0.7607 (tp30) REVERT: B 422 GLN cc_start: 0.8694 (mt0) cc_final: 0.8188 (mt0) REVERT: B 430 MET cc_start: 0.8394 (OUTLIER) cc_final: 0.8142 (tmm) REVERT: B 444 ARG cc_start: 0.8890 (tpp80) cc_final: 0.8677 (tpp80) REVERT: B 512 LEU cc_start: 0.8901 (mt) cc_final: 0.8641 (mp) REVERT: B 778 TYR cc_start: 0.8995 (t80) cc_final: 0.7953 (t80) REVERT: B 782 ASP cc_start: 0.7464 (p0) cc_final: 0.7171 (p0) REVERT: B 807 GLU cc_start: 0.7919 (tt0) cc_final: 0.7615 (tt0) REVERT: B 816 ASN cc_start: 0.6220 (OUTLIER) cc_final: 0.5382 (m110) REVERT: B 900 THR cc_start: 0.9545 (m) cc_final: 0.9070 (p) REVERT: B 1085 SER cc_start: 0.9395 (OUTLIER) cc_final: 0.9187 (t) REVERT: E 136 ASN cc_start: 0.9298 (t0) cc_final: 0.9046 (t0) REVERT: E 215 MET cc_start: 0.8647 (mmt) cc_final: 0.8351 (mmm) REVERT: F 140 ASP cc_start: 0.9262 (p0) cc_final: 0.8622 (p0) REVERT: F 142 SER cc_start: 0.9376 (m) cc_final: 0.8826 (p) REVERT: F 144 GLU cc_start: 0.7859 (mt-10) cc_final: 0.7542 (mt-10) REVERT: G 53 TYR cc_start: 0.8646 (m-80) cc_final: 0.8236 (m-80) REVERT: G 64 GLN cc_start: 0.8677 (mt0) cc_final: 0.8200 (mt0) REVERT: G 71 MET cc_start: 0.8398 (mmm) cc_final: 0.8059 (mmm) REVERT: G 99 ASP cc_start: 0.8770 (p0) cc_final: 0.8469 (p0) REVERT: G 126 GLN cc_start: 0.8093 (tm-30) cc_final: 0.7721 (tm-30) REVERT: G 229 LEU cc_start: 0.9456 (tt) cc_final: 0.9054 (mp) REVERT: G 237 HIS cc_start: 0.8707 (m170) cc_final: 0.8436 (m90) REVERT: H 14 GLU cc_start: 0.8510 (tp30) cc_final: 0.7913 (tp30) REVERT: H 27 GLU cc_start: 0.8208 (mt-10) cc_final: 0.7742 (mp0) REVERT: H 142 LEU cc_start: 0.9618 (tp) cc_final: 0.9414 (tt) REVERT: J 1 MET cc_start: 0.8355 (tpp) cc_final: 0.8056 (tpt) REVERT: K 43 ASP cc_start: 0.7609 (t70) cc_final: 0.6808 (t70) REVERT: K 44 ARG cc_start: 0.9046 (mtp85) cc_final: 0.8789 (mtp85) REVERT: K 81 MET cc_start: 0.8384 (mmm) cc_final: 0.8138 (mmm) REVERT: K 86 VAL cc_start: 0.9363 (t) cc_final: 0.9142 (p) REVERT: K 129 ASP cc_start: 0.8793 (m-30) cc_final: 0.8513 (m-30) REVERT: L 49 LYS cc_start: 0.9262 (mtmm) cc_final: 0.8802 (mtmt) REVERT: M 41 TYR cc_start: 0.9039 (m-80) cc_final: 0.8761 (m-80) REVERT: M 62 TYR cc_start: 0.5879 (p90) cc_final: 0.5012 (p90) REVERT: M 91 TYR cc_start: 0.8514 (m-80) cc_final: 0.8057 (m-80) REVERT: M 92 LYS cc_start: 0.8832 (mtpt) cc_final: 0.8585 (mtmt) REVERT: N 54 TRP cc_start: 0.9400 (m-10) cc_final: 0.9101 (m-90) REVERT: N 63 ASP cc_start: 0.9334 (t0) cc_final: 0.9043 (p0) REVERT: N 67 LEU cc_start: 0.9314 (tp) cc_final: 0.9095 (tt) REVERT: N 114 GLU cc_start: 0.7967 (pt0) cc_final: 0.7546 (mm-30) REVERT: O 221 ARG cc_start: 0.7737 (OUTLIER) cc_final: 0.7038 (mmm160) REVERT: O 313 GLN cc_start: 0.8809 (OUTLIER) cc_final: 0.8388 (pp30) REVERT: O 326 ILE cc_start: 0.5967 (OUTLIER) cc_final: 0.5687 (pt) REVERT: O 401 ASN cc_start: 0.8854 (m110) cc_final: 0.8117 (t0) REVERT: O 439 LYS cc_start: 0.8264 (OUTLIER) cc_final: 0.8016 (pttm) REVERT: O 471 MET cc_start: 0.8976 (mtt) cc_final: 0.8739 (mmm) REVERT: O 485 LYS cc_start: 0.8607 (OUTLIER) cc_final: 0.8317 (mmtm) REVERT: P 127 LYS cc_start: 0.8883 (mtpt) cc_final: 0.8654 (mmmt) REVERT: P 131 HIS cc_start: 0.9216 (m90) cc_final: 0.8342 (m90) REVERT: P 497 GLN cc_start: 0.8891 (OUTLIER) cc_final: 0.8206 (tp-100) REVERT: P 512 ARG cc_start: 0.5699 (OUTLIER) cc_final: 0.4980 (mtm180) REVERT: Q 138 PHE cc_start: 0.8221 (OUTLIER) cc_final: 0.7691 (t80) REVERT: Q 204 GLU cc_start: 0.8494 (OUTLIER) cc_final: 0.7912 (pm20) REVERT: Q 255 VAL cc_start: 0.9258 (OUTLIER) cc_final: 0.9022 (m) REVERT: Q 278 TYR cc_start: 0.8868 (m-80) cc_final: 0.8600 (m-80) REVERT: Q 304 HIS cc_start: 0.7866 (t-90) cc_final: 0.7033 (t-90) REVERT: Q 307 LYS cc_start: 0.9243 (tppp) cc_final: 0.9030 (tppp) outliers start: 289 outliers final: 164 residues processed: 1027 average time/residue: 0.2645 time to fit residues: 461.8596 Evaluate side-chains 907 residues out of total 4950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 181 poor density : 726 time to evaluate : 1.868 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 ASP Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 229 SER Chi-restraints excluded: chain A residue 323 ILE Chi-restraints excluded: chain A residue 346 SER Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 403 LEU Chi-restraints excluded: chain A residue 419 ILE Chi-restraints excluded: chain A residue 442 LYS Chi-restraints excluded: chain A residue 450 LYS Chi-restraints excluded: chain A residue 484 ILE Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 553 GLN Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 586 VAL Chi-restraints excluded: chain A residue 601 MET Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain A residue 678 VAL Chi-restraints excluded: chain A residue 685 SER Chi-restraints excluded: chain A residue 721 LYS Chi-restraints excluded: chain A residue 862 THR Chi-restraints excluded: chain A residue 891 ILE Chi-restraints excluded: chain A residue 947 LEU Chi-restraints excluded: chain A residue 957 VAL Chi-restraints excluded: chain A residue 1016 SER Chi-restraints excluded: chain A residue 1019 LEU Chi-restraints excluded: chain A residue 1033 SER Chi-restraints excluded: chain A residue 1118 VAL Chi-restraints excluded: chain A residue 1119 LYS Chi-restraints excluded: chain A residue 1216 THR Chi-restraints excluded: chain A residue 1222 LEU Chi-restraints excluded: chain A residue 1323 HIS Chi-restraints excluded: chain A residue 1489 VAL Chi-restraints excluded: chain A residue 1491 GLU Chi-restraints excluded: chain A residue 1543 SER Chi-restraints excluded: chain A residue 1563 VAL Chi-restraints excluded: chain A residue 1634 LEU Chi-restraints excluded: chain A residue 1649 VAL Chi-restraints excluded: chain B residue 35 PHE Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 46 ILE Chi-restraints excluded: chain B residue 53 THR Chi-restraints excluded: chain B residue 68 ILE Chi-restraints excluded: chain B residue 75 ASP Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 218 ILE Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 249 VAL Chi-restraints excluded: chain B residue 288 ILE Chi-restraints excluded: chain B residue 343 ASP Chi-restraints excluded: chain B residue 409 TYR Chi-restraints excluded: chain B residue 424 ILE Chi-restraints excluded: chain B residue 430 MET Chi-restraints excluded: chain B residue 455 GLU Chi-restraints excluded: chain B residue 462 GLN Chi-restraints excluded: chain B residue 472 SER Chi-restraints excluded: chain B residue 502 MET Chi-restraints excluded: chain B residue 516 THR Chi-restraints excluded: chain B residue 564 ILE Chi-restraints excluded: chain B residue 592 ILE Chi-restraints excluded: chain B residue 620 LEU Chi-restraints excluded: chain B residue 647 SER Chi-restraints excluded: chain B residue 725 THR Chi-restraints excluded: chain B residue 816 ASN Chi-restraints excluded: chain B residue 819 ASP Chi-restraints excluded: chain B residue 858 ILE Chi-restraints excluded: chain B residue 985 ILE Chi-restraints excluded: chain B residue 1069 ILE Chi-restraints excluded: chain B residue 1085 SER Chi-restraints excluded: chain B residue 1178 ILE Chi-restraints excluded: chain C residue 73 SER Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain C residue 201 GLU Chi-restraints excluded: chain C residue 328 LEU Chi-restraints excluded: chain D residue 31 VAL Chi-restraints excluded: chain D residue 85 SER Chi-restraints excluded: chain F residue 89 GLU Chi-restraints excluded: chain F residue 93 ILE Chi-restraints excluded: chain G residue 47 VAL Chi-restraints excluded: chain G residue 61 VAL Chi-restraints excluded: chain G residue 69 LEU Chi-restraints excluded: chain G residue 95 LEU Chi-restraints excluded: chain G residue 97 LYS Chi-restraints excluded: chain G residue 104 LEU Chi-restraints excluded: chain G residue 110 ASP Chi-restraints excluded: chain G residue 138 PHE Chi-restraints excluded: chain G residue 226 ASP Chi-restraints excluded: chain G residue 245 VAL Chi-restraints excluded: chain G residue 246 ASP Chi-restraints excluded: chain H residue 57 VAL Chi-restraints excluded: chain H residue 109 LYS Chi-restraints excluded: chain H residue 112 ILE Chi-restraints excluded: chain I residue 6 SER Chi-restraints excluded: chain I residue 29 GLU Chi-restraints excluded: chain I residue 39 LYS Chi-restraints excluded: chain I residue 42 PHE Chi-restraints excluded: chain I residue 60 LEU Chi-restraints excluded: chain J residue 50 ILE Chi-restraints excluded: chain J residue 57 ILE Chi-restraints excluded: chain K residue 117 LEU Chi-restraints excluded: chain L residue 46 VAL Chi-restraints excluded: chain L residue 55 ILE Chi-restraints excluded: chain M residue 66 THR Chi-restraints excluded: chain M residue 69 SER Chi-restraints excluded: chain M residue 77 VAL Chi-restraints excluded: chain M residue 98 SER Chi-restraints excluded: chain N residue 25 ILE Chi-restraints excluded: chain N residue 32 CYS Chi-restraints excluded: chain N residue 110 LEU Chi-restraints excluded: chain N residue 111 VAL Chi-restraints excluded: chain N residue 131 LEU Chi-restraints excluded: chain N residue 151 SER Chi-restraints excluded: chain N residue 160 VAL Chi-restraints excluded: chain N residue 173 THR Chi-restraints excluded: chain O residue 202 ILE Chi-restraints excluded: chain O residue 210 THR Chi-restraints excluded: chain O residue 221 ARG Chi-restraints excluded: chain O residue 224 THR Chi-restraints excluded: chain O residue 254 ILE Chi-restraints excluded: chain O residue 260 LEU Chi-restraints excluded: chain O residue 274 ILE Chi-restraints excluded: chain O residue 292 LEU Chi-restraints excluded: chain O residue 313 GLN Chi-restraints excluded: chain O residue 326 ILE Chi-restraints excluded: chain O residue 329 ILE Chi-restraints excluded: chain O residue 344 ILE Chi-restraints excluded: chain O residue 384 ASP Chi-restraints excluded: chain O residue 406 LYS Chi-restraints excluded: chain O residue 439 LYS Chi-restraints excluded: chain O residue 480 VAL Chi-restraints excluded: chain O residue 485 LYS Chi-restraints excluded: chain O residue 533 LEU Chi-restraints excluded: chain O residue 583 GLU Chi-restraints excluded: chain O residue 622 TYR Chi-restraints excluded: chain O residue 626 LEU Chi-restraints excluded: chain O residue 659 LEU Chi-restraints excluded: chain O residue 661 ASN Chi-restraints excluded: chain O residue 668 SER Chi-restraints excluded: chain O residue 707 ASP Chi-restraints excluded: chain O residue 726 SER Chi-restraints excluded: chain P residue 95 LEU Chi-restraints excluded: chain P residue 147 GLN Chi-restraints excluded: chain P residue 150 GLU Chi-restraints excluded: chain P residue 154 LEU Chi-restraints excluded: chain P residue 215 LEU Chi-restraints excluded: chain P residue 259 GLN Chi-restraints excluded: chain P residue 262 LEU Chi-restraints excluded: chain P residue 304 LEU Chi-restraints excluded: chain P residue 367 PHE Chi-restraints excluded: chain P residue 370 SER Chi-restraints excluded: chain P residue 371 GLU Chi-restraints excluded: chain P residue 374 THR Chi-restraints excluded: chain P residue 437 THR Chi-restraints excluded: chain P residue 453 PHE Chi-restraints excluded: chain P residue 479 LEU Chi-restraints excluded: chain P residue 493 ILE Chi-restraints excluded: chain P residue 497 GLN Chi-restraints excluded: chain P residue 512 ARG Chi-restraints excluded: chain Q residue 4 VAL Chi-restraints excluded: chain Q residue 10 ASN Chi-restraints excluded: chain Q residue 27 ILE Chi-restraints excluded: chain Q residue 127 PHE Chi-restraints excluded: chain Q residue 128 TRP Chi-restraints excluded: chain Q residue 138 PHE Chi-restraints excluded: chain Q residue 155 GLN Chi-restraints excluded: chain Q residue 158 THR Chi-restraints excluded: chain Q residue 168 ILE Chi-restraints excluded: chain Q residue 186 LEU Chi-restraints excluded: chain Q residue 187 TYR Chi-restraints excluded: chain Q residue 204 GLU Chi-restraints excluded: chain Q residue 240 ILE Chi-restraints excluded: chain Q residue 247 ILE Chi-restraints excluded: chain Q residue 248 LYS Chi-restraints excluded: chain Q residue 251 TRP Chi-restraints excluded: chain Q residue 255 VAL Chi-restraints excluded: chain Q residue 269 ASP Chi-restraints excluded: chain Q residue 298 GLN Chi-restraints excluded: chain Q residue 317 LEU Chi-restraints excluded: chain Q residue 390 ASN Chi-restraints excluded: chain Q residue 401 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 555 random chunks: chunk 193 optimal weight: 0.9980 chunk 390 optimal weight: 30.0000 chunk 13 optimal weight: 4.9990 chunk 399 optimal weight: 10.0000 chunk 185 optimal weight: 0.9980 chunk 15 optimal weight: 6.9990 chunk 130 optimal weight: 8.9990 chunk 205 optimal weight: 0.9980 chunk 484 optimal weight: 7.9990 chunk 187 optimal weight: 5.9990 chunk 32 optimal weight: 9.9990 overall best weight: 2.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 93 GLN ** A 382 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 431 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 580 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 636 HIS ** A 656 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 128 GLN ** B 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 504 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 720 GLN ** B1163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 100 GLN ** G 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 64 GLN ** G 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 137 GLN H 139 ASN ** M 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 128 ASN ** P 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 497 GLN Q 221 HIS ** Q 372 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.117043 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.084097 restraints weight = 142098.680| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.086949 restraints weight = 66228.948| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.087841 restraints weight = 34261.301| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.088022 restraints weight = 28152.853| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.088127 restraints weight = 26060.555| |-----------------------------------------------------------------------------| r_work (final): 0.3243 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7693 moved from start: 0.5262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 47752 Z= 0.204 Angle : 0.882 23.455 64966 Z= 0.449 Chirality : 0.050 0.373 7264 Planarity : 0.007 0.134 7978 Dihedral : 14.722 166.531 7249 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 19.25 Ramachandran Plot: Outliers : 0.90 % Allowed : 7.53 % Favored : 91.57 % Rotamer: Outliers : 4.45 % Allowed : 18.17 % Favored : 77.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.65 % Twisted General : 0.10 % 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: -1.29 (0.11), residues: 5432 helix: 0.23 (0.11), residues: 1996 sheet: -1.09 (0.18), residues: 761 loop : -1.63 (0.12), residues: 2675 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG G 15 TYR 0.048 0.002 TYR P 211 PHE 0.111 0.002 PHE Q 358 TRP 0.031 0.002 TRP O 324 HIS 0.007 0.001 HIS P 157 Details of bonding type rmsd/Z covalent geometry : bond 0.00443 / 0.20 (47712) covalent geometry : angle 0.86549 / 0.45 (64930) hydrogen bonds : bond 0.05540 / 3.75 ( 2015) hydrogen bonds : angle 5.99284 / 4.22 ( 5581) metal coordination : bond 0.01328 / 0.78 ( 24) metal coordination : angle 7.55325 / 5.65 ( 33) Misc. bond : bond 0.01060 / 0.55 ( 15) link_TRANS : bond 0.00125 / 0.07 ( 1) link_TRANS : angle 0.15812 / 0.09 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10864 Ramachandran restraints generated. 5432 Oldfield, 0 Emsley, 5432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10864 Ramachandran restraints generated. 