Starting phenix.real_space_refine on Wed Aug 27 02:44:16 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/5w64_8774/08_2025/5w64_8774.cif Found real_map, /net/cci-nas-00/data/ceres_data/5w64_8774/08_2025/5w64_8774.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/5w64_8774/08_2025/5w64_8774.cif" } default_model = "/net/cci-nas-00/data/ceres_data/5w64_8774/08_2025/5w64_8774.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/5w64_8774/08_2025/5w64_8774.map" default_real_map = "/net/cci-nas-00/data/ceres_data/5w64_8774/08_2025/5w64_8774.map" } resolution = 4.2 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= 0.012 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 99 5.49 5 S 205 5.16 5 C 29205 2.51 5 N 8042 2.21 5 O 8955 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 30 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 46512 Number of models: 1 Model: "" Number of chains: 25 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: 5063 Number of conformers: 1 Conformer: "" Number of residues, atoms: 640, 5063 Classifications: {'peptide': 640} Incomplete info: {'truncation_to_alanine': 53} Link IDs: {'PTRANS': 19, 'TRANS': 620} Chain breaks: 4 Unresolved non-hydrogen bonds: 106 Unresolved non-hydrogen angles: 159 Unresolved non-hydrogen dihedrals: 53 Planarities with less than four sites: {'UNK:plan-1': 53} Unresolved non-hydrogen planarities: 53 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: {'RNA': 6} Modifications used: {'5*END': 1, 'rna3p_pur': 4, 'rna3p_pyr': 2} Link IDs: {'rna3p': 5} Chain: "S" Number of atoms: 875 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 875 Classifications: {'DNA': 42} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 41} 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 102 178.656 82.727 78.840 1.00 0.00 S ATOM 806 SG CYS A 105 179.184 80.150 78.938 1.00 0.00 S ATOM 1605 SG CYS A 233 180.237 82.777 81.378 1.00 0.00 S ATOM 1627 SG CYS A 236 180.629 82.118 79.185 1.00 0.00 S ATOM 461 SG CYS A 62 131.998 64.491 79.271 1.00 0.00 S ATOM 480 SG CYS A 65 131.219 61.823 81.301 1.00 0.00 S ATOM 535 SG CYS A 72 130.124 63.736 82.231 1.00 0.00 S ATOM 20196 SG CYS B1104 145.151 57.313 87.204 1.00 0.00 S ATOM 20222 SG CYS B1107 145.563 60.028 88.059 1.00 0.00 S ATOM 20369 SG CYS B1128 144.613 58.261 85.487 1.00 0.00 S ATOM 20397 SG CYS B1131 146.391 56.083 85.595 1.00 0.00 S ATOM 28948 SG CYS I 10 162.559 150.943 85.754 1.00 0.00 S ATOM 28970 SG CYS I 13 159.662 149.034 84.867 1.00 0.00 S ATOM 29090 SG CYS I 30 162.050 147.959 83.845 1.00 0.00 S ATOM 29111 SG CYS I 33 162.275 150.622 84.187 1.00 0.00 S ATOM 29418 SG CYS J 7 91.006 99.175 128.458 1.00 0.00 S ATOM 29441 SG CYS J 10 88.745 98.160 129.875 1.00 0.00 S ATOM 29721 SG CYS J 45 90.583 99.696 131.584 1.00 0.00 S ATOM 29727 SG CYS J 46 87.728 100.544 130.829 1.00 0.00 S ATOM 30794 SG CYS L 31 88.979 105.101 84.474 1.00 0.00 S ATOM 30814 SG CYS L 34 86.036 105.370 84.091 1.00 0.00 S ATOM 30918 SG CYS L 48 86.899 105.080 82.106 1.00 0.00 S ATOM 30941 SG CYS L 51 88.955 106.519 82.405 1.00 0.00 S Residues with excluded nonbonded symmetry interactions: 102 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 90 not shown) Time building chain proxies: 10.51, per 1000 atoms: 0.23 Number of scatterers: 46512 At special positions: 0 Unit cell: (213.2, 193.7, 195, 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 99 15.00 O 8955 8.00 N 8042 7.00 C 29205 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=21, symmetry=0 Number of additional bonds: simple=21, symmetry=0 Coordination: Other bonds: Time building additional restraints: 4.95 Conformation dependent library (CDL) restraints added in 1.8 seconds Enol-peptide restraints added in 953.7 nanoseconds 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 233 " pdb="ZN ZN A1701 " - pdb=" SG CYS A 102 " 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 72 " pdb="ZN ZN A1702 " - pdb=" SG CYS A 62 " pdb="ZN ZN A1702 " - pdb=" SG CYS A 65 " pdb=" ZN B1301 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1104 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1128 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1131 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1107 " pdb=" ZN I 201 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 10 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 33 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 30 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 13 " pdb=" ZN J 101 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 45 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 7 " 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 34 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 51 " 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: 215 helices and 60 sheets defined 42.5% alpha, 16.7% beta 31 base pairs and 79 stacking pairs defined. Time for finding SS restraints: 6.90 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 90 through 101 removed outlier: 3.705A pdb=" N SER A 101 " --> pdb=" O TYR A 97 " (cutoff:3.500A) Processing helix chain 'A' and resid 111 through 127 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: 3.819A 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: 3.608A pdb=" N THR A 326 " --> pdb=" O ASN A 322 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 339 removed outlier: 4.885A pdb=" N TYR A 337 " --> pdb=" O CYS A 333 " (cutoff:3.500A) Processing helix chain 'A' and resid 351 through 354 Processing helix chain 'A' and resid 364 through 368 Processing helix chain 'A' and resid 380 through 406 Processing helix chain 'A' and resid 415 through 439 removed outlier: 3.886A 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 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 617 through 619 No H-bonds generated for 'chain 'A' and resid 617 through 619' 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: 3.501A 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 782 through 787 Processing helix chain 'A' and resid 793 through 802 Processing helix chain 'A' and resid 802 through 825 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: 3.644A pdb=" N THR A 853 " --> pdb=" O THR A 849 " (cutoff:3.500A) removed outlier: 4.267A 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 916 Proline residue: A 913 - end of helix Processing helix chain 'A' and resid 923 through 932 Processing helix chain 'A' and resid 936 through 945 Processing helix chain 'A' and resid 991 through 1013 removed outlier: 3.752A pdb=" N PHE A 997 " --> pdb=" O GLN A 993 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N THR A1013 " --> pdb=" O THR A1009 " (cutoff:3.500A) Processing helix chain 'A' and resid 1013 through 1028 removed outlier: 3.744A pdb=" N GLY A1017 " --> pdb=" O THR A1013 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N TYR A1018 " --> pdb=" O SER A1014 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N LEU A1019 " --> pdb=" O ARG A1015 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N LEU A1023 " --> pdb=" O LEU A1019 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N GLN A1026 " --> pdb=" O CYS A1022 " (cutoff:3.500A) Processing helix chain 'A' and resid 1056 through 1064 removed outlier: 4.132A pdb=" N SER A1061 " --> pdb=" O ILE A1057 " (cutoff:3.500A) removed outlier: 7.361A pdb=" N HIS A1062 " --> pdb=" O THR A1058 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N MET A1063 " --> pdb=" O LYS A1059 " (cutoff:3.500A) removed outlier: 3.646A 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: 3.851A 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: 3.682A 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 1164 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 1264 through 1267 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: 3.719A 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: 3.801A pdb=" N TYR A1573 " --> pdb=" O VAL A1569 " (cutoff:3.500A) Processing helix chain 'A' and resid 1578 through 1590 removed outlier: 3.764A pdb=" N LEU A1582 " --> pdb=" O SER A1578 " (cutoff:3.500A) Processing helix chain 'A' and resid 1599 through 1605 removed outlier: 4.335A 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 17 through 27 Processing helix chain 'B' and resid 35 through 42 removed outlier: 4.275A pdb=" N VAL B 42 " --> pdb=" O LEU B 38 " (cutoff:3.500A) Processing helix chain 'B' and resid 42 through 51 removed outlier: 3.690A pdb=" N SER B 48 " --> pdb=" O PRO B 44 " (cutoff:3.500A) Processing helix chain 'B' and resid 59 through 69 removed outlier: 3.604A pdb=" N LEU B 63 " --> pdb=" O GLY B 59 " (cutoff:3.500A) removed outlier: 3.719A 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: 3.960A pdb=" N LYS B 174 " --> pdb=" O HIS B 171 " (cutoff:3.500A) removed outlier: 3.555A 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: 3.653A pdb=" N ALA B 223 " --> pdb=" O ARG B 219 " (cutoff:3.500A) Processing helix chain 'B' and resid 273 through 281 removed outlier: 3.717A 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: 3.799A pdb=" N LYS B 460 " --> pdb=" O ASN B 456 " (cutoff:3.500A) Processing helix chain 'B' and resid 474 through 478 removed outlier: 3.711A pdb=" N ASP B 477 " --> pdb=" O SER B 474 " (cutoff:3.500A) Processing helix chain 'B' and resid 492 through 500 removed outlier: 4.142A pdb=" N PHE B 500 " --> pdb=" O PHE B 496 " (cutoff:3.500A) Processing helix chain 'B' and resid 506 through 512 removed outlier: 3.626A pdb=" N LEU B 512 " --> pdb=" O PHE B 508 " (cutoff:3.500A) Processing helix chain 'B' and resid 515 through 519 Processing helix chain 'B' and resid 521 through 525 removed outlier: 3.533A pdb=" N SER B 524 " --> pdb=" O LEU B 521 " (cutoff:3.500A) Processing helix chain 'B' and resid 560 through 569 Processing helix chain 'B' and resid 573 through 577 removed outlier: 3.901A 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: 3.774A 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 Processing helix chain 'B' and resid 711 through 725 Processing helix chain 'B' and resid 731 through 736 removed outlier: 4.594A pdb=" N CYS B 734 " --> pdb=" O VAL B 731 " (cutoff:3.500A) Processing helix chain 'B' and resid 754 through 760 removed outlier: 4.126A 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: 3.584A pdb=" N ARG B 957 " --> pdb=" O ALA B 953 " (cutoff:3.500A) Processing helix chain 'B' and resid 959 through 976 removed outlier: 3.656A 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 1072 through 1082 Processing helix chain 'B' and resid 1084 through 1093 Processing helix chain 'B' and resid 1173 through 1186 Proline residue: B1179 - end of helix removed outlier: 4.164A 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: 3.588A pdb=" N LEU C 113 " --> pdb=" O PRO C 110 " (cutoff:3.500A) Processing helix chain 'C' and resid 121 through 126 Processing helix chain 'C' and resid 152 through 156 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: 3.904A 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 removed outlier: 3.830A pdb=" N ASN D 49 " --> pdb=" O ASP D 45 " (cutoff:3.500A) Processing helix chain 'D' and resid 81 through 96 removed outlier: 3.785A 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 removed outlier: 3.554A pdb=" N CYS E 47 " --> pdb=" O LYS E 43 " (cutoff:3.500A) 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: 4.092A 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 169 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 128 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 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 14 through 16 No H-bonds generated for 'chain 'J' and resid 14 through 16' 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: 3.778A pdb=" N ILE J 50 " --> pdb=" O CYS J 46 " (cutoff:3.500A) Processing helix chain 'J' and resid 56 through 62 removed outlier: 3.720A 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 83 removed outlier: 4.380A pdb=" N ALA K 75 " --> pdb=" O THR K 71 " (cutoff:3.500A) Processing helix chain 'K' and resid 95 through 98 Processing helix chain 'K' and resid 112 through 142 Processing helix chain 'M' and resid 67 through 72 Processing helix chain 'M' and resid 104 through 107 removed outlier: 3.505A 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 70 through 75 removed outlier: 3.759A pdb=" N ASP N 73 " --> pdb=" O LEU N 70 " (cutoff:3.500A) Processing helix chain 'N' and resid 149 through 154 Processing helix chain 'N' and resid 176 through 180 removed outlier: 3.618A pdb=" N ASP N 179 " --> pdb=" O ASP N 176 " (cutoff:3.500A) Processing helix chain 'O' and resid 294 through 298 removed outlier: 3.914A pdb=" N ILE O 297 " --> pdb=" O PHE O 294 " (cutoff:3.500A) Processing helix chain 'O' and resid 571 through 576 removed outlier: 3.832A pdb=" N SER O 576 " --> pdb=" O PRO O 572 " (cutoff:3.500A) Processing helix chain 'O' and resid 577 through 579 No H-bonds generated for 'chain 'O' and resid 577 through 579' Processing helix chain 'O' and resid 582 through 614 removed outlier: 3.790A pdb=" N SER O 588 " --> pdb=" O ARG O 584 " (cutoff:3.500A) Processing helix chain 'O' and resid 618 through 644 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 712 through 723 removed outlier: 3.582A pdb=" N ASN O 716 " --> pdb=" O ASP O 712 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N GLN O 720 " --> pdb=" O ASN O 716 " (cutoff:3.500A) Processing helix chain 'O' and resid 732 through 744 removed outlier: 3.750A pdb=" N ILE O 736 " --> pdb=" O LEU O 732 " (cutoff:3.500A) removed outlier: 3.810A 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 96 through 124 Processing helix chain 'P' and resid 125 through 147 removed outlier: 3.757A pdb=" N GLU P 130 " --> pdb=" O PRO P 126 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N THR P 143 " --> pdb=" O LYS P 139 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ASP P 146 " --> pdb=" O LYS P 142 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLN P 147 " --> pdb=" O THR P 143 " (cutoff:3.500A) Processing helix chain 'P' and resid 157 through 173 removed outlier: 3.846A 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 225 through 238 removed outlier: 3.668A pdb=" N ALA P 231 " --> pdb=" O TYR P 227 " (cutoff:3.500A) 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: 3.733A pdb=" N CYS P 260 " --> pdb=" O LEU P 256 " (cutoff:3.500A) Processing helix chain 'P' and resid 265 through 278 Processing helix chain 'P' and resid 301 through 319 Processing helix chain 'P' and resid 327 through 339 removed outlier: 4.145A pdb=" N LEU P 332 " --> pdb=" O LEU P 328 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N SER P 333 " --> pdb=" O LYS P 329 " (cutoff:3.500A) Processing helix chain 'P' and resid 345 through 355 Processing helix chain 'P' and resid 362 through 369 removed outlier: 3.554A pdb=" N PHE P 367 " --> pdb=" O SER P 363 " (cutoff:3.500A) Processing helix chain 'P' and resid 371 through 385 Processing helix chain 'P' and resid 405 through 417 Processing helix chain 'P' and resid 437 through 449 Processing helix chain 'P' and resid 470 through 491 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 36 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: 4.033A pdb=" N ILE Q 175 " --> pdb=" O ARG Q 171 " (cutoff:3.500A) Proline residue: Q 176 - end of helix removed outlier: 4.028A 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: 3.666A pdb=" N THR Q 215 " --> pdb=" O ARG Q 211 " (cutoff:3.500A) Processing helix chain 'Q' and resid 228 through 242 removed outlier: 3.541A pdb=" N TYR Q 233 " --> pdb=" O TRP Q 229 " (cutoff:3.500A) removed outlier: 4.611A 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: 4.116A pdb=" N VAL Q 255 " --> pdb=" O TRP Q 251 " (cutoff:3.500A) removed outlier: 4.449A 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 278 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: 3.532A pdb=" N THR Q 413 " --> pdb=" O HIS Q 409 " (cutoff:3.500A) Processing helix chain 'Q' and resid 427 through 443 removed outlier: 3.799A pdb=" N ILE Q 431 " --> pdb=" O PRO Q 427 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ARG Q 441 " --> pdb=" O SER Q 437 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 1631 through 1632 removed outlier: 3.539A pdb=" N ASP A 15 " --> pdb=" O SER B1190 " (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 85 through 86 Processing sheet with id=AA5, first strand: chain 'A' and resid 243 through 245 removed outlier: 4.708A pdb=" N ILE A 251 " --> pdb=" O ILE A 315 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 371 through 373 removed outlier: 3.751A pdb=" N GLU A 376 " --> pdb=" O LEU A 373 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 474 through 475 Processing sheet with id=AA8, first strand: chain 'B' and resid 1045 through 1047 removed outlier: 5.542A pdb=" N ILE A 495 " --> pdb=" O ARG A 606 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 506 through 510 removed outlier: 4.012A pdb=" N GLN A 535 " --> pdb=" O TYR A 578 " (cutoff:3.500A) removed outlier: 6.159A pdb=" N HIS A 580 " --> pdb=" O ALA A 533 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N ALA A 533 " --> pdb=" O HIS A 580 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 686 through 688 Processing sheet with id=AB2, first strand: chain 'A' and resid 749 through 752 removed outlier: 6.340A pdb=" N LEU A 770 " --> pdb=" O LEU A 777 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 826 through 827 removed outlier: 8.807A pdb=" N ILE B 947 " --> pdb=" O ASN B 770 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N VAL B 772 " --> pdb=" O ILE B 947 " (cutoff:3.500A) removed outlier: 7.541A pdb=" N ILE B 949 " --> pdb=" O VAL B 772 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N ALA B 774 " --> pdb=" O ILE B 949 " (cutoff:3.500A) removed outlier: 7.948A pdb=" N ILE B 789 " --> pdb=" O SER B 928 " (cutoff:3.500A) removed outlier: 4.712A pdb=" N LYS B 930 " --> pdb=" O ILE B 789 " (cutoff:3.500A) removed outlier: 5.883A pdb=" N MET B1013 " --> pdb=" O LEU B1022 " (cutoff:3.500A) removed outlier: 7.330A pdb=" N ALA B1024 " --> pdb=" O GLU B1011 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N GLU B1011 " --> pdb=" O ALA B1024 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 826 through 827 removed outlier: 4.485A pdb=" N TYR B1027 " --> pdb=" O VAL B 775 " (cutoff:3.500A) removed outlier: 10.132A pdb=" N SER B 777 " --> pdb=" O ASP B1025 " (cutoff:3.500A) removed outlier: 11.292A pdb=" N ASP B1025 " --> pdb=" O SER B 777 " (cutoff:3.500A) removed outlier: 5.883A pdb=" N MET B1013 " --> pdb=" O LEU B1022 " (cutoff:3.500A) removed outlier: 7.330A pdb=" N ALA B1024 " --> pdb=" O GLU B1011 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N GLU B1011 " --> pdb=" O ALA B1024 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 948 through 949 Processing sheet with id=AB6, first strand: chain 'A' and resid 1030 through 1032 removed outlier: 6.475A pdb=" N ILE A1038 " --> pdb=" O VAL A1046 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 1504 through 1508 removed outlier: 3.907A pdb=" N ARG A1506 " --> pdb=" O GLU A1522 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 1261 through 1262 removed outlier: 6.045A pdb=" N VAL A1261 " --> pdb=" O ILE A1498 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 1461 through 1462 Processing sheet with id=AC1, first strand: chain 'F' and resid 143 through 147 Processing sheet with id=AC2, first strand: chain 'B' and resid 71 through 74 removed outlier: 4.428A pdb=" N VAL B 97 " --> pdb=" O SER B 144 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N SER B 144 " --> pdb=" O VAL B 97 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N VAL B 99 " --> pdb=" O LYS B 142 " (cutoff:3.500A) removed outlier: 5.937A pdb=" N LYS B 142 " --> pdb=" O VAL B 99 " (cutoff:3.500A) removed outlier: 5.292A pdb=" N GLY B 135 " --> pdb=" O GLY B 160 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N GLY B 160 " --> pdb=" O GLY B 135 " (cutoff:3.500A) removed outlier: 5.222A 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 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: 6.834A 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: 5.565A pdb=" N TYR B 232 " --> pdb=" O TYR B 252 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N TYR B 252 " --> pdb=" O TYR B 232 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N THR B 247 " --> pdb=" O SER B 263 " (cutoff:3.500A) removed outlier: 4.462A 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: 6.623A pdb=" N VAL B 586 " --> pdb=" O ILE B 593 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N TRP B 595 " --> pdb=" O CYS B 584 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N CYS B 584 " --> pdb=" O TRP B 595 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N CYS B 585 " --> pdb=" O LEU B 640 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N LEU B 642 " --> pdb=" O CYS B 585 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N GLN B 587 " --> pdb=" O LEU B 642 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 741 through 744 removed outlier: 7.740A pdb=" N THR B 900 " --> pdb=" O LEU B 887 " (cutoff:3.500A) removed outlier: 5.201A pdb=" N LEU B 887 " --> pdb=" O THR B 900 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N SER B 902 " --> pdb=" O VAL B 885 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N VAL B 885 " --> pdb=" O SER B 902 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N LYS B 904 " --> pdb=" O GLU B 883 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 741 through 744 removed outlier: 7.740A pdb=" N THR B 900 " --> pdb=" O LEU B 887 " (cutoff:3.500A) removed outlier: 5.201A pdb=" N LEU B 887 " --> pdb=" O THR B 900 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N SER B 902 " --> pdb=" O VAL B 885 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N VAL B 885 " --> pdb=" O SER B 902 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N LYS B 904 " --> pdb=" O GLU B 883 " (cutoff:3.500A) removed outlier: 5.122A 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 857 through 863 removed outlier: 6.584A pdb=" N LYS B 872 " --> pdb=" O ILE B 858 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N ALA B 860 " --> pdb=" O LYS B 870 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N LYS B 870 " --> pdb=" O ALA B 860 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N PHE B 862 " --> pdb=" O LYS B 868 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N LYS B 868 " --> pdb=" O PHE B 862 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 1098 through 1104 Processing sheet with id=AD6, first strand: chain 'B' and resid 1113 through 1115 Processing sheet with id=AD7, first strand: chain 'B' and resid 1132 through 1134 Processing sheet with id=AD8, first strand: chain 'C' and resid 41 through 47 removed outlier: 5.387A pdb=" N VAL C 42 " --> pdb=" O ILE C 57 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N ILE C 57 " --> pdb=" O VAL C 42 " (cutoff:3.500A) removed outlier: 5.288A pdb=" N ILE C 44 " --> pdb=" O ASP C 55 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N ASP C 55 " --> pdb=" O ILE C 44 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N LEU C 230 " --> pdb=" O VAL C 294 " (cutoff:3.500A) removed outlier: 9.200A pdb=" N ASN C 296 " --> pdb=" O ARG C 228 " (cutoff:3.500A) removed outlier: 10.018A pdb=" N ARG C 228 " --> pdb=" O ASN C 296 " (cutoff:3.500A) removed outlier: 9.790A pdb=" N PHE C 298 " --> pdb=" O SER C 226 " (cutoff:3.500A) removed outlier: 10.652A pdb=" N SER C 226 " --> pdb=" O PHE C 298 " (cutoff:3.500A) removed outlier: 9.963A pdb=" N PHE C 300 " --> pdb=" O THR C 224 " (cutoff:3.500A) removed outlier: 11.327A pdb=" N THR C 224 " --> pdb=" O PHE C 300 " (cutoff:3.500A) removed outlier: 9.895A pdb=" N VAL C 302 " --> pdb=" O VAL C 222 " (cutoff:3.500A) removed outlier: 8.696A pdb=" N VAL C 222 " --> pdb=" O VAL C 302 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 168 through 170 removed outlier: 4.170A pdb=" N VAL C 133 " --> pdb=" O GLU C 170 " (cutoff:3.500A) removed outlier: 5.993A pdb=" N GLU C 201 " --> pdb=" O ASN C 87 " (cutoff:3.500A) removed outlier: 5.751A pdb=" N ASN C 87 " --> pdb=" O GLU C 201 " (cutoff:3.500A) removed outlier: 7.360A pdb=" N SER C 203 " --> pdb=" O PHE C 85 " (cutoff:3.500A) removed outlier: 4.772A pdb=" N PHE C 85 " --> pdb=" O SER C 203 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N LYS C 205 " --> pdb=" O VAL C 83 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N VAL C 83 " --> pdb=" O LYS C 205 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N HIS C 207 " --> pdb=" O GLU C 81 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 141 through 142 Processing sheet with id=AE2, first strand: chain 'C' and resid 161 through 163 removed outlier: 6.676A pdb=" N VAL C 162 " --> pdb=" O LEU C 193 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 256 through 257 Processing sheet with id=AE4, first strand: chain 'D' and resid 21 through 24 removed outlier: 3.894A pdb=" N VAL D 21 " --> pdb=" O TYR G 46 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N ASN G 121 " --> pdb=" O GLY G 86 " (cutoff:3.500A) removed outlier: 5.238A pdb=" N GLY G 86 " --> pdb=" O ASN G 121 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N TYR G 123 " --> pdb=" O TYR G 84 " (cutoff:3.500A) removed outlier: 5.642A pdb=" N TYR G 84 " --> pdb=" O TYR G 123 " (cutoff:3.500A) removed outlier: 7.466A pdb=" N TRP G 125 " --> pdb=" O LEU G 82 " (cutoff:3.500A) removed outlier: 7.189A pdb=" N LEU G 82 " --> pdb=" O TRP G 125 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N LYS G 72 " --> pdb=" O VAL G 81 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'E' and resid 60 through 62 removed outlier: 6.257A pdb=" N TRP E 79 " --> pdb=" O ILE E 109 " (cutoff:3.500A) removed outlier: 7.446A pdb=" N VAL E 111 " --> pdb=" O TRP E 79 " (cutoff:3.500A) removed outlier: 6.406A 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: 3.806A pdb=" N TYR G 136 " --> pdb=" O LEU G 148 " (cutoff:3.500A) removed outlier: 5.918A pdb=" N GLY G 146 " --> pdb=" O PHE G 138 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N GLN G 140 " --> pdb=" O HIS G 144 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N HIS G 144 " --> pdb=" O GLN G 140 " (cutoff:3.500A) removed outlier: 7.116A pdb=" N ASN G 154 " --> pdb=" O VAL G 245 " (cutoff:3.500A) removed outlier: 7.502A pdb=" N GLY G 247 " --> pdb=" O ASN G 154 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N SER G 156 " --> pdb=" O GLY G 247 " (cutoff:3.500A) removed outlier: 6.044A pdb=" N THR G 248 " --> pdb=" O VAL G 233 " (cutoff:3.500A) removed outlier: 5.414A 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: 6.324A pdb=" N GLU H 27 " --> pdb=" O SER H 13 " (cutoff:3.500A) removed outlier: 4.752A pdb=" N VAL H 15 " --> pdb=" O ARG H 25 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N ARG H 25 " --> pdb=" O VAL H 15 " (cutoff:3.500A) removed outlier: 5.093A pdb=" N LEU H 122 " --> pdb=" O ASP H 41 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LYS H 103 " --> pdb=" O TYR H 115 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N SER H 117 " --> pdb=" O ALA H 101 " (cutoff:3.500A) removed outlier: 6.083A 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 95 through 97 removed outlier: 7.072A pdb=" N VAL M 23 " --> pdb=" O LEU M 96 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'M' and resid 48 through 50 removed outlier: 4.758A pdb=" N THR M 37 " --> pdb=" O GLU M 56 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N GLU M 56 " --> pdb=" O THR M 37 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LYS M 99 " --> pdb=" O GLU M 63 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'M' and resid 48 through 50 Processing sheet with id=AF7, first strand: chain 'M' and resid 87 through 91 removed outlier: 3.651A pdb=" N SER M 87 " --> pdb=" O ASN M 82 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N VAL M 77 " --> pdb=" O ILE N 56 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ILE N 56 " --> pdb=" O VAL M 77 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N VAL N 53 " --> pdb=" O LYS N 135 " (cutoff:3.500A) removed outlier: 8.183A pdb=" N PHE N 137 " --> pdb=" O VAL N 53 " (cutoff:3.500A) removed outlier: 6.093A pdb=" N LEU N 55 " --> pdb=" O PHE N 137 " (cutoff:3.500A) removed outlier: 7.689A pdb=" N VAL N 139 " --> pdb=" O LEU N 55 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N LYS N 57 " --> pdb=" O VAL N 139 " (cutoff:3.500A) removed outlier: 4.701A pdb=" N VAL N 136 " --> pdb=" O ASP N 92 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ASP N 92 " --> pdb=" O VAL N 136 " (cutoff:3.500A) Processing sheet with id=AF8, 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: 6.311A pdb=" N LEU O 538 " --> pdb=" O ILE O 508 " (cutoff:3.500A) removed outlier: 4.427A 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=AF9, first strand: chain 'O' and resid 201 through 205 removed outlier: 4.243A pdb=" N GLU O 201 " --> pdb=" O LEU O 219 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'O' and resid 242 through 245 removed outlier: 6.628A pdb=" N ILE O 264 " --> pdb=" O LYS O 243 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'O' and resid 305 through 306 Processing sheet with id=AG3, first strand: chain 'O' and resid 361 through 365 removed outlier: 3.732A pdb=" N GLU O 382 " --> pdb=" O THR O 391 " (cutoff:3.500A) Processing sheet with id=AG4, 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=AG5, first strand: chain 'O' and resid 452 through 457 Processing sheet with id=AG6, first strand: chain 'O' and resid 452 through 457 1968 hydrogen bonds defined for protein. 5391 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 66 hydrogen bonds 88 hydrogen bond angles 0 basepair planarities 31 basepair parallelities 79 stacking parallelities Total time for adding SS restraints: 14.43 Time building geometry restraints manager: 6.26 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: 7773 1.32 - 1.44: 12844 1.44 - 1.57: 26463 1.57 - 1.69: 241 1.69 - 1.82: 326 Bond restraints: 47647 Sorted by residual: bond pdb=" N PRO B 78 " pdb=" CD PRO B 78 " ideal model delta sigma weight residual 1.473 1.324 0.149 1.40e-02 5.10e+03 1.14e+02 bond pdb=" CA GLU O 573 " pdb=" C GLU O 573 " ideal model delta sigma weight residual 1.523 1.642 -0.119 1.34e-02 5.57e+03 7.90e+01 bond pdb=" CA ILE O 297 " pdb=" C ILE O 297 " ideal model delta sigma weight residual 1.530 1.627 -0.097 1.12e-02 7.97e+03 7.47e+01 bond pdb=" CA LEU A 460 " pdb=" C LEU A 460 " ideal model delta sigma weight residual 1.522 1.634 -0.112 1.38e-02 5.25e+03 6.54e+01 bond pdb=" CA LEU P 262 " pdb=" C LEU P 262 " ideal model delta sigma weight residual 1.524 1.623 -0.099 1.26e-02 6.30e+03 6.16e+01 ... (remaining 47642 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.45: 63949 5.45 - 10.89: 759 10.89 - 16.34: 95 16.34 - 21.79: 23 21.79 - 27.24: 5 Bond angle restraints: 64831 Sorted by residual: angle pdb=" N HIS O 617 " pdb=" CA HIS O 617 " pdb=" C HIS O 617 " ideal model delta sigma weight residual 113.19 85.95 27.24 1.19e+00 7.06e-01 5.24e+02 angle pdb=" N VAL P 356 " pdb=" CA VAL P 356 " pdb=" C VAL P 356 " ideal model delta sigma weight residual 112.17 92.41 19.76 9.50e-01 1.11e+00 4.33e+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 90.99 22.22 1.15e+00 7.56e-01 3.73e+02 angle pdb=" N ILE Q 152 " pdb=" CA ILE Q 152 " pdb=" C ILE Q 152 " ideal model delta sigma weight residual 113.20 95.13 18.07 9.60e-01 1.09e+00 3.54e+02 angle pdb=" C LYS B 77 " pdb=" N PRO B 78 " pdb=" CA PRO B 78 " ideal model delta sigma weight residual 120.11 100.39 19.72 1.12e+00 7.97e-01 3.10e+02 ... (remaining 64826 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.00: 27982 35.00 - 70.00: 721 70.00 - 105.00: 40 105.00 - 140.00: 0 140.00 - 175.00: 1 Dihedral angle restraints: 28744 sinusoidal: 12487 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 -157.47 34.87 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 122.80 157.09 -34.29 0 2.50e+00 1.60e-01 1.88e+02 dihedral pdb=" C GLN Q 147 " pdb=" N GLN Q 147 " pdb=" CA GLN Q 147 " pdb=" CB GLN Q 147 " ideal model delta harmonic sigma weight residual -122.60 -143.26 20.66 0 2.50e+00 1.60e-01 6.83e+01 ... (remaining 28741 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.296: 7134 0.296 - 0.591: 107 0.591 - 0.887: 7 0.887 - 1.182: 3 1.182 - 1.478: 1 Chirality restraints: 7252 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 5.46e+01 chirality pdb=" CB ILE M 113 " pdb=" CA ILE M 113 " pdb=" CG1 ILE M 113 " pdb=" CG2 ILE M 113 " both_signs ideal model delta sigma weight residual False 2.64 1.59 1.05 2.00e-01 2.50e+01 2.78e+01 chirality pdb=" CA GLU P 122 " pdb=" N GLU P 122 " pdb=" C GLU P 122 " pdb=" CB GLU P 122 " both_signs ideal model delta sigma weight residual False 2.51 1.57 0.94 2.00e-01 2.50e+01 2.23e+01 ... (remaining 7249 not shown) Planarity restraints: 7976 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 6.60e+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 " 0.008 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 HIS O 701 " -0.080 2.00e-02 2.50e+03 6.00e-02 5.40e+01 pdb=" CG HIS O 701 " 0.086 2.00e-02 2.50e+03 pdb=" ND1 HIS O 701 " 0.045 2.00e-02 2.50e+03 pdb=" CD2 HIS O 701 " 0.039 2.00e-02 2.50e+03 pdb=" CE1 HIS O 701 " -0.051 2.00e-02 2.50e+03 pdb=" NE2 HIS O 701 " -0.039 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 4.72e+01 pdb=" CG PHE Q 270 " -0.056 2.00e-02 2.50e+03 pdb=" CD1 PHE Q 270 " -0.062 2.00e-02 2.50e+03 pdb=" CD2 PHE Q 270 " -0.039 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 ... (remaining 7973 not shown) Histogram of nonbonded interaction distances: 1.01 - 1.78: 196 1.78 - 2.56: 2324 2.56 - 3.34: 68355 3.34 - 4.12: 123881 4.12 - 4.90: 212911 Nonbonded interactions: 407667 Sorted by model distance: nonbonded pdb=" CA LEU O 732 " pdb=" OE2 GLU O 735 " model vdw 1.006 3.470 nonbonded pdb=" NZ LYS A 111 " pdb=" N GLU A 114 " model vdw 1.008 3.200 nonbonded pdb=" OE1 GLU O 614 " pdb=" CB ALA O 670 " model vdw 1.009 3.460 nonbonded pdb=" CD LYS Q 136 " pdb=" CG HIS Q 304 " model vdw 1.010 3.660 nonbonded pdb=" CE2 PHE N 23 " pdb=" CD1 ILE N 25 " model vdw 1.020 3.760 ... (remaining 407662 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: 0.440 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.040 Extract box with map and model: 0.730 Check model and map are aligned: 0.140 Set scattering table: 0.130 Process input model: 58.570 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.080 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:1.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 61.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5920 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 : 0.011 0.483 47692 Z= 0.751 Angle : 1.738 57.708 64864 Z= 0.986 Chirality : 0.090 1.478 7252 Planarity : 0.011 0.122 7976 Dihedral : 15.064 175.004 18200 Min Nonbonded Distance : 1.006 Molprobity Statistics. All-atom Clashscore : 104.20 Ramachandran Plot: Outliers : 4.09 % Allowed : 8.80 % Favored : 87.11 % Rotamer: Outliers : 5.36 % Allowed : 5.11 % Favored : 89.53 % Cbeta Deviations : 1.10 % 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 aren not related in a simple way. whole: -3.53 (0.10), residues: 5432 helix: -1.96 (0.09), residues: 1918 sheet: -1.64 (0.17), residues: 750 loop : -2.87 (0.10), residues: 2764 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.096 0.011 ARG F 136 TYR 0.096 0.007 TYR Q 443 PHE 0.100 0.004 PHE Q 188 TRP 0.061 0.005 TRP Q 273 HIS 0.019 0.003 HIS A 998 Details of bonding type rmsd covalent geometry : bond 0.00850 (47647) covalent geometry : angle 1.55791 (64831) hydrogen bonds : bond 0.22531 ( 1994) hydrogen bonds : angle 10.38921 ( 5479) metal coordination : bond 0.23823 ( 24) metal coordination : angle 34.20532 ( 33) Misc. bond : bond 0.26207 ( 21) *********************** 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 1721 residues out of total 4950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 265 poor density : 1456 time to evaluate : 1.894 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 434 VAL cc_start: 0.7090 (t) cc_final: 0.6678 (t) REVERT: A 450 LYS cc_start: 0.5724 (OUTLIER) cc_final: 0.3159 (mttp) REVERT: A 460 LEU cc_start: 0.5431 (pp) cc_final: 0.4877 (pp) REVERT: A 472 MET cc_start: 0.7725 (mmp) cc_final: 0.7375 (mmt) REVERT: A 634 ASN cc_start: 0.6816 (m-40) cc_final: 0.6303 (m-40) REVERT: A 738 ASN cc_start: 0.6243 (t0) cc_final: 0.5656 (t0) REVERT: A 821 ILE cc_start: 0.7740 (mm) cc_final: 0.7510 (mm) REVERT: A 993 GLN cc_start: 0.1323 (mt0) cc_final: 0.0826 (mp10) REVERT: A 1000 MET cc_start: 0.1809 (mtt) cc_final: 0.1114 (mmt) REVERT: A 1004 GLU cc_start: -0.0679 (tm-30) cc_final: -0.1156 (pp20) REVERT: A 1007 ILE cc_start: 0.1135 (mt) cc_final: 0.0336 (mm) REVERT: A 1008 ASP cc_start: -0.0177 (t0) cc_final: -0.0403 (m-30) REVERT: A 1011 VAL cc_start: -0.2668 (m) cc_final: -0.3023 (p) REVERT: A 1012 LYS cc_start: 0.0317 (pttp) cc_final: -0.0224 (ttmt) REVERT: A 1013 THR cc_start: 0.2029 (m) cc_final: 0.1049 (t) REVERT: A 1089 LEU cc_start: 0.6580 (OUTLIER) cc_final: 0.6145 (pt) REVERT: A 1170 MET cc_start: 0.5980 (mmm) cc_final: 0.5632 (mmm) REVERT: A 1188 ILE cc_start: 0.8709 (mt) cc_final: 0.8429 (mt) REVERT: B 80 ASN cc_start: -0.1405 (t0) cc_final: -0.1961 (t0) REVERT: B 231 HIS cc_start: 0.4801 (m-70) cc_final: 0.4595 (m-70) REVERT: B 411 MET cc_start: 0.7052 (mtp) cc_final: 0.6795 (mtm) REVERT: B 496 PHE cc_start: 0.7945 (t80) cc_final: 0.7491 (t80) REVERT: B 733 LEU cc_start: 0.7551 (mt) cc_final: 0.6985 (mp) REVERT: B 813 LEU cc_start: 0.4890 (OUTLIER) cc_final: 0.3261 (pp) REVERT: B 905 TYR cc_start: 0.6497 (m-10) cc_final: 0.5897 (m-10) REVERT: B 1086 PHE cc_start: 0.6711 (m-80) cc_final: 0.6449 (m-80) REVERT: C 71 MET cc_start: 0.7219 (mtm) cc_final: 0.6665 (mtm) REVERT: D 25 THR cc_start: 0.7519 (p) cc_final: 0.7284 (p) REVERT: F 137 TYR cc_start: 0.6316 (m-80) cc_final: 0.5998 (m-80) REVERT: F 145 ASP cc_start: 0.6916 (m-30) cc_final: 0.5990 (m-30) REVERT: G 96 SER cc_start: 0.5451 (OUTLIER) cc_final: 0.5062 (p) REVERT: G 110 ASP cc_start: 0.6624 (p0) cc_final: 0.5621 (p0) REVERT: I 11 LEU cc_start: 0.5621 (tp) cc_final: 0.4900 (mt) REVERT: J 48 ARG cc_start: 0.7914 (ptt90) cc_final: 0.7333 (ptt90) REVERT: J 49 MET cc_start: 0.8064 (tpp) cc_final: 0.7397 (tpp) REVERT: K 103 ILE cc_start: 0.7620 (tt) cc_final: 0.7344 (tt) REVERT: L 46 VAL cc_start: 0.8593 (t) cc_final: 0.8275 (p) REVERT: L 57 LEU cc_start: 0.6429 (tp) cc_final: 0.6094 (tt) REVERT: M 66 THR cc_start: 0.6982 (OUTLIER) cc_final: 0.6610 (p) REVERT: M 74 ASN cc_start: 0.7779 (t0) cc_final: 0.6720 (t0) REVERT: O 485 LYS cc_start: 0.8831 (OUTLIER) cc_final: 0.8582 (mmtm) REVERT: O 747 LEU cc_start: 0.7530 (OUTLIER) cc_final: 0.7292 (mt) REVERT: P 254 LEU cc_start: 0.7757 (tp) cc_final: 0.7552 (tp) REVERT: P 291 ASP cc_start: 0.7522 (OUTLIER) cc_final: 0.7290 (m-30) REVERT: P 512 ARG cc_start: 0.0245 (OUTLIER) cc_final: -0.0108 (mpp80) REVERT: Q 166 GLU cc_start: 0.7667 (tt0) cc_final: 0.6790 (tt0) REVERT: Q 204 GLU cc_start: 0.6773 (OUTLIER) cc_final: 0.6538 (mp0) REVERT: Q 271 LEU cc_start: 0.9052 (mt) cc_final: 0.8596 (mt) outliers start: 265 outliers final: 130 residues processed: 1676 average time/residue: 0.3064 time to fit residues: 833.3817 Evaluate side-chains 975 residues out of total 4950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 140 poor density : 835 time to evaluate : 1.994 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 556 random chunks: chunk 394 optimal weight: 30.0000 chunk 430 optimal weight: 3.9990 chunk 41 optimal weight: 0.9980 chunk 265 optimal weight: 6.9990 chunk 523 optimal weight: 7.9990 chunk 497 optimal weight: 9.9990 chunk 414 optimal weight: 30.0000 chunk 310 optimal weight: 7.9990 chunk 488 optimal weight: 8.9990 chunk 366 optimal weight: 5.9990 chunk 223 optimal weight: 3.9990 overall best weight: 4.