Starting phenix.real_space_refine on Tue Sep 15 22:21:19 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/5w64_8774/09_2026/5w64_8774.cif Found real_map, /net/cci-nas-00/data/ceres_data/5w64_8774/09_2026/5w64_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 { restraint_files = "/net/cci-nas-00/data/ceres_data/5w64_8774/09_2026/5w64_8774.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/5w64_8774/09_2026/5w64_8774.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/5w64_8774/09_2026/5w64_8774.map" default_real_map = "/net/cci-nas-00/data/ceres_data/5w64_8774/09_2026/5w64_8774.map" model { file = "/net/cci-nas-00/data/ceres_data/5w64_8774/09_2026/5w64_8774.cif" } default_model = "/net/cci-nas-00/data/ceres_data/5w64_8774/09_2026/5w64_8774.cif" } 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): 0.24s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 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: {'RNAv2': 6} Modifications used: {'rna3p_pur': 4, 'rna3p_pyr': 2} Link IDs: {'rna3p': 5} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "S" Number of atoms: 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: 9.55, per 1000 atoms: 0.21 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: 5.06 Conformation dependent library (CDL) restraints added in 2.4 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1701 " pdb="ZN ZN A1701 " - pdb=" SG CYS A 105 " pdb="ZN ZN A1701 " - pdb=" SG CYS A 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: 7.12 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: 16.91 Time building geometry restraints manager: 6.48 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: 63943 5.45 - 10.89: 765 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: 27967 35.00 - 70.00: 717 70.00 - 105.00: 39 105.00 - 140.00: 0 140.00 - 175.00: 1 Dihedral angle restraints: 28724 sinusoidal: 12467 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=" O4' C R 4 " pdb=" C2' C R 4 " pdb=" C1' C R 4 " pdb=" C3' C R 4 " ideal model delta sinusoidal sigma weight residual 25.59 -4.57 30.17 3 3.80e+00 6.93e-02 7.45e+01 ... (remaining 28721 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.296: 7133 0.296 - 0.591: 108 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: 0.660 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 0.800 Check model and map are aligned: 0.140 Set scattering table: 0.120 Process input model: 62.550 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.100 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:1.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 66.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5747 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 : 0.012 0.483 47692 Z= 0.783 Angle : 1.745 57.708 64864 Z= 1.008 Chirality : 0.091 1.478 7252 Planarity : 0.011 0.122 7976 Dihedral : 15.028 175.004 18180 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 are 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/Z covalent geometry : bond 0.00859 / 0.53 (47647) covalent geometry : angle 1.56535 / 1.00 (64831) hydrogen bonds : bond 0.22531 / 14.94 ( 1994) hydrogen bonds : angle 10.38921 / 7.31 ( 5479) metal coordination : bond 0.23823 / 15.23 ( 24) metal coordination : angle 34.20532 / 20.93 ( 33) Misc. bond : bond 0.26207 / 16.41 ( 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 : 1.754 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: 0.0827 (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: 0.1136 (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: 0.0318 (pttp) cc_final: -0.0223 (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: 0.5979 (mmm) cc_final: 0.5631 (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: -0.1962 (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: 0.7946 (t80) cc_final: 0.7491 (t80) REVERT: B 733 LEU cc_start: 0.7551 (mt) cc_final: 0.6984 (mp) REVERT: B 813 LEU cc_start: 0.4891 (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: 0.6664 (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: 0.5061 (p) REVERT: G 110 ASP cc_start: 0.6623 (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: 0.7345 (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: -0.0109 (mpp80) REVERT: Q 166 GLU cc_start: 0.7667 (tt0) cc_final: 0.6790 (tt0) REVERT: Q 204 GLU cc_start: 0.6774 (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: 0.2898 time to fit residues: 793.3703 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 : 1.945 ------------------------------------------------------------------------------- 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... A 43 HIS A 93 GLN ** A 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 221 HIS A 224 HIS A 332 GLN A 344 ASN ** A 435 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 553 GLN A 580 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** A1314 GLN ** A1320 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1532 GLN A1647 ASN B 39 GLN ** 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 ** 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 975 HIS B1010 ASN ** B1038 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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 29 GLN ** E 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 348 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 388 ASN ** O 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 579 ASN ** O 580 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 656 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 701 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 98 HIS ** P 115 GLN ** 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 315 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 389 GLN P 449 GLN P 511 HIS ** Q 372 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 387 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 407 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 40 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.092493 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.072294 restraints weight = 237550.508| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.074254 restraints weight = 128982.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.075540 restraints weight = 83308.202| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 52)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.076372 restraints weight = 60761.103| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.076848 restraints weight = 49048.310| |-----------------------------------------------------------------------------| r_work (final): 0.3414 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7224 moved from start: 0.3960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.139 47692 Z= 0.310 Angle : 1.252 54.123 64864 Z= 0.598 Chirality : 0.059 0.661 7252 Planarity : 0.009 0.178 7976 Dihedral : 13.881 179.740 7127 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 30.50 Ramachandran Plot: Outliers : 1.49 % Allowed : 7.79 % Favored : 90.72 % Rotamer: Outliers : 0.63 % Allowed : 4.08 % Favored : 95.29 % Cbeta Deviations : 0.04 % 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 are not related in a simple way. whole: -2.31 (0.10), residues: 5432 helix: -0.81 (0.10), residues: 1943 sheet: -1.28 (0.17), residues: 750 loop : -2.15 (0.11), residues: 2739 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.060 0.001 ARG O 197 TYR 0.058 0.003 TYR O 196 PHE 0.104 0.004 PHE Q 358 TRP 0.044 0.005 TRP Q 352 HIS 0.029 0.003 HIS P 157 Details of bonding type rmsd/Z covalent geometry : bond 0.00673 / 0.31 (47647) covalent geometry : angle 1.13624 / 0.59 (64831) hydrogen bonds : bond 0.07954 / 5.27 ( 1994) hydrogen bonds : angle 7.55143 / 5.32 ( 5479) metal coordination : bond 0.02500 / 1.47 ( 24) metal coordination : angle 23.36589 / 14.64 ( 33) Misc. bond : bond 0.01338 / 0.78 ( 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 1157 residues out of total 4950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 1126 time to evaluate : 1.841 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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: 0.9199 (mmpt) cc_final: 0.8885 (mmmt) REVERT: A 324 LEU cc_start: 0.9775 (mp) cc_final: 0.9552 (mm) REVERT: A 339 PHE cc_start: 0.8513 (m-80) cc_final: 0.8141 (m-80) REVERT: A 431 GLN cc_start: 0.8478 (tm-30) cc_final: 0.8027 (tm-30) REVERT: A 453 ILE cc_start: 0.9486 (pt) cc_final: 0.9068 (pt) REVERT: A 461 GLU cc_start: 0.7188 (tt0) cc_final: 0.6812 (tt0) REVERT: A 470 HIS cc_start: 0.8093 (m-70) cc_final: 0.6717 (m-70) REVERT: A 505 LEU cc_start: 0.8927 (mp) cc_final: 0.8685 (mp) REVERT: A 518 GLU cc_start: 0.9025 (tt0) cc_final: 0.8549 (tm-30) REVERT: A 589 MET cc_start: 0.8154 (mmm) cc_final: 0.7755 (mmm) REVERT: A 632 GLU cc_start: 0.8634 (mt-10) cc_final: 0.8321 (pt0) REVERT: A 669 LEU cc_start: 0.9057 (mt) cc_final: 0.8835 (mt) REVERT: A 686 PHE cc_start: 0.8892 (m-10) cc_final: 0.8669 (m-80) REVERT: A 699 CYS cc_start: 0.8532 (p) cc_final: 0.8287 (p) REVERT: A 925 MET cc_start: 0.9508 (tpt) cc_final: 0.9079 (tmm) REVERT: A 960 MET cc_start: 0.8443 (mtm) cc_final: 0.7937 (mtp) REVERT: A 994 GLU cc_start: -0.4079 (mt-10) cc_final: -0.4475 (mt-10) REVERT: A 1000 MET cc_start: -0.2310 (mtt) cc_final: -0.2676 (mmm) REVERT: A 1007 ILE cc_start: -0.4304 (mt) cc_final: -0.4587 (mm) REVERT: A 1013 THR cc_start: 0.2974 (m) cc_final: 0.2125 (t) REVERT: A 1056 ASP cc_start: 0.9051 (t0) cc_final: 0.8847 (t0) REVERT: A 1063 MET cc_start: 0.8385 (mmm) cc_final: 0.8184 (mmm) REVERT: A 1175 MET cc_start: 0.8830 (ttm) cc_final: 0.8526 (ttm) REVERT: A 1183 GLU cc_start: 0.8075 (tp30) cc_final: 0.7746 (tp30) REVERT: A 1185 VAL cc_start: 0.9488 (m) cc_final: 0.8897 (m) REVERT: A 1294 MET cc_start: 0.8926 (mtm) cc_final: 0.8586 (mtm) REVERT: A 1490 GLU cc_start: 0.9105 (mt-10) cc_final: 0.8825 (mm-30) REVERT: A 1505 ASP cc_start: 0.8126 (t0) cc_final: 0.7265 (t0) REVERT: A 1507 CYS cc_start: 0.7736 (t) cc_final: 0.7250 (t) REVERT: A 1519 LEU cc_start: 0.9159 (mt) cc_final: 0.8665 (mt) REVERT: A 1589 MET cc_start: 0.9510 (mtt) cc_final: 0.9081 (mmm) REVERT: A 1611 MET cc_start: 0.9600 (ttp) cc_final: 0.8877 (ttp) REVERT: A 1619 CYS cc_start: 0.8918 (m) cc_final: 0.8426 (m) REVERT: A 1620 GLN cc_start: 0.9026 (mp10) cc_final: 0.8786 (mp10) REVERT: A 1621 PHE cc_start: 0.9288 (m-80) cc_final: 0.8936 (m-80) REVERT: B 136 LYS cc_start: 0.8784 (tppt) cc_final: 0.7923 (ttmt) REVERT: B 157 ASP cc_start: 0.9148 (p0) cc_final: 0.8406 (t0) REVERT: B 163 VAL cc_start: 0.9628 (m) cc_final: 0.9357 (p) REVERT: B 166 GLN cc_start: 0.8198 (mp10) cc_final: 0.7941 (mp10) REVERT: B 174 LYS cc_start: 0.9061 (mmpt) cc_final: 0.8804 (mmmt) REVERT: B 215 MET cc_start: 0.7658 (mtt) cc_final: 0.7001 (mtt) REVERT: B 304 ASP cc_start: 0.9506 (m-30) cc_final: 0.9299 (m-30) REVERT: B 359 LEU cc_start: 0.9703 (mt) cc_final: 0.9454 (mt) REVERT: B 373 MET cc_start: 0.8856 (tmm) cc_final: 0.7308 (tmm) REVERT: B 415 GLU cc_start: 0.8729 (tp30) cc_final: 0.8424 (tp30) REVERT: B 416 LYS cc_start: 0.9238 (mmmt) cc_final: 0.8985 (mmtt) REVERT: B 462 GLN cc_start: 0.9431 (tt0) cc_final: 0.9081 (tt0) REVERT: B 496 PHE cc_start: 0.9139 (t80) cc_final: 0.8570 (t80) REVERT: B 515 THR cc_start: 0.9294 (p) cc_final: 0.9083 (t) REVERT: B 543 ASN cc_start: 0.8758 (m-40) cc_final: 0.8492 (m-40) REVERT: B 671 TYR cc_start: 0.8720 (m-80) cc_final: 0.8499 (m-10) REVERT: B 685 VAL cc_start: 0.9523 (OUTLIER) cc_final: 0.9232 (p) REVERT: B 702 ASN cc_start: 0.8916 (m-40) cc_final: 0.8584 (m110) REVERT: B 778 TYR cc_start: 0.8368 (t80) cc_final: 0.7822 (t80) REVERT: B 787 MET cc_start: 0.8299 (pmm) cc_final: 0.7903 (pmm) REVERT: B 790 ASN cc_start: 0.9323 (t0) cc_final: 0.9037 (t0) REVERT: B 905 TYR cc_start: 0.8775 (m-10) cc_final: 0.8067 (m-10) REVERT: B 965 GLU cc_start: 0.8591 (tm-30) cc_final: 0.8348 (tm-30) REVERT: B 982 THR cc_start: 0.9367 (m) cc_final: 0.9144 (p) REVERT: B 1057 MET cc_start: 0.8864 (mpp) cc_final: 0.8612 (mpp) REVERT: B 1074 MET cc_start: 0.8427 (ttm) cc_final: 0.7990 (ttm) REVERT: B 1086 PHE cc_start: 0.7298 (m-80) cc_final: 0.6865 (m-80) REVERT: B 1157 GLN cc_start: 0.9346 (mp-120) cc_final: 0.9060 (mp10) REVERT: B 1174 THR cc_start: 0.9541 (p) cc_final: 0.9197 (p) REVERT: B 1175 THR cc_start: 0.9197 (m) cc_final: 0.8949 (m) REVERT: B 1186 ASP cc_start: 0.9475 (m-30) cc_final: 0.9231 (m-30) REVERT: C 103 LEU cc_start: 0.9388 (mt) cc_final: 0.9106 (mt) REVERT: C 273 ASP cc_start: 0.8658 (t70) cc_final: 0.8351 (t70) REVERT: D 88 GLN cc_start: 0.9270 (mm110) cc_final: 0.8768 (mt0) REVERT: E 28 TYR cc_start: 0.8785 (m-80) cc_final: 0.8372 (m-80) REVERT: E 82 PHE cc_start: 0.9111 (m-10) cc_final: 0.8861 (m-80) REVERT: E 140 LEU cc_start: 0.9366 (mm) cc_final: 0.9058 (mm) REVERT: E 174 GLN cc_start: 0.9198 (mt0) cc_final: 0.8802 (mt0) REVERT: E 182 ASP cc_start: 0.9027 (t70) cc_final: 0.8801 (t70) REVERT: E 215 MET cc_start: 0.8425 (mmt) cc_final: 0.8099 (mmm) REVERT: F 76 LYS cc_start: 0.9277 (mmmm) cc_final: 0.9055 (mmmm) REVERT: F 88 TYR cc_start: 0.8035 (m-80) cc_final: 0.7674 (m-80) REVERT: F 93 ILE cc_start: 0.9730 (OUTLIER) cc_final: 0.9448 (tp) REVERT: F 97 ARG cc_start: 0.9267 (tpt170) cc_final: 0.8810 (tpp80) REVERT: F 111 LEU cc_start: 0.9366 (tt) cc_final: 0.9128 (tt) REVERT: F 132 LEU cc_start: 0.9465 (mt) cc_final: 0.9098 (mt) REVERT: G 45 LEU cc_start: 0.9332 (pp) cc_final: 0.9096 (pp) REVERT: G 75 ASN cc_start: 0.9348 (p0) cc_final: 0.9130 (p0) REVERT: G 110 ASP cc_start: 0.9052 (p0) cc_final: 0.8475 (p0) REVERT: G 113 PHE cc_start: 0.8888 (m-10) cc_final: 0.8402 (m-10) REVERT: H 36 CYS cc_start: 0.8140 (t) cc_final: 0.7933 (t) REVERT: H 116 TYR cc_start: 0.8634 (m-80) cc_final: 0.8429 (m-80) REVERT: H 141 TYR cc_start: 0.8604 (m-80) cc_final: 0.8244 (m-80) REVERT: I 12 ASP cc_start: 0.9545 (m-30) cc_final: 0.9266 (m-30) REVERT: I 64 LYS cc_start: 0.9458 (mtpp) cc_final: 0.9006 (pttt) REVERT: J 1 MET cc_start: 0.7671 (tpt) cc_final: 0.7436 (tpt) REVERT: J 48 ARG cc_start: 0.9390 (ptt90) cc_final: 0.9118 (ptt90) REVERT: J 49 MET cc_start: 0.9507 (tpp) cc_final: 0.8399 (tpp) REVERT: J 59 LYS cc_start: 0.9363 (mmmm) cc_final: 0.8895 (mmmt) REVERT: K 67 GLU cc_start: 0.8347 (tm-30) cc_final: 0.7697 (tm-30) REVERT: K 74 ASN cc_start: 0.9369 (t0) cc_final: 0.8823 (t0) REVERT: K 91 TYR cc_start: 0.8857 (p90) cc_final: 0.8305 (p90) REVERT: K 125 MET cc_start: 0.8613 (mtt) cc_final: 0.7803 (tpp) REVERT: L 53 HIS cc_start: 0.8621 (t70) cc_final: 0.7255 (t-170) REVERT: L 55 ILE cc_start: 0.9647 (mm) cc_final: 0.9323 (mm) REVERT: L 67 PHE cc_start: 0.8436 (m-10) cc_final: 0.8057 (m-10) REVERT: M 12 ILE cc_start: 0.8461 (mm) cc_final: 0.8257 (mm) REVERT: M 26 PHE cc_start: 0.8379 (m-10) cc_final: 0.7589 (m-10) REVERT: M 27 PHE cc_start: 0.7904 (p90) cc_final: 0.7525 (p90) REVERT: M 30 PHE cc_start: 0.9017 (t80) cc_final: 0.8668 (t80) REVERT: M 38 PHE cc_start: 0.9301 (m-10) cc_final: 0.9000 (m-10) REVERT: M 41 TYR cc_start: 0.8710 (m-80) cc_final: 0.8342 (m-80) REVERT: M 75 GLN cc_start: 0.8255 (pp30) cc_final: 0.7850 (pp30) REVERT: N 105 SER cc_start: 0.7993 (OUTLIER) cc_final: 0.7766 (p) REVERT: N 119 LEU cc_start: 0.8100 (mm) cc_final: 0.7720 (tp) REVERT: N 135 LYS cc_start: 0.8179 (mttp) cc_final: 0.7908 (mtpt) REVERT: O 285 MET cc_start: 0.8870 (tmm) cc_final: 0.8542 (pmm) REVERT: O 467 PHE cc_start: 0.9428 (m-80) cc_final: 0.9106 (m-80) REVERT: O 471 MET cc_start: 0.7162 (mtt) cc_final: 0.6829 (mtm) REVERT: O 537 PHE cc_start: 0.9469 (p90) cc_final: 0.9162 (p90) REVERT: P 123 MET cc_start: 0.8766 (mtt) cc_final: 0.8492 (mmt) REVERT: P 207 LEU cc_start: 0.8833 (OUTLIER) cc_final: 0.8534 (tt) REVERT: P 227 TYR cc_start: 0.8184 (m-10) cc_final: 0.7776 (m-80) REVERT: P 254 LEU cc_start: 0.9719 (tp) cc_final: 0.9503 (tp) REVERT: P 258 MET cc_start: 0.9086 (ptt) cc_final: 0.8619 (ptt) REVERT: P 381 MET cc_start: 0.9170 (mmp) cc_final: 0.8839 (mmm) REVERT: P 415 LYS cc_start: 0.9163 (ttpp) cc_final: 0.8951 (ttpp) REVERT: Q 212 HIS cc_start: 0.9501 (m-70) cc_final: 0.9083 (m-70) REVERT: Q 251 TRP cc_start: 0.7365 (p-90) cc_final: 0.5652 (p-90) REVERT: Q 274 MET cc_start: 0.9468 (tpt) cc_final: 0.8708 (tpt) REVERT: Q 308 PHE cc_start: 0.8896 (p90) cc_final: 0.8076 (p90) REVERT: Q 343 GLN cc_start: 0.9024 (mm110) cc_final: 0.8528 (mp10) REVERT: Q 365 TRP cc_start: 0.8067 (m100) cc_final: 0.7632 (m100) outliers start: 31 outliers final: 11 residues processed: 1153 average time/residue: 0.2752 time to fit residues: 525.8091 Evaluate side-chains 795 residues out of total 4950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 780 time to evaluate : 1.811 ------------------------------------------------------------------------------- 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: 8.9990 chunk 133 optimal weight: 20.0000 chunk 345 optimal weight: 8.9990 chunk 450 optimal weight: 0.7980 chunk 375 optimal weight: 3.9990 chunk 544 optimal weight: 6.9990 chunk 214 optimal weight: 20.0000 chunk 163 optimal weight: 8.9990 chunk 104 optimal weight: 3.9990 chunk 159 optimal weight: 9.9990 chunk 332 optimal weight: 8.9990 overall best weight: 4.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 107 HIS A 116 HIS A 382 GLN ** A 435 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 470 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 636 HIS A 738 ASN A1036 ASN A1088 HIS A1113 HIS ** A1320 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1581 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 473 GLN ** 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 715 ASN ** B1100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** J 26 GLN ** K 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 53 HIS 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 490 GLN O 580 ASN ** O 701 HIS ** 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 259 GLN ** P 272 GLN ** 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 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: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.091307 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.071130 restraints weight = 235141.420| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.073053 restraints weight = 129099.333| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.074289 restraints weight = 83666.332| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 56)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.075110 restraints weight = 61606.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.075663 restraints weight = 49656.233| |-----------------------------------------------------------------------------| r_work (final): 0.3387 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7282 moved from start: 0.4862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.212 47692 Z= 0.261 Angle : 1.071 43.841 64864 Z= 0.510 Chirality : 0.054 0.735 7252 Planarity : 0.008 0.343 7976 Dihedral : 14.182 177.405 7127 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 25.90 Ramachandran Plot: Outliers : 1.23 % Allowed : 7.62 % Favored : 91.15 % Rotamer: Outliers : 0.36 % Allowed : 4.53 % Favored : 95.11 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.41 % Twisted General : 0.27 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.85 (0.11), residues: 5432 helix: -0.39 (0.11), residues: 1969 sheet: -1.22 (0.18), residues: 729 loop : -1.85 (0.12), residues: 2734 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.022 0.001 ARG O 197 TYR 0.047 0.003 TYR Q 131 PHE 0.100 0.003 PHE Q 358 TRP 0.048 0.003 TRP O 324 HIS 0.017 0.002 HIS L 53 Details of bonding type rmsd/Z covalent geometry : bond 0.00562 / 0.26 (47647) covalent geometry : angle 0.96582 / 0.50 (64831) hydrogen bonds : bond 0.06656 / 4.45 ( 1994) hydrogen bonds : angle 7.01801 / 4.93 ( 5479) metal coordination : bond 0.01885 / 1.10 ( 24) metal coordination : angle 20.52118 / 12.91 ( 33) Misc. bond : bond 0.01181 / 0.70 ( 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 1024 residues out of total 4950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 1006 time to evaluate : 1.411 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: A 90 PHE cc_start: 0.9344 (m-10) cc_final: 0.9076 (m-10) REVERT: A 214 ASP cc_start: 0.9271 (t70) cc_final: 0.8908 (t0) REVERT: A 218 LYS cc_start: 0.9378 (mtmt) cc_final: 0.9081 (ptpt) REVERT: A 226 LYS cc_start: 0.9266 (mmpt) cc_final: 0.9011 (mmmt) REVERT: A 252 PHE cc_start: 0.7814 (OUTLIER) cc_final: 0.7514 (m-10) REVERT: A 324 LEU cc_start: 0.9788 (mp) cc_final: 0.9570 (mm) REVERT: A 339 PHE cc_start: 0.8747 (m-80) cc_final: 0.8244 (m-80) REVERT: A 437 PHE cc_start: 0.9047 (t80) cc_final: 0.8669 (t80) REVERT: A 470 HIS cc_start: 0.8194 (m-70) cc_final: 0.7932 (m-70) REVERT: A 518 GLU cc_start: 0.9039 (tt0) cc_final: 0.8731 (tm-30) REVERT: A 589 MET cc_start: 0.8440 (mmm) cc_final: 0.7852 (mmm) REVERT: A 597 LYS cc_start: 0.8703 (ptmm) cc_final: 0.8198 (ptmt) REVERT: A 654 ASP cc_start: 0.8933 (m-30) cc_final: 0.8659 (m-30) REVERT: A 674 ILE cc_start: 0.9570 (mt) cc_final: 0.9317 (mm) REVERT: A 686 PHE cc_start: 0.8908 (m-10) cc_final: 0.8697 (m-80) REVERT: A 699 CYS cc_start: 0.8537 (p) cc_final: 0.8245 (p) REVERT: A 925 MET cc_start: 0.9506 (tpt) cc_final: 0.9112 (tmm) REVERT: A 947 LEU cc_start: 0.9067 (mp) cc_final: 0.8832 (mp) REVERT: A 956 ARG cc_start: 0.8476 (ttp80) cc_final: 0.8196 (ttp-110) REVERT: A 960 MET cc_start: 0.8342 (mtm) cc_final: 0.8090 (mtp) REVERT: A 994 GLU cc_start: -0.4521 (mt-10) cc_final: -0.4845 (mt-10) REVERT: A 1000 MET cc_start: -0.1661 (mtt) cc_final: -0.1948 (mmm) REVERT: A 1007 ILE cc_start: -0.4236 (mt) cc_final: -0.4608 (mm) REVERT: A 1008 ASP cc_start: -0.0223 (m-30) cc_final: -0.0472 (m-30) REVERT: A 1019 LEU cc_start: -0.2658 (tp) cc_final: -0.4031 (tp) REVERT: A 1049 MET cc_start: 0.8988 (ptm) cc_final: 0.8675 (ptm) REVERT: A 1056 ASP cc_start: 0.9013 (t0) cc_final: 0.8791 (t0) REVERT: A 1183 GLU cc_start: 0.7982 (tp30) cc_final: 0.7763 (tp30) REVERT: A 1185 VAL cc_start: 0.9512 (m) cc_final: 0.8958 (m) REVERT: A 1238 MET cc_start: 0.7963 (ttm) cc_final: 0.7562 (mtp) REVERT: A 1294 MET cc_start: 0.8949 (mtm) cc_final: 0.8338 (ptp) REVERT: A 1439 MET cc_start: 0.8388 (mmp) cc_final: 0.8139 (mmm) REVERT: A 1476 LEU cc_start: 0.9257 (mt) cc_final: 0.9008 (mt) REVERT: A 1489 VAL cc_start: 0.9697 (t) cc_final: 0.9431 (t) REVERT: A 1504 ILE cc_start: 0.9308 (mm) cc_final: 0.9079 (mm) REVERT: A 1505 ASP cc_start: 0.7893 (t0) cc_final: 0.7152 (t0) REVERT: A 1519 LEU cc_start: 0.9247 (mt) cc_final: 0.8718 (mt) REVERT: A 1589 MET cc_start: 0.9490 (mtt) cc_final: 0.8973 (mmm) REVERT: A 1611 MET cc_start: 0.9165 (ttp) cc_final: 0.8801 (tmm) REVERT: A 1620 GLN cc_start: 0.9032 (mp10) cc_final: 0.8596 (mp10) REVERT: A 1621 PHE cc_start: 0.9283 (m-80) cc_final: 0.8913 (m-80) REVERT: B 125 GLU cc_start: 0.9183 (mt-10) cc_final: 0.8813 (mt-10) REVERT: B 136 LYS cc_start: 0.9009 (tppt) cc_final: 0.8338 (tptp) REVERT: B 138 LEU cc_start: 0.9415 (mm) cc_final: 0.9212 (mm) REVERT: B 163 VAL cc_start: 0.9603 (m) cc_final: 0.9387 (p) REVERT: B 174 LYS cc_start: 0.9143 (mmpt) cc_final: 0.8934 (mmmt) REVERT: B 206 LEU cc_start: 0.9440 (tp) cc_final: 0.9221 (tp) REVERT: B 285 ASP cc_start: 0.8855 (m-30) cc_final: 0.8571 (m-30) REVERT: B 304 ASP cc_start: 0.9457 (m-30) cc_final: 0.9097 (p0) REVERT: B 354 LEU cc_start: 0.9332 (mp) cc_final: 0.9081 (tt) REVERT: B 359 LEU cc_start: 0.9678 (mt) cc_final: 0.9463 (mt) REVERT: B 373 MET cc_start: 0.9058 (tmm) cc_final: 0.8197 (tmm) REVERT: B 374 LEU cc_start: 0.9543 (tp) cc_final: 0.9315 (tp) REVERT: B 419 GLU cc_start: 0.9017 (pt0) cc_final: 0.8672 (pt0) REVERT: B 496 PHE cc_start: 0.9114 (t80) cc_final: 0.8521 (t80) REVERT: B 502 MET cc_start: 0.8900 (ttt) cc_final: 0.7901 (tmm) REVERT: B 515 THR cc_start: 0.9280 (p) cc_final: 0.9063 (t) REVERT: B 640 LEU cc_start: 0.9189 (tp) cc_final: 0.8869 (tp) REVERT: B 778 TYR cc_start: 0.8353 (t80) cc_final: 0.7910 (t80) REVERT: B 790 ASN cc_start: 0.9319 (t0) cc_final: 0.9115 (t0) REVERT: B 982 THR cc_start: 0.9347 (m) cc_final: 0.9111 (p) REVERT: B 1057 MET cc_start: 0.8881 (mpp) cc_final: 0.8599 (mpp) REVERT: B 1073 GLU cc_start: 0.8179 (tp30) cc_final: 0.7957 (tp30) REVERT: B 1074 MET cc_start: 0.8299 (ttm) cc_final: 0.7683 (ttp) REVERT: B 1075 GLU cc_start: 0.8660 (mp0) cc_final: 0.8097 (mm-30) REVERT: B 1086 PHE cc_start: 0.7623 (m-80) cc_final: 0.7248 (m-80) REVERT: B 1157 GLN cc_start: 0.9347 (mp-120) cc_final: 0.8966 (mp10) REVERT: B 1175 THR cc_start: 0.9074 (m) cc_final: 0.8858 (m) REVERT: C 95 GLU cc_start: 0.8163 (mm-30) cc_final: 0.6910 (mm-30) REVERT: C 103 LEU cc_start: 0.9459 (mt) cc_final: 0.9204 (mt) REVERT: C 273 ASP cc_start: 0.8534 (t70) cc_final: 0.8195 (t70) REVERT: E 164 LEU cc_start: 0.9531 (tp) cc_final: 0.9316 (tt) REVERT: E 215 MET cc_start: 0.8514 (mmt) cc_final: 0.8208 (mmm) REVERT: F 76 LYS cc_start: 0.9269 (mmmm) cc_final: 0.9020 (mmmm) REVERT: F 97 ARG cc_start: 0.9205 (tpt170) cc_final: 0.8683 (tpt-90) REVERT: G 45 LEU cc_start: 0.9214 (pp) cc_final: 0.8994 (pp) REVERT: G 110 ASP cc_start: 0.8984 (p0) cc_final: 0.8438 (p0) REVERT: H 102 TYR cc_start: 0.8633 (p90) cc_final: 0.8346 (p90) REVERT: H 141 TYR cc_start: 0.8557 (m-80) cc_final: 0.7950 (m-80) REVERT: I 64 LYS cc_start: 0.9439 (mtpp) cc_final: 0.9027 (pttt) REVERT: J 17 LYS cc_start: 0.9206 (mmtt) cc_final: 0.8986 (mmmt) REVERT: J 48 ARG cc_start: 0.9325 (ptt90) cc_final: 0.9094 (ttp80) REVERT: J 49 MET cc_start: 0.9433 (tpp) cc_final: 0.7864 (tpp) REVERT: J 59 LYS cc_start: 0.9429 (mmmm) cc_final: 0.9013 (mmmt) REVERT: K 67 GLU cc_start: 0.8403 (tm-30) cc_final: 0.7674 (tm-30) REVERT: K 91 TYR cc_start: 0.8985 (p90) cc_final: 0.8711 (p90) REVERT: K 100 LEU cc_start: 0.7956 (mt) cc_final: 0.7642 (mp) REVERT: K 125 MET cc_start: 0.8546 (mtt) cc_final: 0.8146 (mmm) REVERT: L 53 HIS cc_start: 0.7965 (t-90) cc_final: 0.7127 (t-90) REVERT: L 55 ILE cc_start: 0.9435 (mm) cc_final: 0.8692 (mm) REVERT: L 67 PHE cc_start: 0.8355 (m-10) cc_final: 0.8109 (m-10) REVERT: M 26 PHE cc_start: 0.8473 (m-10) cc_final: 0.7619 (m-10) REVERT: M 27 PHE cc_start: 0.7708 (p90) cc_final: 0.7377 (p90) REVERT: M 30 PHE cc_start: 0.8918 (t80) cc_final: 0.8439 (t80) REVERT: M 38 PHE cc_start: 0.9247 (m-10) cc_final: 0.8919 (m-10) REVERT: M 41 TYR cc_start: 0.8706 (m-80) cc_final: 0.8222 (m-80) REVERT: N 119 LEU cc_start: 0.8298 (mm) cc_final: 0.7889 (tp) REVERT: N 135 LYS cc_start: 0.8246 (mttp) cc_final: 0.7885 (mtpt) REVERT: O 467 PHE cc_start: 0.9553 (m-80) cc_final: 0.9218 (m-80) REVERT: O 471 MET cc_start: 0.7009 (mtt) cc_final: 0.6773 (mtm) REVERT: O 537 PHE cc_start: 0.9481 (p90) cc_final: 0.9006 (p90) REVERT: P 226 LEU cc_start: 0.9395 (pp) cc_final: 0.8841 (pp) REVERT: P 227 TYR cc_start: 