5432 Oldfield, 0 Emsley, 5432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1051 residues out of total 4950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 220 poor density : 831 time to evaluate : 1.877 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.8533 (tpp) cc_final: 0.8181 (tpp) REVERT: A 30 LYS cc_start: 0.9103 (tppt) cc_final: 0.8793 (tptp) REVERT: A 93 GLN cc_start: 0.9258 (OUTLIER) cc_final: 0.8831 (mt0) REVERT: A 108 PHE cc_start: 0.9311 (m-80) cc_final: 0.8685 (m-80) REVERT: A 315 ILE cc_start: 0.9140 (pt) cc_final: 0.8860 (mt) REVERT: A 365 THR cc_start: 0.9279 (m) cc_final: 0.9075 (p) REVERT: A 394 LEU cc_start: 0.9508 (tp) cc_final: 0.9269 (pp) REVERT: A 424 MET cc_start: 0.8709 (mmt) cc_final: 0.8322 (mmp) REVERT: A 450 LYS cc_start: 0.4829 (OUTLIER) cc_final: 0.3034 (mmtp) REVERT: A 721 LYS cc_start: 0.8333 (OUTLIER) cc_final: 0.7886 (tptt) REVERT: A 723 TYR cc_start: 0.7662 (m-80) cc_final: 0.7445 (m-10) REVERT: A 819 ASN cc_start: 0.9190 (m-40) cc_final: 0.8649 (m-40) REVERT: A 881 GLU cc_start: 0.8679 (tt0) cc_final: 0.8300 (tp30) REVERT: A 882 ILE cc_start: 0.9495 (mm) cc_final: 0.9276 (mt) REVERT: A 1004 GLU cc_start: 0.0970 (tm-30) cc_final: 0.0495 (tp30) REVERT: A 1024 THR cc_start: -0.1537 (m) cc_final: -0.2200 (t) REVERT: A 1294 MET cc_start: 0.8986 (mtm) cc_final: 0.8635 (ptp) REVERT: A 1545 ASP cc_start: 0.9202 (t0) cc_final: 0.8989 (t0) REVERT: A 1576 SER cc_start: 0.9010 (m) cc_final: 0.8453 (p) REVERT: A 1611 MET cc_start: 0.8670 (tmm) cc_final: 0.8308 (tmm) REVERT: B 54 GLU cc_start: 0.8437 (tm-30) cc_final: 0.8176 (tm-30) REVERT: B 97 VAL cc_start: 0.9489 (t) cc_final: 0.9189 (m) REVERT: B 108 MET cc_start: 0.9172 (mmt) cc_final: 0.8880 (mmp) REVERT: B 373 MET cc_start: 0.8793 (tpp) cc_final: 0.8581 (tpp) REVERT: B 419 GLU cc_start: 0.8281 (tp30) cc_final: 0.7302 (tp30) REVERT: B 422 GLN cc_start: 0.8736 (mt0) cc_final: 0.8258 (mt0) REVERT: B 430 MET cc_start: 0.8298 (OUTLIER) cc_final: 0.7931 (tmm) REVERT: B 512 LEU cc_start: 0.8894 (mt) cc_final: 0.8661 (mp) REVERT: B 778 TYR cc_start: 0.8880 (t80) cc_final: 0.7849 (t80) REVERT: B 807 GLU cc_start: 0.7931 (tt0) cc_final: 0.7652 (tt0) REVERT: B 900 THR cc_start: 0.9522 (m) cc_final: 0.9104 (p) REVERT: B 1186 ASP cc_start: 0.7816 (OUTLIER) cc_final: 0.7173 (t70) REVERT: B 1192 MET cc_start: 0.7960 (mpp) cc_final: 0.7602 (mpp) REVERT: B 1194 ILE cc_start: 0.3762 (OUTLIER) cc_final: 0.3199 (mt) REVERT: C 71 MET cc_start: 0.9222 (ttm) cc_final: 0.8874 (ttp) REVERT: D 15 THR cc_start: 0.9317 (p) cc_final: 0.9040 (t) REVERT: E 78 LEU cc_start: 0.9417 (tt) cc_final: 0.9009 (tt) REVERT: E 112 TYR cc_start: 0.9026 (p90) cc_final: 0.7998 (p90) REVERT: E 114 ASN cc_start: 0.9403 (t0) cc_final: 0.8987 (t0) REVERT: E 136 ASN cc_start: 0.9297 (t0) cc_final: 0.8869 (t0) REVERT: E 211 TYR cc_start: 0.9305 (m-80) cc_final: 0.8717 (m-10) REVERT: E 215 MET cc_start: 0.8501 (mmt) cc_final: 0.8284 (mmm) REVERT: F 77 ASP cc_start: 0.8513 (p0) cc_final: 0.8305 (p0) REVERT: F 108 PHE cc_start: 0.8304 (m-10) cc_final: 0.8076 (m-10) REVERT: F 140 ASP cc_start: 0.9292 (p0) cc_final: 0.8632 (p0) REVERT: F 142 SER cc_start: 0.9355 (m) cc_final: 0.8917 (p) REVERT: F 144 GLU cc_start: 0.7725 (mt-10) cc_final: 0.7523 (mt-10) REVERT: F 151 LEU cc_start: 0.9458 (tp) cc_final: 0.9195 (tp) REVERT: G 64 GLN cc_start: 0.8589 (mt0) cc_final: 0.7851 (mt0) REVERT: G 126 GLN cc_start: 0.8049 (tm-30) cc_final: 0.7584 (tm-30) REVERT: G 229 LEU cc_start: 0.9433 (tt) cc_final: 0.8997 (mp) REVERT: G 237 HIS cc_start: 0.8657 (m170) cc_final: 0.8385 (m90) REVERT: H 14 GLU cc_start: 0.8496 (tp30) cc_final: 0.8044 (tp30) REVERT: H 27 GLU cc_start: 0.8366 (mt-10) cc_final: 0.7911 (mp0) REVERT: K 43 ASP cc_start: 0.7459 (t70) cc_final: 0.7127 (t70) REVERT: K 86 VAL cc_start: 0.9346 (t) cc_final: 0.9141 (p) REVERT: K 97 SER cc_start: 0.9245 (m) cc_final: 0.8731 (t) REVERT: K 122 LYS cc_start: 0.9252 (tppt) cc_final: 0.9028 (tppt) REVERT: K 125 MET cc_start: 0.8703 (mtp) cc_final: 0.8472 (mtp) REVERT: K 129 ASP cc_start: 0.8853 (m-30) cc_final: 0.8498 (m-30) REVERT: M 62 TYR cc_start: 0.5839 (p90) cc_final: 0.5061 (p90) REVERT: N 54 TRP cc_start: 0.9393 (m-10) cc_final: 0.9087 (m-90) REVERT: N 87 TYR cc_start: 0.8714 (m-80) cc_final: 0.8091 (m-80) REVERT: N 114 GLU cc_start: 0.7976 (pt0) cc_final: 0.7614 (mm-30) REVERT: O 313 GLN cc_start: 0.8694 (OUTLIER) cc_final: 0.8377 (pp30) REVERT: O 471 MET cc_start: 0.9034 (mtt) cc_final: 0.8757 (mmm) REVERT: O 574 TRP cc_start: 0.8179 (OUTLIER) cc_final: 0.6685 (m-10) REVERT: P 131 HIS cc_start: 0.9281 (m90) cc_final: 0.8436 (m90) REVERT: P 192 TYR cc_start: 0.7593 (t80) cc_final: 0.7385 (t80) REVERT: P 366 TYR cc_start: 0.7653 (t80) cc_final: 0.7400 (t80) REVERT: P 497 GLN cc_start: 0.9170 (tt0) cc_final: 0.8681 (tp-100) REVERT: P 512 ARG cc_start: 0.6443 (OUTLIER) cc_final: 0.5690 (mtm180) REVERT: Q 138 PHE cc_start: 0.8443 (OUTLIER) cc_final: 0.7880 (t80) REVERT: Q 204 GLU cc_start: 0.8496 (OUTLIER) cc_final: 0.8185 (pm20) REVERT: Q 218 ASP cc_start: 0.8128 (m-30) cc_final: 0.7873 (m-30) REVERT: Q 298 GLN cc_start: 0.7838 (OUTLIER) cc_final: 0.6998 (pm20) REVERT: Q 304 HIS cc_start: 0.8028 (t-90) cc_final: 0.7295 (t-90) outliers start: 220 outliers final: 137 residues processed: 980 average time/residue: 0.2311 time to fit residues: 383.7672 Evaluate side-chains 896 residues out of total 4950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 149 poor density : 747 time to evaluate : 1.093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 ILE Chi-restraints excluded: chain A residue 93 GLN Chi-restraints excluded: chain A residue 94 LEU Chi-restraints excluded: chain A residue 346 SER Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 403 LEU Chi-restraints excluded: chain A residue 419 ILE Chi-restraints excluded: chain A residue 450 LYS Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 601 MET Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain A residue 678 VAL Chi-restraints excluded: chain A residue 685 SER Chi-restraints excluded: chain A residue 721 LYS Chi-restraints excluded: chain A residue 947 LEU Chi-restraints excluded: chain A residue 957 VAL Chi-restraints excluded: chain A residue 1019 LEU Chi-restraints excluded: chain A residue 1063 MET Chi-restraints excluded: chain A residue 1118 VAL Chi-restraints excluded: chain A residue 1119 LYS Chi-restraints excluded: chain A residue 1222 LEU Chi-restraints excluded: chain A residue 1323 HIS Chi-restraints excluded: chain A residue 1470 CYS Chi-restraints excluded: chain A residue 1491 GLU Chi-restraints excluded: chain A residue 1543 SER Chi-restraints excluded: chain A residue 1634 LEU Chi-restraints excluded: chain A residue 1649 VAL Chi-restraints excluded: chain B residue 35 PHE Chi-restraints excluded: chain B residue 68 ILE Chi-restraints excluded: chain B residue 75 ASP Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 190 ILE Chi-restraints excluded: chain B residue 218 ILE Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 288 ILE Chi-restraints excluded: chain B residue 409 TYR Chi-restraints excluded: chain B residue 424 ILE Chi-restraints excluded: chain B residue 430 MET Chi-restraints excluded: chain B residue 455 GLU Chi-restraints excluded: chain B residue 462 GLN Chi-restraints excluded: chain B residue 564 ILE Chi-restraints excluded: chain B residue 592 ILE Chi-restraints excluded: chain B residue 620 LEU Chi-restraints excluded: chain B residue 712 SER Chi-restraints excluded: chain B residue 725 THR Chi-restraints excluded: chain B residue 819 ASP Chi-restraints excluded: chain B residue 910 THR Chi-restraints excluded: chain B residue 918 SER Chi-restraints excluded: chain B residue 1087 LEU Chi-restraints excluded: chain B residue 1178 ILE Chi-restraints excluded: chain B residue 1186 ASP Chi-restraints excluded: chain B residue 1194 ILE Chi-restraints excluded: chain C residue 73 SER Chi-restraints excluded: chain C residue 120 LEU Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain C residue 167 LEU Chi-restraints excluded: chain C residue 201 GLU Chi-restraints excluded: chain C residue 328 LEU Chi-restraints excluded: chain D residue 85 SER Chi-restraints excluded: chain D residue 99 LEU Chi-restraints excluded: chain F residue 93 ILE Chi-restraints excluded: chain G residue 47 VAL Chi-restraints excluded: chain G residue 61 VAL Chi-restraints excluded: chain G residue 69 LEU Chi-restraints excluded: chain G residue 104 LEU Chi-restraints excluded: chain G residue 138 PHE Chi-restraints excluded: chain G residue 226 ASP Chi-restraints excluded: chain G residue 245 VAL Chi-restraints excluded: chain G residue 246 ASP Chi-restraints excluded: chain H residue 137 GLN Chi-restraints excluded: chain H residue 139 ASN Chi-restraints excluded: chain I residue 6 SER Chi-restraints excluded: chain I residue 39 LYS Chi-restraints excluded: chain I residue 42 PHE Chi-restraints excluded: chain I residue 60 LEU Chi-restraints excluded: chain J residue 50 ILE Chi-restraints excluded: chain J residue 57 ILE Chi-restraints excluded: chain L residue 46 VAL Chi-restraints excluded: chain L residue 65 VAL Chi-restraints excluded: chain M residue 77 VAL Chi-restraints excluded: chain M residue 78 VAL Chi-restraints excluded: chain N residue 25 ILE Chi-restraints excluded: chain N residue 32 CYS Chi-restraints excluded: chain N residue 111 VAL Chi-restraints excluded: chain N residue 128 ASN Chi-restraints excluded: chain N residue 131 LEU Chi-restraints excluded: chain N residue 160 VAL Chi-restraints excluded: chain N residue 173 THR Chi-restraints excluded: chain O residue 202 ILE Chi-restraints excluded: chain O residue 254 ILE Chi-restraints excluded: chain O residue 258 SER Chi-restraints excluded: chain O residue 260 LEU Chi-restraints excluded: chain O residue 274 ILE Chi-restraints excluded: chain O residue 313 GLN Chi-restraints excluded: chain O residue 343 LEU Chi-restraints excluded: chain O residue 344 ILE Chi-restraints excluded: chain O residue 353 ASP Chi-restraints excluded: chain O residue 384 ASP Chi-restraints excluded: chain O residue 405 TYR Chi-restraints excluded: chain O residue 416 LEU Chi-restraints excluded: chain O residue 421 ILE Chi-restraints excluded: chain O residue 480 VAL Chi-restraints excluded: chain O residue 533 LEU Chi-restraints excluded: chain O residue 569 VAL Chi-restraints excluded: chain O residue 574 TRP Chi-restraints excluded: chain O residue 583 GLU Chi-restraints excluded: chain O residue 622 TYR Chi-restraints excluded: chain O residue 626 LEU Chi-restraints excluded: chain O residue 659 LEU Chi-restraints excluded: chain O residue 668 SER Chi-restraints excluded: chain O residue 707 ASP Chi-restraints excluded: chain O residue 726 SER Chi-restraints excluded: chain P residue 95 LEU Chi-restraints excluded: chain P residue 145 ASN Chi-restraints excluded: chain P residue 147 GLN Chi-restraints excluded: chain P residue 215 LEU Chi-restraints excluded: chain P residue 259 GLN Chi-restraints excluded: chain P residue 304 LEU Chi-restraints excluded: chain P residue 367 PHE Chi-restraints excluded: chain P residue 370 SER Chi-restraints excluded: chain P residue 408 ILE Chi-restraints excluded: chain P residue 437 THR Chi-restraints excluded: chain P residue 479 LEU Chi-restraints excluded: chain P residue 512 ARG Chi-restraints excluded: chain Q residue 4 VAL Chi-restraints excluded: chain Q residue 10 ASN Chi-restraints excluded: chain Q residue 27 ILE Chi-restraints excluded: chain Q residue 128 TRP Chi-restraints excluded: chain Q residue 138 PHE Chi-restraints excluded: chain Q residue 155 GLN Chi-restraints excluded: chain Q residue 158 THR Chi-restraints excluded: chain Q residue 168 ILE Chi-restraints excluded: chain Q residue 180 CYS Chi-restraints excluded: chain Q residue 187 TYR Chi-restraints excluded: chain Q residue 204 GLU Chi-restraints excluded: chain Q residue 216 LEU Chi-restraints excluded: chain Q residue 240 ILE Chi-restraints excluded: chain Q residue 247 ILE Chi-restraints excluded: chain Q residue 248 LYS Chi-restraints excluded: chain Q residue 251 TRP Chi-restraints excluded: chain Q residue 280 SER Chi-restraints excluded: chain Q residue 289 ASN Chi-restraints excluded: chain Q residue 298 GLN Chi-restraints excluded: chain Q residue 317 LEU Chi-restraints excluded: chain Q residue 390 ASN Chi-restraints excluded: chain Q residue 400 LYS Chi-restraints excluded: chain Q residue 401 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 555 random chunks: chunk 75 optimal weight: 5.9990 chunk 116 optimal weight: 8.9990 chunk 534 optimal weight: 10.0000 chunk 278 optimal weight: 20.0000 chunk 288 optimal weight: 7.9990 chunk 176 optimal weight: 8.9990 chunk 433 optimal weight: 6.9990 chunk 542 optimal weight: 0.4980 chunk 319 optimal weight: 5.9990 chunk 283 optimal weight: 8.9990 chunk 281 optimal weight: 5.9990 overall best weight: 5.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 107 HIS ** A 382 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 431 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 580 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 656 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1113 HIS ** A1116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1314 GLN B 27 ASN ** B 504 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 555 GLN B 720 GLN ** B1163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 100 GLN ** G 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 139 ASN ** L 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 131 HIS ** P 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 221 HIS ** Q 287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 372 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.115254 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.081880 restraints weight = 142839.961| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.084560 restraints weight = 67044.597| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.085657 restraints weight = 35194.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.085768 restraints weight = 27878.604| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.085857 restraints weight = 26284.193| |-----------------------------------------------------------------------------| r_work (final): 0.3213 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7738 moved from start: 0.5546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.080 47752 Z= 0.255 Angle : 0.871 21.566 64966 Z= 0.443 Chirality : 0.050 0.353 7264 Planarity : 0.006 0.131 7978 Dihedral : 14.566 165.049 7220 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 19.24 Ramachandran Plot: Outliers : 0.81 % Allowed : 8.04 % Favored : 91.15 % Rotamer: Outliers : 4.55 % Allowed : 19.20 % Favored : 76.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.24 % 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: -1.17 (0.11), residues: 5432 helix: 0.38 (0.11), residues: 1996 sheet: -1.09 (0.18), residues: 769 loop : -1.58 (0.12), residues: 2667 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.030 0.001 ARG O 377 TYR 0.048 0.002 TYR P 211 PHE 0.107 0.002 PHE Q 358 TRP 0.042 0.002 TRP G 125 HIS 0.014 0.002 HIS Q 212 Details of bonding type rmsd/Z covalent geometry : bond 0.00562 / 0.25 (47712) covalent geometry : angle 0.85653 / 0.44 (64930) hydrogen bonds : bond 0.05427 / 3.62 ( 2015) hydrogen bonds : angle 5.86677 / 4.14 ( 5581) metal coordination : bond 0.01641 / 1.01 ( 24) metal coordination : angle 7.12613 / 5.24 ( 33) Misc. bond : bond 0.01019 / 0.53 ( 15) link_TRANS : bond 0.00140 / 0.07 ( 1) link_TRANS : angle 0.11321 / 0.06 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10864 Ramachandran restraints generated. 5432 Oldfield, 0 Emsley, 5432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10864 Ramachandran restraints generated. 