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 43 HIS A 93 GLN A 116 HIS A 221 HIS A 224 HIS A 344 ASN ** A 431 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 435 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 470 HIS A 553 GLN A 580 HIS A 636 HIS A 656 GLN A 798 HIS ** A1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1180 ASN ** A1191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1320 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1532 GLN A1647 ASN B 39 GLN B 110 ASN ** B 212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 248 ASN B 282 HIS ** B 400 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 532 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 547 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 555 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 575 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 673 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 683 ASN B1010 ASN B1038 HIS B1089 GLN ** B1163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 23 HIS D 29 GLN E 3 GLN E 5 ASN ** E 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 78 GLN ** G 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 36 ASN ** G 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 119 HIS ** H 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 64 GLN ** K 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 54 HIS ** M 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 51 GLN N 132 GLN O 267 ASN O 301 GLN O 308 ASN ** O 346 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 348 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 490 GLN O 579 ASN O 580 ASN ** O 656 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 701 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 238 HIS ** P 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 259 GLN ** P 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 283 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 315 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 449 GLN ** Q 372 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 407 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 43 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.092600 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.072333 restraints weight = 237661.018| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.074301 restraints weight = 128341.326| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.075573 restraints weight = 82742.107| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.076424 restraints weight = 60637.968| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.076940 restraints weight = 49001.480| |-----------------------------------------------------------------------------| r_work (final): 0.3411 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7330 moved from start: 0.4230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.107 47692 Z= 0.293 Angle : 1.152 49.091 64864 Z= 0.550 Chirality : 0.056 0.619 7252 Planarity : 0.008 0.156 7976 Dihedral : 13.984 177.884 7147 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 27.94 Ramachandran Plot: Outliers : 1.42 % Allowed : 7.62 % Favored : 90.96 % Rotamer: Outliers : 0.53 % Allowed : 3.84 % Favored : 95.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.41 % Twisted General : 0.17 % 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 aren not related in a simple way. whole: -2.09 (0.11), residues: 5432 helix: -0.55 (0.11), residues: 1950 sheet: -1.21 (0.17), residues: 749 loop : -2.08 (0.11), residues: 2733 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG O 194 TYR 0.061 0.003 TYR O 196 PHE 0.122 0.004 PHE Q 358 TRP 0.039 0.004 TRP O 324 HIS 0.030 0.002 HIS P 157 Details of bonding type rmsd covalent geometry : bond 0.00630 (47647) covalent geometry : angle 1.04417 (64831) hydrogen bonds : bond 0.07035 ( 1994) hydrogen bonds : angle 7.21417 ( 5479) metal coordination : bond 0.02260 ( 24) metal coordination : angle 21.56193 ( 33) Misc. bond : bond 0.01407 ( 21) *********************** 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 1167 residues out of total 4950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 1141 time to evaluate : 1.850 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: A 214 ASP cc_start: 0.9273 (t70) cc_final: 0.8719 (t0) REVERT: A 218 LYS cc_start: 0.9338 (mtmt) cc_final: 0.9029 (ptpp) REVERT: A 226 LYS cc_start: 0.9186 (mmpt) cc_final: 0.8873 (mmmt) REVERT: A 339 PHE cc_start: 0.8686 (m-80) cc_final: 0.8199 (m-80) REVERT: A 431 GLN cc_start: 0.8695 (tm-30) cc_final: 0.8190 (tm-30) REVERT: A 453 ILE cc_start: 0.9507 (pt) cc_final: 0.9160 (pt) REVERT: A 469 LYS cc_start: 0.7642 (tptm) cc_final: 0.7423 (ttpt) REVERT: A 470 HIS cc_start: 0.8114 (m170) cc_final: 0.7024 (m170) REVERT: A 505 LEU cc_start: 0.8954 (mp) cc_final: 0.8647 (mp) REVERT: A 518 GLU cc_start: 0.9035 (tt0) cc_final: 0.8549 (tm-30) REVERT: A 589 MET cc_start: 0.8220 (mmm) cc_final: 0.7842 (mmm) REVERT: A 635 MET cc_start: 0.8582 (ttm) cc_final: 0.8355 (ttp) REVERT: A 699 CYS cc_start: 0.8474 (p) cc_final: 0.8147 (p) REVERT: A 821 ILE cc_start: 0.9367 (mm) cc_final: 0.9150 (mm) REVERT: A 925 MET cc_start: 0.9517 (tpt) cc_final: 0.9143 (tmm) REVERT: A 947 LEU cc_start: 0.9094 (mp) cc_final: 0.8890 (mp) REVERT: A 960 MET cc_start: 0.8360 (mtm) cc_final: 0.8020 (mtp) REVERT: A 994 GLU cc_start: -0.4137 (mt-10) cc_final: -0.4663 (mt-10) REVERT: A 1000 MET cc_start: -0.2183 (mtt) cc_final: -0.2568 (mmm) REVERT: A 1007 ILE cc_start: -0.4248 (mt) cc_final: -0.4536 (mm) REVERT: A 1013 THR cc_start: 0.2572 (m) cc_final: 0.1423 (t) REVERT: A 1019 LEU cc_start: -0.3571 (tp) cc_final: -0.3985 (tp) REVERT: A 1056 ASP cc_start: 0.9004 (t0) cc_final: 0.8789 (t0) REVERT: A 1175 MET cc_start: 0.8881 (ttm) cc_final: 0.8645 (ttm) REVERT: A 1183 GLU cc_start: 0.8026 (tp30) cc_final: 0.7703 (tp30) REVERT: A 1185 VAL cc_start: 0.9509 (m) cc_final: 0.8939 (m) REVERT: A 1294 MET cc_start: 0.9008 (mtm) cc_final: 0.8594 (mtm) REVERT: A 1505 ASP cc_start: 0.8104 (t0) cc_final: 0.7390 (t0) REVERT: A 1507 CYS cc_start: 0.7725 (t) cc_final: 0.7405 (t) REVERT: A 1519 LEU cc_start: 0.9252 (mt) cc_final: 0.8718 (mt) REVERT: A 1562 ILE cc_start: 0.9654 (mt) cc_final: 0.9389 (mm) REVERT: A 1589 MET cc_start: 0.9485 (mtt) cc_final: 0.9047 (mmm) REVERT: A 1611 MET cc_start: 0.9588 (ttp) cc_final: 0.8796 (ttp) REVERT: A 1620 GLN cc_start: 0.9102 (mp10) cc_final: 0.8710 (mp10) REVERT: A 1621 PHE cc_start: 0.9294 (m-80) cc_final: 0.8898 (m-80) REVERT: B 80 ASN cc_start: -0.1752 (t0) cc_final: -0.2019 (m110) REVERT: B 110 ASN cc_start: 0.6344 (OUTLIER) cc_final: 0.5656 (p0) REVERT: B 136 LYS cc_start: 0.8736 (tppt) cc_final: 0.7834 (ttmt) REVERT: B 157 ASP cc_start: 0.9192 (p0) cc_final: 0.8423 (t0) REVERT: B 163 VAL cc_start: 0.9617 (m) cc_final: 0.9309 (p) REVERT: B 174 LYS cc_start: 0.9112 (mmpt) cc_final: 0.8806 (mmmt) REVERT: B 275 MET cc_start: 0.9223 (ttm) cc_final: 0.8966 (ttm) REVERT: B 304 ASP cc_start: 0.9540 (m-30) cc_final: 0.9068 (p0) REVERT: B 330 LEU cc_start: 0.9610 (mt) cc_final: 0.9384 (mt) REVERT: B 354 LEU cc_start: 0.9296 (mp) cc_final: 0.9080 (tt) REVERT: B 359 LEU cc_start: 0.9716 (mt) cc_final: 0.9386 (mt) REVERT: B 373 MET cc_start: 0.8840 (tmm) cc_final: 0.8496 (tmm) REVERT: B 377 MET cc_start: 0.8758 (mtm) cc_final: 0.8451 (mtm) REVERT: B 415 GLU cc_start: 0.8764 (tp30) cc_final: 0.8477 (tp30) REVERT: B 416 LYS cc_start: 0.9221 (mmmt) cc_final: 0.8952 (mmtt) REVERT: B 462 GLN cc_start: 0.9455 (tt0) cc_final: 0.9126 (tt0) REVERT: B 496 PHE cc_start: 0.9127 (t80) cc_final: 0.8593 (t80) REVERT: B 515 THR cc_start: 0.9296 (p) cc_final: 0.9082 (t) REVERT: B 543 ASN cc_start: 0.8799 (m-40) cc_final: 0.8569 (m110) REVERT: B 733 LEU cc_start: 0.9192 (mt) cc_final: 0.8901 (mt) REVERT: B 778 TYR cc_start: 0.8435 (t80) cc_final: 0.7957 (t80) REVERT: B 787 MET cc_start: 0.8291 (pmm) cc_final: 0.7844 (pmm) REVERT: B 790 ASN cc_start: 0.9382 (t0) cc_final: 0.9086 (t0) REVERT: B 905 TYR cc_start: 0.8733 (m-10) cc_final: 0.8443 (m-10) REVERT: B 982 THR cc_start: 0.9362 (m) cc_final: 0.9125 (p) REVERT: B 1057 MET cc_start: 0.8845 (mpp) cc_final: 0.8533 (mpp) REVERT: B 1074 MET cc_start: 0.8394 (ttm) cc_final: 0.7955 (ttm) REVERT: B 1086 PHE cc_start: 0.7292 (m-80) cc_final: 0.6851 (m-80) REVERT: B 1157 GLN cc_start: 0.9351 (mp-120) cc_final: 0.9036 (mp10) REVERT: B 1174 THR cc_start: 0.9495 (p) cc_final: 0.9179 (p) REVERT: B 1186 ASP cc_start: 0.9491 (m-30) cc_final: 0.9197 (m-30) REVERT: E 2 ASP cc_start: 0.9256 (p0) cc_final: 0.9050 (p0) REVERT: E 28 TYR cc_start: 0.8817 (m-80) cc_final: 0.8442 (m-80) REVERT: E 82 PHE cc_start: 0.9034 (m-10) cc_final: 0.8727 (m-80) REVERT: E 140 LEU cc_start: 0.9398 (mm) cc_final: 0.9076 (mm) REVERT: E 150 VAL cc_start: 0.9351 (t) cc_final: 0.9130 (p) REVERT: E 153 HIS cc_start: 0.8978 (m90) cc_final: 0.8644 (m90) REVERT: E 174 GLN cc_start: 0.9223 (mt0) cc_final: 0.8782 (mt0) REVERT: E 182 ASP cc_start: 0.9035 (t70) cc_final: 0.8799 (t70) REVERT: E 215 MET cc_start: 0.8516 (mmt) cc_final: 0.8122 (mmm) REVERT: F 84 TYR cc_start: 0.8449 (m-10) cc_final: 0.8118 (m-10) REVERT: F 88 TYR cc_start: 0.7892 (m-80) cc_final: 0.7610 (m-80) REVERT: F 93 ILE cc_start: 0.9721 (mp) cc_final: 0.9473 (tp) REVERT: F 97 ARG cc_start: 0.9200 (tpt170) cc_final: 0.8785 (tpt-90) REVERT: F 134 ILE cc_start: 0.9516 (mm) cc_final: 0.9309 (mm) REVERT: G 45 LEU cc_start: 0.9330 (pp) cc_final: 0.9114 (pp) REVERT: G 75 ASN cc_start: 0.9363 (p0) cc_final: 0.9150 (p0) REVERT: G 110 ASP cc_start: 0.9104 (p0) cc_final: 0.8623 (p0) REVERT: H 116 TYR cc_start: 0.8672 (m-80) cc_final: 0.8166 (m-80) REVERT: H 121 LEU cc_start: 0.9553 (mp) cc_final: 0.9341 (mm) REVERT: H 141 TYR cc_start: 0.8680 (m-80) cc_final: 0.8031 (m-80) REVERT: I 12 ASP cc_start: 0.9549 (m-30) cc_final: 0.9284 (m-30) REVERT: I 64 LYS cc_start: 0.9488 (mtpp) cc_final: 0.9038 (pttt) REVERT: J 17 LYS cc_start: 0.9227 (mmtt) cc_final: 0.9017 (mmtt) REVERT: J 48 ARG cc_start: 0.9348 (ptt90) cc_final: 0.8852 (ptt90) REVERT: J 49 MET cc_start: 0.9472 (tpp) cc_final: 0.8138 (tpp) REVERT: J 59 LYS cc_start: 0.9421 (mmmm) cc_final: 0.8934 (mmmt) REVERT: K 67 GLU cc_start: 0.8489 (tm-30) cc_final: 0.7802 (tm-30) REVERT: K 74 ASN cc_start: 0.9378 (t0) cc_final: 0.8828 (t0) REVERT: K 91 TYR cc_start: 0.8883 (p90) cc_final: 0.8608 (p90) REVERT: K 125 MET cc_start: 0.8656 (mtt) cc_final: 0.8054 (mmt) REVERT: L 53 HIS cc_start: 0.8865 (t70) cc_final: 0.7541 (t-170) REVERT: L 55 ILE cc_start: 0.9665 (mm) cc_final: 0.9289 (mm) REVERT: L 67 PHE cc_start: 0.8508 (m-10) cc_final: 0.7957 (m-10) REVERT: M 26 PHE cc_start: 0.8285 (m-10) cc_final: 0.7466 (m-10) REVERT: M 27 PHE cc_start: 0.7818 (p90) cc_final: 0.7331 (p90) REVERT: M 30 PHE cc_start: 0.9025 (t80) cc_final: 0.8619 (t80) REVERT: M 38 PHE cc_start: 0.9255 (m-10) cc_final: 0.8955 (m-80) REVERT: M 41 TYR cc_start: 0.8748 (m-80) cc_final: 0.8311 (m-80) REVERT: M 75 GLN cc_start: 0.8110 (pp30) cc_final: 0.7702 (pp30) REVERT: N 117 GLU cc_start: 0.8230 (tt0) cc_final: 0.8029 (tm-30) REVERT: N 135 LYS cc_start: 0.8300 (mttp) cc_final: 0.8000 (mtpt) REVERT: O 436 ILE cc_start: 0.6203 (OUTLIER) cc_final: 0.4716 (mp) REVERT: O 467 PHE cc_start: 0.9485 (m-80) cc_final: 0.9196 (m-80) REVERT: O 471 MET cc_start: 0.7221 (mtt) cc_final: 0.6863 (mtm) REVERT: O 537 PHE cc_start: 0.9518 (p90) cc_final: 0.8944 (p90) REVERT: P 227 TYR cc_start: 0.8325 (m-10) cc_final: 0.7899 (m-80) REVERT: P 238 HIS cc_start: 0.9232 (m-70) cc_final: 0.8928 (m90) REVERT: P 258 MET cc_start: 0.9047 (ptt) cc_final: 0.8597 (ptt) REVERT: P 284 LEU cc_start: 0.6649 (OUTLIER) cc_final: 0.6319 (tt) REVERT: P 381 MET cc_start: 0.9148 (mmp) cc_final: 0.8870 (mmm) REVERT: P 411 ARG cc_start: 0.9221 (mtt180) cc_final: 0.8992 (mmp-170) REVERT: P 415 LYS cc_start: 0.9104 (ttpp) cc_final: 0.8886 (ttpp) REVERT: P 497 GLN cc_start: 0.9306 (OUTLIER) cc_final: 0.8720 (tp-100) REVERT: Q 1 MET cc_start: 0.8187 (tmm) cc_final: 0.7928 (tmm) REVERT: Q 157 MET cc_start: 0.4597 (ttt) cc_final: 0.4243 (ttt) REVERT: Q 173 MET cc_start: 0.8269 (mmt) cc_final: 0.7983 (mmt) REVERT: Q 212 HIS cc_start: 0.9458 (m-70) cc_final: 0.9042 (m-70) REVERT: Q 248 LYS cc_start: 0.9389 (tppt) cc_final: 0.9057 (tppt) REVERT: Q 259 ASP cc_start: 0.9225 (t0) cc_final: 0.9022 (t0) REVERT: Q 274 MET cc_start: 0.9474 (tpt) cc_final: 0.8413 (tpt) REVERT: Q 281 LYS cc_start: 0.7997 (mttt) cc_final: 0.7783 (mtmm) REVERT: Q 308 PHE cc_start: 0.8997 (p90) cc_final: 0.7917 (p90) REVERT: Q 343 GLN cc_start: 0.9058 (mm110) cc_final: 0.8568 (mp10) REVERT: Q 365 TRP cc_start: 0.7957 (m100) cc_final: 0.7404 (m100) outliers start: 26 outliers final: 6 residues processed: 1161 average time/residue: 0.2912 time to fit residues: 557.1235 Evaluate side-chains 805 residues out of total 4950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 795 time to evaluate : 1.883 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 556 random chunks: chunk 546 optimal weight: 4.9990 chunk 133 optimal weight: 20.0000 chunk 345 optimal weight: 50.0000 chunk 450 optimal weight: 9.9990 chunk 375 optimal weight: 7.9990 chunk 544 optimal weight: 10.0000 chunk 214 optimal weight: 0.9990 chunk 163 optimal weight: 7.9990 chunk 104 optimal weight: 6.9990 chunk 159 optimal weight: 6.9990 chunk 332 optimal weight: 6.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 107 HIS A 332 GLN ** A 431 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 432 ASN ** A 435 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 738 ASN A 819 ASN A1036 ASN A1113 HIS ** A1191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1314 GLN ** A1320 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 473 GLN ** B 532 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 547 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 575 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 702 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 899 GLN B 944 GLN B 975 HIS B 999 GLN ** B1100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 3 GLN E 113 GLN ** G 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 119 HIS ** H 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 134 ASN ** K 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 132 GLN O 313 GLN ** O 346 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 348 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 454 GLN O 461 HIS O 613 HIS O 728 GLN ** P 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 283 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 315 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 449 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 511 HIS ** Q 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 319 ASN ** Q 372 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 407 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 409 HIS Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.090912 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.070770 restraints weight = 236268.367| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.072675 restraints weight = 128617.100| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.073862 restraints weight = 82936.795| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.074608 restraints weight = 61269.877| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.075186 restraints weight = 50100.956| |-----------------------------------------------------------------------------| r_work (final): 0.3377 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7407 moved from start: 0.5123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.085 47692 Z= 0.250 Angle : 0.990 43.607 64864 Z= 0.477 Chirality : 0.051 0.675 7252 Planarity : 0.007 0.267 7976 Dihedral : 14.270 178.082 7147 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 23.84 Ramachandran Plot: Outliers : 1.05 % Allowed : 7.66 % Favored : 91.29 % Rotamer: Outliers : 0.26 % Allowed : 4.06 % Favored : 95.