0.8332 (m-10) cc_final: 0.7962 (m-80) REVERT: P 254 LEU cc_start: 0.9722 (tp) cc_final: 0.9395 (tp) REVERT: P 258 MET cc_start: 0.8893 (ptt) cc_final: 0.8235 (ptt) REVERT: P 363 SER cc_start: 0.8539 (t) cc_final: 0.8298 (m) REVERT: P 381 MET cc_start: 0.9141 (mmp) cc_final: 0.8897 (mmm) REVERT: P 413 LEU cc_start: 0.9768 (mt) cc_final: 0.9472 (mt) REVERT: P 415 LYS cc_start: 0.9147 (ttpp) cc_final: 0.8902 (ttpp) REVERT: Q 157 MET cc_start: 0.4419 (ttt) cc_final: 0.3886 (tpp) REVERT: Q 173 MET cc_start: 0.8312 (mmt) cc_final: 0.8066 (mmt) REVERT: Q 212 HIS cc_start: 0.9433 (m-70) cc_final: 0.8957 (m-70) REVERT: Q 251 TRP cc_start: 0.7097 (p-90) cc_final: 0.6498 (p-90) REVERT: Q 259 ASP cc_start: 0.9301 (t0) cc_final: 0.8915 (t0) REVERT: Q 274 MET cc_start: 0.9569 (tpt) cc_final: 0.8765 (tpt) REVERT: Q 281 LYS cc_start: 0.8118 (mttt) cc_final: 0.7913 (mtmm) REVERT: Q 343 GLN cc_start: 0.8945 (mm110) cc_final: 0.8515 (mp10) REVERT: Q 344 GLU cc_start: 0.9138 (OUTLIER) cc_final: 0.8821 (tp30) REVERT: Q 352 TRP cc_start: 0.7856 (m-10) cc_final: 0.7081 (m-10) REVERT: Q 365 TRP cc_start: 0.9035 (m100) cc_final: 0.8438 (m100) outliers start: 18 outliers final: 7 residues processed: 1017 average time/residue: 0.2554 time to fit residues: 433.8338 Evaluate side-chains 753 residues out of total 4950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 744 time to evaluate : 1.496 ------------------------------------------------------------------------------- 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: 30.0000 chunk 492 optimal weight: 10.0000 chunk 110 optimal weight: 4.9990 chunk 165 optimal weight: 3.9990 chunk 64 optimal weight: 0.9990 chunk 33 optimal weight: 20.0000 chunk 147 optimal weight: 0.0770 chunk 307 optimal weight: 6.9990 chunk 544 optimal weight: 1.9990 chunk 285 optimal weight: 0.2980 chunk 49 optimal weight: 20.0000 overall best weight: 1.4744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 106 HIS ** A 435 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 470 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 649 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 656 GLN A 819 ASN ** A1180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1320 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 462 GLN ** 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 600 GLN ** B 636 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 673 ASN ** B 702 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 899 GLN ** B1041 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1058 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 3 GLN E 99 HIS ** G 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 11 GLN H 134 ASN ** K 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 89 GLN ** O 346 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 348 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 483 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 701 HIS ** 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 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 260 ASN Q 319 ASN ** Q 407 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 409 HIS Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.092407 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.072342 restraints weight = 229585.237| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.074278 restraints weight = 125934.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.075513 restraints weight = 82434.852| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.076384 restraints weight = 60525.445| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.076909 restraints weight = 48542.384| |-----------------------------------------------------------------------------| r_work (final): 0.3423 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7238 moved from start: 0.5346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.191 47692 Z= 0.197 Angle : 0.974 40.448 64864 Z= 0.468 Chirality : 0.052 0.733 7252 Planarity : 0.008 0.377 7976 Dihedral : 14.258 178.441 7127 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 22.82 Ramachandran Plot: Outliers : 1.09 % Allowed : 7.60 % Favored : 91.31 % Rotamer: Outliers : 0.10 % Allowed : 3.46 % Favored : 96.44 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.83 % Twisted General : 0.21 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.59 (0.11), residues: 5432 helix: -0.13 (0.11), residues: 1969 sheet: -1.14 (0.18), residues: 730 loop : -1.73 (0.12), residues: 2733 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.072 0.001 ARG O 197 TYR 0.044 0.003 TYR A 478 PHE 0.103 0.002 PHE Q 358 TRP 0.053 0.003 TRP N 54 HIS 0.017 0.002 HIS B1038 Details of bonding type rmsd/Z covalent geometry : bond 0.00424 / 0.19 (47647) covalent geometry : angle 0.89593 / 0.46 (64831) hydrogen bonds : bond 0.06078 / 4.06 ( 1994) hydrogen bonds : angle 6.68846 / 4.70 ( 5479) metal coordination : bond 0.01748 / 0.96 ( 24) metal coordination : angle 17.01434 / 10.65 ( 33) Misc. bond : bond 0.01410 / 0.82 ( 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 997 residues out of total 4950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 992 time to evaluate : 1.733 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: A 213 ASN cc_start: 0.9303 (t0) cc_final: 0.9102 (t0) REVERT: A 214 ASP cc_start: 0.9251 (t70) cc_final: 0.8286 (t0) REVERT: A 215 GLU cc_start: 0.8389 (mp0) cc_final: 0.8120 (mp0) REVERT: A 218 LYS cc_start: 0.9345 (mtmt) cc_final: 0.8970 (ptpt) REVERT: A 226 LYS cc_start: 0.9369 (mmpt) cc_final: 0.9024 (mmmt) REVERT: A 339 PHE cc_start: 0.8676 (m-80) cc_final: 0.8149 (m-80) REVERT: A 437 PHE cc_start: 0.9086 (t80) cc_final: 0.8810 (t80) REVERT: A 470 HIS cc_start: 0.7977 (m-70) cc_final: 0.7739 (m-70) REVERT: A 484 ILE cc_start: 0.9722 (pt) cc_final: 0.9348 (mp) REVERT: A 518 GLU cc_start: 0.9003 (tt0) cc_final: 0.8739 (tm-30) REVERT: A 589 MET cc_start: 0.8382 (mmm) cc_final: 0.7776 (mmm) REVERT: A 597 LYS cc_start: 0.8575 (ptmm) cc_final: 0.8336 (ptmt) REVERT: A 654 ASP cc_start: 0.8822 (m-30) cc_final: 0.8537 (m-30) REVERT: A 674 ILE cc_start: 0.9529 (mt) cc_final: 0.9277 (mm) REVERT: A 675 SER cc_start: 0.9524 (m) cc_final: 0.9281 (p) REVERT: A 699 CYS cc_start: 0.8384 (p) cc_final: 0.8074 (p) REVERT: A 821 ILE cc_start: 0.9267 (mm) cc_final: 0.9038 (mm) REVERT: A 925 MET cc_start: 0.9483 (tpt) cc_final: 0.9078 (tmm) REVERT: A 943 ILE cc_start: 0.9645 (mt) cc_final: 0.9303 (pt) REVERT: A 944 MET cc_start: 0.8843 (mmp) cc_final: 0.8642 (mmm) REVERT: A 947 LEU cc_start: 0.9086 (mp) cc_final: 0.8771 (mp) REVERT: A 1007 ILE cc_start: -0.4755 (mt) cc_final: -0.5085 (mm) REVERT: A 1008 ASP cc_start: -0.0214 (m-30) cc_final: -0.0538 (m-30) REVERT: A 1009 THR cc_start: 0.0447 (m) cc_final: 0.0147 (m) REVERT: A 1063 MET cc_start: 0.8591 (mmp) cc_final: 0.8358 (mmm) REVERT: A 1183 GLU cc_start: 0.8129 (tp30) cc_final: 0.7910 (tp30) REVERT: A 1185 VAL cc_start: 0.9458 (m) cc_final: 0.8936 (m) REVERT: A 1195 GLU cc_start: 0.9050 (tm-30) cc_final: 0.8579 (tt0) REVERT: A 1238 MET cc_start: 0.7824 (ttm) cc_final: 0.7586 (mtp) REVERT: A 1294 MET cc_start: 0.8888 (mtm) cc_final: 0.8353 (ptp) REVERT: A 1485 MET cc_start: 0.8762 (pmm) cc_final: 0.8525 (pmm) REVERT: A 1489 VAL cc_start: 0.9676 (t) cc_final: 0.9443 (t) REVERT: A 1504 ILE cc_start: 0.9284 (mm) cc_final: 0.9044 (mm) REVERT: A 1505 ASP cc_start: 0.8002 (t0) cc_final: 0.7206 (t0) REVERT: A 1519 LEU cc_start: 0.9231 (mt) cc_final: 0.8641 (mt) REVERT: A 1589 MET cc_start: 0.9456 (mtt) cc_final: 0.8912 (mmm) REVERT: A 1620 GLN cc_start: 0.9011 (mp10) cc_final: 0.8638 (mp10) REVERT: A 1621 PHE cc_start: 0.9230 (m-80) cc_final: 0.8749 (m-80) REVERT: A 1655 ASP cc_start: 0.8467 (m-30) cc_final: 0.7989 (m-30) REVERT: B 125 GLU cc_start: 0.9169 (mt-10) cc_final: 0.8852 (mt-10) REVERT: B 136 LYS cc_start: 0.8957 (tppt) cc_final: 0.8217 (tptp) REVERT: B 164 MET cc_start: 0.7706 (ttt) cc_final: 0.7332 (ttt) REVERT: B 166 GLN cc_start: 0.8479 (mp10) cc_final: 0.8076 (mm-40) REVERT: B 174 LYS cc_start: 0.9132 (mmpt) cc_final: 0.8887 (mmmt) REVERT: B 206 LEU cc_start: 0.9425 (tp) cc_final: 0.9110 (tp) REVERT: B 285 ASP cc_start: 0.8923 (m-30) cc_final: 0.8616 (m-30) REVERT: B 304 ASP cc_start: 0.9436 (m-30) cc_final: 0.9088 (p0) REVERT: B 398 GLN cc_start: 0.9113 (pt0) cc_final: 0.8740 (pt0) REVERT: B 495 ARG cc_start: 0.8473 (tpt170) cc_final: 0.8269 (tpt170) REVERT: B 496 PHE cc_start: 0.9080 (t80) cc_final: 0.8512 (t80) REVERT: B 514 THR cc_start: 0.8512 (p) cc_final: 0.7627 (p) REVERT: B 515 THR cc_start: 0.9267 (p) cc_final: 0.9046 (t) REVERT: B 543 ASN cc_start: 0.8890 (m110) cc_final: 0.8616 (m110) REVERT: B 588 ILE cc_start: 0.9603 (tp) cc_final: 0.9385 (tp) REVERT: B 778 TYR cc_start: 0.8287 (t80) cc_final: 0.7966 (t80) REVERT: B 982 THR cc_start: 0.9400 (m) cc_final: 0.9111 (p) REVERT: B 1074 MET cc_start: 0.8282 (ttm) cc_final: 0.7620 (ttp) REVERT: B 1075 GLU cc_start: 0.8643 (mp0) cc_final: 0.8051 (mm-30) REVERT: B 1086 PHE cc_start: 0.7589 (m-80) cc_final: 0.7199 (m-80) REVERT: B 1157 GLN cc_start: 0.9384 (mp-120) cc_final: 0.8982 (mp10) REVERT: C 95 GLU cc_start: 0.8058 (mm-30) cc_final: 0.7065 (mm-30) REVERT: C 273 ASP cc_start: 0.8467 (t70) cc_final: 0.8136 (t70) REVERT: D 25 THR cc_start: 0.9302 (p) cc_final: 0.8849 (p) REVERT: E 2 ASP cc_start: 0.9132 (p0) cc_final: 0.8813 (p0) REVERT: E 140 LEU cc_start: 0.9382 (mm) cc_final: 0.9111 (mm) REVERT: E 164 LEU cc_start: 0.9466 (tp) cc_final: 0.9169 (tt) REVERT: E 174 GLN cc_start: 0.9163 (mt0) cc_final: 0.8733 (mt0) REVERT: E 182 ASP cc_start: 0.9096 (t70) cc_final: 0.8890 (t70) REVERT: E 215 MET cc_start: 0.8647 (mmt) cc_final: 0.8262 (mmm) REVERT: F 76 LYS cc_start: 0.9260 (mmmm) cc_final: 0.9031 (mmmm) REVERT: F 88 TYR cc_start: 0.7961 (m-80) cc_final: 0.7336 (m-80) REVERT: F 97 ARG cc_start: 0.9211 (tpt170) cc_final: 0.8825 (tpp80) REVERT: F 122 MET cc_start: 0.9141 (mtp) cc_final: 0.8891 (mtp) REVERT: F 136 ARG cc_start: 0.7893 (mtt180) cc_final: 0.7683 (mtt180) REVERT: G 45 LEU cc_start: 0.9225 (pp) cc_final: 0.9016 (pp) REVERT: G 110 ASP cc_start: 0.8819 (p0) cc_final: 0.8397 (p0) REVERT: H 102 TYR cc_start: 0.8609 (p90) cc_final: 0.8156 (p90) REVERT: I 64 LYS cc_start: 0.9417 (mtpp) cc_final: 0.8833 (mtpp) REVERT: J 28 ASP cc_start: 0.8892 (t70) cc_final: 0.8461 (t0) REVERT: J 48 ARG cc_start: 0.9233 (ptt90) cc_final: 0.8888 (tmm-80) REVERT: J 49 MET cc_start: 0.9381 (tpp) cc_final: 0.8534 (tpp) REVERT: J 52 THR cc_start: 0.9184 (p) cc_final: 0.8966 (p) REVERT: J 59 LYS cc_start: 0.9415 (mmmm) cc_final: 0.9012 (mmmt) REVERT: K 67 GLU cc_start: 0.8463 (tm-30) cc_final: 0.7749 (tm-30) REVERT: K 74 ASN cc_start: 0.9355 (t0) cc_final: 0.9096 (t0) REVERT: K 102 ASN cc_start: 0.8301 (p0) cc_final: 0.7943 (p0) REVERT: K 125 MET cc_start: 0.8514 (mtt) cc_final: 0.8047 (mmt) REVERT: L 67 PHE cc_start: 0.8271 (m-10) cc_final: 0.7802 (m-10) REVERT: M 12 ILE cc_start: 0.8634 (mm) cc_final: 0.8425 (mm) REVERT: M 26 PHE cc_start: 0.8483 (m-10) cc_final: 0.7539 (m-10) REVERT: M 27 PHE cc_start: 0.7595 (p90) cc_final: 0.7283 (p90) REVERT: M 30 PHE cc_start: 0.8974 (t80) cc_final: 0.8424 (t80) REVERT: M 38 PHE cc_start: 0.9236 (m-10) cc_final: 0.8917 (m-10) REVERT: M 41 TYR cc_start: 0.8672 (m-80) cc_final: 0.8184 (m-80) REVERT: M 92 LYS cc_start: 0.8465 (ttpt) cc_final: 0.8170 (ttpt) REVERT: N 29 PHE cc_start: 0.8980 (m-80) cc_final: 0.8533 (m-80) REVERT: N 107 MET cc_start: 0.9055 (tmm) cc_final: 0.8762 (mmt) REVERT: N 117 GLU cc_start: 0.8540 (tt0) cc_final: 0.8335 (tm-30) REVERT: N 135 LYS cc_start: 0.8312 (mttp) cc_final: 0.8075 (mtpt) REVERT: O 380 MET cc_start: 0.9022 (mtp) cc_final: 0.8605 (mtp) REVERT: O 408 ILE cc_start: 0.7670 (tp) cc_final: 0.7452 (tp) REVERT: O 467 PHE cc_start: 0.9566 (m-80) cc_final: 0.9166 (m-80) REVERT: O 471 MET cc_start: 0.6862 (mtt) cc_final: 0.6611 (mtm) REVERT: O 537 PHE cc_start: 0.9484 (p90) cc_final: 0.9011 (p90) REVERT: P 226 LEU cc_start: 0.9332 (pp) cc_final: 0.8881 (pp) REVERT: P 227 TYR cc_start: 0.8067 (m-10) cc_final: 0.7812 (m-80) REVERT: P 254 LEU cc_start: 0.9718 (tp) cc_final: 0.9356 (tp) REVERT: P 258 MET cc_start: 0.8920 (ptt) cc_final: 0.8225 (ptt) REVERT: P 355 VAL cc_start: 0.9085 (m) cc_final: 0.8630 (t) REVERT: P 381 MET cc_start: 0.9237 (mmp) cc_final: 0.8951 (mmm) REVERT: P 402 MET cc_start: 0.8124 (mpp) cc_final: 0.7919 (mpp) REVERT: P 413 LEU cc_start: 0.9763 (mt) cc_final: 0.9500 (mt) REVERT: P 415 LYS cc_start: 0.8990 (ttpp) cc_final: 0.8754 (ptmt) REVERT: Q 1 MET cc_start: 0.7777 (tmm) cc_final: 0.6171 (tmm) REVERT: Q 157 MET cc_start: 0.4239 (ttt) cc_final: 0.3511 (tpp) REVERT: Q 212 HIS cc_start: 0.9456 (m-70) cc_final: 0.8901 (m-70) REVERT: Q 229 TRP cc_start: 0.6153 (t60) cc_final: 0.5822 (t60) REVERT: Q 251 TRP cc_start: 0.6908 (p-90) cc_final: 0.6317 (p-90) REVERT: Q 257 ILE cc_start: 0.9313 (tp) cc_final: 0.8823 (tp) REVERT: Q 259 ASP cc_start: 0.9256 (t0) cc_final: 0.9022 (t0) REVERT: Q 274 MET cc_start: 0.9562 (tpt) cc_final: 0.8895 (tpp) REVERT: Q 343 GLN cc_start: 0.8955 (mm110) cc_final: 0.8398 (mp10) REVERT: Q 365 TRP cc_start: 0.9079 (m100) cc_final: 0.8357 (m100) outliers start: 5 outliers final: 0 residues processed: 996 average time/residue: 0.2427 time to fit residues: 406.0719 Evaluate side-chains 741 residues out of total 4950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 