5432 Oldfield, 0 Emsley, 5432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 999 residues out of total 4950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 225 poor density : 774 time to evaluate : 1.779 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 93 GLN cc_start: 0.9397 (mm-40) cc_final: 0.9033 (mt0) REVERT: A 108 PHE cc_start: 0.9289 (m-80) cc_final: 0.8727 (m-80) REVERT: A 342 ARG cc_start: 0.8070 (ptp-110) cc_final: 0.7706 (mtp85) REVERT: A 361 VAL cc_start: 0.8236 (OUTLIER) cc_final: 0.7970 (p) REVERT: A 365 THR cc_start: 0.9274 (m) cc_final: 0.9069 (p) REVERT: A 394 LEU cc_start: 0.9571 (tp) cc_final: 0.9294 (pp) REVERT: A 435 ASN cc_start: 0.8600 (m-40) cc_final: 0.8196 (m110) REVERT: A 450 LYS cc_start: 0.4770 (OUTLIER) cc_final: 0.2996 (mmtt) REVERT: A 721 LYS cc_start: 0.8451 (OUTLIER) cc_final: 0.8026 (tptt) REVERT: A 881 GLU cc_start: 0.8734 (tt0) cc_final: 0.8369 (tp30) REVERT: A 882 ILE cc_start: 0.9502 (mm) cc_final: 0.9292 (mt) REVERT: A 1024 THR cc_start: -0.2492 (m) cc_final: -0.2711 (t) REVERT: A 1294 MET cc_start: 0.8982 (mtm) cc_final: 0.8709 (ptp) REVERT: A 1576 SER cc_start: 0.9068 (m) cc_final: 0.8531 (p) REVERT: A 1611 MET cc_start: 0.8704 (tmm) cc_final: 0.8337 (tmm) REVERT: A 1627 LEU cc_start: 0.9446 (mt) cc_final: 0.9213 (mp) REVERT: B 97 VAL cc_start: 0.9546 (t) cc_final: 0.9262 (m) REVERT: B 125 GLU cc_start: 0.8938 (tt0) cc_final: 0.8466 (tt0) REVERT: B 175 MET cc_start: 0.8826 (mtp) cc_final: 0.8363 (mtp) REVERT: B 373 MET cc_start: 0.8838 (tpp) cc_final: 0.8592 (tpp) REVERT: B 418 ASP cc_start: 0.8602 (t70) cc_final: 0.8331 (t0) REVERT: B 419 GLU cc_start: 0.8351 (tp30) cc_final: 0.7378 (tp30) REVERT: B 422 GLN cc_start: 0.8697 (mt0) cc_final: 0.7928 (mt0) REVERT: B 430 MET cc_start: 0.8388 (OUTLIER) cc_final: 0.8118 (tmm) REVERT: B 448 ARG cc_start: 0.8979 (ttp-110) cc_final: 0.8756 (ttp-110) REVERT: B 473 GLN cc_start: 0.8307 (mm-40) cc_final: 0.8098 (mm-40) REVERT: B 502 MET cc_start: 0.8584 (ttp) cc_final: 0.8321 (ttp) REVERT: B 512 LEU cc_start: 0.8783 (mt) cc_final: 0.8581 (mp) REVERT: B 778 TYR cc_start: 0.8749 (t80) cc_final: 0.7786 (t80) REVERT: B 807 GLU cc_start: 0.7900 (tt0) cc_final: 0.7616 (tt0) REVERT: B 900 THR cc_start: 0.9541 (m) cc_final: 0.9177 (p) REVERT: B 1085 SER cc_start: 0.9369 (OUTLIER) cc_final: 0.9116 (t) REVERT: B 1134 ARG cc_start: 0.8410 (tpp80) cc_final: 0.8183 (tpp80) REVERT: B 1192 MET cc_start: 0.8010 (mpp) cc_final: 0.7419 (mpp) REVERT: C 71 MET cc_start: 0.9226 (ttm) cc_final: 0.8872 (ttp) REVERT: D 15 THR cc_start: 0.9376 (p) cc_final: 0.9142 (t) REVERT: D 44 ILE cc_start: 0.9482 (mt) cc_final: 0.9203 (pt) REVERT: D 89 LEU cc_start: 0.9723 (tp) cc_final: 0.9486 (mt) REVERT: E 78 LEU cc_start: 0.9406 (tt) cc_final: 0.8988 (tt) REVERT: E 112 TYR cc_start: 0.9035 (p90) cc_final: 0.8044 (p90) REVERT: E 114 ASN cc_start: 0.9423 (t0) cc_final: 0.8954 (t0) REVERT: E 119 SER cc_start: 0.9307 (OUTLIER) cc_final: 0.9039 (p) REVERT: E 136 ASN cc_start: 0.9355 (t0) cc_final: 0.8911 (t0) REVERT: E 211 TYR cc_start: 0.9361 (m-80) cc_final: 0.8798 (m-10) REVERT: E 215 MET cc_start: 0.8489 (mmt) cc_final: 0.8221 (mmm) REVERT: F 77 ASP cc_start: 0.8521 (p0) cc_final: 0.8172 (p0) REVERT: F 140 ASP cc_start: 0.9322 (p0) cc_final: 0.8664 (p0) REVERT: F 142 SER cc_start: 0.9348 (m) cc_final: 0.8917 (p) REVERT: F 144 GLU cc_start: 0.7780 (mt-10) cc_final: 0.7550 (mt-10) REVERT: F 151 LEU cc_start: 0.9507 (tp) cc_final: 0.9125 (tp) REVERT: G 64 GLN cc_start: 0.8755 (mt0) cc_final: 0.8053 (mt0) REVERT: G 126 GLN cc_start: 0.8105 (tm-30) cc_final: 0.7429 (tm-30) REVERT: G 229 LEU cc_start: 0.9439 (tt) cc_final: 0.9020 (mp) REVERT: G 237 HIS cc_start: 0.8637 (m170) cc_final: 0.8358 (m90) REVERT: H 14 GLU cc_start: 0.8480 (tp30) cc_final: 0.7953 (tp30) REVERT: H 27 GLU cc_start: 0.8314 (mt-10) cc_final: 0.7851 (mp0) REVERT: H 43 ASN cc_start: 0.8883 (t0) cc_final: 0.8662 (t0) REVERT: I 18 GLU cc_start: 0.8974 (tp30) cc_final: 0.8477 (tp30) REVERT: I 45 LEU cc_start: 0.9230 (mm) cc_final: 0.9011 (mm) REVERT: K 81 MET cc_start: 0.8391 (mmm) cc_final: 0.8010 (mmm) REVERT: K 86 VAL cc_start: 0.9405 (t) cc_final: 0.9196 (p) REVERT: K 97 SER cc_start: 0.9277 (m) cc_final: 0.8799 (t) REVERT: K 122 LYS cc_start: 0.9320 (tppt) cc_final: 0.9071 (tppt) REVERT: K 125 MET cc_start: 0.8718 (mtp) cc_final: 0.8433 (mtp) REVERT: K 129 ASP cc_start: 0.8890 (m-30) cc_final: 0.8494 (m-30) REVERT: M 59 ARG cc_start: 0.9112 (mtm-85) cc_final: 0.8893 (mtm180) REVERT: M 62 TYR cc_start: 0.5919 (p90) cc_final: 0.5062 (p90) REVERT: N 54 TRP cc_start: 0.9425 (m-10) cc_final: 0.8957 (m-10) REVERT: N 87 TYR cc_start: 0.8780 (m-80) cc_final: 0.8251 (m-80) REVERT: N 113 SER cc_start: 0.1533 (OUTLIER) cc_final: -0.2390 (p) REVERT: N 114 GLU cc_start: 0.8211 (pt0) cc_final: 0.7815 (mm-30) REVERT: O 221 ARG cc_start: 0.7916 (OUTLIER) cc_final: 0.7166 (mmm160) REVERT: O 313 GLN cc_start: 0.8619 (OUTLIER) cc_final: 0.8305 (pp30) REVERT: O 471 MET cc_start: 0.9041 (mtt) cc_final: 0.8750 (mmm) REVERT: O 574 TRP cc_start: 0.8191 (OUTLIER) cc_final: 0.6753 (m-10) REVERT: O 583 GLU cc_start: 0.8598 (OUTLIER) cc_final: 0.8171 (pm20) REVERT: P 131 HIS cc_start: 0.9323 (m-70) cc_final: 0.8967 (m-70) REVERT: P 158 MET cc_start: 0.6196 (mmp) cc_final: 0.5077 (mmp) REVERT: P 258 MET cc_start: 0.9309 (mmp) cc_final: 0.8889 (mmm) REVERT: P 300 ASN cc_start: 0.8351 (t0) cc_final: 0.7901 (m110) REVERT: P 369 TRP cc_start: 0.8239 (m-10) cc_final: 0.7807 (m100) REVERT: P 491 PHE cc_start: 0.8009 (OUTLIER) cc_final: 0.7347 (m-10) REVERT: P 497 GLN cc_start: 0.9208 (tt0) cc_final: 0.8554 (tp-100) REVERT: P 512 ARG cc_start: 0.6577 (OUTLIER) cc_final: 0.5825 (mtm180) REVERT: Q 138 PHE cc_start: 0.8720 (OUTLIER) cc_final: 0.8231 (t80) REVERT: Q 212 HIS cc_start: 0.8502 (OUTLIER) cc_final: 0.8150 (t70) REVERT: Q 218 ASP cc_start: 0.8092 (m-30) cc_final: 0.7753 (m-30) REVERT: Q 278 TYR cc_start: 0.8948 (m-80) cc_final: 0.8705 (m-80) REVERT: Q 304 HIS cc_start: 0.8243 (t-90) cc_final: 0.7722 (t-90) outliers start: 225 outliers final: 155 residues processed: 923 average time/residue: 0.2347 time to fit residues: 368.2039 Evaluate side-chains 887 residues out of total 4950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 170 poor density : 717 time to evaluate : 1.706 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 LEU Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 346 SER Chi-restraints excluded: chain A residue 357 MET Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 403 LEU Chi-restraints excluded: chain A residue 450 LYS Chi-restraints excluded: chain A residue 495 ILE Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 586 VAL Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain A residue 678 VAL Chi-restraints excluded: chain A residue 685 SER Chi-restraints excluded: chain A residue 713 VAL Chi-restraints excluded: chain A residue 721 LYS Chi-restraints excluded: chain A residue 891 ILE Chi-restraints excluded: chain A residue 922 CYS Chi-restraints excluded: chain A residue 947 LEU Chi-restraints excluded: chain A residue 957 VAL Chi-restraints excluded: chain A residue 1019 LEU Chi-restraints excluded: chain A residue 1063 MET Chi-restraints excluded: chain A residue 1118 VAL Chi-restraints excluded: chain A residue 1119 LYS Chi-restraints excluded: chain A residue 1222 LEU Chi-restraints excluded: chain A residue 1238 MET Chi-restraints excluded: chain A residue 1323 HIS Chi-restraints excluded: chain A residue 1470 CYS Chi-restraints excluded: chain A residue 1489 VAL Chi-restraints excluded: chain A residue 1491 GLU Chi-restraints excluded: chain A residue 1543 SER Chi-restraints excluded: chain A residue 1634 LEU Chi-restraints excluded: chain A residue 1649 VAL Chi-restraints excluded: chain B residue 35 PHE Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 68 ILE Chi-restraints excluded: chain B residue 75 ASP Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 218 ILE Chi-restraints excluded: chain B residue 249 VAL Chi-restraints excluded: chain B residue 288 ILE Chi-restraints excluded: chain B residue 409 TYR Chi-restraints excluded: chain B residue 424 ILE Chi-restraints excluded: chain B residue 430 MET Chi-restraints excluded: chain B residue 447 SER Chi-restraints excluded: chain B residue 462 GLN Chi-restraints excluded: chain B residue 489 GLU Chi-restraints excluded: chain B residue 516 THR Chi-restraints excluded: chain B residue 564 ILE Chi-restraints excluded: chain B residue 592 ILE Chi-restraints excluded: chain B residue 620 LEU Chi-restraints excluded: chain B residue 647 SER Chi-restraints excluded: chain B residue 712 SER Chi-restraints excluded: chain B residue 725 THR Chi-restraints excluded: chain B residue 819 ASP Chi-restraints excluded: chain B residue 910 THR Chi-restraints excluded: chain B residue 918 SER Chi-restraints excluded: chain B residue 1085 SER Chi-restraints excluded: chain B residue 1087 LEU Chi-restraints excluded: chain B residue 1113 THR Chi-restraints excluded: chain B residue 1178 ILE Chi-restraints excluded: chain C residue 73 SER Chi-restraints excluded: chain C residue 120 LEU Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain C residue 167 LEU Chi-restraints excluded: chain C residue 201 GLU Chi-restraints excluded: chain C residue 273 ASP Chi-restraints excluded: chain C residue 328 LEU Chi-restraints excluded: chain E residue 119 SER Chi-restraints excluded: chain F residue 93 ILE Chi-restraints excluded: chain G residue 47 VAL Chi-restraints excluded: chain G residue 61 VAL Chi-restraints excluded: chain G residue 69 LEU Chi-restraints excluded: chain G residue 138 PHE Chi-restraints excluded: chain G residue 226 ASP Chi-restraints excluded: chain G residue 245 VAL Chi-restraints excluded: chain G residue 246 ASP Chi-restraints excluded: chain H residue 57 VAL Chi-restraints excluded: chain H residue 61 SER Chi-restraints excluded: chain H residue 109 LYS Chi-restraints excluded: chain H residue 129 TYR Chi-restraints excluded: chain I residue 39 LYS Chi-restraints excluded: chain I residue 42 PHE Chi-restraints excluded: chain I residue 60 LEU Chi-restraints excluded: chain J residue 50 ILE Chi-restraints excluded: chain J residue 57 ILE Chi-restraints excluded: chain L residue 46 VAL Chi-restraints excluded: chain L residue 65 VAL Chi-restraints excluded: chain M residue 23 VAL Chi-restraints excluded: chain M residue 66 THR Chi-restraints excluded: chain M residue 77 VAL Chi-restraints excluded: chain M residue 98 SER Chi-restraints excluded: chain N residue 25 ILE Chi-restraints excluded: chain N residue 32 CYS Chi-restraints excluded: chain N residue 53 VAL Chi-restraints excluded: chain N residue 108 THR Chi-restraints excluded: chain N residue 111 VAL Chi-restraints excluded: chain N residue 113 SER Chi-restraints excluded: chain N residue 131 LEU Chi-restraints excluded: chain N residue 160 VAL Chi-restraints excluded: chain N residue 168 LEU Chi-restraints excluded: chain N residue 173 THR Chi-restraints excluded: chain O residue 202 ILE Chi-restraints excluded: chain O residue 203 ILE Chi-restraints excluded: chain O residue 221 ARG Chi-restraints excluded: chain O residue 254 ILE Chi-restraints excluded: chain O residue 258 SER Chi-restraints excluded: chain O residue 260 LEU Chi-restraints excluded: chain O residue 300 LEU Chi-restraints excluded: chain O residue 313 GLN Chi-restraints excluded: chain O residue 344 ILE Chi-restraints excluded: chain O residue 353 ASP Chi-restraints excluded: chain O residue 384 ASP Chi-restraints excluded: chain O residue 405 TYR Chi-restraints excluded: chain O residue 408 ILE Chi-restraints excluded: chain O residue 416 LEU Chi-restraints excluded: chain O residue 421 ILE Chi-restraints excluded: chain O residue 451 ILE Chi-restraints excluded: chain O residue 464 LEU Chi-restraints excluded: chain O residue 480 VAL Chi-restraints excluded: chain O residue 533 LEU Chi-restraints excluded: chain O residue 535 VAL Chi-restraints excluded: chain O residue 569 VAL Chi-restraints excluded: chain O residue 574 TRP Chi-restraints excluded: chain O residue 583 GLU Chi-restraints excluded: chain O residue 622 TYR Chi-restraints excluded: chain O residue 659 LEU Chi-restraints excluded: chain O residue 668 SER Chi-restraints excluded: chain O residue 688 ASP Chi-restraints excluded: chain O residue 707 ASP Chi-restraints excluded: chain O residue 726 SER Chi-restraints excluded: chain P residue 95 LEU Chi-restraints excluded: chain P residue 147 GLN Chi-restraints excluded: chain P residue 215 LEU Chi-restraints excluded: chain P residue 259 GLN Chi-restraints excluded: chain P residue 262 LEU Chi-restraints excluded: chain P residue 304 LEU Chi-restraints excluded: chain P residue 367 PHE Chi-restraints excluded: chain P residue 388 THR Chi-restraints excluded: chain P residue 400 MET Chi-restraints excluded: chain P residue 408 ILE Chi-restraints excluded: chain P residue 437 THR Chi-restraints excluded: chain P residue 479 LEU Chi-restraints excluded: chain P residue 491 PHE Chi-restraints excluded: chain P residue 512 ARG Chi-restraints excluded: chain Q residue 4 VAL Chi-restraints excluded: chain Q residue 10 ASN Chi-restraints excluded: chain Q residue 128 TRP Chi-restraints excluded: chain Q residue 138 PHE Chi-restraints excluded: chain Q residue 155 GLN Chi-restraints excluded: chain Q residue 158 THR Chi-restraints excluded: chain Q residue 168 ILE Chi-restraints excluded: chain Q residue 180 CYS Chi-restraints excluded: chain Q residue 187 TYR Chi-restraints excluded: chain Q residue 212 HIS Chi-restraints excluded: chain Q residue 216 LEU Chi-restraints excluded: chain Q residue 240 ILE Chi-restraints excluded: chain Q residue 247 ILE Chi-restraints excluded: chain Q residue 248 LYS Chi-restraints excluded: chain Q residue 251 TRP Chi-restraints excluded: chain Q residue 269 ASP Chi-restraints excluded: chain Q residue 272 GLN Chi-restraints excluded: chain Q residue 280 SER Chi-restraints excluded: chain Q residue 298 GLN Chi-restraints excluded: chain Q residue 310 ILE Chi-restraints excluded: chain Q residue 317 LEU Chi-restraints excluded: chain Q residue 390 ASN Chi-restraints excluded: chain Q residue 400 LYS Chi-restraints excluded: chain Q residue 401 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 555 random chunks: chunk 210 optimal weight: 5.9990 chunk 129 optimal weight: 7.9990 chunk 47 optimal weight: 10.0000 chunk 485 optimal weight: 5.9990 chunk 133 optimal weight: 0.0020 chunk 204 optimal weight: 0.0870 chunk 334 optimal weight: 0.9980 chunk 366 optimal weight: 3.9990 chunk 506 optimal weight: 30.0000 chunk 374 optimal weight: 3.9990 chunk 34 optimal weight: 4.9990 overall best weight: 1.8170 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 93 GLN A 382 GLN A 431 GLN ** A 580 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 656 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 950 GLN ** A1116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 504 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 547 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 720 GLN B 767 ASN ** B1163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 52 GLN H 133 ASN ** L 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 406 GLN ** Q 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 372 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.116575 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.083236 restraints weight = 142842.744| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.085961 restraints weight = 68120.809| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.086730 restraints weight = 35698.092| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.087127 restraints weight = 29672.181| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.087260 restraints weight = 27882.747| |-----------------------------------------------------------------------------| r_work (final): 0.3242 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7720 moved from start: 0.5782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 47752 Z= 0.172 Angle : 0.835 19.722 64966 Z= 0.421 Chirality : 0.049 0.362 7264 Planarity : 0.006 0.124 7978 Dihedral : 14.454 164.047 7213 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 17.58 Ramachandran Plot: Outliers : 0.72 % Allowed : 7.38 % Favored : 91.90 % Rotamer: Outliers : 4.30 % Allowed : 19.77 % Favored : 75.