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.83 % Twisted General : 0.15 % 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 aren not related in a simple way. whole: -1.59 (0.11), residues: 5432 helix: -0.04 (0.11), residues: 1949 sheet: -1.11 (0.17), residues: 743 loop : -1.81 (0.12), residues: 2740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.001 ARG O 197 TYR 0.038 0.002 TYR Q 131 PHE 0.105 0.003 PHE Q 358 TRP 0.044 0.003 TRP O 324 HIS 0.015 0.002 HIS P 157 Details of bonding type rmsd covalent geometry : bond 0.00531 (47647) covalent geometry : angle 0.90848 (64831) hydrogen bonds : bond 0.06026 ( 1994) hydrogen bonds : angle 6.67627 ( 5479) metal coordination : bond 0.01927 ( 24) metal coordination : angle 17.49644 ( 33) Misc. bond : bond 0.01147 ( 21) *********************** 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 1022 residues out of total 4950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 1009 time to evaluate : 1.879 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: A 226 LYS cc_start: 0.9502 (mmpt) cc_final: 0.9169 (mmmt) REVERT: A 339 PHE cc_start: 0.8804 (m-80) cc_final: 0.8275 (m-80) REVERT: A 437 PHE cc_start: 0.9071 (t80) cc_final: 0.8867 (t80) REVERT: A 453 ILE cc_start: 0.9536 (pt) cc_final: 0.9204 (pt) REVERT: A 470 HIS cc_start: 0.8213 (m170) cc_final: 0.7604 (m170) REVERT: A 472 MET cc_start: 0.8429 (mmm) cc_final: 0.7958 (mmt) REVERT: A 518 GLU cc_start: 0.9062 (tt0) cc_final: 0.8750 (tm-30) REVERT: A 589 MET cc_start: 0.8448 (mmm) cc_final: 0.7936 (mmm) REVERT: A 654 ASP cc_start: 0.8834 (m-30) cc_final: 0.8632 (m-30) REVERT: A 686 PHE cc_start: 0.8816 (m-10) cc_final: 0.8551 (m-80) REVERT: A 699 CYS cc_start: 0.8466 (p) cc_final: 0.8154 (p) REVERT: A 822 THR cc_start: 0.9336 (p) cc_final: 0.9030 (t) REVERT: A 830 MET cc_start: 0.8714 (mmm) cc_final: 0.8389 (mmm) REVERT: A 925 MET cc_start: 0.9501 (tpt) cc_final: 0.9138 (tmm) REVERT: A 956 ARG cc_start: 0.8523 (ttp80) cc_final: 0.8224 (ttp-110) REVERT: A 994 GLU cc_start: -0.4395 (mt-10) cc_final: -0.4718 (mt-10) REVERT: A 1000 MET cc_start: -0.1688 (mtt) cc_final: -0.1985 (mmm) REVERT: A 1007 ILE cc_start: -0.4458 (mt) cc_final: -0.4833 (mm) REVERT: A 1008 ASP cc_start: 0.1171 (t0) cc_final: 0.0613 (m-30) REVERT: A 1019 LEU cc_start: -0.2190 (tp) cc_final: -0.3306 (tp) REVERT: A 1056 ASP cc_start: 0.9069 (t0) cc_final: 0.8853 (t0) REVERT: A 1183 GLU cc_start: 0.8186 (tp30) cc_final: 0.7815 (tp30) REVERT: A 1185 VAL cc_start: 0.9539 (m) cc_final: 0.9060 (t) REVERT: A 1238 MET cc_start: 0.8026 (ttm) cc_final: 0.7645 (mtp) REVERT: A 1476 LEU cc_start: 0.9182 (mt) cc_final: 0.8935 (mt) REVERT: A 1485 MET cc_start: 0.8812 (pmm) cc_final: 0.8559 (pmm) REVERT: A 1489 VAL cc_start: 0.9703 (t) cc_final: 0.9444 (t) REVERT: A 1504 ILE cc_start: 0.9318 (mm) cc_final: 0.9083 (mm) REVERT: A 1505 ASP cc_start: 0.8156 (t0) cc_final: 0.7393 (t0) REVERT: A 1507 CYS cc_start: 0.7359 (t) cc_final: 0.7014 (t) REVERT: A 1519 LEU cc_start: 0.9256 (mt) cc_final: 0.8694 (mt) REVERT: A 1589 MET cc_start: 0.9418 (mtt) cc_final: 0.8925 (mmm) REVERT: A 1603 MET cc_start: 0.8721 (tpt) cc_final: 0.8347 (mmm) REVERT: A 1620 GLN cc_start: 0.9074 (mp10) cc_final: 0.8685 (mp10) REVERT: A 1621 PHE cc_start: 0.9287 (m-80) cc_final: 0.8852 (m-80) REVERT: B 157 ASP cc_start: 0.9243 (p0) cc_final: 0.8996 (p0) REVERT: B 158 CYS cc_start: 0.8635 (m) cc_final: 0.8357 (m) REVERT: B 174 LYS cc_start: 0.9158 (mmpt) cc_final: 0.8904 (mmmt) REVERT: B 206 LEU cc_start: 0.9471 (tp) cc_final: 0.9230 (tp) REVERT: B 215 MET cc_start: 0.7652 (mtt) cc_final: 0.7168 (mtt) REVERT: B 275 MET cc_start: 0.9165 (ttm) cc_final: 0.8850 (ttm) REVERT: B 285 ASP cc_start: 0.8907 (m-30) cc_final: 0.8571 (m-30) REVERT: B 304 ASP cc_start: 0.9503 (m-30) cc_final: 0.9090 (p0) REVERT: B 330 LEU cc_start: 0.9617 (mt) cc_final: 0.9362 (mt) REVERT: B 354 LEU cc_start: 0.9354 (mp) cc_final: 0.9142 (mp) REVERT: B 359 LEU cc_start: 0.9651 (mt) cc_final: 0.9335 (mt) REVERT: B 373 MET cc_start: 0.8956 (tmm) cc_final: 0.8374 (tmm) REVERT: B 374 LEU cc_start: 0.9612 (tp) cc_final: 0.9279 (tp) REVERT: B 398 GLN cc_start: 0.9088 (pt0) cc_final: 0.8820 (pt0) REVERT: B 419 GLU cc_start: 0.9120 (pt0) cc_final: 0.8760 (pt0) REVERT: B 496 PHE cc_start: 0.9129 (t80) cc_final: 0.8651 (t80) REVERT: B 515 THR cc_start: 0.9285 (p) cc_final: 0.9061 (t) REVERT: B 543 ASN cc_start: 0.8845 (m-40) cc_final: 0.8558 (m-40) REVERT: B 640 LEU cc_start: 0.9243 (tp) cc_final: 0.8987 (tp) REVERT: B 803 MET cc_start: 0.8938 (ttp) cc_final: 0.8693 (ttm) REVERT: B 898 LEU cc_start: 0.9177 (tp) cc_final: 0.8767 (tp) REVERT: B 982 THR cc_start: 0.9383 (m) cc_final: 0.9110 (p) REVERT: B 1074 MET cc_start: 0.8308 (ttm) cc_final: 0.7910 (ttp) REVERT: B 1075 GLU cc_start: 0.8666 (mp0) cc_final: 0.8461 (mp0) REVERT: B 1086 PHE cc_start: 0.7706 (m-80) cc_final: 0.7302 (m-80) REVERT: B 1157 GLN cc_start: 0.9370 (mp-120) cc_final: 0.8983 (mp10) REVERT: C 95 GLU cc_start: 0.7944 (mm-30) cc_final: 0.7023 (mm-30) REVERT: C 273 ASP cc_start: 0.8421 (t70) cc_final: 0.8108 (t70) REVERT: D 34 ASP cc_start: 0.9116 (p0) cc_final: 0.8665 (p0) REVERT: E 140 LEU cc_start: 0.9354 (mm) cc_final: 0.9134 (mm) REVERT: E 215 MET cc_start: 0.8664 (mmt) cc_final: 0.8209 (mmm) REVERT: F 76 LYS cc_start: 0.9280 (mmmm) cc_final: 0.9057 (mmmm) REVERT: F 88 TYR cc_start: 0.7963 (m-80) cc_final: 0.7564 (m-80) REVERT: F 122 MET cc_start: 0.9133 (mtp) cc_final: 0.8875 (mtp) REVERT: F 151 LEU cc_start: 0.9196 (tp) cc_final: 0.8989 (tp) REVERT: G 45 LEU cc_start: 0.9195 (pp) cc_final: 0.8991 (pp) REVERT: G 110 ASP cc_start: 0.8950 (p0) cc_final: 0.8421 (p0) REVERT: G 166 TRP cc_start: 0.7871 (m100) cc_final: 0.7579 (m-90) REVERT: H 102 TYR cc_start: 0.8695 (p90) cc_final: 0.8226 (p90) REVERT: H 116 TYR cc_start: 0.8521 (m-80) cc_final: 0.8065 (m-80) REVERT: H 118 PHE cc_start: 0.8763 (m-80) cc_final: 0.7828 (m-80) REVERT: H 141 TYR cc_start: 0.8493 (m-80) cc_final: 0.8040 (m-80) REVERT: I 45 LEU cc_start: 0.9496 (mm) cc_final: 0.9269 (mm) REVERT: I 64 LYS cc_start: 0.9472 (mtpp) cc_final: 0.9128 (pttt) REVERT: J 28 ASP cc_start: 0.8859 (t70) cc_final: 0.8592 (t0) REVERT: J 48 ARG cc_start: 0.9338 (ptt90) cc_final: 0.9064 (ttp80) REVERT: J 49 MET cc_start: 0.9422 (tpp) cc_final: 0.8027 (tpp) REVERT: K 67 GLU cc_start: 0.8471 (tm-30) cc_final: 0.7728 (tm-30) REVERT: K 100 LEU cc_start: 0.8048 (mt) cc_final: 0.7743 (mp) REVERT: K 125 MET cc_start: 0.8497 (mtt) cc_final: 0.8123 (mmt) REVERT: L 33 GLU cc_start: 0.8716 (mm-30) cc_final: 0.8378 (mm-30) REVERT: L 53 HIS cc_start: 0.8810 (t70) cc_final: 0.7824 (t70) REVERT: L 67 PHE cc_start: 0.8374 (m-10) cc_final: 0.8008 (m-10) REVERT: M 26 PHE cc_start: 0.8293 (m-10) cc_final: 0.7316 (m-10) REVERT: M 27 PHE cc_start: 0.7663 (p90) cc_final: 0.7217 (p90) REVERT: M 30 PHE cc_start: 0.9018 (t80) cc_final: 0.8638 (t80) REVERT: M 41 TYR cc_start: 0.8640 (m-80) cc_final: 0.8159 (m-80) REVERT: M 92 LYS cc_start: 0.8449 (ttpt) cc_final: 0.8160 (ttpt) REVERT: N 29 PHE cc_start: 0.9323 (m-80) cc_final: 0.8524 (m-80) REVERT: N 135 LYS cc_start: 0.8165 (mttp) cc_final: 0.7775 (mtpt) REVERT: O 467 PHE cc_start: 0.9598 (m-80) cc_final: 0.9175 (m-80) REVERT: O 537 PHE cc_start: 0.9500 (p90) cc_final: 0.8937 (p90) REVERT: P 226 LEU cc_start: 0.9361 (pp) cc_final: 0.8784 (pp) REVERT: P 227 TYR cc_start: 0.8419 (m-10) cc_final: 0.7941 (m-80) REVERT: P 238 HIS cc_start: 0.9400 (m-70) cc_final: 0.9022 (m90) REVERT: P 254 LEU cc_start: 0.9745 (tp) cc_final: 0.9374 (tp) REVERT: P 258 MET cc_start: 0.8903 (ptt) cc_final: 0.8215 (ptt) REVERT: P 317 MET cc_start: 0.8804 (tpt) cc_final: 0.8595 (tpt) REVERT: P 363 SER cc_start: 0.8889 (t) cc_final: 0.8597 (m) REVERT: P 381 MET cc_start: 0.9201 (mmp) cc_final: 0.8907 (mmm) REVERT: P 402 MET cc_start: 0.7825 (mtp) cc_final: 0.6905 (ttm) REVERT: P 413 LEU cc_start: 0.9776 (mt) cc_final: 0.9544 (mt) REVERT: Q 1 MET cc_start: 0.8124 (tmm) cc_final: 0.6468 (ppp) REVERT: Q 212 HIS cc_start: 0.9417 (m-70) cc_final: 0.8889 (m-70) REVERT: Q 251 TRP cc_start: 0.7435 (p-90) cc_final: 0.6568 (p-90) REVERT: Q 274 MET cc_start: 0.9481 (tpt) cc_final: 0.8661 (tpp) REVERT: Q 286 GLN cc_start: 0.9380 (mp10) cc_final: 0.9156 (mp10) REVERT: Q 308 PHE cc_start: 0.8974 (p90) cc_final: 0.8113 (p90) REVERT: Q 343 GLN cc_start: 0.9111 (mm110) cc_final: 0.8620 (mp10) REVERT: Q 365 TRP cc_start: 0.9130 (m100) cc_final: 0.8244 (m100) outliers start: 13 outliers final: 4 residues processed: 1020 average time/residue: 0.2876 time to fit residues: 485.5441 Evaluate side-chains 746 residues out of total 4950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 742 time to evaluate : 1.985 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 556 random chunks: chunk 296 optimal weight: 20.0000 chunk 492 optimal weight: 7.9990 chunk 110 optimal weight: 4.9990 chunk 165 optimal weight: 10.0000 chunk 64 optimal weight: 3.9990 chunk 33 optimal weight: 6.9990 chunk 147 optimal weight: 0.9980 chunk 307 optimal weight: 10.0000 chunk 544 optimal weight: 8.9990 chunk 285 optimal weight: 0.0980 chunk 49 optimal weight: 20.0000 overall best weight: 3.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 106 HIS A 382 GLN A 649 ASN A 738 ASN A 819 ASN A 950 GLN A1065 GLN ** A1320 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1629 ASN ** B 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 532 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 547 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 575 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 600 GLN ** B 702 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1100 GLN ** D 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 99 HIS ** G 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 36 ASN ** G 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 106 GLN M 89 GLN ** O 346 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 348 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 769 GLN ** P 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 194 GLN ** P 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 315 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 449 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 319 ASN ** Q 372 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 407 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 409 HIS Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.091227 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.071008 restraints weight = 235930.222| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.072956 restraints weight = 127548.398| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.074176 restraints weight = 82110.209| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.074913 restraints weight = 60126.133| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.075497 restraints weight = 49118.365| |-----------------------------------------------------------------------------| r_work (final): 0.3382 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7382 moved from start: 0.5675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.098 47692 Z= 0.197 Angle : 0.880 35.168 64864 Z= 0.432 Chirality : 0.049 0.673 7252 Planarity : 0.008 0.443 7976 Dihedral : 14.203 179.372 7147 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 21.21 Ramachandran Plot: Outliers : 0.99 % Allowed : 7.01 % Favored : 91.99 % Rotamer: Outliers : 0.06 % Allowed : 3.66 % Favored : 96.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.65 % Twisted General : 0.13 % 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 aren not related in a simple way. whole: -1.30 (0.11), residues: 5432 helix: 0.23 (0.11), residues: 1951 sheet: -1.11 (0.17), residues: 762 loop : -1.60 (0.12), residues: 2719 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.001 ARG O 197 TYR 0.040 0.002 TYR A 478 PHE 0.105 0.002 PHE Q 358 TRP 0.040 0.002 TRP N 54 HIS 0.011 0.001 HIS E 99 Details of bonding type rmsd covalent geometry : bond 0.00430 (47647) covalent geometry : angle 0.82682 (64831) hydrogen bonds : bond 0.05438 ( 1994) hydrogen bonds : angle 6.28800 ( 5479) metal coordination : bond 0.02017 ( 24) metal coordination : angle 13.39647 ( 33) Misc. bond : bond 0.01183 ( 21) *********************** 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 972 residues out of total 4950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 969 time to evaluate : 1.861 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: A 214 ASP cc_start: 0.9303 (t70) cc_final: 0.8517 (t0) REVERT: A 223 PHE cc_start: 0.9071 (t80) cc_final: 0.8852 (t80) REVERT: A 226 LYS cc_start: 0.9475 (mmpt) cc_final: 0.9040 (mmmt) REVERT: A 339 PHE cc_start: 0.8841 (m-80) cc_final: 0.8355 (m-80) REVERT: A 437 PHE cc_start: 0.9112 (t80) cc_final: 0.8891 (t80) REVERT: A 453 ILE cc_start: 0.9536 (pt) cc_final: 0.9125 (pt) REVERT: A 470 HIS cc_start: 0.8322 (m170) cc_final: 0.8102 (m170) REVERT: A 472 MET cc_start: 0.8482 (mmm) cc_final: 0.8102 (mmt) REVERT: A 505 LEU cc_start: 0.8848 (mp) cc_final: 0.8594 (mp) REVERT: A 518 GLU cc_start: 0.9096 (tt0) cc_final: 0.8823 (tm-30) REVERT: A 589 MET cc_start: 0.8257 (mmm) cc_final: 0.7841 (mmm) REVERT: A 590 ASN cc_start: 0.8989 (t0) cc_final: 0.8778 (t0) REVERT: A 654 ASP cc_start: 0.8750 (m-30) cc_final: 0.8523 (m-30) REVERT: A 669 LEU cc_start: 0.8949 (mt) cc_final: 0.8714 (mt) REVERT: A 672 ASP cc_start: 0.8112 (t70) cc_final: 0.7874 (t70) REVERT: A 675 SER cc_start: 0.9504 (m) cc_final: 0.9254 (p) REVERT: A 686 PHE cc_start: 0.8920 (m-10) cc_final: 0.8680 (m-80) REVERT: A 699 CYS cc_start: 0.8470 (p) cc_final: 0.8183 (p) REVERT: A 830 MET cc_start: 0.8788 (mmm) cc_final: 0.8382 (mmm) REVERT: A 925 MET cc_start: 0.9510 (tpt) cc_final: 0.9137 (tmm) REVERT: A 943 ILE cc_start: 0.9651 (mt) cc_final: 0.9356 (pt) REVERT: A 960 MET cc_start: 0.7719 (mtp) cc_final: 0.7393 (mtp) REVERT: A 1007 ILE cc_start: -0.4620 (mt) cc_final: -0.5101 (mm) REVERT: A 1008 ASP cc_start: 0.1241 (t0) cc_final: 0.0585 (m-30) REVERT: A 1009 THR cc_start: 0.0457 (m) cc_final: 0.0107 (m) REVERT: A 1185 VAL cc_start: 0.9478 (m) cc_final: 0.9128 (t) REVERT: A 1238 MET cc_start: 0.8038 (ttm) cc_final: 0.7680 (mtp) REVERT: A 1439 MET cc_start: 0.8414 (mmp) cc_final: 0.8180 (mmm) REVERT: A 1476 LEU cc_start: 0.9247 (mt) cc_final: 0.8978 (mt) REVERT: A 1485 MET cc_start: 0.8882 (pmm) cc_final: 0.8653 (pmm) REVERT: A 1490 GLU cc_start: 0.9224 (mt-10) cc_final: 0.8747 (mm-30) REVERT: A 1504 ILE cc_start: 0.9305 (mm) cc_final: 0.9049 (mm) REVERT: A 1505 ASP cc_start: 0.8428 (t0) cc_final: 0.7699 (t0) REVERT: A 1589 MET cc_start: 0.9425 (mtt) cc_final: 0.8933 (mmm) REVERT: A 1610 PHE cc_start: 0.9516 (m-80) cc_final: 0.9154 (m-80) REVERT: A 1620 GLN cc_start: 0.9021 (mp10) cc_final: 0.8582 (mp10) REVERT: A 1621 PHE cc_start: 0.9319 (m-80) cc_final: 0.8787 (m-80) REVERT: B 80 ASN cc_start: -0.0323 (p0) cc_final: -0.0560 (t0) REVERT: B 136 LYS cc_start: 0.8850 (ttmt) cc_final: 0.8164 (tptm) REVERT: B 157 ASP cc_start: 0.9286 (p0) cc_final: 0.8556 (p0) REVERT: B 174 LYS cc_start: 0.9142 (mmpt) cc_final: 0.8907 (mmmt) REVERT: B 188 ASP cc_start: 0.8927 (m-30) cc_final: 0.8551 (m-30) REVERT: B 206 LEU cc_start: 0.9500 (tp) cc_final: 0.9174 (tp) REVERT: B 215 MET cc_start: 0.7634 (mtt) cc_final: 0.7151 (mtt) REVERT: B 224 ASN cc_start: 0.8625 (m110) cc_final: 0.8401 (m110) REVERT: B 275 MET cc_start: 0.9159 (ttm) cc_final: 0.8839 (ttm) REVERT: B 285 ASP cc_start: 0.8923 (m-30) cc_final: 0.8562 (m-30) REVERT: B 304 ASP cc_start: 0.9529 (m-30) cc_final: 0.9116 (p0) REVERT: B 330 LEU cc_start: 0.9657 (mt) cc_final: 0.9391 (mt) REVERT: B 374 LEU cc_start: 0.9636 (tp) cc_final: 0.9433 (tp) REVERT: B 398 GLN cc_start: 0.9070 (pt0) cc_final: 0.8841 (pt0) REVERT: B 411 MET cc_start: 0.9501 (mtm) cc_final: 0.9199 (mtp) REVERT: B 414 LYS cc_start: 0.9632 (ttpp) cc_final: 0.9057 (ttpp) REVERT: B 420 TYR cc_start: 0.9382 (t80) cc_final: 0.9123 (t80) REVERT: B 495 ARG cc_start: 0.8450 (tpt170) cc_final: 0.8144 (tpt-90) REVERT: B 496 PHE cc_start: 0.9131 (t80) cc_final: 0.8605 (t80) REVERT: B 502 MET cc_start: 0.9006 (ttt) cc_final: 0.8737 (tmm) REVERT: B 515 THR cc_start: 0.9245 (p) cc_final: 0.8999 (t) REVERT: B 543 ASN cc_start: 0.8805 (m-40) cc_final: 0.8572 (m-40) REVERT: B 726 MET cc_start: 0.9073 (ttp) cc_final: 0.8847 (ttp) REVERT: B 783 MET cc_start: 0.7412 (mmm) cc_final: 0.7105 (mmm) REVERT: B 785 ASP cc_start: 0.7875 (m-30) cc_final: 0.7620 (m-30) REVERT: B 898 LEU cc_start: 0.9280 (tp) cc_final: 0.8867 (tp) REVERT: B 982 THR cc_start: 0.9394 (m) cc_final: 0.9112 (p) REVERT: B 1074 MET cc_start: 0.8280 (ttm) cc_final: 0.7811 (ttp) REVERT: B 1075 GLU cc_start: 0.8610 (mp0) cc_final: 0.8395 (mp0) REVERT: B 1086 PHE cc_start: 0.7665 (m-80) cc_final: 0.4975 (m-80) REVERT: B 1157 GLN cc_start: 0.9369 (mp-120) cc_final: 0.9062 (mp10) REVERT: C 181 ASP cc_start: 0.8915 (m-30) cc_final: 0.8679 (p0) REVERT: C 247 PHE cc_start: 0.9139 (t80) cc_final: 0.8727 (t80) REVERT: C 273 ASP cc_start: 0.8526 (t70) cc_final: 0.8078 (t70) REVERT: E 2 ASP cc_start: 0.9172 (p0) cc_final: 0.8810 (p0) REVERT: E 140 LEU cc_start: 0.9406 (mm) cc_final: 0.9193 (mm) REVERT: E 174 GLN cc_start: 0.9242 (mt0) cc_final: 0.8737 (mt0) REVERT: E 215 MET cc_start: 0.8807 (mmt) cc_final: 0.8319 (mmm) REVERT: F 74 ILE cc_start: 0.9419 (mm) cc_final: 0.9178 (tp) REVERT: F 76 LYS cc_start: 0.9355 (mmmm) cc_final: 0.9092 (mmmm) REVERT: F 87 LYS cc_start: 0.8864 (ptpp) cc_final: 0.8558 (ptpp) REVERT: F 88 TYR cc_start: 0.8071 (m-80) cc_final: 0.7409 (m-80) REVERT: F 90 ARG cc_start: 0.9459 (ptm-80) cc_final: 0.8959 (ttp80) REVERT: F 92 ARG cc_start: 0.9232 (tpt-90) cc_final: 0.8631 (tpt-90) REVERT: F 122 MET cc_start: 0.9120 (mtp) cc_final: 0.8814 (mtp) REVERT: F 127 GLU cc_start: 0.8518 (mp0) cc_final: 0.8309 (mp0) REVERT: G 45 LEU cc_start: 0.9234 (pp) cc_final: 0.9005 (pp) REVERT: G 98 GLU cc_start: 0.8444 (mm-30) cc_final: 0.8062 (mp0) REVERT: G 110 ASP cc_start: 0.8956 (p0) cc_final: 0.8411 (p0) REVERT: G 166 TRP cc_start: 0.7579 (m100) cc_final: 0.7253 (m-90) REVERT: H 45 GLU cc_start: 0.8681 (tm-30) cc_final: 0.8437 (tm-30) REVERT: H 102 TYR cc_start: 0.8686 (p90) cc_final: 0.8225 (p90) REVERT: H 116 TYR cc_start: 0.8634 (m-80) cc_final: 0.8103 (m-80) REVERT: H 118 PHE cc_start: 0.8885 (m-80) cc_final: 0.8146 (m-80) REVERT: I 9 PHE cc_start: 0.8879 (m-80) cc_final: 0.8555 (m-80) REVERT: I 37 TYR cc_start: 0.8215 (m-10) cc_final: 0.8002 (m-10) REVERT: I 64 LYS cc_start: 0.9425 (mtpp) cc_final: 0.8862 (mtpp) REVERT: J 28 ASP cc_start: 0.8832 (t70) cc_final: 0.8566 (t0) REVERT: J 49 MET cc_start: 0.9479 (tpp) cc_final: 0.8229 (tpp) REVERT: K 67 GLU cc_start: 0.8497 (tm-30) cc_final: 0.7416 (tm-30) REVERT: K 68 GLU cc_start: 0.8678 (mm-30) cc_final: 0.8431 (mm-30) REVERT: K 76 LEU cc_start: 0.9333 (tp) cc_final: 0.9105 (tp) REVERT: K 82 LYS cc_start: 0.9384 (mmtt) cc_final: 0.8844 (mmmm) REVERT: K 100 LEU cc_start: 0.8043 (mt) cc_final: 0.7812 (mp) REVERT: K 102 ASN cc_start: 0.8359 (p0) cc_final: 0.8076 (p0) REVERT: K 125 MET cc_start: 0.8652 (mtt) cc_final: 0.8132 (mmm) REVERT: L 33 GLU cc_start: 0.8669 (mm-30) cc_final: 0.8339 (mm-30) REVERT: L 53 HIS cc_start: 0.8875 (t70) cc_final: 0.7804 (t70) REVERT: L 55 ILE cc_start: 0.9642 (mm) cc_final: 0.9396 (mm) REVERT: M 12 ILE cc_start: 0.8717 (mm) cc_final: 0.8497 (mm) REVERT: M 23 VAL cc_start: 0.9165 (t) cc_final: 0.8938 (t) REVERT: M 26 PHE cc_start: 0.8216 (m-10) cc_final: 0.7361 (m-10) REVERT: M 30 PHE cc_start: 0.9133 (t80) cc_final: 0.8481 (t80) REVERT: M 38 PHE cc_start: 0.9381 (m-10) cc_final: 0.9161 (m-80) REVERT: M 41 TYR cc_start: 0.8607 (m-80) cc_final: 0.8108 (m-80) REVERT: N 29 PHE cc_start: 0.9255 (m-80) cc_final: 0.8596 (m-80) REVERT: N 52 GLN cc_start: 0.8956 (mp10) cc_final: 0.8514 (mp10) REVERT: N 117 GLU cc_start: 0.8724 (tt0) cc_final: 0.8460 (tm-30) REVERT: N 119 LEU cc_start: 0.9000 (mm) cc_final: 0.8686 (tp) REVERT: O 380 MET cc_start: 0.9354 (mtp) cc_final: 0.9031 (mtp) REVERT: O 463 LEU cc_start: 0.9038 (pt) cc_final: 0.8797 (mm) REVERT: O 467 PHE cc_start: 0.9665 (m-80) cc_final: 0.9164 (m-80) REVERT: O 537 PHE cc_start: 0.9570 (p90) cc_final: 0.8963 (p90) REVERT: O 538 LEU cc_start: 0.9644 (mp) cc_final: 0.9297 (mt) REVERT: P 226 LEU cc_start: 0.9358 (pp) cc_final: 0.8804 (pp) REVERT: P 227 TYR cc_start: 0.8262 (m-80) cc_final: 0.7793 (m-80) REVERT: P 238 HIS cc_start: 0.9431 (m-70) cc_final: 0.9107 (m90) REVERT: P 254 LEU cc_start: 0.9757 (tp) cc_final: 0.9406 (tp) REVERT: P 258 MET cc_start: 0.8761 (ptt) cc_final: 0.8170 (ptt) REVERT: P 363 SER cc_start: 0.9057 (t) cc_final: 0.8485 (m) REVERT: P 381 MET cc_start: 0.9306 (mmp) cc_final: 0.9015 (mmm) REVERT: P 413 LEU cc_start: 0.9800 (mt) cc_final: 0.9490 (mt) REVERT: Q 157 MET cc_start: 0.4022 (ttm) cc_final: 0.3550 (ttm) REVERT: Q 173 MET cc_start: 0.8953 (mpp) cc_final: 0.8645 (mpp) REVERT: Q 212 HIS cc_start: 0.9378 (m-70) cc_final: 0.8861 (m-70) REVERT: Q 248 LYS cc_start: 0.9425 (tptt) cc_final: 0.9170 (tptt) REVERT: Q 251 TRP cc_start: 0.7228 (p-90) cc_final: 0.5800 (p-90) REVERT: Q 274 MET cc_start: 0.9478 (tpt) cc_final: 0.8629 (tpp) REVERT: Q 308 PHE cc_start: 0.8821 (p90) cc_final: 0.8123 (p90) REVERT: Q 365 TRP cc_start: 0.9161 (m100) cc_final: 0.8076 (m100) outliers start: 3 outliers final: 1 residues processed: 970 average time/residue: 0.2837 time to fit residues: 457.5689 Evaluate side-chains 743 residues out of total 4950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 742 time to evaluate : 1.755 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 556 random chunks: chunk 336 optimal weight: 3.9990 chunk 306 optimal weight: 30.0000 chunk 241 optimal weight: 9.9990 chunk 144 optimal weight: 10.0000 chunk 20 optimal weight: 0.9990 chunk 128 optimal weight: 20.0000 chunk 454 optimal weight: 50.0000 chunk 320 optimal weight: 1.9990 chunk 61 optimal weight: 5.9990 chunk 217 optimal weight: 9.9990 chunk 552 optimal weight: 20.0000 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 382 GLN A 470 HIS A 819 ASN A1320 GLN ** B 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 231 HIS ** B 532 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 547 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 575 HIS B 673 ASN ** B 702 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 715 ASN ** D 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 32 GLN J 26 GLN M 54 HIS ** M 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 346 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 348 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 757 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 315 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 449 GLN Q 260 ASN Q 319 ASN ** Q 372 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 407 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 409 HIS Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.090516 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.070304 restraints weight = 237197.961| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.072191 restraints weight = 128525.845| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.073438 restraints weight = 82477.