741 time to evaluate : 1.371 ------------------------------------------------------------------------------- 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: 2.9990 chunk 306 optimal weight: 20.0000 chunk 241 optimal weight: 20.0000 chunk 144 optimal weight: 7.9990 chunk 20 optimal weight: 0.0770 chunk 128 optimal weight: 10.0000 chunk 454 optimal weight: 50.0000 chunk 320 optimal weight: 1.9990 chunk 61 optimal weight: 9.9990 chunk 217 optimal weight: 9.9990 chunk 552 optimal weight: 50.0000 overall best weight: 4.6146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 382 GLN A 432 ASN A 649 ASN ** A1191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1320 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 231 HIS B 248 ASN B 351 GLN ** B 547 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 575 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 636 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 702 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 715 ASN B 764 ASN B 999 GLN B1041 ASN ** B1100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 3 GLN ** E 153 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** I 32 GLN ** K 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 54 HIS ** O 346 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 348 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 483 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 769 GLN ** P 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 155 GLN ** 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 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: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.091129 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.071048 restraints weight = 235892.214| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.072958 restraints weight = 128123.464| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.074192 restraints weight = 82393.050| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.074923 restraints weight = 60744.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.075470 restraints weight = 49638.846| |-----------------------------------------------------------------------------| r_work (final): 0.3383 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7310 moved from start: 0.5680 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= 0.225 Angle : 0.941 38.497 64864 Z= 0.456 Chirality : 0.050 0.708 7252 Planarity : 0.007 0.146 7976 Dihedral : 14.331 179.236 7127 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 22.96 Ramachandran Plot: Outliers : 0.94 % Allowed : 7.77 % Favored : 91.29 % Rotamer: Outliers : 0.04 % Allowed : 3.15 % Favored : 96.81 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.24 % Twisted General : 0.21 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.46 (0.11), residues: 5432 helix: 0.05 (0.11), residues: 1956 sheet: -1.19 (0.18), residues: 735 loop : -1.67 (0.12), residues: 2741 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.001 ARG B 815 TYR 0.040 0.002 TYR A 478 PHE 0.100 0.003 PHE Q 358 TRP 0.057 0.002 TRP N 54 HIS 0.017 0.001 HIS P 157 Details of bonding type rmsd/Z covalent geometry : bond 0.00471 / 0.22 (47647) covalent geometry : angle 0.87771 / 0.45 (64831) hydrogen bonds : bond 0.05784 / 3.85 ( 1994) hydrogen bonds : angle 6.49614 / 4.57 ( 5479) metal coordination : bond 0.01982 / 1.06 ( 24) metal coordination : angle 15.04069 / 9.31 ( 33) Misc. bond : bond 0.01572 / 0.82 ( 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 915 residues out of total 4950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 913 time to evaluate : 1.217 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: A 90 PHE cc_start: 0.9521 (m-80) cc_final: 0.9204 (m-10) REVERT: A 226 LYS cc_start: 0.9499 (mmpt) cc_final: 0.9082 (mmmt) REVERT: A 339 PHE cc_start: 0.8824 (m-80) cc_final: 0.8272 (m-80) REVERT: A 437 PHE cc_start: 0.9061 (t80) cc_final: 0.8814 (t80) REVERT: A 470 HIS cc_start: 0.8088 (m-70) cc_final: 0.7639 (m-70) REVERT: A 471 MET cc_start: 0.8287 (mmp) cc_final: 0.7843 (mmp) REVERT: A 589 MET cc_start: 0.8317 (mmm) cc_final: 0.7969 (mmm) REVERT: A 618 TYR cc_start: 0.8609 (m-80) cc_final: 0.8371 (m-10) REVERT: A 654 ASP cc_start: 0.8771 (m-30) cc_final: 0.8549 (m-30) REVERT: A 672 ASP cc_start: 0.8355 (t70) cc_final: 0.7999 (t0) REVERT: A 686 PHE cc_start: 0.8850 (m-10) cc_final: 0.8585 (m-80) REVERT: A 699 CYS cc_start: 0.8541 (p) cc_final: 0.8242 (p) REVERT: A 736 LEU cc_start: 0.9673 (mt) cc_final: 0.9441 (mt) REVERT: A 822 THR cc_start: 0.9294 (p) cc_final: 0.8950 (t) REVERT: A 830 MET cc_start: 0.8783 (mmm) cc_final: 0.8506 (mmm) REVERT: A 925 MET cc_start: 0.9456 (tpt) cc_final: 0.9057 (tmm) REVERT: A 943 ILE cc_start: 0.9653 (mt) cc_final: 0.9321 (pt) REVERT: A 960 MET cc_start: 0.7709 (mtp) cc_final: 0.7282 (mtp) REVERT: A 1000 MET cc_start: -0.1519 (mtt) cc_final: -0.1753 (mmm) REVERT: A 1007 ILE cc_start: -0.4903 (mt) cc_final: -0.5110 (mm) REVERT: A 1009 THR cc_start: 0.0384 (m) cc_final: 0.0042 (m) REVERT: A 1183 GLU cc_start: 0.8269 (tp30) cc_final: 0.7929 (tp30) REVERT: A 1185 VAL cc_start: 0.9542 (m) cc_final: 0.9049 (m) REVERT: A 1224 GLU cc_start: 0.9045 (mp0) cc_final: 0.8738 (mp0) REVERT: A 1238 MET cc_start: 0.7846 (ttm) cc_final: 0.7642 (mtp) REVERT: A 1294 MET cc_start: 0.8875 (mtm) cc_final: 0.8495 (ptp) REVERT: A 1439 MET cc_start: 0.8461 (mmp) cc_final: 0.8244 (mmm) REVERT: A 1476 LEU cc_start: 0.9246 (mt) cc_final: 0.8971 (mt) REVERT: A 1485 MET cc_start: 0.8817 (pmm) cc_final: 0.8608 (pmm) REVERT: A 1504 ILE cc_start: 0.9293 (mm) cc_final: 0.9063 (mm) REVERT: A 1565 GLU cc_start: 0.8629 (mm-30) cc_final: 0.8409 (mt-10) REVERT: A 1589 MET cc_start: 0.9418 (mtt) cc_final: 0.8908 (mmm) REVERT: A 1610 PHE cc_start: 0.9537 (m-80) cc_final: 0.9244 (m-80) REVERT: A 1620 GLN cc_start: 0.9053 (mp10) cc_final: 0.8637 (mp10) REVERT: A 1621 PHE cc_start: 0.9269 (m-80) cc_final: 0.8834 (m-80) REVERT: A 1655 ASP cc_start: 0.8499 (m-30) cc_final: 0.8231 (m-30) REVERT: B 108 MET cc_start: 0.8889 (mmp) cc_final: 0.8601 (mmp) REVERT: B 125 GLU cc_start: 0.9155 (mt-10) cc_final: 0.8709 (mt-10) REVERT: B 136 LYS cc_start: 0.9005 (tppt) cc_final: 0.8524 (tptp) REVERT: B 164 MET cc_start: 0.7967 (ttt) cc_final: 0.7766 (ttt) REVERT: B 174 LYS cc_start: 0.9186 (mmpt) cc_final: 0.8937 (mmmt) REVERT: B 206 LEU cc_start: 0.9467 (tp) cc_final: 0.9148 (tp) REVERT: B 215 MET cc_start: 0.7530 (mtt) cc_final: 0.6954 (mtt) REVERT: B 285 ASP cc_start: 0.8957 (m-30) cc_final: 0.8655 (m-30) REVERT: B 304 ASP cc_start: 0.9480 (m-30) cc_final: 0.9105 (p0) REVERT: B 359 LEU cc_start: 0.9371 (mt) cc_final: 0.9168 (mm) REVERT: B 398 GLN cc_start: 0.9026 (pt0) cc_final: 0.8774 (pt0) REVERT: B 422 GLN cc_start: 0.9170 (tm-30) cc_final: 0.8762 (tm-30) REVERT: B 489 GLU cc_start: 0.8203 (tt0) cc_final: 0.7643 (tt0) REVERT: B 495 ARG cc_start: 0.8467 (tpt170) cc_final: 0.8016 (tpt-90) REVERT: B 514 THR cc_start: 0.8531 (p) cc_final: 0.8128 (p) REVERT: B 515 THR cc_start: 0.9269 (p) cc_final: 0.9034 (t) REVERT: B 543 ASN cc_start: 0.8958 (m110) cc_final: 0.8708 (m110) REVERT: B 568 LEU cc_start: 0.9054 (mt) cc_final: 0.8670 (mt) REVERT: B 575 HIS cc_start: 0.8320 (m-70) cc_final: 0.8100 (m-70) REVERT: B 778 TYR cc_start: 0.8499 (t80) cc_final: 0.7943 (t80) REVERT: B 783 MET cc_start: 0.7305 (mmm) cc_final: 0.6819 (mmm) REVERT: B 790 ASN cc_start: 0.9409 (t0) cc_final: 0.9203 (t0) REVERT: B 803 MET cc_start: 0.8586 (ttm) cc_final: 0.8044 (mtp) REVERT: B 898 LEU cc_start: 0.9310 (tp) cc_final: 0.8949 (tp) REVERT: B 965 GLU cc_start: 0.8742 (tm-30) cc_final: 0.8482 (tm-30) REVERT: B 982 THR cc_start: 0.9405 (m) cc_final: 0.9123 (p) REVERT: B 1074 MET cc_start: 0.8223 (ttm) cc_final: 0.7725 (ttp) REVERT: B 1086 PHE cc_start: 0.7697 (m-80) cc_final: 0.5182 (m-80) REVERT: B 1098 TYR cc_start: 0.8864 (t80) cc_final: 0.8010 (t80) REVERT: B 1157 GLN cc_start: 0.9384 (mp-120) cc_final: 0.9084 (mp10) REVERT: C 95 GLU cc_start: 0.7977 (mm-30) cc_final: 0.7174 (mm-30) REVERT: C 181 ASP cc_start: 0.8865 (m-30) cc_final: 0.8642 (p0) REVERT: C 273 ASP cc_start: 0.8527 (t70) cc_final: 0.8163 (t70) REVERT: D 25 THR cc_start: 0.9412 (p) cc_final: 0.8919 (p) REVERT: D 34 ASP cc_start: 0.9082 (p0) cc_final: 0.8655 (p0) REVERT: D 91 ARG cc_start: 0.9318 (ptp90) cc_final: 0.9103 (ptp-170) REVERT: D 96 PHE cc_start: 0.8314 (m-80) cc_final: 0.7311 (m-80) REVERT: E 2 ASP cc_start: 0.9113 (p0) cc_final: 0.8792 (p0) REVERT: E 140 LEU cc_start: 0.9383 (mm) cc_final: 0.9116 (mm) REVERT: E 164 LEU cc_start: 0.9412 (tp) cc_final: 0.9208 (tt) REVERT: E 215 MET cc_start: 0.8664 (mmt) cc_final: 0.8294 (mmm) REVERT: F 76 LYS cc_start: 0.9317 (mmmm) cc_final: 0.9094 (mmmm) REVERT: F 77 ASP cc_start: 0.8711 (t0) cc_final: 0.8491 (p0) REVERT: F 88 TYR cc_start: 0.8108 (m-80) cc_final: 0.7444 (m-80) REVERT: F 92 ARG cc_start: 0.9188 (tpt-90) cc_final: 0.8647 (tpt-90) REVERT: F 122 MET cc_start: 0.9141 (mtp) cc_final: 0.8904 (mtp) REVERT: F 151 LEU cc_start: 0.9202 (mm) cc_final: 0.8470 (tp) REVERT: G 52 MET cc_start: 0.8936 (ptm) cc_final: 0.7878 (tmm) REVERT: G 98 GLU cc_start: 0.8407 (mm-30) cc_final: 0.8121 (mp0) REVERT: G 110 ASP cc_start: 0.8903 (p0) cc_final: 0.8446 (p0) REVERT: G 119 HIS cc_start: 0.7922 (t-90) cc_final: 0.7441 (t-90) REVERT: H 40 LEU cc_start: 0.9063 (tp) cc_final: 0.8850 (tp) REVERT: H 102 TYR cc_start: 0.8641 (p90) cc_final: 0.8145 (p90) REVERT: H 139 ASN cc_start: 0.9267 (p0) cc_final: 0.8997 (t0) REVERT: I 64 LYS cc_start: 0.9380 (mtpp) cc_final: 0.8780 (mtpp) REVERT: J 28 ASP cc_start: 0.8955 (t70) cc_final: 0.8502 (t0) REVERT: J 49 MET cc_start: 0.9403 (tpp) cc_final: 0.8179 (tpp) REVERT: J 59 LYS cc_start: 0.9460 (mmmm) cc_final: 0.9063 (mmmt) REVERT: K 67 GLU cc_start: 0.8388 (tm-30) cc_final: 0.7766 (tm-30) REVERT: K 76 LEU cc_start: 0.9288 (tp) cc_final: 0.9062 (tp) REVERT: K 125 MET cc_start: 0.8596 (mtt) cc_final: 0.8313 (mmm) REVERT: L 53 HIS cc_start: 0.8653 (t-90) cc_final: 0.8040 (t-90) REVERT: L 67 PHE cc_start: 0.8317 (m-10) cc_final: 0.7808 (m-10) REVERT: M 12 ILE cc_start: 0.8672 (mm) cc_final: 0.8448 (mm) REVERT: M 26 PHE cc_start: 0.8519 (m-10) cc_final: 0.7597 (m-10) REVERT: M 30 PHE cc_start: 0.9031 (t80) cc_final: 0.8617 (t80) REVERT: M 41 TYR cc_start: 0.8657 (m-80) cc_final: 0.8205 (m-80) REVERT: M 92 LYS cc_start: 0.8398 (ttpt) cc_final: 0.8091 (ttpt) REVERT: N 29 PHE cc_start: 0.8892 (m-80) cc_final: 0.8325 (m-80) REVERT: O 293 TYR cc_start: 0.8406 (t80) cc_final: 0.8063 (t80) REVERT: O 408 ILE cc_start: 0.7769 (tp) cc_final: 0.7533 (tp) REVERT: O 463 LEU cc_start: 0.8976 (pt) cc_final: 0.8651 (mm) REVERT: O 467 PHE cc_start: 0.9605 (m-80) cc_final: 0.9166 (m-80) REVERT: O 537 PHE cc_start: 0.9487 (p90) cc_final: 0.8940 (p90) REVERT: P 227 TYR cc_start: 0.8257 (m-80) cc_final: 0.7765 (m-80) REVERT: P 238 HIS cc_start: 0.9328 (m-70) cc_final: 0.8967 (m90) REVERT: P 254 LEU cc_start: 0.9724 (tp) cc_final: 0.9346 (tp) REVERT: P 258 MET cc_start: 0.8766 (ptt) cc_final: 0.8115 (ptt) REVERT: P 317 MET cc_start: 0.8898 (tpt) cc_final: 0.8684 (tpt) REVERT: P 355 VAL cc_start: 0.9074 (m) cc_final: 0.8666 (t) REVERT: P 381 MET cc_start: 0.9321 (mmp) cc_final: 0.8995 (mmm) REVERT: P 402 MET cc_start: 0.8153 (mpp) cc_final: 0.7913 (mpp) REVERT: P 413 LEU cc_start: 0.9795 (mt) cc_final: 0.9468 (mt) REVERT: Q 157 MET cc_start: 0.4701 (ttt) cc_final: 0.3707 (tpp) REVERT: Q 173 MET cc_start: 0.8907 (mpp) cc_final: 0.8524 (mpp) REVERT: Q 212 HIS cc_start: 0.9448 (m-70) cc_final: 0.8908 (m-70) REVERT: Q 228 ASN cc_start: 0.8613 (m110) cc_final: 0.8383 (m110) REVERT: Q 251 TRP cc_start: 0.6908 (p-90) cc_final: 0.6268 (p-90) REVERT: Q 257 ILE cc_start: 0.9419 (tp) cc_final: 0.8926 (tp) REVERT: Q 259 ASP cc_start: 0.9287 (t0) cc_final: 0.9070 (t0) REVERT: Q 274 MET cc_start: 0.9558 (tpt) cc_final: 0.8887 (tpp) REVERT: Q 343 GLN cc_start: 0.8992 (mm110) cc_final: 0.8505 (mp10) REVERT: Q 365 TRP cc_start: 0.9146 (m100) cc_final: 0.8250 (m100) outliers start: 2 outliers final: 2 residues processed: 915 average time/residue: 0.2283 time to fit residues: 352.8373 Evaluate side-chains 704 residues out of total 4950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 702 time to evaluate : 1.654 ------------------------------------------------------------------------------- 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: 6.9990 chunk 278 optimal weight: 7.9990 chunk 3 optimal weight: 10.0000 chunk 144 optimal weight: 9.9990 chunk 17 optimal weight: 30.0000 chunk 87 optimal weight: 0.8980 chunk 74 optimal weight: 0.8980 chunk 534 optimal weight: 20.0000 chunk 149 optimal weight: 0.7980 chunk 538 optimal weight: 9.9990 chunk 334 optimal weight: 0.9990 overall best weight: 2.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 819 ASN A 950 GLN A1065 GLN ** A1320 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 45 HIS ** B 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 547 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 575 HIS ** B 636 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 673 ASN ** B 702 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1038 HIS B1041 ASN B1100 GLN ** D 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 3 GLN E 99 HIS ** G 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 150 HIS K 106 GLN ** 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 155 GLN ** 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 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 315 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 449 GLN ** 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: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.092193 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.071930 restraints weight = 233857.070| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.073892 restraints weight = 126638.