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.24 % Twisted General : 0.06 % 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: -1.03 (0.11), residues: 5432 helix: 0.50 (0.11), residues: 2001 sheet: -1.01 (0.18), residues: 732 loop : -1.50 (0.12), residues: 2699 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG O 601 TYR 0.046 0.002 TYR P 211 PHE 0.110 0.002 PHE Q 358 TRP 0.038 0.002 TRP G 125 HIS 0.009 0.001 HIS Q 212 Details of bonding type rmsd/Z covalent geometry : bond 0.00381 / 0.17 (47712) covalent geometry : angle 0.82303 / 0.42 (64930) hydrogen bonds : bond 0.05154 / 3.44 ( 2015) hydrogen bonds : angle 5.66161 / 4.00 ( 5581) metal coordination : bond 0.00899 / 0.60 ( 24) metal coordination : angle 6.24416 / 4.67 ( 33) Misc. bond : bond 0.00958 / 0.50 ( 15) link_TRANS : bond 0.00108 / 0.06 ( 1) link_TRANS : angle 0.13994 / 0.08 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10864 Ramachandran restraints generated. 5432 Oldfield, 0 Emsley, 5432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10864 Ramachandran restraints generated. 5432 Oldfield, 0 Emsley, 5432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1021 residues out of total 4950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 213 poor density : 808 time to evaluate : 1.528 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 76 GLN cc_start: 0.8018 (tp40) cc_final: 0.7691 (tp40) REVERT: A 93 GLN cc_start: 0.9246 (OUTLIER) cc_final: 0.8949 (mt0) REVERT: A 108 PHE cc_start: 0.9311 (m-80) cc_final: 0.8664 (m-80) REVERT: A 238 MET cc_start: 0.7987 (mmp) cc_final: 0.7529 (mmp) REVERT: A 342 ARG cc_start: 0.8042 (ptp-110) cc_final: 0.7740 (mtt-85) REVERT: A 365 THR cc_start: 0.9286 (m) cc_final: 0.9053 (p) REVERT: A 394 LEU cc_start: 0.9562 (tp) cc_final: 0.9316 (pp) REVERT: A 419 ILE cc_start: 0.7768 (OUTLIER) cc_final: 0.4914 (mp) REVERT: A 435 ASN cc_start: 0.8625 (m-40) cc_final: 0.8353 (m110) REVERT: A 450 LYS cc_start: 0.4923 (OUTLIER) cc_final: 0.2931 (mmtt) REVERT: A 461 GLU cc_start: 0.7195 (mt-10) cc_final: 0.6963 (mm-30) REVERT: A 721 LYS cc_start: 0.8604 (OUTLIER) cc_final: 0.8191 (tptt) REVERT: A 819 ASN cc_start: 0.9106 (m-40) cc_final: 0.8569 (m-40) REVERT: A 881 GLU cc_start: 0.8656 (tt0) cc_final: 0.8253 (tp30) REVERT: A 882 ILE cc_start: 0.9479 (mm) cc_final: 0.9265 (mt) REVERT: A 1024 THR cc_start: -0.2326 (m) cc_final: -0.2584 (t) REVERT: A 1265 GLU cc_start: 0.8648 (mt-10) cc_final: 0.8365 (mt-10) REVERT: A 1576 SER cc_start: 0.8948 (m) cc_final: 0.8399 (p) REVERT: A 1611 MET cc_start: 0.8645 (tmm) cc_final: 0.8253 (tmm) REVERT: A 1627 LEU cc_start: 0.9497 (mt) cc_final: 0.8982 (mp) REVERT: B 97 VAL cc_start: 0.9507 (t) cc_final: 0.9177 (m) REVERT: B 125 GLU cc_start: 0.8838 (tt0) cc_final: 0.8363 (tt0) REVERT: B 175 MET cc_start: 0.8757 (mtp) cc_final: 0.8512 (mtp) REVERT: B 373 MET cc_start: 0.8855 (tpp) cc_final: 0.8639 (tpp) REVERT: B 418 ASP cc_start: 0.8556 (t70) cc_final: 0.8266 (t0) REVERT: B 419 GLU cc_start: 0.8356 (tp30) cc_final: 0.7370 (tp30) REVERT: B 422 GLN cc_start: 0.8708 (mt0) cc_final: 0.8015 (mt0) REVERT: B 430 MET cc_start: 0.8287 (OUTLIER) cc_final: 0.8020 (tmm) REVERT: B 448 ARG cc_start: 0.8954 (ttp-110) cc_final: 0.8551 (ttp-110) REVERT: B 512 LEU cc_start: 0.8859 (mt) cc_final: 0.8657 (mp) REVERT: B 778 TYR cc_start: 0.8665 (t80) cc_final: 0.7727 (t80) REVERT: B 802 THR cc_start: 0.9364 (m) cc_final: 0.8955 (p) REVERT: B 807 GLU cc_start: 0.7782 (tt0) cc_final: 0.7535 (tt0) REVERT: B 815 ARG cc_start: 0.5838 (tpp-160) cc_final: 0.5084 (tpp-160) REVERT: B 900 THR cc_start: 0.9511 (m) cc_final: 0.9203 (p) REVERT: B 962 MET cc_start: 0.8924 (tpp) cc_final: 0.8692 (tpp) REVERT: B 1186 ASP cc_start: 0.7804 (OUTLIER) cc_final: 0.7257 (t70) REVERT: B 1192 MET cc_start: 0.8166 (mpp) cc_final: 0.7476 (mpp) REVERT: C 71 MET cc_start: 0.9185 (ttm) cc_final: 0.8845 (ttp) REVERT: D 15 THR cc_start: 0.9383 (p) cc_final: 0.9152 (t) REVERT: D 44 ILE cc_start: 0.9477 (mt) cc_final: 0.9179 (pt) REVERT: E 78 LEU cc_start: 0.9395 (tt) cc_final: 0.8961 (tt) REVERT: E 112 TYR cc_start: 0.8990 (p90) cc_final: 0.8001 (p90) REVERT: E 114 ASN cc_start: 0.9403 (t0) cc_final: 0.8869 (t0) REVERT: E 119 SER cc_start: 0.9369 (OUTLIER) cc_final: 0.9131 (p) REVERT: E 136 ASN cc_start: 0.9354 (t0) cc_final: 0.8901 (t0) REVERT: E 211 TYR cc_start: 0.9269 (m-80) cc_final: 0.8702 (m-10) REVERT: E 215 MET cc_start: 0.8407 (mmt) cc_final: 0.8181 (mmm) REVERT: F 77 ASP cc_start: 0.8492 (p0) cc_final: 0.8229 (p0) REVERT: F 89 GLU cc_start: 0.9000 (OUTLIER) cc_final: 0.8748 (pm20) REVERT: F 138 LEU cc_start: 0.9138 (mm) cc_final: 0.8926 (mp) REVERT: F 140 ASP cc_start: 0.9314 (p0) cc_final: 0.8675 (p0) REVERT: F 142 SER cc_start: 0.9333 (m) cc_final: 0.8937 (p) REVERT: G 64 GLN cc_start: 0.8695 (mt0) cc_final: 0.7974 (mt0) REVERT: G 71 MET cc_start: 0.8751 (mtp) cc_final: 0.8121 (mtp) REVERT: G 91 ASP cc_start: 0.8035 (t0) cc_final: 0.7468 (t0) REVERT: G 126 GLN cc_start: 0.7986 (tm-30) cc_final: 0.7258 (tm-30) REVERT: G 229 LEU cc_start: 0.9386 (tt) cc_final: 0.8965 (mp) REVERT: G 237 HIS cc_start: 0.8580 (m170) cc_final: 0.8319 (m90) REVERT: H 14 GLU cc_start: 0.8502 (tp30) cc_final: 0.8055 (tp30) REVERT: H 27 GLU cc_start: 0.8234 (mt-10) cc_final: 0.7809 (mp0) REVERT: H 43 ASN cc_start: 0.8886 (t0) cc_final: 0.8668 (t0) REVERT: I 18 GLU cc_start: 0.8855 (tp30) cc_final: 0.8097 (tp30) REVERT: I 45 LEU cc_start: 0.9283 (mm) cc_final: 0.9014 (mm) REVERT: K 42 PRO cc_start: 0.9395 (Cg_exo) cc_final: 0.9168 (Cg_endo) REVERT: K 43 ASP cc_start: 0.7712 (t70) cc_final: 0.7259 (t70) REVERT: K 81 MET cc_start: 0.8381 (mmm) cc_final: 0.7939 (mmm) REVERT: K 97 SER cc_start: 0.9141 (m) cc_final: 0.8673 (t) REVERT: K 122 LYS cc_start: 0.9298 (tppt) cc_final: 0.9063 (tppt) REVERT: K 125 MET cc_start: 0.8674 (mtp) cc_final: 0.8392 (tpp) REVERT: K 129 ASP cc_start: 0.8870 (m-30) cc_final: 0.8433 (m-30) REVERT: M 62 TYR cc_start: 0.6035 (p90) cc_final: 0.5116 (p90) REVERT: M 75 GLN cc_start: 0.9154 (pp30) cc_final: 0.8765 (pm20) REVERT: N 54 TRP cc_start: 0.9363 (m-10) cc_final: 0.9140 (m-10) REVERT: N 106 ASN cc_start: 0.7345 (m110) cc_final: 0.6821 (m-40) REVERT: N 113 SER cc_start: 0.1535 (OUTLIER) cc_final: -0.2393 (p) REVERT: N 114 GLU cc_start: 0.8305 (pt0) cc_final: 0.7933 (mm-30) REVERT: N 131 LEU cc_start: 0.7895 (OUTLIER) cc_final: 0.7495 (pp) REVERT: O 285 MET cc_start: 0.8828 (pmm) cc_final: 0.8564 (pmm) REVERT: O 313 GLN cc_start: 0.8463 (OUTLIER) cc_final: 0.8199 (pp30) REVERT: O 386 MET cc_start: 0.8700 (ptp) cc_final: 0.8342 (mpp) REVERT: O 471 MET cc_start: 0.8968 (mtt) cc_final: 0.8740 (mmm) REVERT: O 574 TRP cc_start: 0.8235 (OUTLIER) cc_final: 0.6910 (m-10) REVERT: O 583 GLU cc_start: 0.8421 (OUTLIER) cc_final: 0.8073 (pm20) REVERT: P 118 TRP cc_start: 0.8616 (t-100) cc_final: 0.8236 (t-100) REVERT: P 131 HIS cc_start: 0.9378 (m-70) cc_final: 0.8902 (m-70) REVERT: P 158 MET cc_start: 0.6617 (mmp) cc_final: 0.5684 (mmp) REVERT: P 258 MET cc_start: 0.9270 (mmp) cc_final: 0.8612 (mmm) REVERT: P 300 ASN cc_start: 0.8502 (t0) cc_final: 0.8138 (m110) REVERT: P 369 TRP cc_start: 0.8269 (m-10) cc_final: 0.7869 (m100) REVERT: P 491 PHE cc_start: 0.7604 (OUTLIER) cc_final: 0.7046 (m-10) REVERT: P 497 GLN cc_start: 0.9282 (tt0) cc_final: 0.8677 (tp40) REVERT: P 512 ARG cc_start: 0.6697 (OUTLIER) cc_final: 0.6080 (mtm180) REVERT: Q 138 PHE cc_start: 0.8902 (OUTLIER) cc_final: 0.8430 (t80) REVERT: Q 212 HIS cc_start: 0.8582 (OUTLIER) cc_final: 0.8288 (t70) REVERT: Q 214 VAL cc_start: 0.9363 (t) cc_final: 0.9041 (t) REVERT: Q 218 ASP cc_start: 0.8249 (m-30) cc_final: 0.7964 (m-30) REVERT: Q 248 LYS cc_start: 0.9539 (OUTLIER) cc_final: 0.9336 (ttpt) REVERT: Q 304 HIS cc_start: 0.8240 (t-90) cc_final: 0.7817 (t-90) REVERT: Q 344 GLU cc_start: 0.8977 (mm-30) cc_final: 0.8717 (mp0) REVERT: Q 372 HIS cc_start: 0.7842 (OUTLIER) cc_final: 0.7499 (t70) REVERT: Q 410 TYR cc_start: 0.8770 (m-10) cc_final: 0.8506 (m-10) outliers start: 213 outliers final: 130 residues processed: 949 average time/residue: 0.2068 time to fit residues: 334.9940 Evaluate side-chains 889 residues out of total 4950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 149 poor density : 740 time to evaluate : 1.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 GLN Chi-restraints excluded: chain A residue 94 LEU Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 222 GLU Chi-restraints excluded: chain A residue 346 SER Chi-restraints excluded: chain A residue 357 MET Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 403 LEU Chi-restraints excluded: chain A residue 419 ILE Chi-restraints excluded: chain A residue 450 LYS Chi-restraints excluded: chain A residue 495 ILE Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 678 VAL Chi-restraints excluded: chain A residue 713 VAL Chi-restraints excluded: chain A residue 721 LYS Chi-restraints excluded: chain A residue 891 ILE Chi-restraints excluded: chain A residue 947 LEU Chi-restraints excluded: chain A residue 957 VAL Chi-restraints excluded: chain A residue 1019 LEU Chi-restraints excluded: chain A residue 1063 MET Chi-restraints excluded: chain A residue 1118 VAL Chi-restraints excluded: chain A residue 1119 LYS Chi-restraints excluded: chain A residue 1470 CYS Chi-restraints excluded: chain A residue 1491 GLU Chi-restraints excluded: chain A residue 1543 SER Chi-restraints excluded: chain A residue 1634 LEU Chi-restraints excluded: chain A residue 1649 VAL Chi-restraints excluded: chain B residue 35 PHE Chi-restraints excluded: chain B residue 68 ILE Chi-restraints excluded: chain B residue 75 ASP Chi-restraints excluded: chain B residue 164 MET Chi-restraints excluded: chain B residue 190 ILE Chi-restraints excluded: chain B residue 218 ILE Chi-restraints excluded: chain B residue 409 TYR Chi-restraints excluded: chain B residue 424 ILE Chi-restraints excluded: chain B residue 430 MET Chi-restraints excluded: chain B residue 447 SER Chi-restraints excluded: chain B residue 462 GLN Chi-restraints excluded: chain B residue 564 ILE Chi-restraints excluded: chain B residue 592 ILE Chi-restraints excluded: chain B residue 712 SER Chi-restraints excluded: chain B residue 725 THR Chi-restraints excluded: chain B residue 819 ASP Chi-restraints excluded: chain B residue 910 THR Chi-restraints excluded: chain B residue 918 SER Chi-restraints excluded: chain B residue 1087 LEU Chi-restraints excluded: chain B residue 1096 SER Chi-restraints excluded: chain B residue 1178 ILE Chi-restraints excluded: chain B residue 1186 ASP Chi-restraints excluded: chain C residue 73 SER Chi-restraints excluded: chain C residue 120 LEU Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain C residue 167 LEU Chi-restraints excluded: chain C residue 201 GLU Chi-restraints excluded: chain C residue 328 LEU Chi-restraints excluded: chain D residue 31 VAL Chi-restraints excluded: chain D residue 85 SER Chi-restraints excluded: chain D residue 99 LEU Chi-restraints excluded: chain E residue 119 SER Chi-restraints excluded: chain F residue 89 GLU Chi-restraints excluded: chain F residue 93 ILE Chi-restraints excluded: chain G residue 47 VAL Chi-restraints excluded: chain G residue 69 LEU Chi-restraints excluded: chain G residue 104 LEU Chi-restraints excluded: chain G residue 138 PHE Chi-restraints excluded: chain G residue 162 ILE Chi-restraints excluded: chain G residue 226 ASP Chi-restraints excluded: chain G residue 245 VAL Chi-restraints excluded: chain G residue 246 ASP Chi-restraints excluded: chain H residue 129 TYR Chi-restraints excluded: chain H residue 133 ASN Chi-restraints excluded: chain H residue 139 ASN Chi-restraints excluded: chain I residue 39 LYS Chi-restraints excluded: chain I residue 42 PHE Chi-restraints excluded: chain I residue 60 LEU Chi-restraints excluded: chain J residue 50 ILE Chi-restraints excluded: chain J residue 57 ILE Chi-restraints excluded: chain L residue 46 VAL Chi-restraints excluded: chain L residue 65 VAL Chi-restraints excluded: chain M residue 23 VAL Chi-restraints excluded: chain M residue 66 THR Chi-restraints excluded: chain N residue 25 ILE Chi-restraints excluded: chain N residue 32 CYS Chi-restraints excluded: chain N residue 72 VAL Chi-restraints excluded: chain N residue 111 VAL Chi-restraints excluded: chain N residue 113 SER Chi-restraints excluded: chain N residue 131 LEU Chi-restraints excluded: chain N residue 160 VAL Chi-restraints excluded: chain N residue 173 THR Chi-restraints excluded: chain O residue 202 ILE Chi-restraints excluded: chain O residue 203 ILE Chi-restraints excluded: chain O residue 254 ILE Chi-restraints excluded: chain O residue 258 SER Chi-restraints excluded: chain O residue 260 LEU Chi-restraints excluded: chain O residue 300 LEU Chi-restraints excluded: chain O residue 313 GLN Chi-restraints excluded: chain O residue 344 ILE Chi-restraints excluded: chain O residue 353 ASP Chi-restraints excluded: chain O residue 384 ASP Chi-restraints excluded: chain O residue 405 TYR Chi-restraints excluded: chain O residue 416 LEU Chi-restraints excluded: chain O residue 421 ILE Chi-restraints excluded: chain O residue 451 ILE Chi-restraints excluded: chain O residue 480 VAL Chi-restraints excluded: chain O residue 533 LEU Chi-restraints excluded: chain O residue 569 VAL Chi-restraints excluded: chain O residue 574 TRP Chi-restraints excluded: chain O residue 583 GLU Chi-restraints excluded: chain O residue 622 TYR Chi-restraints excluded: chain O residue 659 LEU Chi-restraints excluded: chain O residue 668 SER Chi-restraints excluded: chain O residue 688 ASP Chi-restraints excluded: chain O residue 707 ASP Chi-restraints excluded: chain O residue 724 LEU Chi-restraints excluded: chain O residue 726 SER Chi-restraints excluded: chain P residue 95 LEU Chi-restraints excluded: chain P residue 147 GLN Chi-restraints excluded: chain P residue 178 THR Chi-restraints excluded: chain P residue 215 LEU Chi-restraints excluded: chain P residue 262 LEU Chi-restraints excluded: chain P residue 304 LEU Chi-restraints excluded: chain P residue 367 PHE Chi-restraints excluded: chain P residue 400 MET Chi-restraints excluded: chain P residue 408 ILE Chi-restraints excluded: chain P residue 437 THR Chi-restraints excluded: chain P residue 479 LEU Chi-restraints excluded: chain P residue 491 PHE Chi-restraints excluded: chain P residue 512 ARG Chi-restraints excluded: chain Q residue 4 VAL Chi-restraints excluded: chain Q residue 128 TRP Chi-restraints excluded: chain Q residue 138 PHE Chi-restraints excluded: chain Q residue 155 GLN Chi-restraints excluded: chain Q residue 158 THR Chi-restraints excluded: chain Q residue 168 ILE Chi-restraints excluded: chain Q residue 187 TYR Chi-restraints excluded: chain Q residue 212 HIS Chi-restraints excluded: chain Q residue 240 ILE Chi-restraints excluded: chain Q residue 247 ILE Chi-restraints excluded: chain Q residue 248 LYS Chi-restraints excluded: chain Q residue 251 TRP Chi-restraints excluded: chain Q residue 269 ASP Chi-restraints excluded: chain Q residue 280 SER Chi-restraints excluded: chain Q residue 289 ASN Chi-restraints excluded: chain Q residue 298 GLN Chi-restraints excluded: chain Q residue 372 HIS Chi-restraints excluded: chain Q residue 390 ASN Chi-restraints excluded: chain Q residue 400 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 555 random chunks: chunk 191 optimal weight: 10.0000 chunk 407 optimal weight: 20.0000 chunk 100 optimal weight: 10.0000 chunk 372 optimal weight: 9.9990 chunk 274 optimal weight: 10.0000 chunk 346 optimal weight: 10.0000 chunk 244 optimal weight: 8.9990 chunk 139 optimal weight: 8.9990 chunk 47 optimal weight: 8.9990 chunk 504 optimal weight: 8.9990 chunk 427 optimal weight: 10.0000 overall best weight: 9.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 93 GLN A 336 GLN A 382 GLN A 525 ASN A 580 HIS ** A 656 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 785 GLN ** A1116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 251 HIS ** B 504 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 720 GLN ** B1163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 65 HIS ** G 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 133 ASN ** H 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 194 GLN ** P 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 321 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.113708 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.079574 restraints weight = 145820.246| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.082267 restraints weight = 69728.464| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.083031 restraints weight = 44321.928| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.083923 restraints weight = 32067.997| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.083877 restraints weight = 28474.427| |-----------------------------------------------------------------------------| r_work (final): 0.3198 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7888 moved from start: 0.6029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.103 47752 Z= 0.386 Angle : 0.937 21.515 64966 Z= 0.475 Chirality : 0.052 0.395 7264 Planarity : 0.007 0.126 7978 Dihedral : 14.530 163.447 7211 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 21.42 Ramachandran Plot: Outliers : 0.70 % Allowed : 8.01 % Favored : 91.29 % Rotamer: Outliers : 4.85 % Allowed : 20.17 % Favored : 74.