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.074198 restraints weight = 60583.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.074705 restraints weight = 49715.643| |-----------------------------------------------------------------------------| r_work (final): 0.3361 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7439 moved from start: 0.6067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.093 47692 Z= 0.211 Angle : 0.848 25.782 64864 Z= 0.425 Chirality : 0.048 0.702 7252 Planarity : 0.007 0.397 7976 Dihedral : 14.164 177.314 7147 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 21.15 Ramachandran Plot: Outliers : 0.83 % Allowed : 7.36 % Favored : 91.81 % Rotamer: Outliers : 0.08 % Allowed : 2.93 % Favored : 96.99 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.24 % Twisted General : 0.15 % 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 aren not related in a simple way. whole: -1.18 (0.11), residues: 5432 helix: 0.34 (0.11), residues: 1940 sheet: -1.01 (0.18), residues: 757 loop : -1.55 (0.12), residues: 2735 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B1023 TYR 0.036 0.002 TYR A 478 PHE 0.105 0.002 PHE Q 358 TRP 0.051 0.002 TRP N 54 HIS 0.009 0.001 HIS Q 304 Details of bonding type rmsd covalent geometry : bond 0.00454 (47647) covalent geometry : angle 0.81701 (64831) hydrogen bonds : bond 0.05298 ( 1994) hydrogen bonds : angle 6.11623 ( 5479) metal coordination : bond 0.01710 ( 24) metal coordination : angle 10.09922 ( 33) Misc. bond : bond 0.01057 ( 21) *********************** 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 914 residues out of total 4950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 910 time to evaluate : 1.844 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: A 213 ASN cc_start: 0.9237 (t0) cc_final: 0.9014 (t0) REVERT: A 214 ASP cc_start: 0.9211 (t70) cc_final: 0.8785 (t70) REVERT: A 218 LYS cc_start: 0.9494 (ptpp) cc_final: 0.9115 (pttt) REVERT: A 226 LYS cc_start: 0.9507 (mmpt) cc_final: 0.9079 (mmmt) REVERT: A 325 ASP cc_start: 0.8747 (t70) cc_final: 0.8487 (m-30) REVERT: A 339 PHE cc_start: 0.8875 (m-80) cc_final: 0.8320 (m-80) REVERT: A 437 PHE cc_start: 0.9116 (t80) cc_final: 0.8884 (t80) REVERT: A 466 LEU cc_start: 0.9365 (tt) cc_final: 0.9122 (tt) REVERT: A 478 TYR cc_start: 0.8639 (m-10) cc_final: 0.8407 (m-80) REVERT: A 505 LEU cc_start: 0.8846 (mp) cc_final: 0.8588 (mp) REVERT: A 589 MET cc_start: 0.8424 (mmm) cc_final: 0.8167 (mmm) REVERT: A 600 MET cc_start: 0.8841 (ttm) cc_final: 0.8601 (ttp) REVERT: A 618 TYR cc_start: 0.8621 (m-80) cc_final: 0.8393 (m-80) REVERT: A 675 SER cc_start: 0.9526 (m) cc_final: 0.9279 (p) REVERT: A 686 PHE cc_start: 0.8967 (m-10) cc_final: 0.8763 (m-80) REVERT: A 699 CYS cc_start: 0.8578 (p) cc_final: 0.8370 (p) REVERT: A 830 MET cc_start: 0.8799 (mmm) cc_final: 0.8579 (mmm) REVERT: A 925 MET cc_start: 0.9444 (tpt) cc_final: 0.9087 (tmm) REVERT: A 943 ILE cc_start: 0.9619 (mt) cc_final: 0.9287 (pt) REVERT: A 947 LEU cc_start: 0.9115 (mp) cc_final: 0.8795 (mp) REVERT: A 960 MET cc_start: 0.7666 (mtp) cc_final: 0.7287 (mtp) REVERT: A 1007 ILE cc_start: -0.4628 (mt) cc_final: -0.5055 (mt) REVERT: A 1009 THR cc_start: 0.0660 (m) cc_final: 0.0181 (m) REVERT: A 1092 GLU cc_start: 0.9333 (mt-10) cc_final: 0.9015 (mp0) REVERT: A 1183 GLU cc_start: 0.8315 (tp30) cc_final: 0.7991 (tp30) REVERT: A 1185 VAL cc_start: 0.9482 (m) cc_final: 0.8954 (t) REVERT: A 1238 MET cc_start: 0.7944 (ttm) cc_final: 0.7607 (mtp) REVERT: A 1439 MET cc_start: 0.8333 (mmp) cc_final: 0.8125 (mmm) REVERT: A 1476 LEU cc_start: 0.9183 (mt) cc_final: 0.8929 (mt) REVERT: A 1485 MET cc_start: 0.8857 (pmm) cc_final: 0.8642 (pmm) REVERT: A 1490 GLU cc_start: 0.9206 (mt-10) cc_final: 0.8738 (mm-30) REVERT: A 1504 ILE cc_start: 0.9314 (mm) cc_final: 0.9062 (mm) REVERT: A 1505 ASP cc_start: 0.8560 (t0) cc_final: 0.7828 (t0) REVERT: A 1519 LEU cc_start: 0.9483 (mt) cc_final: 0.9227 (mt) REVERT: A 1565 GLU cc_start: 0.8680 (mm-30) cc_final: 0.8417 (mt-10) REVERT: A 1589 MET cc_start: 0.9439 (mtt) cc_final: 0.8945 (mmm) REVERT: A 1610 PHE cc_start: 0.9490 (m-80) cc_final: 0.9053 (m-80) REVERT: A 1620 GLN cc_start: 0.9112 (mp10) cc_final: 0.8657 (mp10) REVERT: A 1621 PHE cc_start: 0.9338 (m-80) cc_final: 0.8797 (m-80) REVERT: A 1657 LEU cc_start: 0.8799 (tp) cc_final: 0.8431 (tp) REVERT: A 1659 LYS cc_start: 0.9053 (mtpt) cc_final: 0.8777 (mtmm) REVERT: B 80 ASN cc_start: -0.0106 (p0) cc_final: -0.0432 (t0) REVERT: B 136 LYS cc_start: 0.8887 (ttmt) cc_final: 0.8205 (tptm) REVERT: B 174 LYS cc_start: 0.9138 (mmpt) cc_final: 0.8868 (mmmt) REVERT: B 188 ASP cc_start: 0.8908 (m-30) cc_final: 0.8528 (m-30) REVERT: B 205 MET cc_start: 0.8503 (mtp) cc_final: 0.8244 (mtp) REVERT: B 206 LEU cc_start: 0.9425 (tp) cc_final: 0.9133 (tp) REVERT: B 215 MET cc_start: 0.7559 (mtt) cc_final: 0.7233 (mtt) REVERT: B 224 ASN cc_start: 0.8638 (m110) cc_final: 0.8411 (m110) REVERT: B 275 MET cc_start: 0.9135 (ttm) cc_final: 0.8905 (ttm) REVERT: B 285 ASP cc_start: 0.8913 (m-30) cc_final: 0.8617 (m-30) REVERT: B 289 PHE cc_start: 0.9209 (t80) cc_final: 0.9004 (t80) REVERT: B 304 ASP cc_start: 0.9490 (m-30) cc_final: 0.9086 (p0) REVERT: B 330 LEU cc_start: 0.9649 (mt) cc_final: 0.9442 (mt) REVERT: B 414 LYS cc_start: 0.9617 (ttpp) cc_final: 0.9254 (ttpp) REVERT: B 422 GLN cc_start: 0.9218 (tm-30) cc_final: 0.8826 (tm-30) REVERT: B 486 VAL cc_start: 0.9384 (t) cc_final: 0.9077 (p) REVERT: B 496 PHE cc_start: 0.9126 (t80) cc_final: 0.8539 (t80) REVERT: B 502 MET cc_start: 0.8995 (ttt) cc_final: 0.8740 (tmm) REVERT: B 515 THR cc_start: 0.9229 (p) cc_final: 0.8980 (t) REVERT: B 671 TYR cc_start: 0.8584 (m-80) cc_final: 0.8192 (m-10) REVERT: B 783 MET cc_start: 0.7703 (mmm) cc_final: 0.7158 (mmm) REVERT: B 898 LEU cc_start: 0.9229 (tp) cc_final: 0.8788 (tp) REVERT: B 959 THR cc_start: 0.9272 (p) cc_final: 0.8938 (p) REVERT: B 982 THR cc_start: 0.9339 (m) cc_final: 0.9045 (p) REVERT: B 1074 MET cc_start: 0.8280 (ttm) cc_final: 0.7852 (ttp) REVERT: B 1086 PHE cc_start: 0.7620 (m-80) cc_final: 0.4977 (m-80) REVERT: B 1157 GLN cc_start: 0.9379 (mp-120) cc_final: 0.9064 (mp10) REVERT: C 71 MET cc_start: 0.9230 (mtp) cc_final: 0.8550 (mmm) REVERT: C 97 LEU cc_start: 0.9637 (tp) cc_final: 0.9434 (tp) REVERT: C 273 ASP cc_start: 0.8401 (t70) cc_final: 0.7974 (t70) REVERT: D 88 GLN cc_start: 0.9463 (mp10) cc_final: 0.8650 (mp10) REVERT: E 140 LEU cc_start: 0.9424 (mm) cc_final: 0.9147 (mm) REVERT: E 215 MET cc_start: 0.8697 (mmt) cc_final: 0.8417 (mmm) REVERT: F 77 ASP cc_start: 0.8738 (t0) cc_final: 0.8459 (p0) REVERT: F 87 LYS cc_start: 0.8911 (ptpp) cc_final: 0.8651 (ptpp) REVERT: F 88 TYR cc_start: 0.8209 (m-80) cc_final: 0.7506 (m-80) REVERT: F 90 ARG cc_start: 0.9490 (ptm-80) cc_final: 0.9004 (ttp80) REVERT: F 92 ARG cc_start: 0.9203 (tpt-90) cc_final: 0.8672 (tpt-90) REVERT: F 122 MET cc_start: 0.9136 (mtp) cc_final: 0.8775 (mtp) REVERT: F 136 ARG cc_start: 0.7996 (mtt180) cc_final: 0.7572 (mtt180) REVERT: F 151 LEU cc_start: 0.9050 (mm) cc_final: 0.8341 (tp) REVERT: G 98 GLU cc_start: 0.8474 (mm-30) cc_final: 0.8145 (mp0) REVERT: G 110 ASP cc_start: 0.8866 (p0) cc_final: 0.8274 (p0) REVERT: G 166 TRP cc_start: 0.7681 (m100) cc_final: 0.7304 (m-90) REVERT: H 45 GLU cc_start: 0.8683 (tm-30) cc_final: 0.8435 (tm-30) REVERT: H 46 LEU cc_start: 0.9278 (mt) cc_final: 0.9075 (mt) REVERT: H 102 TYR cc_start: 0.8772 (p90) cc_final: 0.8250 (p90) REVERT: H 103 LYS cc_start: 0.9569 (ttpp) cc_final: 0.9361 (tttp) REVERT: H 116 TYR cc_start: 0.8622 (m-80) cc_final: 0.8154 (m-80) REVERT: H 118 PHE cc_start: 0.8892 (m-80) cc_final: 0.8095 (m-80) REVERT: I 9 PHE cc_start: 0.8761 (m-80) cc_final: 0.8539 (m-80) REVERT: I 37 TYR cc_start: 0.7951 (m-10) cc_final: 0.7686 (m-10) REVERT: I 64 LYS cc_start: 0.9433 (mtpp) cc_final: 0.8854 (mtpp) REVERT: J 17 LYS cc_start: 0.9311 (mmtt) cc_final: 0.9058 (mmmt) REVERT: J 28 ASP cc_start: 0.8819 (t70) cc_final: 0.8546 (t0) REVERT: J 49 MET cc_start: 0.9440 (tpp) cc_final: 0.8650 (tpp) REVERT: K 67 GLU cc_start: 0.8497 (tm-30) cc_final: 0.7739 (tm-30) REVERT: K 100 LEU cc_start: 0.8054 (mt) cc_final: 0.7836 (mp) REVERT: K 102 ASN cc_start: 0.8266 (p0) cc_final: 0.7934 (p0) REVERT: K 125 MET cc_start: 0.8611 (mtt) cc_final: 0.8261 (mmt) REVERT: L 33 GLU cc_start: 0.8706 (mm-30) cc_final: 0.8471 (mm-30) REVERT: L 53 HIS cc_start: 0.8940 (t70) cc_final: 0.8085 (t70) REVERT: L 55 ILE cc_start: 0.9639 (mm) cc_final: 0.9408 (mm) REVERT: M 12 ILE cc_start: 0.8790 (mm) cc_final: 0.8550 (mm) REVERT: M 23 VAL cc_start: 0.9113 (t) cc_final: 0.8823 (t) REVERT: M 26 PHE cc_start: 0.8321 (m-10) cc_final: 0.7733 (m-10) REVERT: M 30 PHE cc_start: 0.9153 (t80) cc_final: 0.8571 (t80) REVERT: M 38 PHE cc_start: 0.9374 (m-10) cc_final: 0.9162 (m-80) REVERT: M 41 TYR cc_start: 0.8631 (m-80) cc_final: 0.8204 (m-80) REVERT: N 29 PHE cc_start: 0.9295 (m-80) cc_final: 0.8456 (m-80) REVERT: N 52 GLN cc_start: 0.8826 (mp10) cc_final: 0.8441 (mp10) REVERT: N 85 HIS cc_start: 0.8538 (m90) cc_final: 0.8283 (m90) REVERT: N 117 GLU cc_start: 0.8732 (tt0) cc_final: 0.8487 (tm-30) REVERT: N 119 LEU cc_start: 0.8880 (mm) cc_final: 0.8524 (tp) REVERT: O 293 TYR cc_start: 0.8422 (t80) cc_final: 0.8070 (t80) REVERT: O 356 GLU cc_start: 0.7649 (pm20) cc_final: 0.7261 (pm20) REVERT: O 463 LEU cc_start: 0.9038 (pt) cc_final: 0.8768 (mm) REVERT: O 467 PHE cc_start: 0.9611 (m-80) cc_final: 0.9215 (m-80) REVERT: O 471 MET cc_start: 0.6200 (mtm) cc_final: 0.3544 (mmm) REVERT: O 537 PHE cc_start: 0.9498 (p90) cc_final: 0.8854 (p90) REVERT: P 227 TYR cc_start: 0.8085 (m-80) cc_final: 0.7591 (m-80) REVERT: P 238 HIS cc_start: 0.9435 (m-70) cc_final: 0.9117 (m90) REVERT: P 254 LEU cc_start: 0.9754 (tp) cc_final: 0.9377 (tp) REVERT: P 258 MET cc_start: 0.8763 (ptt) cc_final: 0.8210 (ptt) REVERT: P 317 MET cc_start: 0.8879 (tpt) cc_final: 0.8578 (tpt) REVERT: P 381 MET cc_start: 0.9366 (mmp) cc_final: 0.9052 (mmm) REVERT: P 402 MET cc_start: 0.8258 (mpp) cc_final: 0.8040 (mpp) REVERT: P 411 ARG cc_start: 0.9120 (mpt180) cc_final: 0.8640 (mmt180) REVERT: P 413 LEU cc_start: 0.9798 (mt) cc_final: 0.9576 (mt) REVERT: Q 157 MET cc_start: 0.4105 (ttm) cc_final: 0.3764 (ttm) REVERT: Q 173 MET cc_start: 0.9058 (mpp) cc_final: 0.8749 (mpp) REVERT: Q 212 HIS cc_start: 0.9345 (m-70) cc_final: 0.8816 (m-70) REVERT: Q 251 TRP cc_start: 0.7217 (p-90) cc_final: 0.6069 (p-90) REVERT: Q 259 ASP cc_start: 0.9306 (t0) cc_final: 0.9080 (t70) REVERT: Q 274 MET cc_start: 0.9457 (tpt) cc_final: 0.8763 (tpp) REVERT: Q 308 PHE cc_start: 0.8922 (p90) cc_final: 0.8358 (p90) REVERT: Q 365 TRP cc_start: 0.9087 (m100) cc_final: 0.7967 (m100) outliers start: 4 outliers final: 0 residues processed: 913 average time/residue: 0.2306 time to fit residues: 353.4968 Evaluate side-chains 723 residues out of total 4950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 723 time to evaluate : 1.724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 556 random chunks: chunk 188 optimal weight: 9.9990 chunk 278 optimal weight: 0.0770 chunk 3 optimal weight: 10.0000 chunk 144 optimal weight: 9.9990 chunk 17 optimal weight: 30.0000 chunk 87 optimal weight: 10.0000 chunk 74 optimal weight: 10.0000 chunk 534 optimal weight: 6.9990 chunk 149 optimal weight: 4.9990 chunk 538 optimal weight: 6.9990 chunk 334 optimal weight: 20.0000 overall best weight: 5.8146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 636 HIS A 880 GLN ** B 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 462 GLN ** B 532 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 575 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 636 GLN B 755 ASN ** B1041 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 99 HIS ** G 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 346 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 757 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 287 ASN Q 319 ASN ** Q 372 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 407 HIS ** 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 = 0.3795 r_free = 0.3795 target = 0.089545 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.069537 restraints weight = 239076.454| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.071368 restraints weight = 128284.482| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.072568 restraints weight = 82777.652| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.073305 restraints weight = 60683.588| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.073612 restraints weight = 49869.235| |-----------------------------------------------------------------------------| r_work (final): 0.3337 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7476 moved from start: 0.6329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.089 47692 Z= 0.232 Angle : 0.853 41.396 64864 Z= 0.423 Chirality : 0.048 0.730 7252 Planarity : 0.006 0.099 7976 Dihedral : 14.157 176.990 7147 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 21.15 Ramachandran Plot: Outliers : 0.68 % Allowed : 7.53 % Favored : 91.79 % Rotamer: Outliers : 0.12 % Allowed : 2.51 % Favored : 97.37 % 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 aren not related in a simple way. whole: -1.11 (0.11), residues: 5432 helix: 0.35 (0.11), residues: 1951 sheet: -1.02 (0.18), residues: 751 loop : -1.46 (0.12), residues: 2730 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.024 0.001 ARG O 475 TYR 0.034 0.002 TYR K 78 PHE 0.106 0.002 PHE Q 358 TRP 0.052 0.002 TRP N 54 HIS 0.010 0.001 HIS Q 409 Details of bonding type rmsd covalent geometry : bond 0.00497 (47647) covalent geometry : angle 0.80719 (64831) hydrogen bonds : bond 0.05211 ( 1994) hydrogen bonds : angle 6.03885 ( 5479) metal coordination : bond 0.01879 ( 24) metal coordination : angle 12.28541 ( 33) Misc. bond : bond 0.01020 ( 21) *********************** 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 904 residues out of total 4950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 898 time to evaluate : 1.478 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: A 213 ASN cc_start: 0.9252 (t0) cc_final: 0.9013 (t0) REVERT: A 223 PHE cc_start: 0.9051 (t80) cc_final: 0.8836 (t80) REVERT: A 226 LYS cc_start: 0.9430 (mmpt) cc_final: 0.8961 (mmmt) REVERT: A 325 ASP cc_start: 0.8736 (t70) cc_final: 0.8486 (m-30) REVERT: A 339 PHE cc_start: 0.8953 (m-80) cc_final: 0.8390 (m-80) REVERT: A 437 PHE cc_start: 0.9227 (t80) cc_final: 0.8977 (t80) REVERT: A 466 LEU cc_start: 0.9338 (tt) cc_final: 0.9078 (tt) REVERT: A 470 HIS cc_start: 0.8631 (m-70) cc_final: 0.8413 (m-70) REVERT: A 589 MET cc_start: 0.8580 (mmm) cc_final: 0.8328 (mmm) REVERT: A 618 TYR cc_start: 0.8666 (m-80) cc_final: 0.8449 (m-80) REVERT: A 654 ASP cc_start: 0.8470 (m-30) cc_final: 0.8245 (m-30) REVERT: A 736 LEU cc_start: 0.9676 (mt) cc_final: 0.9475 (mt) REVERT: A 830 MET cc_start: 0.8819 (mmm) cc_final: 0.8585 (mmm) REVERT: A 925 MET cc_start: 0.9475 (tpt) cc_final: 0.9041 (tmm) REVERT: A 943 ILE cc_start: 0.9625 (mt) cc_final: 0.9346 (pt) REVERT: A 947 LEU cc_start: 0.9202 (mp) cc_final: 0.8885 (mp) REVERT: A 1007 ILE cc_start: -0.4626 (mt) cc_final: -0.5154 (mt) REVERT: A 1008 ASP cc_start: -0.1346 (m-30) cc_final: -0.1561 (m-30) REVERT: A 1009 THR cc_start: 0.0783 (m) cc_final: 0.0481 (m) REVERT: A 1019 LEU cc_start: -0.3608 (tp) cc_final: -0.3958 (tp) REVERT: A 1092 GLU cc_start: 0.9308 (mt-10) cc_final: 0.9037 (mp0) REVERT: A 1183 GLU cc_start: 0.8342 (tp30) cc_final: 0.8005 (tp30) REVERT: A 1185 VAL cc_start: 0.9502 (m) cc_final: 0.9020 (t) REVERT: A 1476 LEU cc_start: 0.9178 (mt) cc_final: 0.8924 (mt) REVERT: A 1490 GLU cc_start: 0.9235 (mt-10) cc_final: 0.8800 (mm-30) REVERT: A 1504 ILE cc_start: 0.9313 (mm) cc_final: 0.9083 (mm) REVERT: A 1505 ASP cc_start: 0.8014 (t0) cc_final: 0.7325 (t70) REVERT: A 1519 LEU cc_start: 0.9501 (mt) cc_final: 0.9204 (mt) REVERT: A 1565 GLU cc_start: 0.8622 (mm-30) cc_final: 0.8392 (mt-10) REVERT: A 1587 ASP cc_start: 0.8962 (m-30) cc_final: 0.8516 (m-30) REVERT: A 1589 MET cc_start: 0.9364 (mtt) cc_final: 0.9041 (mmm) REVERT: A 1610 PHE cc_start: 0.9504 (m-80) cc_final: 0.9030 (m-80) REVERT: A 1616 GLU cc_start: 0.7553 (tt0) cc_final: 0.6926 (tm-30) REVERT: A 1620 GLN cc_start: 0.9157 (mp10) cc_final: 0.8676 (mp10) REVERT: A 1621 PHE cc_start: 0.9338 (m-80) cc_final: 0.8798 (m-80) REVERT: A 1657 LEU cc_start: 0.8717 (tp) cc_final: 0.8317 (tp) REVERT: A 1659 LYS cc_start: 0.9139 (mtpt) cc_final: 0.8399 (mtmm) REVERT: B 80 ASN cc_start: -0.0004 (p0) cc_final: -0.0437 (t0) REVERT: B 98 SER cc_start: 0.9251 (p) cc_final: 0.8738 (m) REVERT: B 125 GLU cc_start: 0.9216 (pt0) cc_final: 0.8867 (pm20) REVERT: B 136 LYS cc_start: 0.9015 (ttmt) cc_final: 0.8426 (tptm) REVERT: B 138 LEU cc_start: 0.9242 (mm) cc_final: 0.9031 (mm) REVERT: B 174 LYS cc_start: 0.9156 (mmpt) cc_final: 0.8898 (mmmt) REVERT: B 188 ASP cc_start: 0.8957 (m-30) cc_final: 0.8609 (m-30) REVERT: B 205 MET cc_start: 0.8563 (mtp) cc_final: 0.8306 (mtp) REVERT: B 206 LEU cc_start: 0.9400 (tp) cc_final: 0.9172 (tp) REVERT: B 215 MET cc_start: 0.7467 (mtt) cc_final: 0.7090 (mtt) REVERT: B 224 ASN cc_start: 0.8669 (m110) cc_final: 0.8431 (m110) REVERT: B 242 ASP cc_start: 0.8994 (p0) cc_final: 0.7308 (p0) REVERT: B 275 MET cc_start: 0.9162 (ttm) cc_final: 0.8945 (ttm) REVERT: B 285 ASP cc_start: 0.8827 (m-30) cc_final: 0.8530 (m-30) REVERT: B 289 PHE cc_start: 0.9158 (t80) cc_final: 0.8913 (t80) REVERT: B 304 ASP cc_start: 0.9493 (m-30) cc_final: 0.9066 (p0) REVERT: B 411 MET cc_start: 0.9262 (mtp) cc_final: 0.9017 (mtp) REVERT: B 414 LYS cc_start: 0.9643 (ttpp) cc_final: 0.9058 (ttpp) REVERT: B 422 GLN cc_start: 0.9218 (tm-30) cc_final: 0.8982 (tm-30) REVERT: B 486 VAL cc_start: 0.9411 (t) cc_final: 0.9109 (p) REVERT: B 489 GLU cc_start: 0.8415 (tt0) cc_final: 0.8213 (tt0) REVERT: B 496 PHE cc_start: 0.9101 (t80) cc_final: 0.8578 (t80) REVERT: B 515 THR cc_start: 0.9242 (p) cc_final: 0.9003 (t) REVERT: B 543 ASN cc_start: 0.8875 (m-40) cc_final: 0.8641 (m-40) REVERT: B 575 HIS cc_start: 0.8377 (m-70) cc_final: 0.8015 (m90) REVERT: B 668 GLU cc_start: 0.8313 (pt0) cc_final: 0.8082 (pt0) REVERT: B 671 TYR cc_start: 0.9028 (m-80) cc_final: 0.8545 (m-10) REVERT: B 783 MET cc_start: 0.7669 (mmm) cc_final: 0.7237 (mmm) REVERT: B 908 ARG cc_start: 0.8070 (ptm160) cc_final: 0.7192 (ptm160) REVERT: B 958 MET cc_start: 0.8774 (mtt) cc_final: 0.8558 (mtt) REVERT: B 962 MET cc_start: 0.9005 (ttm) cc_final: 0.8673 (ttm) REVERT: B 982 THR cc_start: 0.9352 (m) cc_final: 0.9061 (p) REVERT: B 1074 MET cc_start: 0.8292 (ttm) cc_final: 0.7988 (ttp) REVERT: B 1075 GLU cc_start: 0.8606 (mp0) cc_final: 0.8332 (mp0) REVERT: B 1086 PHE cc_start: 0.7549 (m-80) cc_final: 0.6970 (m-80) REVERT: B 1157 GLN cc_start: 0.9396 (mp-120) cc_final: 0.9097 (mp10) REVERT: C 71 MET cc_start: 0.9235 (mtp) cc_final: 0.8634 (mmm) REVERT: C 95 GLU cc_start: 0.8303 (mt-10) cc_final: 0.7304 (mt-10) REVERT: C 273 ASP cc_start: 0.8333 (t70) cc_final: 0.8006 (t70) REVERT: E 75 MET cc_start: 0.7470 (ttp) cc_final: 0.7000 (tmm) REVERT: E 140 LEU cc_start: 0.9340 (mm) cc_final: 0.9059 (mm) REVERT: E 215 MET cc_start: 0.8754 (mmt) cc_final: 0.8447 (mmm) REVERT: F 88 TYR cc_start: 0.8361 (m-80) cc_final: 0.7750 (m-80) REVERT: F 90 ARG cc_start: 0.9447 (ptm-80) cc_final: 0.8995 (ttp80) REVERT: F 99 LEU cc_start: 0.9561 (tp) cc_final: 0.9350 (tp) REVERT: F 122 MET cc_start: 0.9130 (mtp) cc_final: 0.8741 (mtp) REVERT: F 136 ARG cc_start: 0.8047 (mtt180) cc_final: 0.7671 (mtt180) REVERT: F 151 LEU cc_start: 0.9161 (mm) cc_final: 0.8498 (tp) REVERT: G 71 MET cc_start: 0.8420 (ttm) cc_final: 0.7984 (ttm) REVERT: G 98 GLU cc_start: 0.8403 (mm-30) cc_final: 0.8051 (mp0) REVERT: G 166 TRP cc_start: 0.7553 (m100) cc_final: 0.7250 (m-90) REVERT: H 45 GLU cc_start: 0.8692 (tm-30) cc_final: 0.8373 (tm-30) REVERT: H 102 TYR cc_start: 0.8815 (p90) cc_final: 0.8289 (p90) REVERT: H 116 TYR cc_start: 0.8605 (m-80) cc_final: 0.8172 (m-80) REVERT: H 118 PHE cc_start: 0.8909 (m-80) cc_final: 0.8152 (m-80) REVERT: I 37 TYR cc_start: 0.7961 (m-10) cc_final: 0.7613 (m-10) REVERT: I 64 LYS cc_start: 0.9435 (mtpp) cc_final: 0.8881 (mtpp) REVERT: J 17 LYS cc_start: 0.9273 (mmtt) cc_final: 0.9067 (mmmt) REVERT: J 28 ASP cc_start: 0.8777 (t70) cc_final: 0.8562 (t0) REVERT: J 49 MET cc_start: 0.9479 (tpp) cc_final: 0.8649 (tpp) REVERT: K 67 GLU cc_start: 0.8397 (tm-30) cc_final: 0.7230 (tm-30) REVERT: K 100 LEU cc_start: 0.7970 (mt) cc_final: 0.7769 (mp) REVERT: K 102 ASN cc_start: 0.8274 (p0) cc_final: 0.7950 (p0) REVERT: K 125 MET cc_start: 0.8656 (mtt) cc_final: 0.8270 (mmt) REVERT: L 33 GLU cc_start: 0.8749 (mm-30) cc_final: 0.8486 (mm-30) REVERT: L 53 HIS cc_start: 0.9009 (t70) cc_final: 0.8080 (t70) REVERT: L 68 GLU cc_start: 0.7212 (tm-30) cc_final: 0.6868 (tm-30) REVERT: M 12 ILE cc_start: 0.8822 (mm) cc_final: 0.8582 (mm) REVERT: M 23 VAL cc_start: 0.9136 (t) cc_final: 0.8880 (t) REVERT: M 26 PHE cc_start: 0.8296 (m-10) cc_final: 0.7732 (m-10) REVERT: M 30 PHE cc_start: 0.9210 (t80) cc_final: 0.8671 (t80) REVERT: M 38 PHE cc_start: 0.9271 (m-10) cc_final: 0.9054 (m-80) REVERT: M 41 TYR cc_start: 0.8707 (m-80) cc_final: 0.8315 (m-80) REVERT: N 29 PHE cc_start: 0.9216 (m-80) cc_final: 0.8520 (m-80) REVERT: N 85 HIS cc_start: 0.8507 (m90) cc_final: 0.8258 (m90) REVERT: N 117 GLU cc_start: 0.8750 (tt0) cc_final: 0.8510 (tm-30) REVERT: N 119 LEU cc_start: 0.8825 (mm) cc_final: 0.8522 (tp) REVERT: O 293 TYR cc_start: 0.8478 (t80) cc_final: 0.8110 (t80) REVERT: O 356 GLU cc_start: 0.7755 (pm20) cc_final: 0.7331 (pm20) REVERT: O 463 LEU cc_start: 0.9056 (pt) cc_final: 0.8740 (mm) REVERT: O 467 PHE cc_start: 0.9613 (m-80) cc_final: 0.9124 (m-80) REVERT: O 537 PHE cc_start: 0.9498 (p90) cc_final: 0.8746 (p90) REVERT: O 538 LEU cc_start: 0.9649 (mp) cc_final: 0.9276 (mt) REVERT: P 227 TYR cc_start: 0.8358 (m-80) cc_final: 0.7877 (m-80) REVERT: P 238 HIS cc_start: 0.9435 (m-70) cc_final: 0.9165 (m90) REVERT: P 254 LEU cc_start: 0.9773 (tp) cc_final: 0.9358 (tp) REVERT: P 258 MET cc_start: 0.8828 (ptt) cc_final: 0.8334 (ptt) REVERT: P 317 MET cc_start: 0.8805 (tpt) cc_final: 0.8490 (tpt) REVERT: P 381 MET cc_start: 0.9366 (mmp) cc_final: 0.9035 (mmm) REVERT: P 402 MET cc_start: 0.8317 (mpp) cc_final: 0.8086 (mpp) REVERT: P 404 ILE cc_start: 0.9196 (mt) cc_final: 0.8850 (tt) REVERT: P 411 ARG cc_start: 0.9124 (mpt180) cc_final: 0.8827 (mmt180) REVERT: P 413 LEU cc_start: 0.9824 (mt) cc_final: 0.9604 (mt) REVERT: P 491 PHE cc_start: 0.8687 (m-10) cc_final: 0.8355 (m-80) REVERT: Q 157 MET cc_start: 0.4189 (ttm) cc_final: 0.3878 (ttm) REVERT: Q 212 HIS cc_start: 0.9348 (m-70) cc_final: 0.8842 (m-70) REVERT: Q 236 PHE cc_start: 0.9396 (t80) cc_final: 0.9186 (t80) REVERT: Q 251 TRP cc_start: 0.7182 (p-90) cc_final: 0.5960 (p-90) REVERT: Q 259 ASP cc_start: 0.9345 (t0) cc_final: 0.9130 (t70) REVERT: Q 274 MET cc_start: 0.9373 (tpt) cc_final: 0.8822 (tpp) REVERT: Q 308 PHE cc_start: 0.8886 (p90) cc_final: 0.8354 (p90) REVERT: Q 363 GLU cc_start: 0.8944 (mm-30) cc_final: 0.8423 (tm-30) REVERT: Q 365 TRP cc_start: 0.9113 (m100) cc_final: 0.7941 (m100) outliers start: 6 outliers final: 3 residues processed: 904 average time/residue: 0.2225 time to fit residues: 335.0845 Evaluate side-chains 709 residues out of total 4950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 706 time to evaluate : 1.610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 556 random chunks: chunk 135 optimal weight: 9.9990 chunk 363 optimal weight: 7.9990 chunk 440 optimal weight: 9.9990 chunk 66 optimal weight: 9.9990 chunk 327 optimal weight: 5.9990 chunk 260 optimal weight: 20.0000 chunk 286 optimal weight: 0.0040 chunk 115 optimal weight: 7.9990 chunk 133 optimal weight: 9.9990 chunk 378 optimal weight: 20.0000 chunk 118 optimal weight: 6.9990 overall best weight: 5.8000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 649 ASN ** B 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 351 GLN ** B 532 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 575 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 673 ASN ** B1041 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 346 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 757 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 319 ASN ** Q 372 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 407 HIS ** 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 = 0.3788 r_free = 0.3788 target = 0.089396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.069234 restraints weight = 239077.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.071085 restraints weight = 129428.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.072214 restraints weight = 84316.161| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.072919 restraints weight = 62628.991| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.073440 restraints weight = 51467.385| |-----------------------------------------------------------------------------| r_work (final): 0.3332 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7475 moved from start: 0.6573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.086 47692 Z= 0.229 Angle : 0.852 39.093 64864 Z= 0.423 Chirality : 0.048 0.475 7252 Planarity : 0.006 0.109 7976 Dihedral : 14.152 177.274 7147 Min Nonbonded Distance : 1.878 Molprobity Statistics. All-atom Clashscore : 21.63 Ramachandran Plot: Outliers : 0.64 % Allowed : 7.73 % Favored : 91.62 % Rotamer: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Cbeta Deviations : 0.02 % 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 aren not related in a simple way. whole: -1.12 (0.11), residues: 5432 helix: 0.33 (0.11), residues: 1965 sheet: -1.02 (0.18), residues: 746 loop : -1.46 (0.12), residues: 2721 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG D 91 TYR 0.035 0.002 TYR K 78 PHE 0.104 0.002 PHE Q 358 TRP 0.037 0.002 TRP N 54 HIS 0.008 0.001 HIS Q 372 Details of bonding type rmsd covalent geometry : bond 0.00491 (47647) covalent geometry : angle 0.81120 (64831) hydrogen bonds : bond 0.05143 ( 1994) hydrogen bonds : angle 6.02599 ( 5479) metal coordination : bond 0.01889 ( 24) metal coordination : angle 11.58314 ( 33) Misc. bond : bond 0.00993 ( 21) *********************** 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 875 residues out of total 4950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 875 time to evaluate : 1.896 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: A 5 LYS cc_start: 0.9052 (ttmm) cc_final: 0.8780 (ttmt) REVERT: A 97 TYR cc_start: 0.9178 (m-80) cc_final: 0.8834 (m-80) REVERT: A 115 VAL cc_start: 0.9412 (t) cc_final: 0.9138 (p) REVERT: A 213 ASN cc_start: 0.9223 (t0) cc_final: 0.8931 (t0) REVERT: A 214 ASP cc_start: 0.9263 (t70) cc_final: 0.8700 (t0) REVERT: A 218 LYS cc_start: 0.9514 (ptpp) cc_final: 0.9125 (pttt) REVERT: A 226 LYS cc_start: 0.9535 (mmpt) cc_final: 0.9039 (mmmt) REVERT: A 339 PHE cc_start: 0.8905 (m-80) cc_final: 0.8451 (m-80) REVERT: A 437 PHE cc_start: 0.9293 (t80) cc_final: 0.9049 (t80) REVERT: A 466 LEU cc_start: 0.9312 (tt) cc_final: 0.8952 (tt) REVERT: A 589 MET cc_start: 0.8657 (mmm) cc_final: 0.8287 (mmm) REVERT: A 618 TYR cc_start: 0.8639 (m-80) cc_final: 0.8184 (m-80) REVERT: A 654 ASP cc_start: 0.8557 (m-30) cc_final: 0.8312 (m-30) REVERT: A 830 MET cc_start: 0.8849 (mmm) cc_final: 0.8621 (mmm) REVERT: A 925 MET cc_start: 0.9495 (tpt) cc_final: 0.9029 (tmm) REVERT: A 943 ILE cc_start: 0.9626 (mt) cc_final: 0.9373 (pt) REVERT: A 947 LEU cc_start: 0.9253 (mp) cc_final: 0.8952 (mp) REVERT: A 960 MET cc_start: 0.7841 (mtp) cc_final: 0.7470 (mtp) REVERT: A 1007 ILE cc_start: -0.4850 (mt) cc_final: -0.5236 (mt) REVERT: A 1060 GLU cc_start: 0.8807 (tm-30) cc_final: 0.8526 (tm-30) REVERT: A 1092 GLU cc_start: 0.9297 (mt-10) cc_final: 0.9064 (mp0) REVERT: A 1183 GLU cc_start: 0.8398 (tp30) cc_final: 0.8002 (tp30) REVERT: A 1185 VAL cc_start: 0.9551 (m) cc_final: 0.9070 (t) REVERT: A 1238 MET cc_start: 0.7733 (ttm) cc_final: 0.7324 (mtp) REVERT: A 1294 MET cc_start: 0.9239 (ptp) cc_final: 0.8925 (ptp) REVERT: A 1476 LEU cc_start: 0.9160 (mt) cc_final: 0.8904 (mt) REVERT: A 1490 GLU cc_start: 0.9241 (mt-10) cc_final: 0.8963 (mm-30) REVERT: A 1504 ILE cc_start: 0.9260 (mm) cc_final: 0.8977 (mm) REVERT: A 1505 ASP cc_start: 0.8175 (t0) cc_final: 0.7419 (t70) REVERT: A 1519 LEU cc_start: 0.9454 (mt) cc_final: 0.9174 (mt) REVERT: A 1565 GLU cc_start: 0.8688 (mm-30) cc_final: 0.8434 (mt-10) REVERT: A 1587 ASP cc_start: 0.8998 (m-30) cc_final: 0.8542 (m-30) REVERT: A 1589 MET cc_start: 0.9381 (mtt) cc_final: 0.9043 (mmm) REVERT: A 1610 PHE cc_start: 0.9481 (m-80) cc_final: 0.8996 (m-80) REVERT: A 1616 GLU cc_start: 0.7540 (tt0) cc_final: 0.6869 (tm-30) REVERT: A 1619 CYS cc_start: 0.8796 (m) cc_final: 0.8520 (m) REVERT: A 1620 GLN cc_start: 0.9222 (mp10) cc_final: 0.8715 (mp10) REVERT: A 1621 PHE cc_start: 0.9349 (m-80) cc_final: 0.8752 (m-80) REVERT: A 1657 LEU cc_start: 0.8797 (tp) cc_final: 0.8441 (tp) REVERT: B 80 ASN cc_start: -0.0034 (p0) cc_final: -0.0253 (t0) REVERT: B 98 SER cc_start: 0.9237 (p) cc_final: 0.8744 (m) REVERT: B 136 LYS cc_start: 0.8978 (ttmt) cc_final: 0.8390 (tptm) REVERT: B 174 LYS cc_start: 0.9212 (mmpt) cc_final: 0.8877 (mmmt) REVERT: B 206 LEU cc_start: 0.9421 (tp) cc_final: 0.9200 (tp) REVERT: B 215 MET cc_start: 0.7490 (mtt) cc_final: 0.7114 (mtt) REVERT: B 224 ASN cc_start: 0.8659 (m110) cc_final: 0.8380 (m110) REVERT: B 242 ASP cc_start: 0.9079 (p0) cc_final: 0.7482 (p0) REVERT: B 275 MET cc_start: 0.9275 (ttm) cc_final: 0.9069 (ttm) REVERT: B 304 ASP cc_start: 0.9501 (m-30) cc_final: 0.9086 (p0) REVERT: B 411 MET cc_start: 0.9270 (mtp) cc_final: 0.9003 (mtp) REVERT: B 414 LYS cc_start: 0.9664 (ttpp) cc_final: 0.9104 (ttpp) REVERT: B 422 GLN cc_start: 0.9321 (tm-30) cc_final: 0.9092 (tm-30) REVERT: B 470 LEU cc_start: 0.9169 (mp) cc_final: 0.8853 (tt) REVERT: B 486 VAL cc_start: 0.9355 (t) cc_final: 0.9044 (p) REVERT: B 496 PHE cc_start: 0.9084 (t80) cc_final: 0.8576 (t80) REVERT: B 515 THR cc_start: 0.9271 (p) cc_final: 0.9031 (t) REVERT: B 543 ASN cc_start: 0.8891 (m-40) cc_final: 0.8629 (m-40) REVERT: B 575 HIS cc_start: 0.8440 (m-70) cc_final: 0.8128 (m-70) REVERT: B 668 GLU cc_start: 0.8355 (pt0) cc_final: 0.7965 (pt0) REVERT: B 671 TYR cc_start: 0.9001 (m-80) cc_final: 0.8702 (m-10) REVERT: B 800 TYR cc_start: 0.7753 (t80) cc_final: 0.6739 (t80) REVERT: B 936 MET cc_start: 0.9351 (ttt) cc_final: 0.9012 (tmm) REVERT: B 958 MET cc_start: 0.8921 (mtt) cc_final: 0.8611 (mtt) REVERT: B 965 GLU cc_start: 0.9045 (tm-30) cc_final: 0.8681 (tm-30) REVERT: B 1034 GLN cc_start: 0.9262 (pt0) cc_final: 0.8960 (pt0) REVERT: B 1074 MET cc_start: 0.8248 (ttm) cc_final: 0.7944 (ttp) REVERT: B 1075 GLU cc_start: 0.8686 (mp0) cc_final: 0.8182 (mm-30) REVERT: B 1086 PHE cc_start: 0.7591 (m-80) cc_final: 0.7114 (m-80) REVERT: B 1157 GLN cc_start: 0.9429 (mp-120) cc_final: 0.9143 (mp10) REVERT: C 71 MET cc_start: 0.9330 (mtp) cc_final: 0.8751 (mmm) REVERT: C 97 LEU cc_start: 0.9678 (tp) cc_final: 0.9473 (tp) REVERT: C 273 ASP cc_start: 0.8367 (t70) cc_final: 0.8081 (t70) REVERT: E 116 ILE cc_start: 0.9130 (pt) cc_final: 0.8737 (pt) REVERT: E 140 LEU cc_start: 0.9333 (mm) cc_final: 0.9048 (mm) REVERT: F 88 TYR cc_start: 0.8325 (m-80) cc_final: 0.7656 (m-80) REVERT: F 90 ARG cc_start: 0.9427 (ptm-80) cc_final: 0.9132 (ttp80) REVERT: F 122 MET cc_start: 0.9115 (mtp) cc_final: 0.8692 (mtp) REVERT: F 136 ARG cc_start: 0.8036 (mtt180) cc_final: 0.7662 (mtt180) REVERT: G 75 ASN cc_start: 0.9320 (p0) cc_final: 0.8688 (t0) REVERT: G 98 GLU cc_start: 0.8426 (mm-30) cc_final: 0.8097 (mp0) REVERT: G 166 TRP cc_start: 0.7607 (m100) cc_final: 0.7251 (m-90) REVERT: H 45 GLU cc_start: 0.8693 (tm-30) cc_final: 0.8360 (tm-30) REVERT: H 116 TYR cc_start: 0.8645 (m-80) cc_final: 0.8201 (m-80) REVERT: H 118 PHE cc_start: 0.8866 (m-80) cc_final: 0.8024 (m-80) REVERT: I 64 LYS cc_start: 0.9342 (mtpp) cc_final: 0.8838 (mtpp) REVERT: J 28 ASP cc_start: 0.8769 (t70) cc_final: 0.8555 (t0) REVERT: J 49 MET cc_start: 0.9523 (tpp) cc_final: 0.8668 (tpp) REVERT: J 58 GLU cc_start: 0.9166 (tp30) cc_final: 0.8833 (tm-30) REVERT: K 46 LYS cc_start: 0.7869 (tptt) cc_final: 0.7356 (tptm) REVERT: K 67 GLU cc_start: 0.8522 (tm-30) cc_final: 0.7358 (tm-30) REVERT: K 102 ASN cc_start: 0.8387 (p0) cc_final: 0.8144 (p0) REVERT: K 125 MET cc_start: 0.8718 (mtt) cc_final: 0.8355 (mmt) REVERT: L 33 GLU cc_start: 0.8847 (mm-30) cc_final: 0.8494 (mm-30) REVERT: L 53 HIS cc_start: 0.8938 (t70) cc_final: 0.8124 (t70) REVERT: L 68 GLU cc_start: 0.7032 (tm-30) cc_final: 0.6654 (tm-30) REVERT: M 12 ILE cc_start: 0.8758 (mm) cc_final: 0.8539 (mm) REVERT: M 26 PHE cc_start: 0.8246 (m-10) cc_final: 0.7356 (m-10) REVERT: M 30 PHE cc_start: 0.9225 (t80) cc_final: 0.8586 (t80) REVERT: M 38 PHE cc_start: 0.9085 (m-10) cc_final: 0.8837 (m-80) REVERT: M 41 TYR cc_start: 0.8732 (m-80) cc_final: 0.8354 (m-80) REVERT: N 29 PHE cc_start: 0.9253 (m-80) cc_final: 0.8464 (m-80) REVERT: N 52 GLN cc_start: 0.8801 (mp10) cc_final: 0.8340 (mp10) REVERT: N 117 GLU cc_start: 0.8830 (tt0) cc_final: 0.8607 (tm-30) REVERT: N 119 LEU cc_start: 0.8810 (mm) cc_final: 0.8507 (tp) REVERT: O 293 TYR cc_start: 0.8561 (t80) cc_final: 0.8160 (t80) REVERT: O 356 GLU cc_start: 0.7679 (pm20) cc_final: 0.7161 (pm20) REVERT: O 463 LEU cc_start: 0.9073 (pt) cc_final: 0.8724 (mm) REVERT: O 467 PHE cc_start: 0.9584 (m-80) cc_final: 0.9177 (m-80) REVERT: O 471 MET cc_start: 0.6108 (mtm) cc_final: 0.5679 (ptp) REVERT: O 537 PHE cc_start: 0.9548 (p90) cc_final: 0.9205 (p90) REVERT: P 118 TRP cc_start: 0.9052 (t60) cc_final: 0.8696 (t60) REVERT: P 227 TYR cc_start: 0.8137 (m-80) cc_final: 0.7489 (m-80) REVERT: P 238 HIS cc_start: 0.9449 (m-70) cc_final: 0.9206 (m90) REVERT: P 254 LEU cc_start: 0.9789 (tp) cc_final: 0.9404 (tp) REVERT: P 258 MET cc_start: 0.8867 (ptt) cc_final: 0.8379 (ptt) REVERT: P 381 MET cc_start: 0.9454 (mmp) cc_final: 0.9166 (mmm) REVERT: P 402 MET cc_start: 0.8477 (mpp) cc_final: 0.8199 (mpp) REVERT: P 404 ILE cc_start: 0.9250 (mt) cc_final: 0.8893 (tt) REVERT: P 411 ARG cc_start: 0.9163 (mpt180) cc_final: 0.8856 (mmt180) REVERT: P 413 LEU cc_start: 0.9846 (mt) cc_final: 0.9624 (mt) REVERT: P 434 HIS cc_start: 0.7674 (m-70) cc_final: 0.7447 (m-70) REVERT: P 491 PHE cc_start: 0.8716 (m-10) cc_final: 0.8329 (m-80) REVERT: Q 157 MET cc_start: 0.3887 (ttm) cc_final: 0.3540 (ttm) REVERT: Q 212 HIS cc_start: 0.9352 (m-70) cc_final: 0.8834 (m-70) REVERT: Q 251 TRP cc_start: 0.7238 (p-90) cc_final: 0.6027 (p-90) REVERT: Q 259 ASP cc_start: 0.9396 (t0) cc_final: 0.9164 (t70) REVERT: Q 274 MET cc_start: 0.9355 (tpt) cc_final: 0.8934 (tpp) REVERT: Q 308 PHE cc_start: 0.8798 (p90) cc_final: 0.8382 (p90) REVERT: Q 363 GLU cc_start: 0.9016 (mm-30) cc_final: 0.8549 (tm-30) REVERT: Q 365 TRP cc_start: 0.9026 (m100) cc_final: 0.7780 (m100) REVERT: Q 414 PHE cc_start: 0.9069 (m-10) cc_final: 0.8828 (m-80) outliers start: 0 outliers final: 0 residues processed: 875 average time/residue: 0.2368 time to fit residues: 346.0111 Evaluate side-chains 688 residues out of total 4950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 688 time to evaluate : 1.037 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 556 random chunks: chunk 369 optimal weight: 3.9990 chunk 92 optimal weight: 10.0000 chunk 56 optimal weight: 0.9990 chunk 517 optimal weight: 30.0000 chunk 390 optimal weight: 10.0000 chunk 119 optimal weight: 9.9990 chunk 97 optimal weight: 4.9990 chunk 483 optimal weight: 7.9990 chunk 60 optimal weight: 6.9990 chunk 7 optimal weight: 9.9990 chunk 139 optimal weight: 0.4980 overall best weight: 3.