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.075145 restraints weight = 81246.127| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.075882 restraints weight = 59836.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.076454 restraints weight = 48842.781| |-----------------------------------------------------------------------------| r_work (final): 0.3402 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7260 moved from start: 0.6030 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= 0.177 Angle : 0.881 28.086 64864 Z= 0.434 Chirality : 0.050 0.648 7252 Planarity : 0.007 0.279 7976 Dihedral : 14.273 178.189 7127 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 20.33 Ramachandran Plot: Outliers : 0.77 % Allowed : 7.25 % Favored : 91.97 % Rotamer: Outliers : 0.04 % Allowed : 2.43 % Favored : 97.53 % Cbeta Deviations : 0.02 % 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 are not related in a simple way. whole: -1.31 (0.11), residues: 5432 helix: 0.14 (0.11), residues: 1969 sheet: -1.09 (0.18), residues: 727 loop : -1.56 (0.12), residues: 2736 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG Q 302 TYR 0.033 0.002 TYR A 478 PHE 0.102 0.002 PHE Q 358 TRP 0.039 0.002 TRP O 324 HIS 0.013 0.001 HIS E 99 Details of bonding type rmsd/Z covalent geometry : bond 0.00375 / 0.17 (47647) covalent geometry : angle 0.84230 / 0.43 (64831) hydrogen bonds : bond 0.05542 / 3.69 ( 1994) hydrogen bonds : angle 6.24068 / 4.39 ( 5479) metal coordination : bond 0.01440 / 0.85 ( 24) metal coordination : angle 11.52876 / 7.19 ( 33) Misc. bond : bond 0.01253 / 0.73 ( 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 933 residues out of total 4950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 931 time to evaluate : 1.358 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 90 PHE cc_start: 0.9444 (m-80) cc_final: 0.9242 (m-10) REVERT: A 214 ASP cc_start: 0.9308 (t70) cc_final: 0.8630 (t0) REVERT: A 218 LYS cc_start: 0.9382 (mtmt) cc_final: 0.9097 (ptpp) REVERT: A 226 LYS cc_start: 0.9533 (mmpt) cc_final: 0.9095 (mmmt) REVERT: A 339 PHE cc_start: 0.8834 (m-80) cc_final: 0.8251 (m-80) REVERT: A 438 ILE cc_start: 0.9536 (mp) cc_final: 0.9318 (mp) REVERT: A 466 LEU cc_start: 0.9346 (tt) cc_final: 0.9081 (tt) REVERT: A 618 TYR cc_start: 0.8581 (m-80) cc_final: 0.8303 (m-10) REVERT: A 654 ASP cc_start: 0.8754 (m-30) cc_final: 0.8537 (m-30) REVERT: A 686 PHE cc_start: 0.8942 (m-10) cc_final: 0.8615 (m-80) REVERT: A 822 THR cc_start: 0.9271 (p) cc_final: 0.8959 (t) REVERT: A 830 MET cc_start: 0.8842 (mmm) cc_final: 0.8492 (mmm) REVERT: A 925 MET cc_start: 0.9490 (tpt) cc_final: 0.9095 (tmm) REVERT: A 943 ILE cc_start: 0.9623 (mt) cc_final: 0.9316 (pt) REVERT: A 960 MET cc_start: 0.7629 (mtp) cc_final: 0.7378 (mtp) REVERT: A 994 GLU cc_start: -0.4524 (mt-10) cc_final: -0.4829 (mt-10) REVERT: A 1000 MET cc_start: -0.1792 (mtt) cc_final: -0.2138 (mmm) REVERT: A 1007 ILE cc_start: -0.5141 (mt) cc_final: -0.5398 (mm) REVERT: A 1183 GLU cc_start: 0.8321 (tp30) cc_final: 0.7949 (tp30) REVERT: A 1185 VAL cc_start: 0.9474 (m) cc_final: 0.9050 (t) REVERT: A 1222 LEU cc_start: 0.9330 (tt) cc_final: 0.9121 (tt) REVERT: A 1226 VAL cc_start: 0.9662 (t) cc_final: 0.9396 (p) REVERT: A 1227 MET cc_start: 0.8510 (tpp) cc_final: 0.8302 (tpp) REVERT: A 1476 LEU cc_start: 0.9261 (mt) cc_final: 0.8987 (mt) REVERT: A 1504 ILE cc_start: 0.9254 (mm) cc_final: 0.8995 (mm) REVERT: A 1505 ASP cc_start: 0.8374 (t0) cc_final: 0.7682 (t70) REVERT: A 1519 LEU cc_start: 0.9335 (mp) cc_final: 0.8908 (mt) REVERT: A 1587 ASP cc_start: 0.8915 (m-30) cc_final: 0.8414 (m-30) REVERT: A 1589 MET cc_start: 0.9389 (mtt) cc_final: 0.8895 (mmm) REVERT: A 1610 PHE cc_start: 0.9535 (m-80) cc_final: 0.9329 (m-80) REVERT: A 1613 MET cc_start: 0.9166 (mtm) cc_final: 0.8519 (ptp) REVERT: A 1620 GLN cc_start: 0.9035 (mp10) cc_final: 0.8570 (mp10) REVERT: A 1621 PHE cc_start: 0.9244 (m-80) cc_final: 0.8769 (m-80) REVERT: B 98 SER cc_start: 0.9366 (p) cc_final: 0.8850 (m) REVERT: B 108 MET cc_start: 0.8681 (mmp) cc_final: 0.8317 (mmp) REVERT: B 125 GLU cc_start: 0.9169 (mt-10) cc_final: 0.8762 (mt-10) REVERT: B 158 CYS cc_start: 0.8741 (m) cc_final: 0.8328 (m) REVERT: B 174 LYS cc_start: 0.9217 (mmpt) cc_final: 0.8942 (mmmt) REVERT: B 206 LEU cc_start: 0.9430 (tp) cc_final: 0.9116 (tp) REVERT: B 275 MET cc_start: 0.9223 (ttm) cc_final: 0.9022 (ttm) REVERT: B 285 ASP cc_start: 0.8614 (m-30) cc_final: 0.8362 (m-30) REVERT: B 304 ASP cc_start: 0.9504 (m-30) cc_final: 0.9137 (p0) REVERT: B 330 LEU cc_start: 0.9685 (mt) cc_final: 0.9470 (mt) REVERT: B 398 GLN cc_start: 0.9182 (pt0) cc_final: 0.8869 (pt0) REVERT: B 411 MET cc_start: 0.9476 (mtt) cc_final: 0.9219 (mtp) REVERT: B 422 GLN cc_start: 0.9226 (tm-30) cc_final: 0.8808 (tm-30) REVERT: B 486 VAL cc_start: 0.9326 (t) cc_final: 0.8962 (p) REVERT: B 489 GLU cc_start: 0.8225 (tt0) cc_final: 0.7919 (tt0) REVERT: B 514 THR cc_start: 0.8707 (p) cc_final: 0.8276 (p) REVERT: B 515 THR cc_start: 0.9240 (p) cc_final: 0.8978 (t) REVERT: B 543 ASN cc_start: 0.8870 (m110) cc_final: 0.8606 (m110) REVERT: B 556 SER cc_start: 0.7109 (p) cc_final: 0.6040 (t) REVERT: B 557 ASP cc_start: 0.7662 (m-30) cc_final: 0.7131 (m-30) REVERT: B 568 LEU cc_start: 0.9068 (mt) cc_final: 0.8688 (mt) REVERT: B 778 TYR cc_start: 0.8434 (t80) cc_final: 0.8065 (t80) REVERT: B 783 MET cc_start: 0.7379 (mmm) cc_final: 0.6788 (mmm) REVERT: B 785 ASP cc_start: 0.7865 (m-30) cc_final: 0.7594 (m-30) REVERT: B 898 LEU cc_start: 0.9295 (tp) cc_final: 0.8909 (tp) REVERT: B 936 MET cc_start: 0.8914 (tpp) cc_final: 0.8623 (tpp) REVERT: B 962 MET cc_start: 0.8964 (ttm) cc_final: 0.8736 (ttm) REVERT: B 965 GLU cc_start: 0.8888 (tm-30) cc_final: 0.8568 (tm-30) REVERT: B 982 THR cc_start: 0.9390 (m) cc_final: 0.9130 (p) REVERT: B 1073 GLU cc_start: 0.8005 (tp30) cc_final: 0.7752 (tp30) REVERT: B 1074 MET cc_start: 0.8269 (ttm) cc_final: 0.7733 (ttp) REVERT: B 1075 GLU cc_start: 0.8545 (mp0) cc_final: 0.8235 (mm-30) REVERT: B 1086 PHE cc_start: 0.7681 (m-80) cc_final: 0.5272 (m-80) REVERT: B 1098 TYR cc_start: 0.8864 (t80) cc_final: 0.7892 (t80) REVERT: C 95 GLU cc_start: 0.8135 (mm-30) cc_final: 0.7607 (mm-30) REVERT: C 273 ASP cc_start: 0.8560 (t70) cc_final: 0.8106 (t70) REVERT: D 25 THR cc_start: 0.9391 (p) cc_final: 0.8880 (p) REVERT: D 91 ARG cc_start: 0.9480 (ptp90) cc_final: 0.9105 (ptp-170) REVERT: E 116 ILE cc_start: 0.9208 (pt) cc_final: 0.8985 (pt) REVERT: E 140 LEU cc_start: 0.9363 (mm) cc_final: 0.9079 (mm) REVERT: E 174 GLN cc_start: 0.9218 (mt0) cc_final: 0.8706 (mt0) REVERT: E 215 MET cc_start: 0.8795 (mmt) cc_final: 0.8470 (mmm) REVERT: F 76 LYS cc_start: 0.9328 (mmmm) cc_final: 0.9102 (mmmm) REVERT: F 77 ASP cc_start: 0.8730 (t0) cc_final: 0.8485 (p0) REVERT: F 92 ARG cc_start: 0.9160 (tpt-90) cc_final: 0.8647 (tpt-90) REVERT: F 111 LEU cc_start: 0.9501 (tp) cc_final: 0.9219 (tt) REVERT: F 122 MET cc_start: 0.9194 (mtp) cc_final: 0.8888 (mtp) REVERT: F 136 ARG cc_start: 0.7933 (mtt180) cc_final: 0.7555 (mtt180) REVERT: G 43 ILE cc_start: 0.8985 (pt) cc_final: 0.8525 (mm) REVERT: G 45 LEU cc_start: 0.9226 (pp) cc_final: 0.8943 (pp) REVERT: G 98 GLU cc_start: 0.8664 (mm-30) cc_final: 0.8305 (mp0) REVERT: G 110 ASP cc_start: 0.8810 (p0) cc_final: 0.8304 (p0) REVERT: G 119 HIS cc_start: 0.7910 (t-90) cc_final: 0.7437 (t-90) REVERT: H 102 TYR cc_start: 0.8657 (p90) cc_final: 0.8048 (p90) REVERT: H 118 PHE cc_start: 0.8699 (m-80) cc_final: 0.7987 (m-80) REVERT: H 141 TYR cc_start: 0.9144 (m-80) cc_final: 0.8549 (m-10) REVERT: I 64 LYS cc_start: 0.9396 (mtpp) cc_final: 0.8845 (mtpp) REVERT: J 28 ASP cc_start: 0.8882 (t70) cc_final: 0.8537 (t0) REVERT: J 49 MET cc_start: 0.9448 (tpp) cc_final: 0.8791 (tpp) REVERT: J 59 LYS cc_start: 0.9460 (mmmm) cc_final: 0.9073 (mmmt) REVERT: K 67 GLU cc_start: 0.8186 (tm-30) cc_final: 0.7196 (tm-30) REVERT: K 125 MET cc_start: 0.8662 (mtt) cc_final: 0.8257 (mmm) REVERT: L 53 HIS cc_start: 0.8772 (t-90) cc_final: 0.7962 (t-90) REVERT: L 67 PHE cc_start: 0.8357 (m-10) cc_final: 0.7831 (m-10) REVERT: M 26 PHE cc_start: 0.8259 (m-10) cc_final: 0.7298 (m-10) REVERT: M 30 PHE cc_start: 0.9031 (t80) cc_final: 0.8662 (t80) REVERT: M 41 TYR cc_start: 0.8743 (m-80) cc_final: 0.8314 (m-80) REVERT: M 92 LYS cc_start: 0.8320 (ttpt) cc_final: 0.7999 (ttpt) REVERT: N 29 PHE cc_start: 0.8946 (m-80) cc_final: 0.8120 (m-80) REVERT: N 107 MET cc_start: 0.9075 (tmm) cc_final: 0.8728 (mmt) REVERT: O 293 TYR cc_start: 0.8527 (t80) cc_final: 0.8139 (t80) REVERT: O 408 ILE cc_start: 0.7726 (tp) cc_final: 0.7493 (tp) REVERT: O 463 LEU cc_start: 0.8998 (pt) cc_final: 0.8736 (mm) REVERT: O 467 PHE cc_start: 0.9659 (m-80) cc_final: 0.9250 (m-80) REVERT: O 537 PHE cc_start: 0.9530 (p90) cc_final: 0.8922 (p90) REVERT: O 538 LEU cc_start: 0.9653 (mp) cc_final: 0.9308 (mt) REVERT: P 123 MET cc_start: 0.9091 (mpp) cc_final: 0.8799 (mmp) REVERT: P 226 LEU cc_start: 0.9353 (pp) cc_final: 0.9056 (pp) REVERT: P 227 TYR cc_start: 0.8516 (m-80) cc_final: 0.7935 (m-80) REVERT: P 238 HIS cc_start: 0.9394 (m-70) cc_final: 0.9092 (m90) REVERT: P 254 LEU cc_start: 0.9749 (tp) cc_final: 0.9364 (tp) REVERT: P 258 MET cc_start: 0.8790 (ptt) cc_final: 0.8151 (ptt) REVERT: P 317 MET cc_start: 0.8911 (tpt) cc_final: 0.8649 (tpt) REVERT: P 353 VAL cc_start: 0.8871 (p) cc_final: 0.8576 (m) REVERT: P 381 MET cc_start: 0.9336 (mmp) cc_final: 0.9045 (mmm) REVERT: P 402 MET cc_start: 0.8414 (mpp) cc_final: 0.8194 (mpp) REVERT: P 413 LEU cc_start: 0.9815 (mt) cc_final: 0.9546 (mt) REVERT: Q 173 MET cc_start: 0.8964 (mpp) cc_final: 0.8641 (mpp) REVERT: Q 212 HIS cc_start: 0.9369 (m-70) cc_final: 0.8829 (m-70) REVERT: Q 228 ASN cc_start: 0.8630 (m110) cc_final: 0.8387 (m110) REVERT: Q 251 TRP cc_start: 0.6897 (p-90) cc_final: 0.6221 (p-90) REVERT: Q 274 MET cc_start: 0.9549 (tpt) cc_final: 0.8929 (tpp) REVERT: Q 343 GLN cc_start: 0.8966 (mm110) cc_final: 0.8450 (mp10) REVERT: Q 365 TRP cc_start: 0.9168 (m100) cc_final: 0.8259 (m100) outliers start: 2 outliers final: 0 residues processed: 933 average time/residue: 0.2193 time to fit residues: 348.4098 Evaluate side-chains 719 residues out of total 4950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 719 time to evaluate : 1.510 ------------------------------------------------------------------------------- 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: 6.9990 chunk 363 optimal weight: 20.0000 chunk 440 optimal weight: 30.0000 chunk 66 optimal weight: 30.0000 chunk 327 optimal weight: 50.0000 chunk 260 optimal weight: 10.0000 chunk 286 optimal weight: 0.0980 chunk 115 optimal weight: 6.9990 chunk 133 optimal weight: 10.0000 chunk 378 optimal weight: 10.0000 chunk 118 optimal weight: 30.0000 overall best weight: 6.8192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 596 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 730 GLN A 880 GLN ** A1320 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 183 HIS ** 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** B 814 ASN ** B 824 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1038 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1041 ASN ** B1058 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 3 GLN ** G 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 65 HIS ** 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 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 435 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: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.089931 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.069839 restraints weight = 238638.678| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.071675 restraints weight = 130929.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.072845 restraints weight = 84996.588| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.073565 restraints weight = 62995.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.074107 restraints weight = 51723.887| |-----------------------------------------------------------------------------| r_work (final): 0.3347 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7360 moved from start: 0.6200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.096 47692 Z= 0.264 Angle : 0.895 29.871 64864 Z= 0.450 Chirality : 0.050 0.450 7252 Planarity : 0.006 0.196 7976 Dihedral : 14.429 177.827 7127 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 23.18 Ramachandran Plot: Outliers : 0.68 % Allowed : 8.10 % Favored : 91.22 % Rotamer: Outliers : 0.04 % Allowed : 1.88 % Favored : 98.