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.24 % Twisted General : 0.06 % 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: -1.14 (0.11), residues: 5432 helix: 0.45 (0.11), residues: 2003 sheet: -1.17 (0.18), residues: 756 loop : -1.58 (0.12), residues: 2673 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A1039 TYR 0.050 0.003 TYR P 211 PHE 0.108 0.003 PHE Q 358 TRP 0.037 0.003 TRP A 530 HIS 0.016 0.002 HIS A1323 Details of bonding type rmsd/Z covalent geometry : bond 0.00845 / 0.39 (47712) covalent geometry : angle 0.92130 / 0.47 (64930) hydrogen bonds : bond 0.05494 / 3.64 ( 2015) hydrogen bonds : angle 5.88964 / 4.16 ( 5581) metal coordination : bond 0.02454 / 1.58 ( 24) metal coordination : angle 7.58609 / 5.38 ( 33) Misc. bond : bond 0.00924 / 0.48 ( 15) link_TRANS : bond 0.00160 / 0.08 ( 1) link_TRANS : angle 0.09955 / 0.06 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10864 Ramachandran restraints generated. 5432 Oldfield, 0 Emsley, 5432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10864 Ramachandran restraints generated. 5432 Oldfield, 0 Emsley, 5432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 976 residues out of total 4950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 240 poor density : 736 time to evaluate : 1.259 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 93 GLN cc_start: 0.9067 (OUTLIER) cc_final: 0.8606 (mt0) REVERT: A 238 MET cc_start: 0.8145 (mmp) cc_final: 0.7744 (mmp) REVERT: A 394 LEU cc_start: 0.9550 (tp) cc_final: 0.9310 (pp) REVERT: A 450 LYS cc_start: 0.5280 (OUTLIER) cc_final: 0.3152 (mmtm) REVERT: A 461 GLU cc_start: 0.7583 (mt-10) cc_final: 0.7365 (mm-30) REVERT: A 530 TRP cc_start: 0.7590 (t60) cc_final: 0.7287 (t60) REVERT: A 721 LYS cc_start: 0.8765 (OUTLIER) cc_final: 0.8327 (tptt) REVERT: A 881 GLU cc_start: 0.8588 (tt0) cc_final: 0.8353 (tp30) REVERT: A 1576 SER cc_start: 0.9159 (m) cc_final: 0.8615 (p) REVERT: A 1611 MET cc_start: 0.8605 (tmm) cc_final: 0.8243 (tmm) REVERT: A 1627 LEU cc_start: 0.9602 (mt) cc_final: 0.9001 (mp) REVERT: B 97 VAL cc_start: 0.9469 (t) cc_final: 0.9264 (m) REVERT: B 175 MET cc_start: 0.8750 (mtp) cc_final: 0.8401 (mtp) REVERT: B 418 ASP cc_start: 0.8504 (t70) cc_final: 0.8173 (t0) REVERT: B 419 GLU cc_start: 0.8333 (tp30) cc_final: 0.7348 (tp30) REVERT: B 422 GLN cc_start: 0.8646 (mt0) cc_final: 0.7799 (mt0) REVERT: B 430 MET cc_start: 0.8407 (OUTLIER) cc_final: 0.8153 (tmm) REVERT: B 448 ARG cc_start: 0.8882 (ttp-110) cc_final: 0.8590 (ttp-110) REVERT: B 473 GLN cc_start: 0.8380 (mm-40) cc_final: 0.8066 (mm-40) REVERT: B 502 MET cc_start: 0.8577 (ttp) cc_final: 0.8207 (tmm) REVERT: B 778 TYR cc_start: 0.8732 (t80) cc_final: 0.7670 (t80) REVERT: B 782 ASP cc_start: 0.7298 (p0) cc_final: 0.6704 (p0) REVERT: B 807 GLU cc_start: 0.7756 (tt0) cc_final: 0.7494 (tt0) REVERT: B 900 THR cc_start: 0.9538 (m) cc_final: 0.9216 (p) REVERT: B 950 ASN cc_start: 0.8900 (t0) cc_final: 0.8430 (t0) REVERT: B 1186 ASP cc_start: 0.7949 (OUTLIER) cc_final: 0.7522 (t70) REVERT: B 1192 MET cc_start: 0.8183 (mpp) cc_final: 0.7458 (mpp) REVERT: C 71 MET cc_start: 0.9105 (ttm) cc_final: 0.8718 (ttp) REVERT: E 75 MET cc_start: 0.8920 (tpp) cc_final: 0.8704 (tpp) REVERT: E 78 LEU cc_start: 0.9366 (tt) cc_final: 0.8975 (tt) REVERT: E 112 TYR cc_start: 0.9080 (p90) cc_final: 0.8116 (p90) REVERT: E 114 ASN cc_start: 0.9419 (t0) cc_final: 0.8961 (t0) REVERT: E 136 ASN cc_start: 0.9459 (t0) cc_final: 0.9057 (t0) REVERT: E 211 TYR cc_start: 0.9375 (m-80) cc_final: 0.8768 (m-10) REVERT: E 215 MET cc_start: 0.8487 (mmt) cc_final: 0.8270 (mmm) REVERT: F 77 ASP cc_start: 0.8515 (p0) cc_final: 0.8117 (p0) REVERT: F 89 GLU cc_start: 0.9069 (OUTLIER) cc_final: 0.8739 (pm20) REVERT: F 140 ASP cc_start: 0.9253 (p0) cc_final: 0.8684 (p0) REVERT: F 142 SER cc_start: 0.9291 (m) cc_final: 0.8954 (p) REVERT: G 49 LEU cc_start: 0.9409 (tp) cc_final: 0.9089 (tt) REVERT: G 64 GLN cc_start: 0.8616 (mt0) cc_final: 0.7949 (mt0) REVERT: G 126 GLN cc_start: 0.8089 (tm-30) cc_final: 0.7196 (tm-30) REVERT: G 229 LEU cc_start: 0.9380 (tt) cc_final: 0.8973 (mp) REVERT: G 237 HIS cc_start: 0.8397 (m170) cc_final: 0.8128 (m90) REVERT: H 14 GLU cc_start: 0.8142 (tp30) cc_final: 0.7746 (tm-30) REVERT: I 18 GLU cc_start: 0.8952 (tp30) cc_final: 0.8599 (tp30) REVERT: I 45 LEU cc_start: 0.9212 (mm) cc_final: 0.8972 (mm) REVERT: K 67 GLU cc_start: 0.7760 (tm-30) cc_final: 0.7527 (tm-30) REVERT: K 81 MET cc_start: 0.8336 (mmm) cc_final: 0.8061 (mmm) REVERT: K 97 SER cc_start: 0.9332 (m) cc_final: 0.8894 (t) REVERT: K 125 MET cc_start: 0.8608 (mtp) cc_final: 0.8223 (tpp) REVERT: K 129 ASP cc_start: 0.8719 (m-30) cc_final: 0.8305 (m-30) REVERT: M 18 GLN cc_start: 0.8012 (pm20) cc_final: 0.7708 (pm20) REVERT: M 62 TYR cc_start: 0.5920 (p90) cc_final: 0.5042 (p90) REVERT: M 71 GLN cc_start: 0.9333 (tm-30) cc_final: 0.9108 (tm-30) REVERT: M 75 GLN cc_start: 0.9149 (pp30) cc_final: 0.8800 (pm20) REVERT: N 113 SER cc_start: 0.2696 (OUTLIER) cc_final: 0.2383 (p) REVERT: O 259 ASN cc_start: 0.7594 (OUTLIER) cc_final: 0.6935 (m110) REVERT: O 271 ILE cc_start: 0.9133 (OUTLIER) cc_final: 0.8825 (mm) REVERT: O 313 GLN cc_start: 0.8514 (OUTLIER) cc_final: 0.8217 (pp30) REVERT: O 471 MET cc_start: 0.8965 (mtt) cc_final: 0.8764 (mmm) REVERT: O 570 ASP cc_start: 0.8937 (t0) cc_final: 0.8448 (p0) REVERT: O 574 TRP cc_start: 0.7995 (OUTLIER) cc_final: 0.6609 (m-10) REVERT: P 131 HIS cc_start: 0.9441 (m-70) cc_final: 0.8921 (m-70) REVERT: P 158 MET cc_start: 0.6848 (mmp) cc_final: 0.5477 (mmm) REVERT: P 258 MET cc_start: 0.9129 (mmp) cc_final: 0.8404 (mmm) REVERT: P 300 ASN cc_start: 0.8478 (t0) cc_final: 0.8148 (m110) REVERT: P 311 MET cc_start: 0.9270 (ppp) cc_final: 0.8732 (pmm) REVERT: P 369 TRP cc_start: 0.8575 (m-10) cc_final: 0.8145 (m-10) REVERT: P 491 PHE cc_start: 0.8081 (OUTLIER) cc_final: 0.7370 (m-10) REVERT: P 497 GLN cc_start: 0.9228 (tt0) cc_final: 0.8519 (tp-100) REVERT: P 512 ARG cc_start: 0.6473 (OUTLIER) cc_final: 0.6037 (mpp-170) REVERT: Q 138 PHE cc_start: 0.8993 (OUTLIER) cc_final: 0.8503 (t80) REVERT: Q 214 VAL cc_start: 0.9448 (t) cc_final: 0.9074 (t) REVERT: Q 218 ASP cc_start: 0.8356 (m-30) cc_final: 0.8074 (m-30) REVERT: Q 340 ASP cc_start: 0.7631 (p0) cc_final: 0.7085 (p0) REVERT: Q 344 GLU cc_start: 0.9067 (mm-30) cc_final: 0.8785 (mt-10) REVERT: Q 372 HIS cc_start: 0.7771 (OUTLIER) cc_final: 0.7467 (t70) REVERT: Q 390 ASN cc_start: 0.4138 (OUTLIER) cc_final: 0.3893 (p0) REVERT: Q 410 TYR cc_start: 0.8770 (m-10) cc_final: 0.8509 (m-10) outliers start: 240 outliers final: 169 residues processed: 894 average time/residue: 0.1909 time to fit residues: 293.3900 Evaluate side-chains 864 residues out of total 4950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 185 poor density : 679 time to evaluate : 1.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 GLN Chi-restraints excluded: chain A residue 94 LEU Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 323 ILE Chi-restraints excluded: chain A residue 346 SER Chi-restraints excluded: chain A residue 357 MET Chi-restraints excluded: chain A residue 387 SER Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 403 LEU Chi-restraints excluded: chain A residue 450 LYS Chi-restraints excluded: chain A residue 482 SER Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain A residue 678 VAL Chi-restraints excluded: chain A residue 685 SER Chi-restraints excluded: chain A residue 713 VAL Chi-restraints excluded: chain A residue 721 LYS Chi-restraints excluded: chain A residue 891 ILE Chi-restraints excluded: chain A residue 922 CYS Chi-restraints excluded: chain A residue 957 VAL Chi-restraints excluded: chain A residue 1019 LEU Chi-restraints excluded: chain A residue 1118 VAL Chi-restraints excluded: chain A residue 1119 LYS Chi-restraints excluded: chain A residue 1188 ILE Chi-restraints excluded: chain A residue 1222 LEU Chi-restraints excluded: chain A residue 1238 MET Chi-restraints excluded: chain A residue 1470 CYS Chi-restraints excluded: chain A residue 1489 VAL Chi-restraints excluded: chain A residue 1491 GLU Chi-restraints excluded: chain A residue 1543 SER Chi-restraints excluded: chain A residue 1569 VAL Chi-restraints excluded: chain A residue 1603 MET Chi-restraints excluded: chain A residue 1634 LEU Chi-restraints excluded: chain A residue 1649 VAL Chi-restraints excluded: chain B residue 33 SER Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 67 ASP Chi-restraints excluded: chain B residue 68 ILE Chi-restraints excluded: chain B residue 75 ASP Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 218 ILE Chi-restraints excluded: chain B residue 343 ASP Chi-restraints excluded: chain B residue 353 VAL Chi-restraints excluded: chain B residue 409 TYR Chi-restraints excluded: chain B residue 424 ILE Chi-restraints excluded: chain B residue 430 MET Chi-restraints excluded: chain B residue 453 VAL Chi-restraints excluded: chain B residue 462 GLN Chi-restraints excluded: chain B residue 472 SER Chi-restraints excluded: chain B residue 564 ILE Chi-restraints excluded: chain B residue 592 ILE Chi-restraints excluded: chain B residue 647 SER Chi-restraints excluded: chain B residue 712 SER Chi-restraints excluded: chain B residue 725 THR Chi-restraints excluded: chain B residue 819 ASP Chi-restraints excluded: chain B residue 858 ILE Chi-restraints excluded: chain B residue 910 THR Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 985 ILE Chi-restraints excluded: chain B residue 1069 ILE Chi-restraints excluded: chain B residue 1085 SER Chi-restraints excluded: chain B residue 1087 LEU Chi-restraints excluded: chain B residue 1096 SER Chi-restraints excluded: chain B residue 1113 THR Chi-restraints excluded: chain B residue 1178 ILE Chi-restraints excluded: chain B residue 1186 ASP Chi-restraints excluded: chain C residue 73 SER Chi-restraints excluded: chain C residue 120 LEU Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain C residue 201 GLU Chi-restraints excluded: chain C residue 273 ASP Chi-restraints excluded: chain C residue 328 LEU Chi-restraints excluded: chain D residue 18 THR Chi-restraints excluded: chain D residue 31 VAL Chi-restraints excluded: chain D residue 85 SER Chi-restraints excluded: chain D residue 99 LEU Chi-restraints excluded: chain E residue 208 TYR Chi-restraints excluded: chain F residue 89 GLU Chi-restraints excluded: chain G residue 47 VAL Chi-restraints excluded: chain G residue 69 LEU Chi-restraints excluded: chain G residue 104 LEU Chi-restraints excluded: chain G residue 138 PHE Chi-restraints excluded: chain G residue 162 ILE Chi-restraints excluded: chain G residue 226 ASP Chi-restraints excluded: chain G residue 245 VAL Chi-restraints excluded: chain G residue 246 ASP Chi-restraints excluded: chain H residue 129 TYR Chi-restraints excluded: chain I residue 11 LEU Chi-restraints excluded: chain I residue 39 LYS Chi-restraints excluded: chain I residue 42 PHE Chi-restraints excluded: chain I residue 47 VAL Chi-restraints excluded: chain I residue 60 LEU Chi-restraints excluded: chain J residue 50 ILE Chi-restraints excluded: chain J residue 57 ILE Chi-restraints excluded: chain L residue 46 VAL Chi-restraints excluded: chain L residue 65 VAL Chi-restraints excluded: chain M residue 12 ILE Chi-restraints excluded: chain M residue 23 VAL Chi-restraints excluded: chain M residue 66 THR Chi-restraints excluded: chain M residue 77 VAL Chi-restraints excluded: chain M residue 78 VAL Chi-restraints excluded: chain M residue 98 SER Chi-restraints excluded: chain N residue 25 ILE Chi-restraints excluded: chain N residue 53 VAL Chi-restraints excluded: chain N residue 72 VAL Chi-restraints excluded: chain N residue 75 GLU Chi-restraints excluded: chain N residue 108 THR Chi-restraints excluded: chain N residue 111 VAL Chi-restraints excluded: chain N residue 113 SER Chi-restraints excluded: chain N residue 131 LEU Chi-restraints excluded: chain N residue 145 ILE Chi-restraints excluded: chain N residue 151 SER Chi-restraints excluded: chain N residue 155 VAL Chi-restraints excluded: chain N residue 160 VAL Chi-restraints excluded: chain N residue 173 THR Chi-restraints excluded: chain O residue 202 ILE Chi-restraints excluded: chain O residue 203 ILE Chi-restraints excluded: chain O residue 226 HIS Chi-restraints excluded: chain O residue 254 ILE Chi-restraints excluded: chain O residue 258 SER Chi-restraints excluded: chain O residue 259 ASN Chi-restraints excluded: chain O residue 260 LEU Chi-restraints excluded: chain O residue 271 ILE Chi-restraints excluded: chain O residue 300 LEU Chi-restraints excluded: chain O residue 313 GLN Chi-restraints excluded: chain O residue 344 ILE Chi-restraints excluded: chain O residue 353 ASP Chi-restraints excluded: chain O residue 384 ASP Chi-restraints excluded: chain O residue 405 TYR Chi-restraints excluded: chain O residue 416 LEU Chi-restraints excluded: chain O residue 421 ILE Chi-restraints excluded: chain O residue 442 LEU Chi-restraints excluded: chain O residue 451 ILE Chi-restraints excluded: chain O residue 480 VAL Chi-restraints excluded: chain O residue 535 VAL Chi-restraints excluded: chain O residue 569 VAL Chi-restraints excluded: chain O residue 574 TRP Chi-restraints excluded: chain O residue 622 TYR Chi-restraints excluded: chain O residue 659 LEU Chi-restraints excluded: chain O residue 668 SER Chi-restraints excluded: chain O residue 688 ASP Chi-restraints excluded: chain O residue 707 ASP Chi-restraints excluded: chain O residue 726 SER Chi-restraints excluded: chain P residue 95 LEU Chi-restraints excluded: chain P residue 147 GLN Chi-restraints excluded: chain P residue 178 THR Chi-restraints excluded: chain P residue 215 LEU Chi-restraints excluded: chain P residue 225 GLN Chi-restraints excluded: chain P residue 262 LEU Chi-restraints excluded: chain P residue 304 LEU Chi-restraints excluded: chain P residue 356 VAL Chi-restraints excluded: chain P residue 366 TYR Chi-restraints excluded: chain P residue 367 PHE Chi-restraints excluded: chain P residue 388 THR Chi-restraints excluded: chain P residue 400 MET Chi-restraints excluded: chain P residue 408 ILE Chi-restraints excluded: chain P residue 437 THR Chi-restraints excluded: chain P residue 479 LEU Chi-restraints excluded: chain P residue 491 PHE Chi-restraints excluded: chain P residue 512 ARG Chi-restraints excluded: chain Q residue 4 VAL Chi-restraints excluded: chain Q residue 10 ASN Chi-restraints excluded: chain Q residue 127 PHE Chi-restraints excluded: chain Q residue 128 TRP Chi-restraints excluded: chain Q residue 138 PHE Chi-restraints excluded: chain Q residue 155 GLN Chi-restraints excluded: chain Q residue 158 THR Chi-restraints excluded: chain Q residue 168 ILE Chi-restraints excluded: chain Q residue 187 TYR Chi-restraints excluded: chain Q residue 216 LEU Chi-restraints excluded: chain Q residue 240 ILE Chi-restraints excluded: chain Q residue 247 ILE Chi-restraints excluded: chain Q residue 248 LYS Chi-restraints excluded: chain Q residue 251 TRP Chi-restraints excluded: chain Q residue 269 ASP Chi-restraints excluded: chain Q residue 279 SER Chi-restraints excluded: chain Q residue 280 SER Chi-restraints excluded: chain Q residue 289 ASN Chi-restraints excluded: chain Q residue 298 GLN Chi-restraints excluded: chain Q residue 354 LEU Chi-restraints excluded: chain Q residue 372 HIS Chi-restraints excluded: chain Q residue 390 ASN Chi-restraints excluded: chain Q residue 400 LYS Chi-restraints excluded: chain Q residue 401 ILE Chi-restraints excluded: chain Q residue 424 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 555 random chunks: chunk 191 optimal weight: 2.9990 chunk 361 optimal weight: 7.9990 chunk 271 optimal weight: 4.9990 chunk 408 optimal weight: 10.0000 chunk 107 optimal weight: 10.0000 chunk 170 optimal weight: 3.9990 chunk 363 optimal weight: 8.9990 chunk 261 optimal weight: 3.9990 chunk 445 optimal weight: 9.9990 chunk 470 optimal weight: 10.0000 chunk 213 optimal weight: 3.