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 596 HIS B 45 HIS ** B 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 212 ASN ** B 532 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 547 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 575 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 702 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1041 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 99 HIS ** G 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 85 HIS ** O 346 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 757 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 319 ASN ** Q 372 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 407 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.089906 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.069850 restraints weight = 238066.544| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.071726 restraints weight = 129750.429| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.072865 restraints weight = 83701.442| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.073570 restraints weight = 61887.742| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.074090 restraints weight = 50894.220| |-----------------------------------------------------------------------------| r_work (final): 0.3348 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7451 moved from start: 0.6790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.099 47692 Z= 0.187 Angle : 0.834 35.534 64864 Z= 0.412 Chirality : 0.048 0.472 7252 Planarity : 0.006 0.260 7976 Dihedral : 14.104 176.831 7147 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 19.97 Ramachandran Plot: Outliers : 0.61 % Allowed : 7.49 % Favored : 91.90 % Rotamer: Outliers : 0.02 % Allowed : 1.27 % Favored : 98.71 % Cbeta Deviations : 0.02 % 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 aren not related in a simple way. whole: -1.02 (0.11), residues: 5432 helix: 0.46 (0.11), residues: 1958 sheet: -0.97 (0.18), residues: 743 loop : -1.44 (0.12), residues: 2731 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.044 0.001 ARG B 815 TYR 0.032 0.002 TYR K 78 PHE 0.107 0.002 PHE Q 358 TRP 0.040 0.002 TRP B 143 HIS 0.008 0.001 HIS E 99 Details of bonding type rmsd covalent geometry : bond 0.00406 (47647) covalent geometry : angle 0.80201 (64831) hydrogen bonds : bond 0.05055 ( 1994) hydrogen bonds : angle 5.87079 ( 5479) metal coordination : bond 0.01446 ( 24) metal coordination : angle 10.12846 ( 33) Misc. bond : bond 0.01165 ( 21) *********************** 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 885 residues out of total 4950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 884 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 5 LYS cc_start: 0.8973 (ttmm) cc_final: 0.8733 (ttmt) REVERT: A 97 TYR cc_start: 0.9209 (m-80) cc_final: 0.8885 (m-80) REVERT: A 213 ASN cc_start: 0.9261 (t0) cc_final: 0.8968 (t0) REVERT: A 214 ASP cc_start: 0.9284 (t70) cc_final: 0.8688 (t0) REVERT: A 215 GLU cc_start: 0.9125 (pm20) cc_final: 0.8789 (pm20) REVERT: A 218 LYS cc_start: 0.9514 (ptpp) cc_final: 0.9123 (pttt) REVERT: A 226 LYS cc_start: 0.9445 (mmpt) cc_final: 0.9002 (mmmt) REVERT: A 339 PHE cc_start: 0.8940 (m-80) cc_final: 0.8403 (m-80) REVERT: A 437 PHE cc_start: 0.9296 (t80) cc_final: 0.9053 (t80) REVERT: A 466 LEU cc_start: 0.9271 (tt) cc_final: 0.8973 (tt) REVERT: A 470 HIS cc_start: 0.8563 (m-70) cc_final: 0.8302 (m-70) REVERT: A 589 MET cc_start: 0.8634 (mmm) cc_final: 0.8407 (mmm) REVERT: A 640 ASN cc_start: 0.8793 (t0) cc_final: 0.8564 (t0) REVERT: A 654 ASP cc_start: 0.8491 (m-30) cc_final: 0.8238 (m-30) REVERT: A 738 ASN cc_start: 0.8731 (m-40) cc_final: 0.8065 (t0) REVERT: A 830 MET cc_start: 0.8824 (mmm) cc_final: 0.8623 (mmm) REVERT: A 925 MET cc_start: 0.9470 (tpt) cc_final: 0.9037 (tmm) REVERT: A 943 ILE cc_start: 0.9611 (mt) cc_final: 0.9364 (pt) REVERT: A 947 LEU cc_start: 0.9229 (mp) cc_final: 0.8902 (mp) REVERT: A 960 MET cc_start: 0.7766 (mtp) cc_final: 0.7538 (mtp) REVERT: A 1007 ILE cc_start: -0.4722 (mt) cc_final: -0.5057 (mt) REVERT: A 1060 GLU cc_start: 0.8834 (tm-30) cc_final: 0.8522 (tm-30) REVERT: A 1092 GLU cc_start: 0.9298 (mt-10) cc_final: 0.9065 (mp0) REVERT: A 1183 GLU cc_start: 0.8512 (tp30) cc_final: 0.7979 (tp30) REVERT: A 1185 VAL cc_start: 0.9453 (m) cc_final: 0.9050 (t) REVERT: A 1227 MET cc_start: 0.8745 (tpt) cc_final: 0.8144 (tpp) REVERT: A 1238 MET cc_start: 0.7720 (ttm) cc_final: 0.7198 (mtp) REVERT: A 1294 MET cc_start: 0.9287 (ptp) cc_final: 0.8983 (ptp) REVERT: A 1439 MET cc_start: 0.8223 (mmp) cc_final: 0.8014 (mmm) REVERT: A 1476 LEU cc_start: 0.9213 (mt) cc_final: 0.8932 (mt) REVERT: A 1490 GLU cc_start: 0.9243 (mt-10) cc_final: 0.8972 (mm-30) REVERT: A 1504 ILE cc_start: 0.9252 (mm) cc_final: 0.8952 (mm) REVERT: A 1505 ASP cc_start: 0.8071 (t0) cc_final: 0.7390 (t70) REVERT: A 1519 LEU cc_start: 0.9470 (mt) cc_final: 0.9181 (mt) REVERT: A 1565 GLU cc_start: 0.8623 (mm-30) cc_final: 0.8389 (mt-10) REVERT: A 1587 ASP cc_start: 0.8780 (m-30) cc_final: 0.8369 (m-30) REVERT: A 1589 MET cc_start: 0.9177 (mtt) cc_final: 0.8822 (mmm) REVERT: A 1610 PHE cc_start: 0.9461 (m-80) cc_final: 0.9037 (m-80) REVERT: A 1620 GLN cc_start: 0.9243 (mp10) cc_final: 0.8755 (mp10) REVERT: A 1621 PHE cc_start: 0.9314 (m-80) cc_final: 0.8791 (m-80) REVERT: A 1657 LEU cc_start: 0.8790 (tp) cc_final: 0.8496 (tp) REVERT: B 80 ASN cc_start: 0.0155 (p0) cc_final: -0.0153 (t0) REVERT: B 98 SER cc_start: 0.9072 (p) cc_final: 0.8645 (m) REVERT: B 136 LYS cc_start: 0.8967 (ttmt) cc_final: 0.8377 (tptm) REVERT: B 157 ASP cc_start: 0.9176 (p0) cc_final: 0.8667 (p0) REVERT: B 174 LYS cc_start: 0.9191 (mmpt) cc_final: 0.8826 (mmmt) REVERT: B 188 ASP cc_start: 0.8960 (m-30) cc_final: 0.8610 (m-30) REVERT: B 206 LEU cc_start: 0.9389 (tp) cc_final: 0.9074 (tp) REVERT: B 215 MET cc_start: 0.7488 (mtt) cc_final: 0.7089 (mtt) REVERT: B 224 ASN cc_start: 0.8646 (m110) cc_final: 0.8359 (m110) REVERT: B 242 ASP cc_start: 0.9094 (p0) cc_final: 0.7451 (p0) REVERT: B 275 MET cc_start: 0.9254 (ttm) cc_final: 0.9042 (ttm) REVERT: B 304 ASP cc_start: 0.9514 (m-30) cc_final: 0.9084 (p0) REVERT: B 330 LEU cc_start: 0.9633 (mt) cc_final: 0.9387 (mt) REVERT: B 411 MET cc_start: 0.9203 (mtp) cc_final: 0.8842 (mtp) REVERT: B 414 LYS cc_start: 0.9663 (ttpp) cc_final: 0.9093 (ttpp) REVERT: B 422 GLN cc_start: 0.9339 (tm-30) cc_final: 0.9093 (tm-30) REVERT: B 470 LEU cc_start: 0.9171 (mp) cc_final: 0.8849 (tt) REVERT: B 486 VAL cc_start: 0.9412 (t) cc_final: 0.9070 (p) REVERT: B 496 PHE cc_start: 0.9068 (t80) cc_final: 0.8553 (t80) REVERT: B 515 THR cc_start: 0.9238 (p) cc_final: 0.8994 (t) REVERT: B 543 ASN cc_start: 0.8880 (m-40) cc_final: 0.8629 (m-40) REVERT: B 556 SER cc_start: 0.7493 (p) cc_final: 0.6313 (t) REVERT: B 557 ASP cc_start: 0.7962 (m-30) cc_final: 0.7497 (m-30) REVERT: B 668 GLU cc_start: 0.8292 (pt0) cc_final: 0.7854 (pt0) REVERT: B 783 MET cc_start: 0.7507 (mmm) cc_final: 0.6904 (mmm) REVERT: B 936 MET cc_start: 0.9314 (ttt) cc_final: 0.9013 (tmm) REVERT: B 958 MET cc_start: 0.8907 (mtt) cc_final: 0.8594 (mtt) REVERT: B 965 GLU cc_start: 0.9088 (tm-30) cc_final: 0.8679 (tm-30) REVERT: B 1074 MET cc_start: 0.8071 (ttm) cc_final: 0.7785 (ttp) REVERT: B 1075 GLU cc_start: 0.8683 (mp0) cc_final: 0.8260 (mp0) REVERT: B 1086 PHE cc_start: 0.7410 (m-80) cc_final: 0.6959 (m-80) REVERT: B 1157 GLN cc_start: 0.9402 (mp-120) cc_final: 0.9174 (mp10) REVERT: C 71 MET cc_start: 0.9347 (mtp) cc_final: 0.8593 (mmm) REVERT: C 88 ASN cc_start: 0.8331 (t0) cc_final: 0.7978 (t0) REVERT: C 273 ASP cc_start: 0.8300 (t70) cc_final: 0.7976 (t70) REVERT: E 140 LEU cc_start: 0.9340 (mm) cc_final: 0.9060 (mm) REVERT: F 87 LYS cc_start: 0.8872 (ptpp) cc_final: 0.8632 (ptpp) REVERT: F 88 TYR cc_start: 0.8293 (m-80) cc_final: 0.7606 (m-80) REVERT: F 90 ARG cc_start: 0.9466 (ptm-80) cc_final: 0.8917 (ttp80) REVERT: F 122 MET cc_start: 0.9146 (mtp) cc_final: 0.8728 (mtp) REVERT: F 127 GLU cc_start: 0.8552 (mp0) cc_final: 0.8335 (mp0) REVERT: F 136 ARG cc_start: 0.7970 (mtt180) cc_final: 0.7438 (mtt180) REVERT: F 151 LEU cc_start: 0.8908 (mm) cc_final: 0.8220 (tp) REVERT: G 52 MET cc_start: 0.8999 (ptm) cc_final: 0.8246 (ppp) REVERT: G 75 ASN cc_start: 0.9308 (p0) cc_final: 0.8695 (t0) REVERT: G 98 GLU cc_start: 0.8576 (mm-30) cc_final: 0.8199 (mp0) REVERT: H 45 GLU cc_start: 0.8718 (tm-30) cc_final: 0.8361 (tm-30) REVERT: H 46 LEU cc_start: 0.9314 (mt) cc_final: 0.9100 (mt) REVERT: H 97 MET cc_start: 0.9128 (mmm) cc_final: 0.8912 (mmm) REVERT: H 102 TYR cc_start: 0.8786 (p90) cc_final: 0.8273 (p90) REVERT: H 116 TYR cc_start: 0.8634 (m-80) cc_final: 0.8300 (m-80) REVERT: I 64 LYS cc_start: 0.9322 (mtpp) cc_final: 0.8831 (mtpp) REVERT: J 28 ASP cc_start: 0.8704 (t70) cc_final: 0.8477 (t0) REVERT: J 49 MET cc_start: 0.9480 (tpp) cc_final: 0.8834 (tpp) REVERT: J 58 GLU cc_start: 0.9138 (tp30) cc_final: 0.8897 (tm-30) REVERT: K 46 LYS cc_start: 0.7832 (tptt) cc_final: 0.7007 (tptm) REVERT: K 67 GLU cc_start: 0.8626 (tm-30) cc_final: 0.7437 (tm-30) REVERT: K 102 ASN cc_start: 0.8419 (p0) cc_final: 0.8172 (p0) REVERT: K 125 MET cc_start: 0.8743 (mtt) cc_final: 0.8405 (mmm) REVERT: L 33 GLU cc_start: 0.8758 (mm-30) cc_final: 0.8468 (mm-30) REVERT: L 53 HIS cc_start: 0.8949 (t70) cc_final: 0.8179 (t70) REVERT: L 68 GLU cc_start: 0.7101 (tm-30) cc_final: 0.6652 (tm-30) REVERT: M 12 ILE cc_start: 0.8809 (mm) cc_final: 0.8590 (mm) REVERT: M 26 PHE cc_start: 0.8335 (m-10) cc_final: 0.7261 (m-10) REVERT: M 30 PHE cc_start: 0.9214 (t80) cc_final: 0.8541 (t80) REVERT: M 38 PHE cc_start: 0.9116 (m-10) cc_final: 0.8846 (m-10) REVERT: M 41 TYR cc_start: 0.8749 (m-80) cc_final: 0.8373 (m-80) REVERT: N 29 PHE cc_start: 0.9220 (m-80) cc_final: 0.8421 (m-80) REVERT: N 52 GLN cc_start: 0.8784 (mp10) cc_final: 0.8329 (mp10) REVERT: N 117 GLU cc_start: 0.8944 (tt0) cc_final: 0.8712 (tm-30) REVERT: N 119 LEU cc_start: 0.8759 (mm) cc_final: 0.8490 (tp) REVERT: O 293 TYR cc_start: 0.8579 (t80) cc_final: 0.8207 (t80) REVERT: O 463 LEU cc_start: 0.9136 (pt) cc_final: 0.8762 (mm) REVERT: O 467 PHE cc_start: 0.9601 (m-80) cc_final: 0.9206 (m-80) REVERT: O 537 PHE cc_start: 0.9580 (p90) cc_final: 0.9195 (p90) REVERT: O 538 LEU cc_start: 0.9690 (mp) cc_final: 0.9387 (mt) REVERT: P 238 HIS cc_start: 0.9430 (m-70) cc_final: 0.9188 (m90) REVERT: P 254 LEU cc_start: 0.9769 (tp) cc_final: 0.9381 (tp) REVERT: P 258 MET cc_start: 0.8732 (ptt) cc_final: 0.8271 (ptt) REVERT: P 304 LEU cc_start: 0.8331 (mp) cc_final: 0.7925 (mp) REVERT: P 381 MET cc_start: 0.9490 (mmp) cc_final: 0.9222 (mmm) REVERT: P 402 MET cc_start: 0.8476 (mpp) cc_final: 0.8197 (mpp) REVERT: P 404 ILE cc_start: 0.9261 (mt) cc_final: 0.8897 (tt) REVERT: P 411 ARG cc_start: 0.9125 (mpt180) cc_final: 0.8855 (mmt180) REVERT: P 413 LEU cc_start: 0.9728 (mt) cc_final: 0.9458 (mt) REVERT: P 491 PHE cc_start: 0.8579 (m-10) cc_final: 0.8015 (m-80) REVERT: Q 157 MET cc_start: 0.4141 (ttm) cc_final: 0.3805 (ttm) REVERT: Q 212 HIS cc_start: 0.9330 (m-70) cc_final: 0.8783 (m90) REVERT: Q 251 TRP cc_start: 0.7274 (p-90) cc_final: 0.6056 (p-90) REVERT: Q 259 ASP cc_start: 0.9383 (t0) cc_final: 0.9146 (t70) REVERT: Q 274 MET cc_start: 0.9337 (tpt) cc_final: 0.8939 (tpp) REVERT: Q 308 PHE cc_start: 0.8753 (p90) cc_final: 0.8364 (p90) REVERT: Q 365 TRP cc_start: 0.8973 (m100) cc_final: 0.7686 (m100) REVERT: Q 414 PHE cc_start: 0.9080 (m-10) cc_final: 0.8864 (m-80) outliers start: 1 outliers final: 0 residues processed: 885 average time/residue: 0.1879 time to fit residues: 280.4886 Evaluate side-chains 700 residues out of total 4950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 700 time to evaluate : 1.052 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 556 random chunks: chunk 389 optimal weight: 5.9990 chunk 518 optimal weight: 0.5980 chunk 427 optimal weight: 50.0000 chunk 444 optimal weight: 30.0000 chunk 190 optimal weight: 10.0000 chunk 221 optimal weight: 8.9990 chunk 354 optimal weight: 30.0000 chunk 256 optimal weight: 9.9990 chunk 498 optimal weight: 20.0000 chunk 1 optimal weight: 20.0000 chunk 80 optimal weight: 3.9990 overall best weight: 5.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 596 HIS ** A 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1088 HIS ** B 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 469 ASN ** B 532 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 547 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 575 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 673 ASN ** B 702 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1038 HIS ** B1041 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 346 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 388 ASN O 395 GLN ** O 757 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 319 ASN ** Q 372 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 407 HIS ** 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 = 0.3780 r_free = 0.3780 target = 0.088987 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.069016 restraints weight = 238052.567| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.070748 restraints weight = 130298.828| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.071924 restraints weight = 86943.318| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.072639 restraints weight = 63299.897| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.073162 restraints weight = 51756.949| |-----------------------------------------------------------------------------| r_work (final): 0.3325 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7493 moved from start: 0.6960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.086 47692 Z= 0.233 Angle : 0.857 33.167 64864 Z= 0.429 Chirality : 0.049 0.519 7252 Planarity : 0.006 0.238 7976 Dihedral : 14.291 177.466 7147 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 22.25 Ramachandran Plot: Outliers : 0.55 % Allowed : 7.93 % Favored : 91.51 % Rotamer: Outliers : 0.00 % Allowed : 0.61 % Favored : 99.39 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.83 % Twisted General : 0.13 % 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 aren not related in a simple way. whole: -1.10 (0.11), residues: 5432 helix: 0.39 (0.11), residues: 1969 sheet: -1.02 (0.18), residues: 758 loop : -1.48 (0.12), residues: 2705 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.030 0.001 ARG O 197 TYR 0.040 0.002 TYR P 366 PHE 0.109 0.002 PHE Q 358 TRP 0.060 0.003 TRP P 287 HIS 0.010 0.001 HIS Q 409 Details of bonding type rmsd covalent geometry : bond 0.00499 (47647) covalent geometry : angle 0.82861 (64831) hydrogen bonds : bond 0.05100 ( 1994) hydrogen bonds : angle 5.94052 ( 5479) metal coordination : bond 0.01775 ( 24) metal coordination : angle 9.65585 ( 33) Misc. bond : bond 0.01112 ( 21) *********************** 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 851 residues out of total 4950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 851 time to evaluate : 1.075 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: A 5 LYS cc_start: 0.8995 (ttmm) cc_final: 0.8745 (ttmt) REVERT: A 97 TYR cc_start: 0.9212 (m-80) cc_final: 0.8851 (m-80) REVERT: A 213 ASN cc_start: 0.9247 (t0) cc_final: 0.8970 (t0) REVERT: A 214 ASP cc_start: 0.9242 (t70) cc_final: 0.8666 (t0) REVERT: A 215 GLU cc_start: 0.9134 (pm20) cc_final: 0.8804 (pm20) REVERT: A 218 LYS cc_start: 0.9526 (ptpp) cc_final: 0.9119 (pttt) REVERT: A 226 LYS cc_start: 0.9479 (mmpt) cc_final: 0.9018 (mmmt) REVERT: A 339 PHE cc_start: 0.8981 (m-80) cc_final: 0.8428 (m-80) REVERT: A 437 PHE cc_start: 0.9311 (t80) cc_final: 0.9081 (t80) REVERT: A 470 HIS cc_start: 0.8569 (m-70) cc_final: 0.8275 (m-70) REVERT: A 589 MET cc_start: 0.8676 (mmm) cc_final: 0.8350 (mmm) REVERT: A 590 ASN cc_start: 0.9354 (t0) cc_final: 0.9025 (t0) REVERT: A 600 MET cc_start: 0.8880 (ttm) cc_final: 0.8616 (ttm) REVERT: A 654 ASP cc_start: 0.8632 (m-30) cc_final: 0.8411 (m-30) REVERT: A 672 ASP cc_start: 0.8313 (t70) cc_final: 0.8105 (t70) REVERT: A 738 ASN cc_start: 0.8745 (m-40) cc_final: 0.8255 (t0) REVERT: A 830 MET cc_start: 0.8872 (mmm) cc_final: 0.8635 (mmm) REVERT: A 925 MET cc_start: 0.9495 (tpt) cc_final: 0.9062 (tmm) REVERT: A 943 ILE cc_start: 0.9624 (mt) cc_final: 0.9364 (pt) REVERT: A 944 MET cc_start: 0.8874 (mmp) cc_final: 0.8671 (mmm) REVERT: A 947 LEU cc_start: 0.9268 (mp) cc_final: 0.8955 (mp) REVERT: A 960 MET cc_start: 0.7782 (mtp) cc_final: 0.7470 (mtp) REVERT: A 1007 ILE cc_start: -0.4660 (mt) cc_final: -0.5079 (mt) REVERT: A 1009 THR cc_start: 0.0310 (m) cc_final: -0.0095 (m) REVERT: A 1060 GLU cc_start: 0.8856 (tm-30) cc_final: 0.8521 (tm-30) REVERT: A 1092 GLU cc_start: 0.9352 (mt-10) cc_final: 0.9145 (mp0) REVERT: A 1183 GLU cc_start: 0.8496 (tp30) cc_final: 0.8030 (tp30) REVERT: A 1185 VAL cc_start: 0.9524 (m) cc_final: 0.9111 (t) REVERT: A 1224 GLU cc_start: 0.8862 (mp0) cc_final: 0.8652 (mp0) REVERT: A 1265 GLU cc_start: 0.8823 (pt0) cc_final: 0.8612 (pt0) REVERT: A 1439 MET cc_start: 0.8202 (mmp) cc_final: 0.7984 (mmm) REVERT: A 1476 LEU cc_start: 0.9206 (mt) cc_final: 0.8956 (mt) REVERT: A 1504 ILE cc_start: 0.9277 (mm) cc_final: 0.9017 (mm) REVERT: A 1505 ASP cc_start: 0.8201 (t0) cc_final: 0.7480 (t70) REVERT: A 1519 LEU cc_start: 0.9480 (mt) cc_final: 0.9164 (mt) REVERT: A 1587 ASP cc_start: 0.8865 (m-30) cc_final: 0.8390 (m-30) REVERT: A 1610 PHE cc_start: 0.9524 (m-80) cc_final: 0.9115 (m-80) REVERT: A 1616 GLU cc_start: 0.7587 (tt0) cc_final: 0.6894 (tm-30) REVERT: A 1620 GLN cc_start: 0.9247 (mp10) cc_final: 0.8754 (mp10) REVERT: A 1621 PHE cc_start: 0.9341 (m-80) cc_final: 0.8734 (m-80) REVERT: A 1657 LEU cc_start: 0.8794 (tp) cc_final: 0.8480 (tp) REVERT: B 80 ASN cc_start: 0.0407 (p0) cc_final: -0.0036 (t0) REVERT: B 98 SER cc_start: 0.9056 (p) cc_final: 0.8693 (m) REVERT: B 136 LYS cc_start: 0.8966 (ttmt) cc_final: 0.8394 (tptm) REVERT: B 157 ASP cc_start: 0.9147 (p0) cc_final: 0.8658 (p0) REVERT: B 164 MET cc_start: 0.8047 (ttp) cc_final: 0.7797 (ttp) REVERT: B 174 LYS cc_start: 0.9200 (mmpt) cc_final: 0.8884 (mmmt) REVERT: B 206 LEU cc_start: 0.9421 (tp) cc_final: 0.9188 (tp) REVERT: B 215 MET cc_start: 0.7545 (mtt) cc_final: 0.7169 (mtt) REVERT: B 224 ASN cc_start: 0.8667 (m110) cc_final: 0.8374 (m110) REVERT: B 242 ASP cc_start: 0.9114 (p0) cc_final: 0.7625 (p0) REVERT: B 275 MET cc_start: 0.9263 (ttm) cc_final: 0.9047 (ttm) REVERT: B 304 ASP cc_start: 0.9533 (m-30) cc_final: 0.9091 (p0) REVERT: B 330 LEU cc_start: 0.9635 (mt) cc_final: 0.9401 (mt) REVERT: B 411 MET cc_start: 0.9176 (mtp) cc_final: 0.8975 (mtp) REVERT: B 414 LYS cc_start: 0.9660 (ttpp) cc_final: 0.9073 (ttpp) REVERT: B 422 GLN cc_start: 0.9309 (tm-30) cc_final: 0.9076 (tm-30) REVERT: B 470 LEU cc_start: 0.9178 (mp) cc_final: 0.8925 (tt) REVERT: B 486 VAL cc_start: 0.9356 (t) cc_final: 0.9056 (p) REVERT: B 496 PHE cc_start: 0.9051 (t80) cc_final: 0.8537 (t80) REVERT: B 515 THR cc_start: 0.9268 (p) cc_final: 0.9027 (t) REVERT: B 543 ASN cc_start: 0.8898 (m-40) cc_final: 0.8625 (m-40) REVERT: B 556 SER cc_start: 0.7338 (p) cc_final: 0.6065 (t) REVERT: B 557 