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.24 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.27 (0.11), residues: 5432 helix: 0.23 (0.11), residues: 1945 sheet: -1.12 (0.18), residues: 737 loop : -1.55 (0.12), residues: 2750 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG B 261 TYR 0.048 0.002 TYR B1184 PHE 0.105 0.003 PHE Q 358 TRP 0.044 0.003 TRP B 143 HIS 0.020 0.002 HIS B1038 Details of bonding type rmsd/Z covalent geometry : bond 0.00556 / 0.26 (47647) covalent geometry : angle 0.86474 / 0.45 (64831) hydrogen bonds : bond 0.05541 / 3.68 ( 1994) hydrogen bonds : angle 6.28649 / 4.43 ( 5479) metal coordination : bond 0.02061 / 1.17 ( 24) metal coordination : angle 10.26168 / 6.31 ( 33) Misc. bond : bond 0.01039 / 0.63 ( 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 863 residues out of total 4950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 861 time to evaluate : 1.292 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: A 90 PHE cc_start: 0.9551 (m-80) cc_final: 0.9306 (m-10) REVERT: A 214 ASP cc_start: 0.9343 (t70) cc_final: 0.8596 (t0) REVERT: A 218 LYS cc_start: 0.9443 (mtmt) cc_final: 0.9224 (ptpt) REVERT: A 226 LYS cc_start: 0.9555 (mmpt) cc_final: 0.9114 (mmmt) REVERT: A 325 ASP cc_start: 0.8805 (t70) cc_final: 0.8498 (m-30) REVERT: A 339 PHE cc_start: 0.8894 (m-80) cc_final: 0.8364 (m-80) REVERT: A 470 HIS cc_start: 0.8560 (m-70) cc_final: 0.8275 (m-70) REVERT: A 736 LEU cc_start: 0.9692 (mt) cc_final: 0.9476 (mt) REVERT: A 822 THR cc_start: 0.9324 (p) cc_final: 0.9023 (t) REVERT: A 830 MET cc_start: 0.8879 (mmm) cc_final: 0.8580 (mmm) REVERT: A 925 MET cc_start: 0.9509 (tpt) cc_final: 0.9069 (tmm) REVERT: A 943 ILE cc_start: 0.9647 (mt) cc_final: 0.9280 (pt) REVERT: A 944 MET cc_start: 0.8885 (mmp) cc_final: 0.8671 (mmm) REVERT: A 947 LEU cc_start: 0.9201 (mp) cc_final: 0.8829 (mp) REVERT: A 960 MET cc_start: 0.7474 (mtp) cc_final: 0.7209 (mtp) REVERT: A 1000 MET cc_start: -0.1838 (mtt) cc_final: -0.2074 (mmm) REVERT: A 1007 ILE cc_start: -0.4755 (mt) cc_final: -0.4955 (mm) REVERT: A 1009 THR cc_start: 0.0467 (m) cc_final: 0.0087 (m) REVERT: A 1092 GLU cc_start: 0.9359 (mt-10) cc_final: 0.9024 (mp0) REVERT: A 1183 GLU cc_start: 0.8369 (tp30) cc_final: 0.8028 (tp30) REVERT: A 1185 VAL cc_start: 0.9541 (m) cc_final: 0.9180 (t) REVERT: A 1224 GLU cc_start: 0.9112 (mp0) cc_final: 0.8841 (pm20) REVERT: A 1227 MET cc_start: 0.8554 (tpp) cc_final: 0.8318 (tpp) REVERT: A 1439 MET cc_start: 0.8391 (mmp) cc_final: 0.8093 (mmm) REVERT: A 1476 LEU cc_start: 0.9112 (mt) cc_final: 0.8839 (mt) REVERT: A 1504 ILE cc_start: 0.9255 (mm) cc_final: 0.9022 (mm) REVERT: A 1505 ASP cc_start: 0.8581 (t0) cc_final: 0.7829 (t0) REVERT: A 1519 LEU cc_start: 0.9403 (mp) cc_final: 0.9034 (mt) REVERT: A 1587 ASP cc_start: 0.8926 (m-30) cc_final: 0.8515 (m-30) REVERT: A 1589 MET cc_start: 0.9478 (mtt) cc_final: 0.8886 (mmm) REVERT: A 1620 GLN cc_start: 0.9080 (mp10) cc_final: 0.8604 (mp10) REVERT: A 1621 PHE cc_start: 0.9297 (m-80) cc_final: 0.8861 (m-80) REVERT: B 98 SER cc_start: 0.9246 (p) cc_final: 0.8767 (m) REVERT: B 108 MET cc_start: 0.8616 (mmp) cc_final: 0.8214 (mmp) REVERT: B 136 LYS cc_start: 0.8817 (ttmt) cc_final: 0.8118 (tptm) REVERT: B 174 LYS cc_start: 0.9175 (mmpt) cc_final: 0.8869 (mmmt) REVERT: B 206 LEU cc_start: 0.9414 (tp) cc_final: 0.9152 (tp) REVERT: B 215 MET cc_start: 0.7564 (mtt) cc_final: 0.6973 (mtt) REVERT: B 304 ASP cc_start: 0.9488 (m-30) cc_final: 0.9117 (p0) REVERT: B 398 GLN cc_start: 0.9217 (pt0) cc_final: 0.8990 (pt0) REVERT: B 411 MET cc_start: 0.9456 (mtt) cc_final: 0.9222 (mtp) REVERT: B 415 GLU cc_start: 0.8673 (tp30) cc_final: 0.8171 (tp30) REVERT: B 419 GLU cc_start: 0.8950 (pt0) cc_final: 0.8744 (pt0) REVERT: B 422 GLN cc_start: 0.9258 (tm-30) cc_final: 0.8864 (tm-30) REVERT: B 486 VAL cc_start: 0.9343 (t) cc_final: 0.9084 (p) REVERT: B 489 GLU cc_start: 0.8322 (tt0) cc_final: 0.8087 (tt0) REVERT: B 514 THR cc_start: 0.8500 (p) cc_final: 0.8085 (p) REVERT: B 515 THR cc_start: 0.9269 (p) cc_final: 0.9013 (t) REVERT: B 543 ASN cc_start: 0.8967 (m110) cc_final: 0.8612 (m-40) REVERT: B 568 LEU cc_start: 0.9078 (mt) cc_final: 0.8694 (mt) REVERT: B 778 TYR cc_start: 0.8636 (t80) cc_final: 0.8043 (t80) REVERT: B 785 ASP cc_start: 0.8164 (m-30) cc_final: 0.7917 (m-30) REVERT: B 898 LEU cc_start: 0.9265 (tp) cc_final: 0.8904 (tp) REVERT: B 965 GLU cc_start: 0.8953 (tm-30) cc_final: 0.8733 (tm-30) REVERT: B 982 THR cc_start: 0.9355 (m) cc_final: 0.9022 (p) REVERT: B 1074 MET cc_start: 0.8277 (ttm) cc_final: 0.7881 (ttp) REVERT: B 1075 GLU cc_start: 0.8545 (mp0) cc_final: 0.8238 (mm-30) REVERT: B 1086 PHE cc_start: 0.7801 (m-80) cc_final: 0.5484 (m-80) REVERT: B 1098 TYR cc_start: 0.9011 (t80) cc_final: 0.8020 (t80) REVERT: B 1111 LEU cc_start: 0.9379 (tp) cc_final: 0.9170 (tt) REVERT: B 1130 ARG cc_start: 0.9029 (ttt180) cc_final: 0.8690 (mtp85) REVERT: C 71 MET cc_start: 0.9302 (mtp) cc_final: 0.8598 (mmm) REVERT: C 95 GLU cc_start: 0.8294 (mm-30) cc_final: 0.6845 (mm-30) REVERT: C 181 ASP cc_start: 0.8383 (p0) cc_final: 0.8084 (p0) REVERT: C 247 PHE cc_start: 0.9160 (t80) cc_final: 0.8801 (t80) REVERT: C 273 ASP cc_start: 0.8371 (t70) cc_final: 0.8145 (t70) REVERT: D 25 THR cc_start: 0.9381 (p) cc_final: 0.8942 (p) REVERT: D 91 ARG cc_start: 0.9449 (ptp90) cc_final: 0.9064 (ptp-170) REVERT: E 140 LEU cc_start: 0.9366 (mm) cc_final: 0.9091 (mm) REVERT: E 215 MET cc_start: 0.8822 (mmt) cc_final: 0.8479 (mmm) REVERT: F 76 LYS cc_start: 0.9371 (mmmm) cc_final: 0.9153 (mmmm) REVERT: F 77 ASP cc_start: 0.8829 (t0) cc_final: 0.8543 (p0) REVERT: F 88 TYR cc_start: 0.8343 (m-80) cc_final: 0.7759 (m-80) REVERT: F 92 ARG cc_start: 0.9213 (tpt-90) cc_final: 0.8662 (tpt-90) REVERT: F 103 MET cc_start: 0.9204 (mmt) cc_final: 0.8905 (mmp) REVERT: F 122 MET cc_start: 0.9163 (mtp) cc_final: 0.8806 (mtp) REVERT: F 151 LEU cc_start: 0.9240 (mm) cc_final: 0.8474 (tp) REVERT: G 98 GLU cc_start: 0.8496 (mm-30) cc_final: 0.8166 (mp0) REVERT: G 110 ASP cc_start: 0.8800 (p0) cc_final: 0.8382 (p0) REVERT: G 119 HIS cc_start: 0.7911 (t-90) cc_final: 0.7478 (t-90) REVERT: H 102 TYR cc_start: 0.8770 (p90) cc_final: 0.8176 (p90) REVERT: H 118 PHE cc_start: 0.8718 (m-80) cc_final: 0.8058 (m-80) REVERT: I 64 LYS cc_start: 0.9397 (mtpp) cc_final: 0.8838 (mtpp) REVERT: J 28 ASP cc_start: 0.9075 (t70) cc_final: 0.8623 (t0) REVERT: J 49 MET cc_start: 0.9547 (tpp) cc_final: 0.8631 (tpp) REVERT: K 46 LYS cc_start: 0.7758 (tptt) cc_final: 0.7276 (tppt) REVERT: K 67 GLU cc_start: 0.8573 (tm-30) cc_final: 0.8134 (tm-30) REVERT: K 76 LEU cc_start: 0.9419 (tp) cc_final: 0.9177 (tp) REVERT: K 82 LYS cc_start: 0.9304 (mmtt) cc_final: 0.8869 (mmmt) REVERT: K 125 MET cc_start: 0.8809 (mtt) cc_final: 0.8524 (mmm) REVERT: L 53 HIS cc_start: 0.8996 (t-90) cc_final: 0.8162 (t-90) REVERT: M 12 ILE cc_start: 0.8730 (mm) cc_final: 0.8523 (mm) REVERT: M 18 GLN cc_start: 0.8887 (mm110) cc_final: 0.8434 (mp10) REVERT: M 26 PHE cc_start: 0.8351 (m-10) cc_final: 0.7534 (m-10) REVERT: M 30 PHE cc_start: 0.9181 (t80) cc_final: 0.8911 (t80) REVERT: M 38 PHE cc_start: 0.9070 (m-80) cc_final: 0.8684 (m-80) REVERT: M 41 TYR cc_start: 0.8753 (m-80) cc_final: 0.8354 (m-80) REVERT: M 61 GLU cc_start: 0.9105 (mp0) cc_final: 0.8901 (mp0) REVERT: N 29 PHE cc_start: 0.8849 (m-80) cc_final: 0.8225 (m-80) REVERT: N 119 LEU cc_start: 0.9021 (mm) cc_final: 0.8479 (tp) REVERT: O 293 TYR cc_start: 0.8492 (t80) cc_final: 0.8141 (t80) REVERT: O 434 ARG cc_start: 0.6340 (tmm160) cc_final: 0.5892 (ttp-170) REVERT: O 463 LEU cc_start: 0.9019 (pt) cc_final: 0.8737 (mm) REVERT: O 467 PHE cc_start: 0.9673 (m-80) cc_final: 0.9293 (m-80) REVERT: O 537 PHE cc_start: 0.9497 (p90) cc_final: 0.8820 (p90) REVERT: O 538 LEU cc_start: 0.9657 (mp) cc_final: 0.9290 (mt) REVERT: P 123 MET cc_start: 0.9125 (mpp) cc_final: 0.8900 (mmm) REVERT: P 227 TYR cc_start: 0.8430 (m-80) cc_final: 0.7813 (m-80) REVERT: P 238 HIS cc_start: 0.9424 (m-70) cc_final: 0.9137 (m90) REVERT: P 258 MET cc_start: 0.8892 (ptt) cc_final: 0.8329 (ptt) REVERT: P 317 MET cc_start: 0.8721 (tpt) cc_final: 0.8481 (tpt) REVERT: P 381 MET cc_start: 0.9428 (mmp) cc_final: 0.9190 (mmm) REVERT: P 402 MET cc_start: 0.8514 (mpp) cc_final: 0.8306 (mpp) REVERT: P 413 LEU cc_start: 0.9817 (mt) cc_final: 0.9586 (mt) REVERT: Q 1 MET cc_start: 0.8229 (tmm) cc_final: 0.7414 (tmm) REVERT: Q 157 MET cc_start: 0.3668 (ttm) cc_final: 0.3105 (ttm) REVERT: Q 173 MET cc_start: 0.9138 (mpp) cc_final: 0.8791 (mpp) REVERT: Q 229 TRP cc_start: 0.6301 (t60) cc_final: 0.5732 (t60) REVERT: Q 251 TRP cc_start: 0.7025 (p-90) cc_final: 0.6197 (p-90) REVERT: Q 257 ILE cc_start: 0.9354 (tp) cc_final: 0.8874 (tp) REVERT: Q 274 MET cc_start: 0.9621 (tpt) cc_final: 0.9101 (tpp) REVERT: Q 363 GLU cc_start: 0.9032 (mm-30) cc_final: 0.8400 (tm-30) REVERT: Q 365 TRP cc_start: 0.9239 (m100) cc_final: 0.8104 (m100) outliers start: 2 outliers final: 1 residues processed: 863 average time/residue: 0.2025 time to fit residues: 295.4689 Evaluate side-chains 675 residues out of total 4950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 674 time to evaluate : 1.293 ------------------------------------------------------------------------------- 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: 2.9990 chunk 92 optimal weight: 8.9990 chunk 56 optimal weight: 5.9990 chunk 517 optimal weight: 9.9990 chunk 390 optimal weight: 50.0000 chunk 119 optimal weight: 5.9990 chunk 97 optimal weight: 0.7980 chunk 483 optimal weight: 5.9990 chunk 60 optimal weight: 5.9990 chunk 7 optimal weight: 40.0000 chunk 139 optimal weight: 4.9990 overall best weight: 4.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A1320 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 575 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 636 GLN B 673 ASN B 755 ASN ** B1038 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1041 ASN ** C 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 30 HIS ** 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** ** J 53 HIS ** 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 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 304 HIS 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: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.090651 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.070598 restraints weight = 237212.052| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.072450 restraints weight = 128960.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.073645 restraints weight = 83242.172| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.074360 restraints weight = 61795.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.074885 restraints weight = 50819.819| |-----------------------------------------------------------------------------| r_work (final): 0.3367 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7328 moved from start: 0.6374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.083 47692 Z= 0.202 Angle : 0.856 29.817 64864 Z= 0.430 Chirality : 0.050 0.590 7252 Planarity : 0.007 0.280 7976 Dihedral : 14.422 178.091 7127 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 21.51 Ramachandran Plot: Outliers : 0.68 % Allowed : 7.75 % Favored : 91.57 % Rotamer: Outliers : 0.02 % Allowed : 1.11 % Favored : 98.87 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.65 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.24 (0.11), residues: 5432 helix: 0.25 (0.11), residues: 1952 sheet: -1.09 (0.18), residues: 748 loop : -1.54 (0.12), residues: 2732 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.037 0.001 ARG Q 291 TYR 0.026 0.002 TYR B 409 PHE 0.101 0.002 PHE Q 358 TRP 0.035 0.002 TRP N 54 HIS 0.030 0.002 HIS B 824 Details of bonding type rmsd/Z covalent geometry : bond 0.00432 / 0.20 (47647) covalent geometry : angle 0.83376 / 0.43 (64831) hydrogen bonds : bond 0.05312 / 3.53 ( 1994) hydrogen bonds : angle 6.15360 / 4.33 ( 5479) metal coordination : bond 0.01582 / 0.92 ( 24) metal coordination : angle 8.68296 / 5.41 ( 33) Misc. bond : bond 0.01214 / 0.69 ( 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 874 residues out of total 4950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 873 time to evaluate : 1.114 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 90 PHE cc_start: 0.9513 (m-80) cc_final: 0.9298 (m-10) REVERT: A 115 VAL cc_start: 0.9466 (t) cc_final: 0.9208 (p) REVERT: A 213 ASN cc_start: 0.9281 (t0) cc_final: 0.9023 (t0) REVERT: A 214 ASP cc_start: 0.9348 (t70) cc_final: 0.8526 (t0) REVERT: A 218 LYS cc_start: 0.9472 (mtmt) cc_final: 0.9249 (ptpt) REVERT: A 225 LYS cc_start: 0.9587 (mmtm) cc_final: 0.9354 (mmtm) REVERT: A 226 LYS cc_start: 0.9528 (mmpt) cc_final: 0.9135 (mmmt) REVERT: A 339 PHE cc_start: 0.8885 (m-80) cc_final: 0.8333 (m-80) REVERT: A 438 ILE cc_start: 0.9233 (mp) cc_final: 0.8941 (mp) REVERT: A 466 LEU cc_start: 0.9366 (tt) cc_final: 0.8898 (tt) REVERT: A 470 HIS cc_start: 0.8494 (m-70) cc_final: 0.8199 (m-70) REVERT: A 589 MET cc_start: 0.8563 (mmp) cc_final: 0.8341 (mmm) REVERT: A 654 ASP cc_start: 0.8893 (m-30) cc_final: 0.8642 (m-30) REVERT: A 699 CYS cc_start: 0.8645 (p) cc_final: 0.8340 (p) REVERT: A 822 THR cc_start: 0.9283 (p) cc_final: 0.8967 (t) REVERT: A 830 MET cc_start: 0.8857 (mmm) cc_final: 0.8527 (mmm) REVERT: A 925 MET cc_start: 0.9496 (tpt) cc_final: 0.9048 (tmm) REVERT: A 943 ILE cc_start: 0.9650 (mt) cc_final: 0.9333 (pt) REVERT: A 947 LEU cc_start: 0.9161 (mp) cc_final: 0.8816 (mp) REVERT: A 960 MET cc_start: 0.7297 (mtp) cc_final: 0.7095 (mtp) REVERT: A 1007 ILE cc_start: -0.4694 (mt) cc_final: -0.5034 (mt) REVERT: A 1092 GLU cc_start: 0.9320 (mt-10) cc_final: 0.9022 (mp0) REVERT: A 1183 GLU