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 93 GLN ** A 525 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 656 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1191 GLN ** B 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 361 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 504 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 547 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 720 GLN ** B1163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 133 ASN ** H 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.115787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.081901 restraints weight = 143671.104| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.084220 restraints weight = 64616.354| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.085666 restraints weight = 39550.581| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 55)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.086563 restraints weight = 29321.527| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.086976 restraints weight = 24657.057| |-----------------------------------------------------------------------------| r_work (final): 0.3272 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7763 moved from start: 0.6200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 47752 Z= 0.215 Angle : 0.853 20.356 64966 Z= 0.430 Chirality : 0.049 0.355 7264 Planarity : 0.006 0.128 7978 Dihedral : 14.469 162.011 7208 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 18.98 Ramachandran Plot: Outliers : 0.70 % Allowed : 7.57 % Favored : 91.73 % Rotamer: Outliers : 3.86 % Allowed : 22.01 % Favored : 74.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.24 % Twisted General : 0.04 % 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: -1.01 (0.11), residues: 5432 helix: 0.57 (0.11), residues: 1989 sheet: -1.04 (0.18), residues: 760 loop : -1.51 (0.12), residues: 2683 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG M 31 TYR 0.051 0.002 TYR P 211 PHE 0.108 0.002 PHE Q 358 TRP 0.033 0.002 TRP G 125 HIS 0.010 0.001 HIS N 170 Details of bonding type rmsd/Z covalent geometry : bond 0.00479 / 0.21 (47712) covalent geometry : angle 0.83971 / 0.43 (64930) hydrogen bonds : bond 0.05058 / 3.37 ( 2015) hydrogen bonds : angle 5.66986 / 4.01 ( 5581) metal coordination : bond 0.01369 / 0.81 ( 24) metal coordination : angle 6.66433 / 4.95 ( 33) Misc. bond : bond 0.00974 / 0.51 ( 15) link_TRANS : bond 0.00141 / 0.07 ( 1) link_TRANS : angle 0.15402 / 0.09 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10864 Ramachandran restraints generated. 5432 Oldfield, 0 Emsley, 5432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10864 Ramachandran restraints generated. 5432 Oldfield, 0 Emsley, 5432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 952 residues out of total 4950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 191 poor density : 761 time to evaluate : 1.092 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 238 MET cc_start: 0.8033 (mmp) cc_final: 0.7685 (mmp) REVERT: A 394 LEU cc_start: 0.9533 (tp) cc_final: 0.9305 (pp) REVERT: A 450 LYS cc_start: 0.5095 (OUTLIER) cc_final: 0.3065 (mmtt) REVERT: A 461 GLU cc_start: 0.7246 (mt-10) cc_final: 0.7016 (mm-30) REVERT: A 530 TRP cc_start: 0.7660 (t60) cc_final: 0.7309 (t60) REVERT: A 608 LEU cc_start: 0.9172 (OUTLIER) cc_final: 0.8944 (mt) REVERT: A 881 GLU cc_start: 0.8711 (tt0) cc_final: 0.8333 (tp30) REVERT: A 882 ILE cc_start: 0.9476 (mt) cc_final: 0.9254 (mm) REVERT: A 1576 SER cc_start: 0.9136 (m) cc_final: 0.8535 (p) REVERT: A 1611 MET cc_start: 0.8615 (tmm) cc_final: 0.8240 (tmm) REVERT: A 1627 LEU cc_start: 0.9619 (mt) cc_final: 0.9144 (mp) REVERT: B 97 VAL cc_start: 0.9449 (t) cc_final: 0.9203 (m) REVERT: B 175 MET cc_start: 0.8756 (mtp) cc_final: 0.8454 (mtp) REVERT: B 418 ASP cc_start: 0.8576 (t70) cc_final: 0.8292 (t0) REVERT: B 419 GLU cc_start: 0.8374 (tp30) cc_final: 0.7336 (tp30) REVERT: B 422 GLN cc_start: 0.8687 (mt0) cc_final: 0.7883 (mt0) REVERT: B 430 MET cc_start: 0.8286 (OUTLIER) cc_final: 0.8016 (tmm) REVERT: B 448 ARG cc_start: 0.8944 (ttp-110) cc_final: 0.8600 (ttp-110) REVERT: B 473 GLN cc_start: 0.8382 (mm-40) cc_final: 0.8018 (mm-40) REVERT: B 502 MET cc_start: 0.8609 (ttp) cc_final: 0.8245 (tmm) REVERT: B 778 TYR cc_start: 0.8712 (t80) cc_final: 0.7687 (t80) REVERT: B 787 MET cc_start: 0.8703 (OUTLIER) cc_final: 0.8077 (ppp) REVERT: B 900 THR cc_start: 0.9478 (m) cc_final: 0.9167 (p) REVERT: B 950 ASN cc_start: 0.8871 (t0) cc_final: 0.8616 (t0) REVERT: B 962 MET cc_start: 0.8934 (tpp) cc_final: 0.8726 (tpp) REVERT: B 1134 ARG cc_start: 0.8529 (tpp80) cc_final: 0.8037 (tpp80) REVERT: B 1186 ASP cc_start: 0.7866 (OUTLIER) cc_final: 0.7401 (t70) REVERT: B 1192 MET cc_start: 0.8172 (mpp) cc_final: 0.7423 (mpp) REVERT: C 71 MET cc_start: 0.9201 (ttm) cc_final: 0.8879 (ttp) REVERT: C 112 MET cc_start: 0.8412 (mpp) cc_final: 0.8057 (mpp) REVERT: D 34 ASP cc_start: 0.9043 (t0) cc_final: 0.8655 (p0) REVERT: D 45 ASP cc_start: 0.8972 (t0) cc_final: 0.8511 (t0) REVERT: E 22 MET cc_start: 0.8633 (ttm) cc_final: 0.8431 (tpt) REVERT: E 78 LEU cc_start: 0.9310 (tt) cc_final: 0.8919 (tt) REVERT: E 112 TYR cc_start: 0.8923 (p90) cc_final: 0.8017 (p90) REVERT: E 114 ASN cc_start: 0.9363 (t0) cc_final: 0.8834 (t0) REVERT: E 119 SER cc_start: 0.9393 (OUTLIER) cc_final: 0.9113 (p) REVERT: E 136 ASN cc_start: 0.9434 (t0) cc_final: 0.9027 (t0) REVERT: E 211 TYR cc_start: 0.9281 (m-80) cc_final: 0.8691 (m-10) REVERT: E 215 MET cc_start: 0.8501 (mmt) cc_final: 0.8261 (mmm) REVERT: F 77 ASP cc_start: 0.8559 (p0) cc_final: 0.8196 (p0) REVERT: F 140 ASP cc_start: 0.9202 (p0) cc_final: 0.8608 (p0) REVERT: F 142 SER cc_start: 0.9332 (m) cc_final: 0.8902 (p) REVERT: G 64 GLN cc_start: 0.8531 (mt0) cc_final: 0.7846 (mt0) REVERT: G 126 GLN cc_start: 0.7964 (tm-30) cc_final: 0.7122 (tm-30) REVERT: G 229 LEU cc_start: 0.9192 (tt) cc_final: 0.8751 (mp) REVERT: G 237 HIS cc_start: 0.8334 (m170) cc_final: 0.8096 (m90) REVERT: I 18 GLU cc_start: 0.8948 (tp30) cc_final: 0.8523 (tp30) REVERT: I 45 LEU cc_start: 0.9152 (mm) cc_final: 0.8949 (mm) REVERT: K 67 GLU cc_start: 0.7733 (tm-30) cc_final: 0.7526 (tm-30) REVERT: K 81 MET cc_start: 0.8478 (mmm) cc_final: 0.8100 (mmm) REVERT: K 97 SER cc_start: 0.9364 (m) cc_final: 0.8908 (t) REVERT: K 107 THR cc_start: 0.8677 (OUTLIER) cc_final: 0.8438 (t) REVERT: K 125 MET cc_start: 0.8674 (mtp) cc_final: 0.8325 (tpp) REVERT: K 129 ASP cc_start: 0.8815 (m-30) cc_final: 0.8381 (m-30) REVERT: M 62 TYR cc_start: 0.6001 (p90) cc_final: 0.5149 (p90) REVERT: M 75 GLN cc_start: 0.9228 (pp30) cc_final: 0.8873 (pm20) REVERT: N 113 SER cc_start: 0.2517 (OUTLIER) cc_final: 0.2136 (p) REVERT: O 259 ASN cc_start: 0.7411 (OUTLIER) cc_final: 0.6889 (m110) REVERT: O 285 MET cc_start: 0.8795 (pmm) cc_final: 0.8500 (pmm) REVERT: O 313 GLN cc_start: 0.8286 (OUTLIER) cc_final: 0.8044 (pp30) REVERT: O 397 LYS cc_start: 0.7857 (OUTLIER) cc_final: 0.7598 (mmtp) REVERT: O 471 MET cc_start: 0.8916 (mtt) cc_final: 0.8679 (mmm) REVERT: O 570 ASP cc_start: 0.8932 (t0) cc_final: 0.8449 (p0) REVERT: O 659 LEU cc_start: 0.5440 (OUTLIER) cc_final: 0.5176 (mt) REVERT: P 118 TRP cc_start: 0.8809 (t-100) cc_final: 0.8537 (t-100) REVERT: P 131 HIS cc_start: 0.9430 (m-70) cc_final: 0.8890 (m-70) REVERT: P 158 MET cc_start: 0.6956 (OUTLIER) cc_final: 0.5765 (mmt) REVERT: P 222 PHE cc_start: 0.8898 (t80) cc_final: 0.8465 (t80) REVERT: P 258 MET cc_start: 0.9185 (mmp) cc_final: 0.8792 (mmm) REVERT: P 300 ASN cc_start: 0.8503 (t0) cc_final: 0.8286 (m110) REVERT: P 369 TRP cc_start: 0.8600 (m-10) cc_final: 0.8268 (m100) REVERT: P 419 LEU cc_start: 0.7468 (pp) cc_final: 0.7249 (pp) REVERT: P 491 PHE cc_start: 0.7799 (OUTLIER) cc_final: 0.7571 (m-10) REVERT: P 497 GLN cc_start: 0.9202 (tt0) cc_final: 0.8583 (tp-100) REVERT: P 512 ARG cc_start: 0.6489 (OUTLIER) cc_final: 0.5850 (mtm180) REVERT: Q 138 PHE cc_start: 0.9150 (OUTLIER) cc_final: 0.8734 (t80) REVERT: Q 214 VAL cc_start: 0.9437 (t) cc_final: 0.9056 (t) REVERT: Q 218 ASP cc_start: 0.8311 (m-30) cc_final: 0.8040 (m-30) REVERT: Q 248 LYS cc_start: 0.9583 (OUTLIER) cc_final: 0.9336 (ttpt) REVERT: Q 372 HIS cc_start: 0.7681 (OUTLIER) cc_final: 0.7381 (t70) REVERT: Q 390 ASN cc_start: 0.4243 (OUTLIER) cc_final: 0.3993 (p0) REVERT: Q 410 TYR cc_start: 0.8726 (m-10) cc_final: 0.8449 (m-10) outliers start: 191 outliers final: 136 residues processed: 882 average time/residue: 0.1715 time to fit residues: 258.8575 Evaluate side-chains 872 residues out of total 4950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 155 poor density : 717 time to evaluate : 1.036 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 LEU Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 222 GLU Chi-restraints excluded: chain A residue 346 SER Chi-restraints excluded: chain A residue 357 MET Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 403 LEU Chi-restraints excluded: chain A residue 419 ILE Chi-restraints excluded: chain A residue 450 LYS Chi-restraints excluded: chain A residue 495 ILE Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 608 LEU Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain A residue 678 VAL Chi-restraints excluded: chain A residue 713 VAL Chi-restraints excluded: chain A residue 891 ILE Chi-restraints excluded: chain A residue 922 CYS Chi-restraints excluded: chain A residue 957 VAL Chi-restraints excluded: chain A residue 1019 LEU Chi-restraints excluded: chain A residue 1118 VAL Chi-restraints excluded: chain A residue 1119 LYS Chi-restraints excluded: chain A residue 1188 ILE Chi-restraints excluded: chain A residue 1222 LEU Chi-restraints excluded: chain A residue 1238 MET Chi-restraints excluded: chain A residue 1470 CYS Chi-restraints excluded: chain A residue 1491 GLU Chi-restraints excluded: chain A residue 1543 SER Chi-restraints excluded: chain A residue 1603 MET Chi-restraints excluded: chain A residue 1634 LEU Chi-restraints excluded: chain A residue 1649 VAL Chi-restraints excluded: chain B residue 57 ASP Chi-restraints excluded: chain B residue 68 ILE Chi-restraints excluded: chain B residue 75 ASP Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 249 VAL Chi-restraints excluded: chain B residue 293 ILE Chi-restraints excluded: chain B residue 306 LEU Chi-restraints excluded: chain B residue 343 ASP Chi-restraints excluded: chain B residue 409 TYR Chi-restraints excluded: chain B residue 421 LEU Chi-restraints excluded: chain B residue 424 ILE Chi-restraints excluded: chain B residue 430 MET Chi-restraints excluded: chain B residue 453 VAL Chi-restraints excluded: chain B residue 462 GLN Chi-restraints excluded: chain B residue 564 ILE Chi-restraints excluded: chain B residue 712 SER Chi-restraints excluded: chain B residue 725 THR Chi-restraints excluded: chain B residue 787 MET Chi-restraints excluded: chain B residue 819 ASP Chi-restraints excluded: chain B residue 910 THR Chi-restraints excluded: chain B residue 918 SER Chi-restraints excluded: chain B residue 1087 LEU Chi-restraints excluded: chain B residue 1113 THR Chi-restraints excluded: chain B residue 1178 ILE Chi-restraints excluded: chain B residue 1186 ASP Chi-restraints excluded: chain C residue 73 SER Chi-restraints excluded: chain C residue 120 LEU Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain C residue 201 GLU Chi-restraints excluded: chain C residue 273 ASP Chi-restraints excluded: chain C residue 328 LEU Chi-restraints excluded: chain D residue 15 THR Chi-restraints excluded: chain D residue 31 VAL Chi-restraints excluded: chain D residue 85 SER Chi-restraints excluded: chain E residue 119 SER Chi-restraints excluded: chain E residue 178 ILE Chi-restraints excluded: chain E residue 199 ILE Chi-restraints excluded: chain G residue 47 VAL Chi-restraints excluded: chain G residue 69 LEU Chi-restraints excluded: chain G residue 104 LEU Chi-restraints excluded: chain G residue 138 PHE Chi-restraints excluded: chain G residue 162 ILE Chi-restraints excluded: chain G residue 226 ASP Chi-restraints excluded: chain G residue 245 VAL Chi-restraints excluded: chain G residue 246 ASP Chi-restraints excluded: chain H residue 129 TYR Chi-restraints excluded: chain I residue 39 LYS Chi-restraints excluded: chain I residue 42 PHE Chi-restraints excluded: chain I residue 53 ASP Chi-restraints excluded: chain I residue 60 LEU Chi-restraints excluded: chain J residue 50 ILE Chi-restraints excluded: chain J residue 57 ILE Chi-restraints excluded: chain K residue 107 THR Chi-restraints excluded: chain L residue 46 VAL Chi-restraints excluded: chain L residue 65 VAL Chi-restraints excluded: chain M residue 23 VAL Chi-restraints excluded: chain M residue 66 THR Chi-restraints excluded: chain M residue 97 VAL Chi-restraints excluded: chain N residue 25 ILE Chi-restraints excluded: chain N residue 32 CYS Chi-restraints excluded: chain N residue 72 VAL Chi-restraints excluded: chain N residue 75 GLU Chi-restraints excluded: chain N residue 111 VAL Chi-restraints excluded: chain N residue 113 SER Chi-restraints excluded: chain N residue 131 LEU Chi-restraints excluded: chain N residue 160 VAL Chi-restraints excluded: chain N residue 168 LEU Chi-restraints excluded: chain N residue 173 THR Chi-restraints excluded: chain O residue 202 ILE Chi-restraints excluded: chain O residue 203 ILE Chi-restraints excluded: chain O residue 254 ILE Chi-restraints excluded: chain O residue 258 SER Chi-restraints excluded: chain O residue 259 ASN Chi-restraints excluded: chain O residue 260 LEU Chi-restraints excluded: chain O residue 300 LEU Chi-restraints excluded: chain O residue 313 GLN Chi-restraints excluded: chain O residue 344 ILE Chi-restraints excluded: chain O residue 353 ASP Chi-restraints excluded: chain O residue 384 ASP Chi-restraints excluded: chain O residue 397 LYS Chi-restraints excluded: chain O residue 416 LEU Chi-restraints excluded: chain O residue 421 ILE Chi-restraints excluded: chain O residue 442 LEU Chi-restraints excluded: chain O residue 451 ILE Chi-restraints excluded: chain O residue 480 VAL Chi-restraints excluded: chain O residue 569 VAL Chi-restraints excluded: chain O residue 622 TYR Chi-restraints excluded: chain O residue 659 LEU Chi-restraints excluded: chain O residue 688 ASP Chi-restraints excluded: chain O residue 724 LEU Chi-restraints excluded: chain O residue 726 SER Chi-restraints excluded: chain P residue 95 LEU Chi-restraints excluded: chain P residue 147 GLN Chi-restraints excluded: chain P residue 158 MET Chi-restraints excluded: chain P residue 215 LEU Chi-restraints excluded: chain P residue 262 LEU Chi-restraints excluded: chain P residue 304 LEU Chi-restraints excluded: chain P residue 356 VAL Chi-restraints excluded: chain P residue 366 TYR Chi-restraints excluded: chain P residue 367 PHE Chi-restraints excluded: chain P residue 400 MET Chi-restraints excluded: chain P residue 408 ILE Chi-restraints excluded: chain P residue 437 THR Chi-restraints excluded: chain P residue 479 LEU Chi-restraints excluded: chain P residue 491 PHE Chi-restraints excluded: chain P residue 512 ARG Chi-restraints excluded: chain Q residue 10 ASN Chi-restraints excluded: chain Q residue 128 TRP Chi-restraints excluded: chain Q residue 138 PHE Chi-restraints excluded: chain Q residue 155 GLN Chi-restraints excluded: chain Q residue 158 THR Chi-restraints excluded: chain Q residue 168 ILE Chi-restraints excluded: chain Q residue 187 TYR Chi-restraints excluded: chain Q residue 240 ILE Chi-restraints excluded: chain Q residue 247 ILE Chi-restraints excluded: chain Q residue 248 LYS Chi-restraints excluded: chain Q residue 251 TRP Chi-restraints excluded: chain Q residue 269 ASP Chi-restraints excluded: chain Q residue 280 SER Chi-restraints excluded: chain Q residue 289 ASN Chi-restraints excluded: chain Q residue 298 GLN Chi-restraints excluded: chain Q residue 372 HIS Chi-restraints excluded: chain Q residue 390 ASN Chi-restraints excluded: chain Q residue 400 LYS Chi-restraints excluded: chain Q residue 401 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 555 random chunks: chunk 381 optimal weight: 7.9990 chunk 186 optimal weight: 1.9990 chunk 544 optimal weight: 5.9990 chunk 335 optimal weight: 0.4980 chunk 398 optimal weight: 2.9990 chunk 143 optimal weight: 0.9990 chunk 240 optimal weight: 0.9990 chunk 125 optimal weight: 20.0000 chunk 64 optimal weight: 7.9990 chunk 494 optimal weight: 0.4980 chunk 363 optimal weight: 1.9990 overall best weight: 0.