ASP cc_start: 0.8095 (m-30) cc_final: 0.7595 (m-30) REVERT: B 575 HIS cc_start: 0.8601 (m-70) cc_final: 0.8167 (m-70) REVERT: B 668 GLU cc_start: 0.8342 (pt0) cc_final: 0.7962 (pt0) REVERT: B 783 MET cc_start: 0.7358 (mmm) cc_final: 0.6902 (mmm) REVERT: B 936 MET cc_start: 0.9313 (ttt) cc_final: 0.9072 (tmm) REVERT: B 958 MET cc_start: 0.8965 (mtt) cc_final: 0.8653 (mtt) REVERT: B 962 MET cc_start: 0.9067 (ttm) cc_final: 0.8779 (ttm) REVERT: B 965 GLU cc_start: 0.9080 (tm-30) cc_final: 0.8691 (tm-30) REVERT: B 1034 GLN cc_start: 0.9277 (pt0) cc_final: 0.9062 (pt0) REVERT: B 1074 MET cc_start: 0.8089 (ttm) cc_final: 0.7852 (ttp) REVERT: B 1075 GLU cc_start: 0.8751 (mp0) cc_final: 0.8355 (mm-30) REVERT: B 1086 PHE cc_start: 0.7689 (m-80) cc_final: 0.7219 (m-80) REVERT: B 1133 MET cc_start: 0.8906 (tmm) cc_final: 0.8655 (tmm) REVERT: B 1157 GLN cc_start: 0.9416 (mp-120) cc_final: 0.9131 (mp10) REVERT: C 71 MET cc_start: 0.9350 (mtp) cc_final: 0.8664 (mmm) REVERT: C 88 ASN cc_start: 0.8276 (t0) cc_final: 0.7957 (t0) REVERT: C 273 ASP cc_start: 0.8380 (t70) cc_final: 0.8138 (t0) REVERT: E 116 ILE cc_start: 0.9187 (pt) cc_final: 0.8887 (pt) REVERT: E 121 MET cc_start: 0.8421 (pmm) cc_final: 0.8193 (tpt) REVERT: E 140 LEU cc_start: 0.9306 (mm) cc_final: 0.9040 (mm) REVERT: F 90 ARG cc_start: 0.9426 (ptm-80) cc_final: 0.9156 (ttp80) REVERT: F 103 MET cc_start: 0.9165 (mmt) cc_final: 0.8912 (mmp) REVERT: F 122 MET cc_start: 0.9111 (mtp) cc_final: 0.8681 (mtp) REVERT: F 127 GLU cc_start: 0.8635 (mp0) cc_final: 0.8393 (mp0) REVERT: G 75 ASN cc_start: 0.9327 (p0) cc_final: 0.8674 (t0) REVERT: G 84 TYR cc_start: 0.7916 (p90) cc_final: 0.7622 (p90) REVERT: G 98 GLU cc_start: 0.8429 (mm-30) cc_final: 0.8081 (mp0) REVERT: H 45 GLU cc_start: 0.8710 (tm-30) cc_final: 0.8341 (tm-30) REVERT: H 46 LEU cc_start: 0.9308 (mt) cc_final: 0.9095 (mt) REVERT: H 116 TYR cc_start: 0.8674 (m-80) cc_final: 0.8211 (m-80) REVERT: H 118 PHE cc_start: 0.8713 (m-80) cc_final: 0.8159 (m-80) REVERT: I 64 LYS cc_start: 0.9228 (mtpp) cc_final: 0.8800 (mtpp) REVERT: J 28 ASP cc_start: 0.8799 (t70) cc_final: 0.8575 (t0) REVERT: J 49 MET cc_start: 0.9507 (tpp) cc_final: 0.8850 (tpp) REVERT: J 58 GLU cc_start: 0.9169 (tp30) cc_final: 0.8965 (tm-30) REVERT: K 46 LYS cc_start: 0.7815 (tptt) cc_final: 0.7103 (tptm) REVERT: K 67 GLU cc_start: 0.8665 (tm-30) cc_final: 0.7479 (tm-30) REVERT: K 102 ASN cc_start: 0.8472 (p0) cc_final: 0.8204 (p0) REVERT: K 125 MET cc_start: 0.8781 (mtt) cc_final: 0.8348 (mmm) REVERT: L 33 GLU cc_start: 0.8855 (mm-30) cc_final: 0.8607 (mm-30) REVERT: L 53 HIS cc_start: 0.9004 (t70) cc_final: 0.8185 (t70) REVERT: L 68 GLU cc_start: 0.6974 (tm-30) cc_final: 0.6666 (tm-30) REVERT: M 23 VAL cc_start: 0.8686 (t) cc_final: 0.8365 (t) REVERT: M 30 PHE cc_start: 0.9136 (t80) cc_final: 0.8671 (t80) REVERT: M 41 TYR cc_start: 0.8784 (m-80) cc_final: 0.8427 (m-80) REVERT: N 29 PHE cc_start: 0.9205 (m-80) cc_final: 0.8399 (m-80) REVERT: N 52 GLN cc_start: 0.8835 (mp10) cc_final: 0.8390 (mp10) REVERT: N 117 GLU cc_start: 0.9013 (tt0) cc_final: 0.8728 (tm-30) REVERT: O 293 TYR cc_start: 0.8583 (t80) cc_final: 0.8234 (t80) REVERT: O 397 LYS cc_start: 0.7682 (mttp) cc_final: 0.7115 (mmtm) REVERT: O 467 PHE cc_start: 0.9599 (m-80) cc_final: 0.9191 (m-80) REVERT: O 538 LEU cc_start: 0.9695 (mp) cc_final: 0.9348 (mt) REVERT: P 238 HIS cc_start: 0.9468 (m-70) cc_final: 0.9215 (m90) REVERT: P 254 LEU cc_start: 0.9760 (tp) cc_final: 0.9367 (tp) REVERT: P 258 MET cc_start: 0.8836 (ptt) cc_final: 0.8366 (ptt) REVERT: P 381 MET cc_start: 0.9477 (mmp) cc_final: 0.9211 (mmm) REVERT: P 402 MET cc_start: 0.8558 (mpp) cc_final: 0.8307 (mpp) REVERT: P 404 ILE cc_start: 0.9245 (mt) cc_final: 0.8881 (tt) REVERT: P 413 LEU cc_start: 0.9742 (mt) cc_final: 0.9467 (mt) REVERT: P 434 HIS cc_start: 0.7720 (m-70) cc_final: 0.7511 (m-70) REVERT: P 491 PHE cc_start: 0.8622 (m-10) cc_final: 0.8370 (m-80) REVERT: Q 157 MET cc_start: 0.4346 (ttm) cc_final: 0.3962 (ttm) REVERT: Q 212 HIS cc_start: 0.9357 (m-70) cc_final: 0.8859 (m-70) REVERT: Q 251 TRP cc_start: 0.7426 (p-90) cc_final: 0.6208 (p-90) REVERT: Q 259 ASP cc_start: 0.9448 (t0) cc_final: 0.9225 (t70) REVERT: Q 274 MET cc_start: 0.9343 (tpt) cc_final: 0.8969 (tpp) REVERT: Q 308 PHE cc_start: 0.8805 (p90) cc_final: 0.8444 (p90) REVERT: Q 365 TRP cc_start: 0.9003 (m100) cc_final: 0.7732 (m100) outliers start: 0 outliers final: 0 residues processed: 851 average time/residue: 0.1702 time to fit residues: 244.7439 Evaluate side-chains 689 residues out of total 4950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 689 time to evaluate : 1.052 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 556 random chunks: chunk 552 optimal weight: 20.0000 chunk 45 optimal weight: 10.0000 chunk 382 optimal weight: 5.9990 chunk 177 optimal weight: 9.9990 chunk 161 optimal weight: 1.9990 chunk 441 optimal weight: 7.9990 chunk 190 optimal weight: 7.9990 chunk 121 optimal weight: 5.9990 chunk 23 optimal weight: 20.0000 chunk 408 optimal weight: 5.9990 chunk 171 optimal weight: 4.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 596 HIS ** A 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 469 ASN ** B 532 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 547 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 575 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 702 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1038 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1041 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 346 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 395 GLN ** O 757 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 372 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 407 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.089210 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.069178 restraints weight = 240360.858| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.071000 restraints weight = 130933.411| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.072142 restraints weight = 85456.893| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.072812 restraints weight = 62917.951| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.073332 restraints weight = 51867.095| |-----------------------------------------------------------------------------| r_work (final): 0.3328 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7490 moved from start: 0.7118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 47692 Z= 0.212 Angle : 0.870 40.707 64864 Z= 0.430 Chirality : 0.049 0.540 7252 Planarity : 0.007 0.239 7976 Dihedral : 14.290 177.665 7147 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 21.65 Ramachandran Plot: Outliers : 0.55 % Allowed : 7.86 % Favored : 91.59 % Rotamer: Outliers : 0.00 % Allowed : 0.36 % Favored : 99.64 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.83 % 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 aren not related in a simple way. whole: -1.07 (0.11), residues: 5432 helix: 0.44 (0.11), residues: 1959 sheet: -1.06 (0.18), residues: 767 loop : -1.45 (0.12), residues: 2706 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.030 0.001 ARG O 197 TYR 0.033 0.002 TYR P 366 PHE 0.110 0.002 PHE Q 358 TRP 0.039 0.003 TRP P 287 HIS 0.017 0.001 HIS B1038 Details of bonding type rmsd covalent geometry : bond 0.00457 (47647) covalent geometry : angle 0.83560 (64831) hydrogen bonds : bond 0.05031 ( 1994) hydrogen bonds : angle 5.87596 ( 5479) metal coordination : bond 0.01533 ( 24) metal coordination : angle 10.78616 ( 33) Misc. bond : bond 0.01138 ( 21) ********************** 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 849 residues out of total 4950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 849 time to evaluate : 1.095 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: A 5 LYS cc_start: 0.8984 (ttmm) cc_final: 0.8708 (ttmt) REVERT: A 97 TYR cc_start: 0.9220 (m-80) cc_final: 0.8852 (m-80) REVERT: A 213 ASN cc_start: 0.9254 (t0) cc_final: 0.8980 (t0) REVERT: A 214 ASP cc_start: 0.9269 (t70) cc_final: 0.8707 (t0) REVERT: A 215 GLU cc_start: 0.9119 (pm20) cc_final: 0.8758 (pm20) REVERT: A 218 LYS cc_start: 0.9533 (ptpp) cc_final: 0.9128 (pttt) REVERT: A 226 LYS cc_start: 0.9462 (mmpt) cc_final: 0.8978 (mmmt) REVERT: A 339 PHE cc_start: 0.8881 (m-80) cc_final: 0.8433 (m-80) REVERT: A 437 PHE cc_start: 0.9328 (t80) cc_final: 0.9100 (t80) REVERT: A 470 HIS cc_start: 0.8582 (m-70) cc_final: 0.8311 (m-70) REVERT: A 589 MET cc_start: 0.8617 (mmm) cc_final: 0.8304 (mmm) REVERT: A 590 ASN cc_start: 0.9410 (t0) cc_final: 0.9084 (t0) REVERT: A 654 ASP cc_start: 0.8639 (m-30) cc_final: 0.8402 (m-30) REVERT: A 738 ASN cc_start: 0.8732 (m-40) cc_final: 0.8110 (t0) REVERT: A 830 MET cc_start: 0.8855 (mmm) cc_final: 0.8610 (mmm) REVERT: A 925 MET cc_start: 0.9443 (tpt) cc_final: 0.9038 (tmm) REVERT: A 943 ILE cc_start: 0.9613 (mt) cc_final: 0.9363 (pt) REVERT: A 960 MET cc_start: 0.7705 (mtp) cc_final: 0.7397 (mtp) REVERT: A 1007 ILE cc_start: -0.4751 (mt) cc_final: -0.5159 (mt) REVERT: A 1060 GLU cc_start: 0.8913 (tm-30) cc_final: 0.8585 (tm-30) REVERT: A 1183 GLU cc_start: 0.8468 (tp30) cc_final: 0.7996 (tp30) REVERT: A 1185 VAL cc_start: 0.9569 (m) cc_final: 0.9123 (t) REVERT: A 1265 GLU cc_start: 0.8821 (pt0) cc_final: 0.8571 (pt0) REVERT: A 1476 LEU cc_start: 0.9227 (mt) cc_final: 0.8943 (mt) REVERT: A 1504 ILE cc_start: 0.9303 (mm) cc_final: 0.9014 (mm) REVERT: A 1505 ASP cc_start: 0.8091 (t0) cc_final: 0.7406 (t70) REVERT: A 1519 LEU cc_start: 0.9479 (mt) cc_final: 0.9192 (mt) REVERT: A 1587 ASP cc_start: 0.8881 (m-30) cc_final: 0.8428 (m-30) REVERT: A 1589 MET cc_start: 0.9268 (mmm) cc_final: 0.8732 (mmm) REVERT: A 1610 PHE cc_start: 0.9527 (m-80) cc_final: 0.9137 (m-80) REVERT: A 1620 GLN cc_start: 0.9280 (mp10) cc_final: 0.8837 (mp10) REVERT: A 1621 PHE cc_start: 0.9326 (m-80) cc_final: 0.8827 (m-80) REVERT: A 1657 LEU cc_start: 0.8788 (tp) cc_final: 0.8465 (tp) REVERT: B 70 GLU cc_start: 0.9053 (mt-10) cc_final: 0.8652 (mm-30) REVERT: B 80 ASN cc_start: 0.0625 (p0) cc_final: 0.0161 (t0) REVERT: B 98 SER cc_start: 0.9054 (p) cc_final: 0.8039 (m) REVERT: B 136 LYS cc_start: 0.8949 (ttmt) cc_final: 0.8388 (tptm) REVERT: B 158 CYS cc_start: 0.8874 (m) cc_final: 0.8562 (m) REVERT: B 174 LYS cc_start: 0.9181 (mmpt) cc_final: 0.8840 (mmmt) REVERT: B 206 LEU cc_start: 0.9413 (tp) cc_final: 0.9090 (tp) REVERT: B 215 MET cc_start: 0.7472 (mtt) cc_final: 0.7059 (mtt) REVERT: B 224 ASN cc_start: 0.8666 (m110) cc_final: 0.8356 (m110) REVERT: B 275 MET cc_start: 0.9253 (ttm) cc_final: 0.9046 (ttm) REVERT: B 304 ASP cc_start: 0.9529 (m-30) cc_final: 0.9081 (p0) REVERT: B 330 LEU cc_start: 0.9642 (mt) cc_final: 0.9401 (mt) REVERT: B 411 MET cc_start: 0.9146 (mtp) cc_final: 0.8935 (mtp) REVERT: B 414 LYS cc_start: 0.9670 (ttpp) cc_final: 0.9316 (tttp) REVERT: B 422 GLN cc_start: 0.9327 (tm-30) cc_final: 0.9103 (tm-30) REVERT: B 457 ILE cc_start: 0.9460 (tp) cc_final: 0.9127 (tp) REVERT: B 470 LEU cc_start: 0.9194 (mp) cc_final: 0.8937 (tt) REVERT: B 486 VAL cc_start: 0.9344 (t) cc_final: 0.9026 (p) REVERT: B 496 PHE cc_start: 0.9036 (t80) cc_final: 0.8500 (t80) REVERT: B 515 THR cc_start: 0.9260 (p) cc_final: 0.9010 (t) REVERT: B 543 ASN cc_start: 0.8866 (m-40) cc_final: 0.8608 (m-40) REVERT: B 556 SER cc_start: 0.7603 (p) cc_final: 0.6508 (t) REVERT: B 557 ASP cc_start: 0.8188 (m-30) cc_final: 0.7625 (m-30) REVERT: B 575 HIS cc_start: 0.8603 (m-70) cc_final: 0.8224 (m-70) REVERT: B 668 GLU cc_start: 0.8291 (pt0) cc_final: 0.7888 (pt0) REVERT: B 783 MET cc_start: 0.7202 (mmm) cc_final: 0.6685 (mmm) REVERT: B 936 MET cc_start: 0.9306 (ttt) cc_final: 0.9009 (tmm) REVERT: B 958 MET cc_start: 0.8965 (mtt) cc_final: 0.8642 (mtt) REVERT: B 965 GLU cc_start: 0.9099 (tm-30) cc_final: 0.8686 (tm-30) REVERT: B 1034 GLN cc_start: 0.9300 (pt0) cc_final: 0.9091 (pt0) REVERT: B 1074 MET cc_start: 0.8118 (ttm) cc_final: 0.7888 (ttp) REVERT: B 1075 GLU cc_start: 0.8698 (mp0) cc_final: 0.8136 (mm-30) REVERT: B 1086 PHE cc_start: 0.7534 (m-80) cc_final: 0.7051 (m-80) REVERT: B 1157 GLN cc_start: 0.9433 (mp-120) cc_final: 0.9210 (mp10) REVERT: C 71 MET cc_start: 0.9314 (mtp) cc_final: 0.8654 (mmm) REVERT: C 88 ASN cc_start: 0.8412 (t0) cc_final: 0.8097 (t0) REVERT: C 273 ASP cc_start: 0.8393 (t70) cc_final: 0.8159 (t0) REVERT: C 308 MET cc_start: 0.8702 (mtm) cc_final: 0.8307 (mmp) REVERT: E 75 MET cc_start: 0.7725 (ppp) cc_final: 0.7374 (tmm) REVERT: E 116 ILE cc_start: 0.9205 (pt) cc_final: 0.8900 (pt) REVERT: E 121 MET cc_start: 0.8442 (pmm) cc_final: 0.8182 (tpt) REVERT: E 140 LEU cc_start: 0.9292 (mm) cc_final: 0.9024 (mm) REVERT: F 74 ILE cc_start: 0.9311 (mm) cc_final: 0.9094 (tp) REVERT: F 90 ARG cc_start: 0.9465 (ptm-80) cc_final: 0.8910 (ttp80) REVERT: F 103 MET cc_start: 0.9237 (mmt) cc_final: 0.8966 (mmp) REVERT: F 112 GLU cc_start: 0.8411 (pm20) cc_final: 0.8148 (pm20) REVERT: F 122 MET cc_start: 0.9113 (mtp) cc_final: 0.8712 (mtp) REVERT: F 127 GLU cc_start: 0.8677 (mp0) cc_final: 0.8402 (mp0) REVERT: F 151 LEU cc_start: 0.8875 (mm) cc_final: 0.8160 (tp) REVERT: G 75 ASN cc_start: 0.9327 (p0) cc_final: 0.8694 (t0) REVERT: G 98 GLU cc_start: 0.8393 (mm-30) cc_final: 0.8111 (mp0) REVERT: H 45 GLU cc_start: 0.8705 (tm-30) cc_final: 0.8308 (tm-30) REVERT: H 46 LEU cc_start: 0.9288 (mt) cc_final: 0.9073 (mt) REVERT: H 102 TYR cc_start: 0.8853 (p90) cc_final: 0.8294 (p90) REVERT: H 116 TYR cc_start: 0.8699 (m-80) cc_final: 0.8202 (m-80) REVERT: H 118 PHE cc_start: 0.8678 (m-80) cc_final: 0.8141 (m-80) REVERT: I 60 LEU cc_start: 0.9489 (mm) cc_final: 0.8990 (mm) REVERT: I 64 LYS cc_start: 0.9165 (mtpp) cc_final: 0.8752 (mtpp) REVERT: J 28 ASP cc_start: 0.8831 (t70) cc_final: 0.8586 (t0) REVERT: J 49 MET cc_start: 0.9502 (tpp) cc_final: 0.8829 (tpp) REVERT: K 46 LYS cc_start: 0.7810 (tptt) cc_final: 0.7573 (tptm) REVERT: K 67 GLU cc_start: 0.8469 (tm-30) cc_final: 0.8009 (tm-30) REVERT: K 102 ASN cc_start: 0.8480 (p0) cc_final: 0.8219 (p0) REVERT: K 125 MET cc_start: 0.8769 (mtt) cc_final: 0.8451 (mmm) REVERT: K 129 ASP cc_start: 0.9348 (m-30) cc_final: 0.9143 (m-30) REVERT: L 33 GLU cc_start: 0.8879 (mm-30) cc_final: 0.8639 (mm-30) REVERT: M 23 VAL cc_start: 0.8965 (t) cc_final: 0.8541 (t) REVERT: M 30 PHE cc_start: 0.9272 (t80) cc_final: 0.8764 (t80) REVERT: M 41 TYR cc_start: 0.8805 (m-80) cc_final: 0.8460 (m-80) REVERT: M 61 GLU cc_start: 0.9173 (mp0) cc_final: 0.8259 (tm-30) REVERT: N 29 PHE cc_start: 0.9130 (m-80) cc_final: 0.8341 (m-80) REVERT: N 52 GLN cc_start: 0.8807 (mp10) cc_final: 0.8386 (mp10) REVERT: O 293 TYR cc_start: 0.8655 (t80) cc_final: 0.8295 (t80) REVERT: O 467 PHE cc_start: 0.9593 (m-80) cc_final: 0.9215 (m-80) REVERT: O 538 LEU cc_start: 0.9669 (mp) cc_final: 0.9358 (mt) REVERT: P 238 HIS cc_start: 0.9482 (m-70) cc_final: 0.9224 (m90) REVERT: P 258 MET cc_start: 0.8816 (ptt) cc_final: 0.8581 (ptt) REVERT: P 304 LEU cc_start: 0.8787 (mp) cc_final: 0.8321 (mp) REVERT: P 381 MET cc_start: 0.9508 (mmp) cc_final: 0.9244 (mmm) REVERT: P 402 MET cc_start: 0.8536 (mpp) cc_final: 0.8284 (mpp) REVERT: P 404 ILE cc_start: 0.9226 (mt) cc_final: 0.8859 (tt) REVERT: P 413 LEU cc_start: 0.9741 (mt) cc_final: 0.9487 (mt) REVERT: P 434 HIS cc_start: 0.7721 (m-70) cc_final: 0.7510 (m-70) REVERT: P 491 PHE cc_start: 0.8554 (m-10) cc_final: 0.8183 (m-80) REVERT: Q 157 MET cc_start: 0.4325 (ttm) cc_final: 0.4029 (ttm) REVERT: Q 212 HIS cc_start: 0.9352 (m-70) cc_final: 0.8861 (m-70) REVERT: Q 221 HIS cc_start: 0.9361 (m90) cc_final: 0.8864 (m-70) REVERT: Q 251 TRP cc_start: 0.7434 (p-90) cc_final: 0.6233 (p-90) REVERT: Q 259 ASP cc_start: 0.9429 (t0) cc_final: 0.9196 (t70) REVERT: Q 274 MET cc_start: 0.9355 (tpt) cc_final: 0.9002 (tpp) REVERT: Q 308 PHE cc_start: 0.8775 (p90) cc_final: 0.8423 (p90) REVERT: Q 365 TRP cc_start: 0.8962 (m100) cc_final: 0.7631 (m100) outliers start: 0 outliers final: 0 residues processed: 849 average time/residue: 0.1676 time to fit residues: 241.8281 Evaluate side-chains 696 residues out of total 4950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 696 time to evaluate : 1.069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 556 random chunks: chunk 13 optimal weight: 3.9990 chunk 203 optimal weight: 1.9990 chunk 105 optimal weight: 20.0000 chunk 450 optimal weight: 0.6980 chunk 542 optimal weight: 2.9990 chunk 305 optimal weight: 5.9990 chunk 185 optimal weight: 1.9990 chunk 489 optimal weight: 40.0000 chunk 423 optimal weight: 4.9990 chunk 507 optimal weight: 30.0000 chunk 102 optimal weight: 10.0000 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 224 HIS A 738 ASN ** A 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 532 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 547 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 575 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 702 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1041 ASN ** C 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 51 GLN ** O 757 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 372 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 407 HIS ** 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 = 0.3811 r_free = 0.3811 target = 0.090499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.070384 restraints weight = 237907.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.072235 restraints weight = 129894.280| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.073314 restraints weight = 84142.790| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.074204 restraints weight = 62868.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.074620 restraints weight = 50822.827| |-----------------------------------------------------------------------------| r_work (final): 0.3360 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7448 moved from start: 0.7347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 47692 Z= 0.168 Angle : 0.844 37.357 64864 Z= 0.418 Chirality : 0.048 0.554 7252 Planarity : 0.006 0.221 7976 Dihedral : 14.204 177.126 7147 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 19.11 Ramachandran Plot: Outliers : 0.52 % Allowed : 7.49 % Favored : 91.99 % Rotamer: Outliers : 0.02 % Allowed : 0.26 % Favored : 99.72 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.83 % 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 aren not related in a simple way. whole: -0.94 (0.11), residues: 5432 helix: 0.54 (0.12), residues: 1946 sheet: -0.94 (0.18), residues: 765 loop : -1.39 (0.12), residues: 2721 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.028 0.001 ARG O 197 TYR 0.055 0.002 TYR P 366 PHE 0.113 0.002 PHE Q 358 TRP 0.033 0.002 TRP O 389 HIS 0.008 0.001 HIS J 53 Details of bonding type rmsd covalent geometry : bond 0.00365 (47647) covalent geometry : angle 0.81689 (64831) hydrogen bonds : bond 0.05013 ( 1994) hydrogen bonds : angle 5.76182 ( 5479) metal coordination : bond 0.01091 ( 24) metal coordination : angle 9.36944 ( 33) Misc. bond : bond 0.01193 ( 21) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9050.83 seconds wall clock time: 157 minutes 4.33 seconds (9424.33 seconds total)