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 525 ASN ** A 656 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1116 GLN ** B 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 504 HIS ** B 547 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 720 GLN ** B1163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 100 GLN F 104 ASN ** G 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 137 GLN J 53 HIS ** M 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.117737 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.084362 restraints weight = 142331.074| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.087233 restraints weight = 68577.719| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.087814 restraints weight = 36437.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.088086 restraints weight = 35469.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.088164 restraints weight = 32247.190| |-----------------------------------------------------------------------------| r_work (final): 0.3283 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7742 moved from start: 0.6386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 47752 Z= 0.164 Angle : 0.853 18.564 64966 Z= 0.428 Chirality : 0.049 0.447 7264 Planarity : 0.006 0.128 7978 Dihedral : 14.387 160.400 7203 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 16.71 Ramachandran Plot: Outliers : 0.63 % Allowed : 7.20 % Favored : 92.18 % Rotamer: Outliers : 3.15 % Allowed : 22.57 % Favored : 74.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.24 % Twisted General : 0.04 % 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: -0.88 (0.11), residues: 5432 helix: 0.63 (0.12), residues: 1991 sheet: -0.87 (0.18), residues: 736 loop : -1.43 (0.12), residues: 2705 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG I 61 TYR 0.045 0.002 TYR P 211 PHE 0.108 0.002 PHE Q 358 TRP 0.064 0.002 TRP P 184 HIS 0.013 0.001 HIS O 571 Details of bonding type rmsd/Z covalent geometry : bond 0.00358 / 0.16 (47712) covalent geometry : angle 0.84290 / 0.43 (64930) hydrogen bonds : bond 0.04887 / 3.26 ( 2015) hydrogen bonds : angle 5.53494 / 3.93 ( 5581) metal coordination : bond 0.00813 / 0.53 ( 24) metal coordination : angle 5.76555 / 4.33 ( 33) Misc. bond : bond 0.00998 / 0.52 ( 15) link_TRANS : bond 0.00109 / 0.06 ( 1) link_TRANS : angle 0.15975 / 0.09 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10864 Ramachandran restraints generated. 5432 Oldfield, 0 Emsley, 5432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10864 Ramachandran restraints generated. 5432 Oldfield, 0 Emsley, 5432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 959 residues out of total 4950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 156 poor density : 803 time to evaluate : 1.100 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 238 MET cc_start: 0.8160 (mmp) cc_final: 0.7738 (mmp) REVERT: A 394 LEU cc_start: 0.9526 (tp) cc_final: 0.9291 (pp) REVERT: A 450 LYS cc_start: 0.5196 (OUTLIER) cc_final: 0.3126 (mmtt) REVERT: A 819 ASN cc_start: 0.9084 (m-40) cc_final: 0.8597 (m-40) REVERT: A 881 GLU cc_start: 0.8692 (tt0) cc_final: 0.8224 (tp30) REVERT: A 1116 GLN cc_start: 0.6524 (OUTLIER) cc_final: 0.5932 (pp30) REVERT: A 1576 SER cc_start: 0.8984 (m) cc_final: 0.8357 (p) REVERT: A 1611 MET cc_start: 0.8610 (tmm) cc_final: 0.8218 (tmm) REVERT: A 1624 LYS cc_start: 0.9236 (OUTLIER) cc_final: 0.8926 (mtmm) REVERT: B 418 ASP cc_start: 0.8563 (t70) cc_final: 0.8250 (t0) REVERT: B 419 GLU cc_start: 0.8386 (tp30) cc_final: 0.7319 (tp30) REVERT: B 422 GLN cc_start: 0.8707 (mt0) cc_final: 0.8021 (mt0) REVERT: B 430 MET cc_start: 0.8355 (OUTLIER) cc_final: 0.8053 (tmm) REVERT: B 448 ARG cc_start: 0.9008 (ttp-110) cc_final: 0.8650 (ttp-110) REVERT: B 473 GLN cc_start: 0.8239 (mm-40) cc_final: 0.7886 (mm-40) REVERT: B 502 MET cc_start: 0.8573 (ttp) cc_final: 0.8160 (tmm) REVERT: B 778 TYR cc_start: 0.8530 (t80) cc_final: 0.7643 (t80) REVERT: B 807 GLU cc_start: 0.7706 (tt0) cc_final: 0.7343 (tt0) REVERT: B 900 THR cc_start: 0.9474 (m) cc_final: 0.9246 (p) REVERT: B 962 MET cc_start: 0.8915 (tpp) cc_final: 0.8659 (tpp) REVERT: B 1065 ARG cc_start: 0.7901 (mtt180) cc_final: 0.7477 (mtp180) REVERT: B 1086 PHE cc_start: 0.8350 (m-80) cc_final: 0.7979 (m-80) REVERT: B 1134 ARG cc_start: 0.8528 (tpp80) cc_final: 0.8075 (tpp80) REVERT: B 1186 ASP cc_start: 0.7794 (OUTLIER) cc_final: 0.7283 (t70) REVERT: B 1192 MET cc_start: 0.8194 (mpp) cc_final: 0.7470 (mpp) REVERT: C 71 MET cc_start: 0.9160 (ttm) cc_final: 0.8701 (ttp) REVERT: C 112 MET cc_start: 0.8377 (mpp) cc_final: 0.8073 (mpp) REVERT: D 34 ASP cc_start: 0.9205 (t0) cc_final: 0.8755 (p0) REVERT: E 75 MET cc_start: 0.8861 (tpp) cc_final: 0.8643 (tpp) REVERT: E 78 LEU cc_start: 0.9404 (tt) cc_final: 0.9006 (tt) REVERT: E 106 GLN cc_start: 0.7480 (tt0) cc_final: 0.7143 (tt0) REVERT: E 112 TYR cc_start: 0.8997 (p90) cc_final: 0.7972 (p90) REVERT: E 114 ASN cc_start: 0.9403 (t0) cc_final: 0.8815 (t0) REVERT: E 119 SER cc_start: 0.9382 (OUTLIER) cc_final: 0.9156 (p) REVERT: E 136 ASN cc_start: 0.9418 (t0) cc_final: 0.8857 (t0) REVERT: E 187 TYR cc_start: 0.8938 (t80) cc_final: 0.8248 (t80) REVERT: E 211 TYR cc_start: 0.9239 (m-80) cc_final: 0.8738 (m-10) REVERT: E 215 MET cc_start: 0.8521 (mmt) cc_final: 0.8287 (mmm) REVERT: F 77 ASP cc_start: 0.8624 (p0) cc_final: 0.8292 (p0) REVERT: F 140 ASP cc_start: 0.9126 (p0) cc_final: 0.8542 (p0) REVERT: F 142 SER cc_start: 0.9346 (m) cc_final: 0.8933 (p) REVERT: G 64 GLN cc_start: 0.8730 (mt0) cc_final: 0.8074 (mt0) REVERT: G 119 HIS cc_start: 0.8420 (m170) cc_final: 0.7851 (m-70) REVERT: G 126 GLN cc_start: 0.7874 (tm-30) cc_final: 0.7124 (tm-30) REVERT: G 229 LEU cc_start: 0.9336 (tt) cc_final: 0.8891 (mp) REVERT: H 27 GLU cc_start: 0.8204 (mp0) cc_final: 0.7949 (mp0) REVERT: H 123 MET cc_start: 0.8424 (ppp) cc_final: 0.8192 (ppp) REVERT: I 18 GLU cc_start: 0.8933 (tp30) cc_final: 0.8410 (tp30) REVERT: I 45 LEU cc_start: 0.9168 (mm) cc_final: 0.8952 (mm) REVERT: J 27 GLU cc_start: 0.8811 (OUTLIER) cc_final: 0.8538 (pp20) REVERT: K 67 GLU cc_start: 0.7615 (tm-30) cc_final: 0.7388 (tm-30) REVERT: K 82 LYS cc_start: 0.9532 (mmtm) cc_final: 0.9328 (mmmm) REVERT: K 97 SER cc_start: 0.9288 (m) cc_final: 0.8743 (t) REVERT: K 107 THR cc_start: 0.8752 (OUTLIER) cc_final: 0.8535 (t) REVERT: K 125 MET cc_start: 0.8651 (mtp) cc_final: 0.8389 (tpp) REVERT: K 129 ASP cc_start: 0.8858 (m-30) cc_final: 0.8415 (m-30) REVERT: M 18 GLN cc_start: 0.8019 (pm20) cc_final: 0.7782 (pm20) REVERT: M 62 TYR cc_start: 0.6022 (p90) cc_final: 0.5180 (p90) REVERT: M 75 GLN cc_start: 0.9172 (pp30) cc_final: 0.8788 (pm20) REVERT: N 106 ASN cc_start: 0.7553 (m110) cc_final: 0.7173 (m-40) REVERT: N 114 GLU cc_start: 0.8496 (pt0) cc_final: 0.8278 (mm-30) REVERT: O 201 GLU cc_start: 0.7996 (OUTLIER) cc_final: 0.7590 (pm20) REVERT: O 259 ASN cc_start: 0.7113 (OUTLIER) cc_final: 0.6887 (m110) REVERT: O 285 MET cc_start: 0.8764 (pmm) cc_final: 0.8455 (pmm) REVERT: O 380 MET cc_start: 0.7984 (tpp) cc_final: 0.7298 (tpt) REVERT: O 450 ARG cc_start: 0.8742 (mtp85) cc_final: 0.8006 (mtm180) REVERT: O 570 ASP cc_start: 0.8908 (t0) cc_final: 0.8467 (p0) REVERT: P 131 HIS cc_start: 0.9390 (m-70) cc_final: 0.8848 (m-70) REVERT: P 158 MET cc_start: 0.6910 (OUTLIER) cc_final: 0.5704 (mmt) REVERT: P 222 PHE cc_start: 0.8991 (t80) cc_final: 0.8612 (t80) REVERT: P 258 MET cc_start: 0.9219 (mmp) cc_final: 0.8678 (mmm) REVERT: P 369 TRP cc_start: 0.8610 (m-10) cc_final: 0.8226 (m100) REVERT: P 497 GLN cc_start: 0.9225 (tt0) cc_final: 0.8679 (tp40) REVERT: Q 138 PHE cc_start: 0.9085 (OUTLIER) cc_final: 0.8786 (t80) REVERT: Q 214 VAL cc_start: 0.9418 (t) cc_final: 0.9024 (t) REVERT: Q 218 ASP cc_start: 0.8228 (m-30) cc_final: 0.7935 (m-30) REVERT: Q 248 LYS cc_start: 0.9533 (OUTLIER) cc_final: 0.9321 (ttpt) REVERT: Q 372 HIS cc_start: 0.7708 (OUTLIER) cc_final: 0.7386 (t70) REVERT: Q 390 ASN cc_start: 0.4318 (OUTLIER) cc_final: 0.4095 (p0) REVERT: Q 410 TYR cc_start: 0.8730 (m-10) cc_final: 0.8441 (m-10) outliers start: 156 outliers final: 110 residues processed: 902 average time/residue: 0.1704 time to fit residues: 262.6927 Evaluate side-chains 857 residues out of total 4950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 732 time to evaluate : 1.090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 LEU Chi-restraints excluded: chain A residue 346 SER Chi-restraints excluded: chain A residue 357 MET Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 403 LEU Chi-restraints excluded: chain A residue 419 ILE Chi-restraints excluded: chain A residue 450 LYS Chi-restraints excluded: chain A residue 495 ILE Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain A residue 713 VAL Chi-restraints excluded: chain A residue 957 VAL Chi-restraints excluded: chain A residue 1019 LEU Chi-restraints excluded: chain A residue 1116 GLN Chi-restraints excluded: chain A residue 1118 VAL Chi-restraints excluded: chain A residue 1119 LYS Chi-restraints excluded: chain A residue 1222 LEU Chi-restraints excluded: chain A residue 1603 MET Chi-restraints excluded: chain A residue 1624 LYS Chi-restraints excluded: chain A residue 1634 LEU Chi-restraints excluded: chain A residue 1649 VAL Chi-restraints excluded: chain B residue 57 ASP Chi-restraints excluded: chain B residue 68 ILE Chi-restraints excluded: chain B residue 75 ASP Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 249 VAL Chi-restraints excluded: chain B residue 306 LEU Chi-restraints excluded: chain B residue 343 ASP Chi-restraints excluded: chain B residue 409 TYR Chi-restraints excluded: chain B residue 421 LEU Chi-restraints excluded: chain B residue 424 ILE Chi-restraints excluded: chain B residue 430 MET Chi-restraints excluded: chain B residue 453 VAL Chi-restraints excluded: chain B residue 564 ILE Chi-restraints excluded: chain B residue 712 SER Chi-restraints excluded: chain B residue 725 THR Chi-restraints excluded: chain B residue 819 ASP Chi-restraints excluded: chain B residue 918 SER Chi-restraints excluded: chain B residue 1087 LEU Chi-restraints excluded: chain B residue 1113 THR Chi-restraints excluded: chain B residue 1178 ILE Chi-restraints excluded: chain B residue 1186 ASP Chi-restraints excluded: chain C residue 73 SER Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain C residue 328 LEU Chi-restraints excluded: chain D residue 31 VAL Chi-restraints excluded: chain E residue 119 SER Chi-restraints excluded: chain E residue 178 ILE Chi-restraints excluded: chain E residue 199 ILE Chi-restraints excluded: chain G residue 69 LEU Chi-restraints excluded: chain G residue 138 PHE Chi-restraints excluded: chain G residue 162 ILE Chi-restraints excluded: chain G residue 226 ASP Chi-restraints excluded: chain G residue 245 VAL Chi-restraints excluded: chain G residue 246 ASP Chi-restraints excluded: chain H residue 129 TYR Chi-restraints excluded: chain I residue 42 PHE Chi-restraints excluded: chain I residue 47 VAL Chi-restraints excluded: chain I residue 60 LEU Chi-restraints excluded: chain J residue 27 GLU Chi-restraints excluded: chain J residue 57 ILE Chi-restraints excluded: chain K residue 107 THR Chi-restraints excluded: chain L residue 46 VAL Chi-restraints excluded: chain L residue 65 VAL Chi-restraints excluded: chain M residue 23 VAL Chi-restraints excluded: chain M residue 66 THR Chi-restraints excluded: chain M residue 97 VAL Chi-restraints excluded: chain N residue 25 ILE Chi-restraints excluded: chain N residue 72 VAL Chi-restraints excluded: chain N residue 75 GLU Chi-restraints excluded: chain N residue 111 VAL Chi-restraints excluded: chain N residue 160 VAL Chi-restraints excluded: chain N residue 168 LEU Chi-restraints excluded: chain N residue 173 THR Chi-restraints excluded: chain O residue 201 GLU Chi-restraints excluded: chain O residue 202 ILE Chi-restraints excluded: chain O residue 203 ILE Chi-restraints excluded: chain O residue 254 ILE Chi-restraints excluded: chain O residue 258 SER Chi-restraints excluded: chain O residue 259 ASN Chi-restraints excluded: chain O residue 300 LEU Chi-restraints excluded: chain O residue 344 ILE Chi-restraints excluded: chain O residue 353 ASP Chi-restraints excluded: chain O residue 384 ASP Chi-restraints excluded: chain O residue 416 LEU Chi-restraints excluded: chain O residue 421 ILE Chi-restraints excluded: chain O residue 442 LEU Chi-restraints excluded: chain O residue 451 ILE Chi-restraints excluded: chain O residue 480 VAL Chi-restraints excluded: chain O residue 569 VAL Chi-restraints excluded: chain O residue 622 TYR Chi-restraints excluded: chain O residue 688 ASP Chi-restraints excluded: chain O residue 707 ASP Chi-restraints excluded: chain P residue 95 LEU Chi-restraints excluded: chain P residue 158 MET Chi-restraints excluded: chain P residue 180 ASP Chi-restraints excluded: chain P residue 184 TRP Chi-restraints excluded: chain P residue 262 LEU Chi-restraints excluded: chain P residue 304 LEU Chi-restraints excluded: chain P residue 356 VAL Chi-restraints excluded: chain P residue 366 TYR Chi-restraints excluded: chain P residue 367 PHE Chi-restraints excluded: chain P residue 400 MET Chi-restraints excluded: chain P residue 408 ILE Chi-restraints excluded: chain P residue 437 THR Chi-restraints excluded: chain P residue 479 LEU Chi-restraints excluded: chain Q residue 10 ASN Chi-restraints excluded: chain Q residue 128 TRP Chi-restraints excluded: chain Q residue 138 PHE Chi-restraints excluded: chain Q residue 155 GLN Chi-restraints excluded: chain Q residue 158 THR Chi-restraints excluded: chain Q residue 168 ILE Chi-restraints excluded: chain Q residue 187 TYR Chi-restraints excluded: chain Q residue 240 ILE Chi-restraints excluded: chain Q residue 247 ILE Chi-restraints excluded: chain Q residue 248 LYS Chi-restraints excluded: chain Q residue 251 TRP Chi-restraints excluded: chain Q residue 269 ASP Chi-restraints excluded: chain Q residue 279 SER Chi-restraints excluded: chain Q residue 289 ASN Chi-restraints excluded: chain Q residue 298 GLN Chi-restraints excluded: chain Q residue 372 HIS Chi-restraints excluded: chain Q residue 390 ASN Chi-restraints excluded: chain Q residue 400 LYS Chi-restraints excluded: chain Q residue 401 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 555 random chunks: chunk 323 optimal weight: 4.9990 chunk 352 optimal weight: 9.9990 chunk 204 optimal weight: 5.9990 chunk 350 optimal weight: 20.0000 chunk 115 optimal weight: 8.9990 chunk 214 optimal weight: 0.7980 chunk 286 optimal weight: 5.9990 chunk 3 optimal weight: 6.9990 chunk 47 optimal weight: 10.0000 chunk 209 optimal weight: 10.0000 chunk 340 optimal weight: 7.9990 overall best weight: 4.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 432 ASN B 183 HIS ** B 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 547 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 720 GLN ** B1163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 49 ASN E 54 GLN F 100 GLN ** G 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 286 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.115827 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.082744 restraints weight = 144309.335| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.085274 restraints weight = 69448.572| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.086304 restraints weight = 37443.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.086427 restraints weight = 30625.984| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.086596 restraints weight = 28766.568| |-----------------------------------------------------------------------------| r_work (final): 0.3252 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7828 moved from start: 0.6512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 47752 Z= 0.245 Angle : 0.886 23.503 64966 Z= 0.445 Chirality : 0.050 0.360 7264 Planarity : 0.006 0.129 7978 Dihedral : 14.342 160.509 7187 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 18.64 Ramachandran Plot: Outliers : 0.63 % Allowed : 7.31 % Favored : 92.07 % Rotamer: Outliers : 2.99 % Allowed : 23.32 % Favored : 73.69 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.24 % Twisted General : 0.02 % 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: -0.92 (0.11), residues: 5432 helix: 0.65 (0.12), residues: 2006 sheet: -0.90 (0.18), residues: 746 loop : -1.52 (0.12), residues: 2680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 25 TYR 0.051 0.002 TYR P 211 PHE 0.109 0.002 PHE Q 358 TRP 0.044 0.002 TRP P 184 HIS 0.015 0.001 HIS B 183 Details of bonding type rmsd/Z covalent geometry : bond 0.00547 / 0.24 (47712) covalent geometry : angle 0.87596 / 0.44 (64930) hydrogen bonds : bond 0.04964 / 3.31 ( 2015) hydrogen bonds : angle 5.60821 / 3.97 ( 5581) metal coordination : bond 0.01489 / 0.89 ( 24) metal coordination : angle 6.04193 / 4.34 ( 33) Misc. bond : bond 0.00964 / 0.50 ( 15) link_TRANS : bond 0.00115 / 0.06 ( 1) link_TRANS : angle 0.09033 / 0.05 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10864 Ramachandran restraints generated. 5432 Oldfield, 0 Emsley, 5432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10864 Ramachandran restraints generated. 5432 Oldfield, 0 Emsley, 5432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 889 residues out of total 4950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 148 poor density : 741 time to evaluate : 1.143 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 238 MET cc_start: 0.8184 (mmp) cc_final: 0.7835 (mmp) REVERT: A 316 LEU cc_start: 0.9405 (mm) cc_final: 0.9009 (tp) REVERT: A 394 LEU cc_start: 0.9539 (tp) cc_final: 0.9316 (pp) REVERT: A 450 LYS cc_start: 0.5361 (OUTLIER) cc_final: 0.3282 (mmtt) REVERT: A 960 MET cc_start: 0.9129 (mtm) cc_final: 0.8792 (mtp) REVERT: A 1576 SER cc_start: 0.9147 (m) cc_final: 0.8564 (p) REVERT: A 1611 MET cc_start: 0.8543 (tmm) cc_final: 0.8184 (tmm) REVERT: A 1620 GLN cc_start: 0.8577 (mp10) cc_final: 0.8270 (mp10) REVERT: A 1624 LYS cc_start: 0.9183 (OUTLIER) cc_final: 0.8871 (mtmm) REVERT: B 173 ASN cc_start: 0.8552 (p0) cc_final: 0.8316 (p0) REVERT: B 418 ASP cc_start: 0.8510 (t70) cc_final: 0.8243 (t0) REVERT: B 419 GLU cc_start: 0.8363 (tp30) cc_final: 0.7332 (tp30) REVERT: B 422 GLN cc_start: 0.8672 (mt0) cc_final: 0.7871 (mt0) REVERT: B 430 MET cc_start: 0.8390 (OUTLIER) cc_final: 0.8123 (tmm) REVERT: B 448 ARG cc_start: 0.8949 (ttp-110) cc_final: 0.8587 (ttp-110) REVERT: B 473 GLN cc_start: 0.8283 (mm-40) cc_final: 0.7862 (mm-40) REVERT: B 502 MET cc_start: 0.8404 (ttp) cc_final: 0.8141 (tmm) REVERT: B 778 TYR cc_start: 0.8617 (t80) cc_final: 0.7685 (t80) REVERT: B 815 ARG cc_start: 0.5224 (tpp-160) cc_final: 0.4333 (tpp-160) REVERT: B 898 LEU cc_start: 0.9244 (tp) cc_final: 0.9043 (tt) REVERT: B 962 MET cc_start: 0.8877 (tpp) cc_final: 0.8650 (tpp) REVERT: B 1065 ARG cc_start: 0.7876 (mtt180) cc_final: 0.7535 (mtp180) REVERT: B 1186 ASP cc_start: 0.7663 (OUTLIER) cc_final: 0.7239 (t70) REVERT: B 1192 MET cc_start: 0.8269 (mpp) cc_final: 0.7544 (mpp) REVERT: C 112 MET cc_start: 0.8351 (mpp) cc_final: 0.8048 (mpp) REVERT: D 34 ASP cc_start: 0.8933 (t0) cc_final: 0.8397 (p0) REVERT: D 37 LEU cc_start: 0.9555 (pt) cc_final: 0.9115 (mm) REVERT: E 78 LEU cc_start: 0.9312 (tt) cc_final: 0.8983 (tt) REVERT: E 90 VAL cc_start: 0.9305 (OUTLIER) cc_final: 0.9022 (p) REVERT: E 106 GLN cc_start: 0.7308 (tt0) cc_final: 0.6971 (tt0) REVERT: E 112 TYR cc_start: 0.8949 (p90) cc_final: 0.7990 (p90) REVERT: E 114 ASN cc_start: 0.9363 (t0) cc_final: 0.8811 (t0) REVERT: E 119 SER cc_start: 0.9367 (OUTLIER) cc_final: 0.9017 (p) REVERT: E 136 ASN cc_start: 0.9462 (t0) cc_final: 0.8961 (t0) REVERT: E 211 TYR cc_start: 0.9251 (m-80) cc_final: 0.8697 (m-10) REVERT: F 77 ASP cc_start: 0.8550 (p0) cc_final: 0.8205 (p0) REVERT: F 118 LEU cc_start: 0.9385 (mt) cc_final: 0.8949 (mt) REVERT: F 122 MET cc_start: 0.9125 (mtm) cc_final: 0.8011 (mpp) REVERT: F 140 ASP cc_start: 0.9157 (p0) cc_final: 0.8645 (p0) REVERT: F 142 SER cc_start: 0.9322 (m) cc_final: 0.9014 (p) REVERT: G 64 GLN cc_start: 0.8649 (mt0) cc_final: 0.7960 (mt0) REVERT: G 126 GLN cc_start: 0.7951 (tm-30) cc_final: 0.7346 (tm-30) REVERT: G 229 LEU cc_start: 0.9291 (tt) cc_final: 0.8850 (mp) REVERT: H 14 GLU cc_start: 0.7756 (tm-30) cc_final: 0.7109 (tm-30) REVERT: I 45 LEU cc_start: 0.9145 (mm) cc_final: 0.8939 (mm) REVERT: I 56 PHE cc_start: 0.8304 (m-80) cc_final: 0.8008 (m-80) REVERT: I 61 ARG cc_start: 0.8928 (tpp80) cc_final: 0.8194 (tpp80) REVERT: J 27 GLU cc_start: 0.8773 (OUTLIER) cc_final: 0.8462 (pp20) REVERT: K 97 SER cc_start: 0.9301 (m) cc_final: 0.8798 (t) REVERT: K 107 THR cc_start: 0.8814 (OUTLIER) cc_final: 0.8581 (t) REVERT: K 125 MET cc_start: 0.8645 (mtp) cc_final: 0.8295 (tpp) REVERT: K 129 ASP cc_start: 0.8724 (m-30) cc_final: 0.8294 (m-30) REVERT: M 18 GLN cc_start: 0.8107 (pm20) cc_final: 0.7841 (pm20) REVERT: M 62 TYR cc_start: 0.6189 (p90) cc_final: 0.5324 (p90) REVERT: M 75 GLN cc_start: 0.9148 (pp30) cc_final: 0.8768 (pm20) REVERT: N 113 SER cc_start: 0.2744 (OUTLIER) cc_final: 0.2380 (p) REVERT: N 141 GLU cc_start: 0.8116 (tt0) cc_final: 0.7115 (tp30) REVERT: O 259 ASN cc_start: 0.6927 (OUTLIER) cc_final: 0.6635 (m110) REVERT: O 343 LEU cc_start: 0.8338 (pp) cc_final: 0.8118 (pt) REVERT: O 450 ARG cc_start: 0.8784 (mtp85) cc_final: 0.8042 (mtm180) REVERT: O 570 ASP cc_start: 0.8947 (t0) cc_final: 0.8589 (p0) REVERT: P 131 HIS cc_start: 0.9388 (m-70) cc_final: 0.8835 (m-70) REVERT: P 158 MET cc_start: 0.6819 (OUTLIER) cc_final: 0.5569 (mmt) REVERT: P 222 PHE cc_start: 0.8954 (t80) cc_final: 0.8587 (t80) REVERT: P 258 MET cc_start: 0.9206 (mmp) cc_final: 0.8696 (mmm) REVERT: P 497 GLN cc_start: 0.9240 (tt0) cc_final: 0.8570 (tp40) REVERT: Q 138 PHE cc_start: 0.9164 (OUTLIER) cc_final: 0.8848 (t80) REVERT: Q 214 VAL cc_start: 0.9370 (t) cc_final: 0.8926 (t) REVERT: Q 218 ASP cc_start: 0.8224 (m-30) cc_final: 0.7873 (m-30) REVERT: Q 359 MET cc_start: 0.8601 (ttp) cc_final: 0.7975 (tmm) REVERT: Q 372 HIS cc_start: 0.7775 (OUTLIER) cc_final: 0.7473 (t70) REVERT: Q 390 ASN cc_start: 0.4227 (OUTLIER) cc_final: 0.3983 (p0) REVERT: Q 410 TYR cc_start: 0.8711 (m-10) cc_final: 0.8414 (m-10) outliers start: 148 outliers final: 118 residues processed: 838 average time/residue: 0.1702 time to fit residues: 243.3905 Evaluate side-chains 845 residues out of total 4950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 132 poor density : 713 time to evaluate : 1.054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 LEU Chi-restraints excluded: chain A residue 346 SER Chi-restraints excluded: chain A residue 357 MET Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 403 LEU Chi-restraints excluded: chain A residue 419 ILE Chi-restraints excluded: chain A residue 450 LYS Chi-restraints excluded: chain A residue 495 ILE Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 633 MET Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain A residue 713 VAL Chi-restraints excluded: chain A residue 891 ILE Chi-restraints excluded: chain A residue 957 VAL Chi-restraints excluded: chain A residue 1019 LEU Chi-restraints excluded: chain A residue 1118 VAL Chi-restraints excluded: chain A residue 1119 LYS Chi-restraints excluded: chain A residue 1222 LEU Chi-restraints excluded: chain A residue 1603 MET Chi-restraints excluded: chain A residue 1624 LYS Chi-restraints excluded: chain A residue 1634 LEU Chi-restraints excluded: chain A residue 1649 VAL Chi-restraints excluded: chain B residue 57 ASP Chi-restraints excluded: chain B residue 68 ILE Chi-restraints excluded: chain B residue 75 ASP Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 190 ILE Chi-restraints excluded: chain B residue 293 ILE Chi-restraints excluded: chain B residue 306 LEU Chi-restraints excluded: chain B residue 343 ASP Chi-restraints excluded: chain B residue 409 TYR Chi-restraints excluded: chain B residue 424 ILE Chi-restraints excluded: chain B residue 430 MET Chi-restraints excluded: chain B residue 453 VAL Chi-restraints excluded: chain B residue 564 ILE Chi-restraints excluded: chain B residue 712 SER Chi-restraints excluded: chain B residue 725 THR Chi-restraints excluded: chain B residue 819 ASP Chi-restraints excluded: chain B residue 910 THR Chi-restraints excluded: chain B residue 918 SER Chi-restraints excluded: chain B residue 1087 LEU Chi-restraints excluded: chain B residue 1113 THR Chi-restraints excluded: chain B residue 1178 ILE Chi-restraints excluded: chain B residue 1186 ASP Chi-restraints excluded: chain C residue 73 SER Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain C residue 328 LEU Chi-restraints excluded: chain D residue 15 THR Chi-restraints excluded: chain D residue 31 VAL Chi-restraints excluded: chain D residue 85 SER Chi-restraints excluded: chain D residue 99 LEU Chi-restraints excluded: chain E residue 90 VAL Chi-restraints excluded: chain E residue 119 SER Chi-restraints excluded: chain E residue 178 ILE Chi-restraints excluded: chain E residue 199 ILE Chi-restraints excluded: chain G residue 69 LEU Chi-restraints excluded: chain G residue 138 PHE Chi-restraints excluded: chain G residue 162 ILE Chi-restraints excluded: chain G residue 226 ASP Chi-restraints excluded: chain G residue 245 VAL Chi-restraints excluded: chain G residue 246 ASP Chi-restraints excluded: chain H residue 129 TYR Chi-restraints excluded: chain I residue 11 LEU Chi-restraints excluded: chain I residue 42 PHE Chi-restraints excluded: chain I residue 47 VAL Chi-restraints excluded: chain I residue 60 LEU Chi-restraints excluded: chain J residue 27 GLU Chi-restraints excluded: chain J residue 50 ILE Chi-restraints excluded: chain K residue 107 THR Chi-restraints excluded: chain L residue 46 VAL Chi-restraints excluded: chain L residue 65 VAL Chi-restraints excluded: chain M residue 23 VAL Chi-restraints excluded: chain M residue 66 THR Chi-restraints excluded: chain M residue 97 VAL Chi-restraints excluded: chain M residue 98 SER Chi-restraints excluded: chain N residue 25 ILE Chi-restraints excluded: chain N residue 72 VAL Chi-restraints excluded: chain N residue 75 GLU Chi-restraints excluded: chain N residue 111 VAL Chi-restraints excluded: chain N residue 113 SER Chi-restraints excluded: chain N residue 160 VAL Chi-restraints excluded: chain N residue 168 LEU Chi-restraints excluded: chain N residue 173 THR Chi-restraints excluded: chain O residue 202 ILE Chi-restraints excluded: chain O residue 203 ILE Chi-restraints excluded: chain O residue 254 ILE Chi-restraints excluded: chain O residue 258 SER Chi-restraints excluded: chain O residue 259 ASN Chi-restraints excluded: chain O residue 300 LEU Chi-restraints excluded: chain O residue 344 ILE Chi-restraints excluded: chain O residue 353 ASP Chi-restraints excluded: chain O residue 384 ASP Chi-restraints excluded: chain O residue 416 LEU Chi-restraints excluded: chain O residue 421 ILE Chi-restraints excluded: chain O residue 442 LEU Chi-restraints excluded: chain O residue 451 ILE Chi-restraints excluded: chain O residue 480 VAL Chi-restraints excluded: chain O residue 569 VAL Chi-restraints excluded: chain O residue 622 TYR Chi-restraints excluded: chain O residue 688 ASP Chi-restraints excluded: chain O residue 707 ASP Chi-restraints excluded: chain P residue 95 LEU Chi-restraints excluded: chain P residue 158 MET Chi-restraints excluded: chain P residue 180 ASP Chi-restraints excluded: chain P residue 184 TRP Chi-restraints excluded: chain P residue 193 PHE Chi-restraints excluded: chain P residue 262 LEU Chi-restraints excluded: chain P residue 304 LEU Chi-restraints excluded: chain P residue 356 VAL Chi-restraints excluded: chain P residue 366 TYR Chi-restraints excluded: chain P residue 367 PHE Chi-restraints excluded: chain P residue 400 MET Chi-restraints excluded: chain P residue 408 ILE Chi-restraints excluded: chain P residue 437 THR Chi-restraints excluded: chain P residue 479 LEU Chi-restraints excluded: chain Q residue 10 ASN Chi-restraints excluded: chain Q residue 128 TRP Chi-restraints excluded: chain Q residue 138 PHE Chi-restraints excluded: chain Q residue 155 GLN Chi-restraints excluded: chain Q residue 158 THR Chi-restraints excluded: chain Q residue 168 ILE Chi-restraints excluded: chain Q residue 187 TYR Chi-restraints excluded: chain Q residue 247 ILE Chi-restraints excluded: chain Q residue 269 ASP Chi-restraints excluded: chain Q residue 279 SER Chi-restraints excluded: chain Q residue 289 ASN Chi-restraints excluded: chain Q residue 298 GLN Chi-restraints excluded: chain Q residue 344 GLU Chi-restraints excluded: chain Q residue 372 HIS Chi-restraints excluded: chain Q residue 390 ASN Chi-restraints excluded: chain Q residue 400 LYS Chi-restraints excluded: chain Q residue 401 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 555 random chunks: chunk 236 optimal weight: 5.9990 chunk 358 optimal weight: 3.9990 chunk 70 optimal weight: 1.9990 chunk 497 optimal weight: 0.0370 chunk 48 optimal weight: 5.9990 chunk 392 optimal weight: 20.0000 chunk 300 optimal weight: 9.9990 chunk 198 optimal weight: 0.7980 chunk 248 optimal weight: 4.9990 chunk 40 optimal weight: 5.9990 chunk 549 optimal weight: 50.0000 overall best weight: 2.3664 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 93 GLN A1191 GLN ** B 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 547 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 720 GLN ** B1163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 22 GLN ** Q 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.117288 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.084159 restraints weight = 143367.956| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.086757 restraints weight = 71203.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.087504 restraints weight = 39246.598| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.088274 restraints weight = 30480.221| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.088288 restraints weight = 29547.027| |-----------------------------------------------------------------------------| r_work (final): 0.3285 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7752 moved from start: 0.6673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 47752 Z= 0.178 Angle : 0.868 20.776 64966 Z= 0.435 Chirality : 0.049 0.341 7264 Planarity : 0.006 0.129 7978 Dihedral : 14.308 159.470 7183 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 17.83 Ramachandran Plot: Outliers : 0.63 % Allowed : 7.16 % Favored : 92.21 % Rotamer: Outliers : 2.87 % Allowed : 23.40 % Favored : 73.73 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.24 % Twisted General : 0.02 % 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: -0.86 (0.11), residues: 5432 helix: 0.69 (0.12), residues: 1996 sheet: -0.87 (0.18), residues: 750 loop : -1.46 (0.12), residues: 2686 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.029 0.001 ARG B 129 TYR 0.047 0.002 TYR P 211 PHE 0.108 0.002 PHE Q 358 TRP 0.052 0.002 TRP P 184 HIS 0.010 0.001 HIS O 348 Details of bonding type rmsd/Z covalent geometry : bond 0.00397 / 0.18 (47712) covalent geometry : angle 0.85944 / 0.43 (64930) hydrogen bonds : bond 0.04839 / 3.24 ( 2015) hydrogen bonds : angle 5.49741 / 3.88 ( 5581) metal coordination : bond 0.00965 / 0.60 ( 24) metal coordination : angle 5.45220 / 4.05 ( 33) Misc. bond : bond 0.01011 / 0.52 ( 15) link_TRANS : bond 0.00105 / 0.06 ( 1) link_TRANS : angle 0.14409 / 0.08 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8985.71 seconds wall clock time: 155 minutes 25.77 seconds (9325.77 seconds total)