cc_start: 0.8329 (tp30) cc_final: 0.7959 (tp30) REVERT: A 1185 VAL cc_start: 0.9490 (m) cc_final: 0.9160 (t) REVERT: A 1226 VAL cc_start: 0.9697 (t) cc_final: 0.9473 (p) REVERT: A 1476 LEU cc_start: 0.9149 (mt) cc_final: 0.8858 (mt) REVERT: A 1504 ILE cc_start: 0.9222 (mm) cc_final: 0.8999 (mm) REVERT: A 1505 ASP cc_start: 0.8647 (t0) cc_final: 0.7968 (t70) REVERT: A 1519 LEU cc_start: 0.9394 (mp) cc_final: 0.9028 (mt) REVERT: A 1587 ASP cc_start: 0.8899 (m-30) cc_final: 0.8463 (m-30) REVERT: A 1589 MET cc_start: 0.9465 (mtt) cc_final: 0.8903 (mmm) REVERT: A 1620 GLN cc_start: 0.9160 (mp10) cc_final: 0.8368 (mp10) REVERT: A 1621 PHE cc_start: 0.9239 (m-80) cc_final: 0.8752 (m-80) REVERT: B 39 GLN cc_start: 0.9265 (mt0) cc_final: 0.8951 (mp10) REVERT: B 98 SER cc_start: 0.9211 (p) cc_final: 0.8794 (m) REVERT: B 108 MET cc_start: 0.8613 (mmp) cc_final: 0.8192 (mmp) REVERT: B 125 GLU cc_start: 0.9123 (mt-10) cc_final: 0.8619 (mt-10) REVERT: B 136 LYS cc_start: 0.8882 (ttmt) cc_final: 0.8245 (tptm) REVERT: B 174 LYS cc_start: 0.9270 (mmpt) cc_final: 0.8933 (mmmt) REVERT: B 206 LEU cc_start: 0.9413 (tp) cc_final: 0.9134 (tp) REVERT: B 215 MET cc_start: 0.7506 (mtt) cc_final: 0.6950 (mtt) REVERT: B 224 ASN cc_start: 0.8652 (m110) cc_final: 0.8443 (m110) REVERT: B 304 ASP cc_start: 0.9481 (m-30) cc_final: 0.9073 (p0) REVERT: B 354 LEU cc_start: 0.9307 (tt) cc_final: 0.9048 (tt) REVERT: B 398 GLN cc_start: 0.9232 (pt0) cc_final: 0.8994 (pt0) REVERT: B 422 GLN cc_start: 0.9245 (tm-30) cc_final: 0.8983 (tm-30) REVERT: B 486 VAL cc_start: 0.9336 (t) cc_final: 0.8985 (p) REVERT: B 489 GLU cc_start: 0.8308 (tt0) cc_final: 0.8066 (tt0) REVERT: B 514 THR cc_start: 0.8479 (p) cc_final: 0.8081 (p) REVERT: B 515 THR cc_start: 0.9291 (p) cc_final: 0.9012 (t) REVERT: B 543 ASN cc_start: 0.9009 (m110) cc_final: 0.8635 (m-40) REVERT: B 556 SER cc_start: 0.7504 (p) cc_final: 0.6298 (t) REVERT: B 557 ASP cc_start: 0.7956 (m-30) cc_final: 0.7407 (m-30) REVERT: B 568 LEU cc_start: 0.9070 (mt) cc_final: 0.8727 (mt) REVERT: B 778 TYR cc_start: 0.8734 (t80) cc_final: 0.8158 (t80) REVERT: B 898 LEU cc_start: 0.9298 (tp) cc_final: 0.8945 (tp) REVERT: B 934 ILE cc_start: 0.9465 (pt) cc_final: 0.9241 (pt) REVERT: B 936 MET cc_start: 0.9296 (ttt) cc_final: 0.8971 (tmm) REVERT: B 965 GLU cc_start: 0.8969 (tm-30) cc_final: 0.8724 (tm-30) REVERT: B 982 THR cc_start: 0.9353 (m) cc_final: 0.9037 (p) REVERT: B 1073 GLU cc_start: 0.8212 (tp30) cc_final: 0.7953 (tp30) REVERT: B 1074 MET cc_start: 0.8269 (ttm) cc_final: 0.7839 (ttp) REVERT: B 1075 GLU cc_start: 0.8561 (mp0) cc_final: 0.8205 (mm-30) REVERT: B 1086 PHE cc_start: 0.7640 (m-80) cc_final: 0.7144 (m-80) REVERT: B 1098 TYR cc_start: 0.8883 (t80) cc_final: 0.7997 (t80) REVERT: B 1111 LEU cc_start: 0.9339 (tp) cc_final: 0.9130 (tt) REVERT: C 71 MET cc_start: 0.9278 (mtp) cc_final: 0.8547 (mmm) REVERT: C 88 ASN cc_start: 0.8271 (t0) cc_final: 0.7976 (t0) REVERT: C 95 GLU cc_start: 0.8387 (mm-30) cc_final: 0.6890 (mm-30) REVERT: C 181 ASP cc_start: 0.8230 (p0) cc_final: 0.7945 (p0) REVERT: C 247 PHE cc_start: 0.9168 (t80) cc_final: 0.8842 (t80) REVERT: D 25 THR cc_start: 0.9286 (p) cc_final: 0.8834 (p) REVERT: D 91 ARG cc_start: 0.9434 (ptp90) cc_final: 0.9045 (ptp-170) REVERT: E 75 MET cc_start: 0.7300 (tmm) cc_final: 0.7080 (tmm) REVERT: E 140 LEU cc_start: 0.9361 (mm) cc_final: 0.9088 (mm) REVERT: E 149 LEU cc_start: 0.9544 (mm) cc_final: 0.9221 (mm) REVERT: E 215 MET cc_start: 0.8820 (mmt) cc_final: 0.8507 (mmm) REVERT: F 77 ASP cc_start: 0.8848 (t0) cc_final: 0.8535 (p0) REVERT: F 90 ARG cc_start: 0.9392 (ptm-80) cc_final: 0.9109 (ttp80) REVERT: F 103 MET cc_start: 0.9196 (mmt) cc_final: 0.8868 (mmp) REVERT: F 122 MET cc_start: 0.9185 (mtp) cc_final: 0.8844 (mtp) REVERT: G 43 ILE cc_start: 0.9060 (pt) cc_final: 0.8617 (mm) REVERT: G 45 LEU cc_start: 0.9205 (pp) cc_final: 0.8986 (pp) REVERT: G 98 GLU cc_start: 0.8637 (mm-30) cc_final: 0.8274 (mp0) REVERT: G 119 HIS cc_start: 0.7860 (t-90) cc_final: 0.7501 (t-90) REVERT: H 102 TYR cc_start: 0.8779 (p90) cc_final: 0.8196 (p90) REVERT: H 118 PHE cc_start: 0.8774 (m-80) cc_final: 0.8164 (m-80) REVERT: I 64 LYS cc_start: 0.9373 (mtpp) cc_final: 0.8826 (mtpp) REVERT: J 28 ASP cc_start: 0.9015 (t70) cc_final: 0.8518 (t0) REVERT: J 49 MET cc_start: 0.9457 (tpp) cc_final: 0.8716 (tpp) REVERT: K 46 LYS cc_start: 0.7692 (tptt) cc_final: 0.7189 (tppt) REVERT: K 67 GLU cc_start: 0.8745 (tm-30) cc_final: 0.8203 (tm-30) REVERT: K 76 LEU cc_start: 0.9432 (tp) cc_final: 0.9169 (tp) REVERT: K 91 TYR cc_start: 0.8777 (p90) cc_final: 0.8356 (p90) REVERT: K 125 MET cc_start: 0.8809 (mtt) cc_final: 0.8346 (mmt) REVERT: L 53 HIS cc_start: 0.8897 (t-90) cc_final: 0.8096 (t-90) REVERT: M 12 ILE cc_start: 0.8748 (mm) cc_final: 0.8548 (mm) REVERT: M 26 PHE cc_start: 0.8291 (m-10) cc_final: 0.7329 (m-10) REVERT: M 30 PHE cc_start: 0.9181 (t80) cc_final: 0.8907 (t80) REVERT: M 38 PHE cc_start: 0.9089 (m-80) cc_final: 0.8719 (m-80) REVERT: M 41 TYR cc_start: 0.8794 (m-80) cc_final: 0.8425 (m-80) REVERT: N 29 PHE cc_start: 0.8877 (m-80) cc_final: 0.8051 (m-80) REVERT: N 107 MET cc_start: 0.9229 (tmm) cc_final: 0.8786 (mmt) REVERT: N 119 LEU cc_start: 0.8912 (mm) cc_final: 0.8389 (tp) REVERT: O 293 TYR cc_start: 0.8490 (t80) cc_final: 0.8121 (t80) REVERT: O 434 ARG cc_start: 0.6386 (tmm160) cc_final: 0.5891 (ttp-170) REVERT: O 463 LEU cc_start: 0.9106 (pt) cc_final: 0.8818 (mm) REVERT: O 467 PHE cc_start: 0.9692 (m-80) cc_final: 0.9267 (m-80) REVERT: O 537 PHE cc_start: 0.9506 (p90) cc_final: 0.8811 (p90) REVERT: O 538 LEU cc_start: 0.9637 (mp) cc_final: 0.9289 (mt) REVERT: P 123 MET cc_start: 0.9090 (mpp) cc_final: 0.8883 (mmm) REVERT: P 227 TYR cc_start: 0.8312 (m-80) cc_final: 0.7690 (m-80) REVERT: P 238 HIS cc_start: 0.9407 (m-70) cc_final: 0.9127 (m90) REVERT: P 254 LEU cc_start: 0.9733 (tp) cc_final: 0.9360 (tp) REVERT: P 258 MET cc_start: 0.8881 (ptt) cc_final: 0.8236 (ptt) REVERT: P 317 MET cc_start: 0.8729 (tpt) cc_final: 0.8464 (tpt) REVERT: P 381 MET cc_start: 0.9357 (mmp) cc_final: 0.9004 (mmm) REVERT: P 402 MET cc_start: 0.8515 (mpp) cc_final: 0.8314 (mpp) REVERT: P 413 LEU cc_start: 0.9818 (mt) cc_final: 0.9535 (mt) REVERT: P 434 HIS cc_start: 0.7682 (m-70) cc_final: 0.7473 (m-70) REVERT: Q 157 MET cc_start: 0.3382 (ttm) cc_final: 0.3102 (tpp) REVERT: Q 173 MET cc_start: 0.9157 (mpp) cc_final: 0.8787 (mpp) REVERT: Q 228 ASN cc_start: 0.8634 (m110) cc_final: 0.8423 (m110) REVERT: Q 229 TRP cc_start: 0.6286 (t60) cc_final: 0.5661 (t60) REVERT: Q 251 TRP cc_start: 0.7030 (p-90) cc_final: 0.6165 (p-90) REVERT: Q 257 ILE cc_start: 0.9300 (tp) cc_final: 0.8790 (tp) REVERT: Q 274 MET cc_start: 0.9575 (tpt) cc_final: 0.9072 (tpp) REVERT: Q 365 TRP cc_start: 0.9196 (m100) cc_final: 0.7951 (m100) outliers start: 1 outliers final: 0 residues processed: 874 average time/residue: 0.1787 time to fit residues: 263.5538 Evaluate side-chains 678 residues out of total 4950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 678 time to evaluate : 1.035 ------------------------------------------------------------------------------- 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: 30.0000 chunk 518 optimal weight: 10.0000 chunk 427 optimal weight: 7.9990 chunk 444 optimal weight: 7.9990 chunk 190 optimal weight: 7.9990 chunk 221 optimal weight: 0.9990 chunk 354 optimal weight: 0.6980 chunk 256 optimal weight: 6.9990 chunk 498 optimal weight: 6.9990 chunk 1 optimal weight: 20.0000 chunk 80 optimal weight: 0.0270 overall best weight: 3.1444 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 224 HIS A1320 GLN ** B 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 101 GLN ** 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** B1041 ASN ** 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** J 53 HIS ** O 346 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 348 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 454 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 315 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 435 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** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.091026 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.070833 restraints weight = 234906.148| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.072726 restraints weight = 126181.693| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.073883 restraints weight = 81289.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.074707 restraints weight = 60819.777| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.075185 restraints weight = 48976.909| |-----------------------------------------------------------------------------| r_work (final): 0.3374 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7310 moved from start: 0.6564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.128 47692 Z= 0.188 Angle : 0.861 29.990 64864 Z= 0.431 Chirality : 0.050 0.633 7252 Planarity : 0.007 0.265 7976 Dihedral : 14.260 177.793 7127 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 21.16 Ramachandran Plot: Outliers : 0.66 % Allowed : 7.62 % Favored : 91.72 % Rotamer: Outliers : 0.00 % Allowed : 0.63 % Favored : 99.37 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.65 % Twisted General : 0.11 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.18 (0.11), residues: 5432 helix: 0.27 (0.11), residues: 1950 sheet: -1.00 (0.18), residues: 737 loop : -1.49 (0.12), residues: 2745 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.037 0.001 ARG B 815 TYR 0.036 0.002 TYR P 366 PHE 0.103 0.002 PHE Q 358 TRP 0.039 0.002 TRP N 54 HIS 0.014 0.001 HIS B 824 Details of bonding type rmsd/Z covalent geometry : bond 0.00410 / 0.19 (47647) covalent geometry : angle 0.84006 / 0.43 (64831) hydrogen bonds : bond 0.05240 / 3.49 ( 1994) hydrogen bonds : angle 6.08675 / 4.29 ( 5479) metal coordination : bond 0.01495 / 0.89 ( 24) metal coordination : angle 8.32272 / 5.14 ( 33) Misc. bond : bond 0.01350 / 0.77 ( 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 867 residues out of total 4950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 867 time to evaluate : 1.058 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: A 90 PHE cc_start: 0.9525 (m-80) cc_final: 0.9315 (m-10) REVERT: A 97 TYR cc_start: 0.9238 (m-80) cc_final: 0.8915 (m-80) REVERT: A 131 ASP cc_start: 0.9289 (p0) cc_final: 0.9062 (t0) REVERT: A 213 ASN cc_start: 0.9302 (t0) cc_final: 0.9046 (t0) REVERT: A 214 ASP cc_start: 0.9381 (t70) cc_final: 0.8527 (t0) REVERT: A 218 LYS cc_start: 0.9490 (mtmt) cc_final: 0.9252 (ptpt) REVERT: A 226 LYS cc_start: 0.9528 (mmpt) cc_final: 0.9096 (mmmt) REVERT: A 339 PHE cc_start: 0.8939 (m-80) cc_final: 0.8340 (m-80) REVERT: A 438 ILE cc_start: 0.9327 (mp) cc_final: 0.9105 (mp) REVERT: A 466 LEU cc_start: 0.9368 (tt) cc_final: 0.8925 (tt) REVERT: A 470 HIS cc_start: 0.8559 (m-70) cc_final: 0.8260 (m-70) REVERT: A 505 LEU cc_start: 0.8894 (mp) cc_final: 0.8631 (mp) REVERT: A 590 ASN cc_start: 0.9135 (t0) cc_final: 0.8821 (t0) REVERT: A 654 ASP cc_start: 0.8858 (m-30) cc_final: 0.8592 (m-30) REVERT: A 699 CYS cc_start: 0.8687 (p) cc_final: 0.8470 (p) REVERT: A 736 LEU cc_start: 0.9716 (mt) cc_final: 0.9500 (mt) REVERT: A 738 ASN cc_start: 0.8858 (m-40) cc_final: 0.8275 (t0) REVERT: A 822 THR cc_start: 0.9270 (p) cc_final: 0.8962 (t) REVERT: A 830 MET cc_start: 0.8859 (mmm) cc_final: 0.8504 (mmm) REVERT: A 925 MET cc_start: 0.9522 (tpt) cc_final: 0.9084 (mmm) REVERT: A 943 ILE cc_start: 0.9637 (mt) cc_final: 0.9389 (pt) REVERT: A 944 MET cc_start: 0.8905 (mmp) cc_final: 0.8697 (mmm) REVERT: A 947 LEU cc_start: 0.9217 (mp) cc_final: 0.8952 (mp) REVERT: A 960 MET cc_start: 0.7394 (mtp) cc_final: 0.7188 (mtp) REVERT: A 1007 ILE cc_start: -0.4843 (mt) cc_final: -0.5207 (mt) REVERT: A 1060 GLU cc_start: 0.8762 (tm-30) cc_final: 0.8528 (tm-30) REVERT: A 1092 GLU cc_start: 0.9327 (mt-10) cc_final: 0.9020 (mp0) REVERT: A 1183 GLU cc_start: 0.8371 (tp30) cc_final: 0.7988 (tp30) REVERT: A 1185 VAL cc_start: 0.9490 (m) cc_final: 0.9171 (t) REVERT: A 1224 GLU cc_start: 0.8978 (mp0) cc_final: 0.8690 (mp0) REVERT: A 1226 VAL cc_start: 0.9674 (t) cc_final: 0.9449 (p) REVERT: A 1227 MET cc_start: 0.8794 (tpp) cc_final: 0.8472 (tpp) REVERT: A 1476 LEU cc_start: 0.9171 (mt) cc_final: 0.8875 (mt) REVERT: A 1504 ILE cc_start: 0.9190 (mm) cc_final: 0.8944 (mm) REVERT: A 1505 ASP cc_start: 0.8697 (t0) cc_final: 0.8012 (t70) REVERT: A 1519 LEU cc_start: 0.9360 (mp) cc_final: 0.8944 (mt) REVERT: A 1587 ASP cc_start: 0.8876 (m-30) cc_final: 0.8415 (m-30) REVERT: A 1589 MET cc_start: 0.9465 (mtt) cc_final: 0.8906 (mmm) REVERT: A 1613 MET cc_start: 0.9027 (mtm) cc_final: 0.8501 (ptp) REVERT: A 1620 GLN cc_start: 0.8937 (mp10) cc_final: 0.8628 (mp10) REVERT: A 1621 PHE cc_start: 0.9290 (m-80) cc_final: 0.8766 (m-80) REVERT: B 39 GLN cc_start: 0.9100 (mt0) cc_final: 0.8862 (mp10) REVERT: B 98 SER cc_start: 0.9214 (p) cc_final: 0.8815 (m) REVERT: B 108 MET cc_start: 0.8728 (mmp) cc_final: 0.8328 (mmp) REVERT: B 125 GLU cc_start: 0.9166 (mt-10) cc_final: 0.8632 (mt-10) REVERT: B 136 LYS cc_start: 0.8905 (ttmt) cc_final: 0.8264 (tptm) REVERT: B 168 ASN cc_start: 0.9284 (t0) cc_final: 0.8903 (t0) REVERT: B 174 LYS cc_start: 0.9220 (mmpt) cc_final: 0.8902 (mmmt) REVERT: B 206 LEU cc_start: 0.9345 (tp) cc_final: 0.9071 (tp) REVERT: B 215 MET cc_start: 0.7567 (mtt) cc_final: 0.7106 (mtt) REVERT: B 224 ASN cc_start: 0.8647 (m110) cc_final: 0.8418 (m110) REVERT: B 304 ASP cc_start: 0.9503 (m-30) cc_final: 0.9107 (p0) REVERT: B 398 GLN cc_start: 0.9245 (pt0) cc_final: 0.9009 (pt0) REVERT: B 422 GLN cc_start: 0.9266 (tm-30) cc_final: 0.9017 (tm-30) REVERT: B 486 VAL cc_start: 0.9375 (t) cc_final: 0.9024 (p) REVERT: B 489 GLU cc_start: 0.8298 (tt0) cc_final: 0.8027 (tt0) REVERT: B 514 THR cc_start: 0.8593 (p) cc_final: 0.8216 (p) REVERT: B 515 THR cc_start: 0.9261 (p) cc_final: 0.8964 (t) REVERT: B 543 ASN cc_start: 0.8978 (m110) cc_final: 0.8613 (m-40) REVERT: B 556 SER cc_start: 0.7405 (p) cc_final: 0.6279 (t) REVERT: B 557 ASP cc_start: 0.7954 (m-30) cc_final: 0.7448 (m-30) REVERT: B 568 LEU cc_start: 0.9071 (mt) cc_final: 0.8748 (mt) REVERT: B 671 TYR cc_start: 0.8948 (m-80) cc_final: 0.8587 (m-10) REVERT: B 778 TYR cc_start: 0.8652 (t80) cc_final: 0.8078 (t80) REVERT: B 783 MET cc_start: 0.7098 (mmm) cc_final: 0.6783 (mmm) REVERT: B 898 LEU cc_start: 0.9329 (tp) cc_final: 0.9012 (tp) REVERT: B 936 MET cc_start: 0.8924 (ttt) cc_final: 0.8606 (tmm) REVERT: B 965 GLU cc_start: 0.8933 (tm-30) cc_final: 0.8676 (tm-30) REVERT: B 982 THR cc_start: 0.9402 (m) cc_final: 0.9099 (p) REVERT: B 1073 GLU cc_start: 0.8026 (tp30) cc_final: 0.7768 (tp30) REVERT: B 1074 MET cc_start: 0.8216 (ttm) cc_final: 0.7813 (ttp) REVERT: B 1075 GLU cc_start: 0.8565 (mp0) cc_final: 0.8175 (mm-30) REVERT: B 1086 PHE cc_start: 0.7625 (m-80) cc_final: 0.7101 (m-80) REVERT: B 1098 TYR cc_start: 0.8855 (t80) cc_final: 0.7912 (t80) REVERT: B 1111 LEU cc_start: 0.9358 (tp) cc_final: 0.9109 (tt) REVERT: C 71 MET cc_start: 0.9310 (mtp) cc_final: 0.8545 (mmm) REVERT: C 88 ASN cc_start: 0.8287 (t0) cc_final: 0.7972 (t0) REVERT: C 95 GLU cc_start: 0.8403 (mm-30) cc_final: 0.7193 (mm-30) REVERT: C 181 ASP cc_start: 0.8160 (p0) cc_final: 0.7900 (p0) REVERT: C 247 PHE cc_start: 0.9162 (t80) cc_final: 0.8825 (t80) REVERT: D 25 THR cc_start: 0.9317 (p) cc_final: 0.8856 (p) REVERT: D 91 ARG cc_start: 0.9437 (ptp90) cc_final: 0.9070 (ptp-170) REVERT: E 75 MET cc_start: 0.7551 (tmm) cc_final: 0.7281 (tmm) REVERT: E 140 LEU cc_start: 0.9369 (mm) cc_final: 0.9082 (mm) REVERT: E 149 LEU cc_start: 0.9531 (mm) cc_final: 0.9245 (mm) REVERT: E 215 MET cc_start: 0.8802 (mmt) cc_final: 0.8529 (mmp) REVERT: F 77 ASP cc_start: 0.8753 (t0) cc_final: 0.8347 (p0) REVERT: F 90 ARG cc_start: 0.9474 (ptm-80) cc_final: 0.8944 (ttp80) REVERT: F 103 MET cc_start: 0.9171 (mmt) cc_final: 0.8826 (mmp) REVERT: F 122 MET cc_start: 0.9184 (mtp) cc_final: 0.8845 (mtp) REVERT: F 127 GLU cc_start: 0.8643 (mp0) cc_final: 0.8433 (mp0) REVERT: F 151 LEU cc_start: 0.9184 (mm) cc_final: 0.8448 (tp) REVERT: G 43 ILE cc_start: 0.9106 (pt) cc_final: 0.8663 (mm) REVERT: G 45 LEU cc_start: 0.9225 (pp) cc_final: 0.9020 (pp) REVERT: G 75 ASN cc_start: 0.9291 (p0) cc_final: 0.8630 (t0) REVERT: G 98 GLU cc_start: 0.8661 (mm-30) cc_final: 0.8309 (mp0) REVERT: G 119 HIS cc_start: 0.7755 (t-90) cc_final: 0.7445 (t-90) REVERT: H 102 TYR cc_start: 0.8760 (p90) cc_final: 0.8176 (p90) REVERT: H 118 PHE cc_start: 0.8772 (m-80) cc_final: 0.8171 (m-80) REVERT: I 60 LEU cc_start: 0.9575 (mm) cc_final: 0.9042 (mm) REVERT: I 64 LYS cc_start: 0.9372 (mtpp) cc_final: 0.8822 (mtpp) REVERT: J 28 ASP cc_start: 0.8977 (t70) cc_final: 0.8475 (t0) REVERT: J 49 MET cc_start: 0.9537 (tpp) cc_final: 0.8529 (tpp) REVERT: K 46 LYS cc_start: 0.7762 (tptt) cc_final: 0.7219 (tppt) REVERT: K 67 GLU cc_start: 0.8836 (tm-30) cc_final: 0.8279 (tm-30) REVERT: K 125 MET cc_start: 0.8838 (mtt) cc_final: 0.8437 (mmm) REVERT: L 53 HIS cc_start: 0.8820 (t-90) cc_final: 0.8047 (t-90) REVERT: M 26 PHE cc_start: 0.8274 (m-10) cc_final: 0.7366 (m-10) REVERT: M 30 PHE cc_start: 0.9210 (t80) cc_final: 0.8977 (t80) REVERT: M 38 PHE cc_start: 0.9078 (m-80) cc_final: 0.8705 (m-80) REVERT: M 41 TYR cc_start: 0.8724 (m-80) cc_final: 0.8348 (m-80) REVERT: M 61 GLU cc_start: 0.9184 (mp0) cc_final: 0.8346 (tm-30) REVERT: M 91 TYR cc_start: 0.8737 (m-80) cc_final: 0.8507 (m-80) REVERT: M 92 LYS cc_start: 0.8306 (ttpt) cc_final: 0.7923 (ttpt) REVERT: N 29 PHE cc_start: 0.8783 (m-80) cc_final: 0.8173 (m-80) REVERT: N 107 MET cc_start: 0.9241 (tmm) cc_final: 0.8757 (mmt) REVERT: N 119 LEU cc_start: 0.8901 (mm) cc_final: 0.8376 (tp) REVERT: O 293 TYR cc_start: 0.8540 (t80) cc_final: 0.8147 (t80) REVERT: O 463 LEU cc_start: 0.9106 (pt) cc_final: 0.8785 (mm) REVERT: O 467 PHE cc_start: 0.9645 (m-80) cc_final: 0.9312 (m-80) REVERT: O 471 MET cc_start: 0.5402 (mtm) cc_final: 0.2934 (mmm) REVERT: O 537 PHE cc_start: 0.9516 (p90) cc_final: 0.8798 (p90) REVERT: O 538 LEU cc_start: 0.9641 (mp) cc_final: 0.9285 (mt) REVERT: P 226 LEU cc_start: 0.9415 (pp) cc_final: 0.8773 (pp) REVERT: P 227 TYR cc_start: 0.8315 (m-80) cc_final: 0.7639 (m-80) REVERT: P 238 HIS cc_start: 0.9408 (m-70) cc_final: 0.9144 (m90) REVERT: P 258 MET cc_start: 0.8951 (ptt) cc_final: 0.8374 (ptt) REVERT: P 317 MET cc_start: 0.8653 (tpt) cc_final: 0.8393 (tpt) REVERT: P 381 MET cc_start: 0.9415 (mmp) cc_final: 0.9064 (mmm) REVERT: P 413 LEU cc_start: 0.9816 (mt) cc_final: 0.9519 (mt) REVERT: P 434 HIS cc_start: 0.7607 (m-70) cc_final: 0.7402 (m-70) REVERT: Q 157 MET cc_start: 0.3241 (ttm) cc_final: 0.3039 (tpp) REVERT: Q 173 MET cc_start: 0.9102 (mpp) cc_final: 0.8707 (mpp) REVERT: Q 228 ASN cc_start: 0.8625 (m110) cc_final: 0.8425 (m110) REVERT: Q 229 TRP cc_start: 0.6312 (t60) cc_final: 0.5659 (t60) REVERT: Q 251 TRP cc_start: 0.6747 (p-90) cc_final: 0.5959 (p-90) REVERT: Q 257 ILE cc_start: 0.9351 (tp) cc_final: 0.8858 (tp) REVERT: Q 274 MET cc_start: 0.9623 (tpt) cc_final: 0.8964 (tpp) REVERT: Q 277 ILE cc_start: 0.9474 (tp) cc_final: 0.8771 (tp) REVERT: Q 278 TYR cc_start: 0.9630 (m-10) cc_final: 0.8902 (m-80) REVERT: Q 365 TRP cc_start: 0.9182 (m100) cc_final: 0.7953 (m100) outliers start: 0 outliers final: 0 residues processed: 867 average time/residue: 0.1609 time to fit residues: 237.5315 Evaluate side-chains 695 residues out of total 4950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 695 time to evaluate : 0.997 ------------------------------------------------------------------------------- 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: 50.0000 chunk 45 optimal weight: 20.0000 chunk 382 optimal weight: 1.9990 chunk 177 optimal weight: 6.9990 chunk 161 optimal weight: 0.9980 chunk 441 optimal weight: 40.0000 chunk 190 optimal weight: 9.9990 chunk 121 optimal weight: 2.9990 chunk 23 optimal weight: 20.0000 chunk 408 optimal weight: 5.9990 chunk 171 optimal weight: 3.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 382 GLN ** A 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 575 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 673 ASN B1041 ASN ** 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** ** O 346 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 454 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 315 ASN ** 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 304 HIS 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: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.090937 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.070969 restraints weight = 235316.726| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.072831 restraints weight = 128174.588| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.073895 restraints weight = 82708.073| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.074716 restraints weight = 62783.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.075066 restraints weight = 50839.920| |-----------------------------------------------------------------------------| r_work (final): 0.3372 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7339 moved from start: 0.6717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 47692 Z= 0.184 Angle : 0.870 35.194 64864 Z= 0.429 Chirality : 0.050 0.650 7252 Planarity : 0.007 0.286 7976 Dihedral : 14.243 177.800 7127 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 20.50 Ramachandran Plot: Outliers : 0.59 % Allowed : 7.77 % Favored : 91.64 % Rotamer: Outliers : 0.00 % Allowed : 0.42 % Favored : 99.58 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.65 % Twisted General : 0.11 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.13 (0.11), residues: 5432 helix: 0.33 (0.11), residues: 1953 sheet: -0.94 (0.18), residues: 711 loop : -1.49 (0.12), residues: 2768 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG B 815 TYR 0.034 0.002 TYR P 366 PHE 0.107 0.002 PHE Q 358 TRP 0.060 0.002 TRP N 54 HIS 0.011 0.001 HIS B1038 Details of bonding type rmsd/Z covalent geometry : bond 0.00394 / 0.18 (47647) covalent geometry : angle 0.83349 / 0.43 (64831) hydrogen bonds : bond 0.05242 / 3.49 ( 1994) hydrogen bonds : angle 6.06803 / 4.29 ( 5479) metal coordination : bond 0.01329 / 0.73 ( 24) metal coordination : angle 11.12219 / 6.87 ( 33) Misc. bond : bond 0.01167 / 0.68 ( 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 864 residues out of total 4950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 864 time to evaluate : 1.046 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: A 90 PHE cc_start: 0.9522 (m-80) cc_final: 0.9281 (m-10) REVERT: A 97 TYR cc_start: 0.9260 (m-80) cc_final: 0.8951 (m-80) REVERT: A 213 ASN cc_start: 0.9243 (t0) cc_final: 0.9000 (t0) REVERT: A 214 ASP cc_start: 0.9315 (t70) cc_final: 0.8405 (t0) REVERT: A 218 LYS cc_start: 0.9470 (mtmt) cc_final: 0.9237 (ptpt) REVERT: A 226 LYS cc_start: 0.9347 (mmpt) cc_final: 0.8919 (mmmt) REVERT: A 339 PHE cc_start: 0.8685 (m-80) cc_final: 0.8272 (m-80) REVERT: A 466 LEU cc_start: 0.9354 (tt) cc_final: 0.8904 (tt) REVERT: A 470 HIS cc_start: 0.8486 (m-70) cc_final: 0.8191 (m-70) REVERT: A 505 LEU cc_start: 0.8835 (mp) cc_final: 0.8607 (mp) REVERT: A 654 ASP cc_start: 0.8778 (m-30) cc_final: 0.8507 (m-30) REVERT: A 672 ASP cc_start: 0.8144 (t70) cc_final: 0.7906 (t70) REVERT: A 699 CYS cc_start: 0.8670 (p) cc_final: 0.8406 (p) REVERT: A 736 LEU cc_start: 0.9677 (mt) cc_final: 0.9468 (mt) REVERT: A 738 ASN cc_start: 0.8814 (m-40) cc_final: 0.8270 (t0) REVERT: A 822 THR cc_start: 0.9215 (p) cc_final: 0.8891 (t) REVERT: A 830 MET cc_start: 0.8832 (mmm) cc_final: 0.8506 (mmm) REVERT: A 925 MET cc_start: 0.9457 (tpt) cc_final: 0.8986 (mmm) REVERT: A 943 ILE cc_start: 0.9608 (mt) cc_final: 0.9347 (pt) REVERT: A 947 LEU cc_start: 0.9209 (mp) cc_final: 0.8939 (mp) REVERT: A 1007 ILE cc_start: -0.4405 (mt) cc_final: -0.4732 (mm) REVERT: A 1019 LEU cc_start: -0.3236 (tp) cc_final: -0.3597 (tp) REVERT: A 1060 GLU cc_start: 0.8783 (tm-30) cc_final: 0.8537 (tm-30) REVERT: A 1092 GLU cc_start: 0.9267 (mt-10) cc_final: 0.9036 (mp0) REVERT: A 1183 GLU cc_start: 0.8319 (tp30) cc_final: 0.7927 (tp30) REVERT: A 1185 VAL cc_start: 0.9486 (m) cc_final: 0.9162 (t) REVERT: A 1226 VAL cc_start: 0.9720 (t) cc_final: 0.9498 (p) REVERT: A 1227 MET cc_start: 0.8617 (tpp) cc_final: 0.8332 (tpp) REVERT: A 1476 LEU cc_start: 0.9159 (mt) cc_final: 0.8892 (mt) REVERT: A 1504 ILE cc_start: 0.9204 (mm) cc_final: 0.8975 (mm) REVERT: A 1505 ASP cc_start: 0.8658 (t0) cc_final: 0.7988 (t70) REVERT: A 1519 LEU cc_start: 0.9306 (mp) cc_final: 0.8925 (mt) REVERT: A 1587 ASP cc_start: 0.8886 (m-30) cc_final: 0.8450 (m-30) REVERT: A 1589 MET cc_start: 0.9341 (mtt) cc_final: 0.8854 (mmm) REVERT: A 1613 MET cc_start: 0.8940 (mtm) cc_final: 0.8472 (ptp) REVERT: A 1620 GLN cc_start: 0.8945 (mp10) cc_final: 0.8662 (mp10) REVERT: A 1621 PHE cc_start: 0.9231 (m-80) cc_final: 0.8703 (m-80) REVERT: B 98 SER cc_start: 0.9158 (p) cc_final: 0.8761 (m) REVERT: B 108 MET cc_start: 0.8732 (mmp) cc_final: 0.8310 (mmp) REVERT: B 125 GLU cc_start: 0.8985 (mt-10) cc_final: 0.8581 (mt-10) REVERT: B 136 LYS cc_start: 0.8908 (ttmt) cc_final: 0.8298 (tptm) REVERT: B 168 ASN cc_start: 0.9215 (t0) cc_final: 0.8842 (t0) REVERT: B 174 LYS cc_start: 0.9202 (mmpt) cc_final: 0.8931 (mmmt) REVERT: B 206 LEU cc_start: 0.9326 (tp) cc_final: 0.9043 (tp) REVERT: B 215 MET cc_start: 0.7402 (mtt) cc_final: 0.6940 (mtt) REVERT: B 224 ASN cc_start: 0.8641 (m110) cc_final: 0.8423 (m110) REVERT: B 285 ASP cc_start: 0.8743 (m-30) cc_final: 0.8460 (m-30) REVERT: B 304 ASP cc_start: 0.9437 (m-30) cc_final: 0.9080 (p0) REVERT: B 354 LEU cc_start: 0.9342 (tt) cc_final: 0.9127 (tt) REVERT: B 398 GLN cc_start: 0.9200 (pt0) cc_final: 0.8975 (pt0) REVERT: B 411 MET cc_start: 0.9373 (mtt) cc_final: 0.9011 (mmm) REVERT: B 422 GLN cc_start: 0.9222 (tm-30) cc_final: 0.8954 (tm-30) REVERT: B 486 VAL cc_start: 0.9360 (t) cc_final: 0.9016 (p) REVERT: B 514 THR cc_start: 0.8546 (p) cc_final: 0.8159 (p) REVERT: B 515 THR cc_start: 0.9286 (p) cc_final: 0.9000 (t) REVERT: B 543 ASN cc_start: 0.8950 (m110) cc_final: 0.8571 (m-40) REVERT: B 556 SER cc_start: 0.7621 (p) cc_final: 0.6664 (t) REVERT: B 557 ASP cc_start: 0.7918 (m-30) cc_final: 0.7361 (m-30) REVERT: B 568 LEU cc_start: 0.9069 (mt) cc_final: 0.8725 (mt) REVERT: B 671 TYR cc_start: 0.8880 (m-80) cc_final: 0.8548 (m-10) REVERT: B 778 TYR cc_start: 0.8632 (t80) cc_final: 0.8035 (t80) REVERT: B 885 VAL cc_start: 0.8907 (t) cc_final: 0.8693 (t) REVERT: B 934 ILE cc_start: 0.9473 (pt) cc_final: 0.9231 (pt) REVERT: B 962 MET cc_start: 0.8915 (ttm) cc_final: 0.8703 (ttm) REVERT: B 965 GLU cc_start: 0.8914 (tm-30) cc_final: 0.8679 (tm-30) REVERT: B 982 THR cc_start: 0.9394 (m) cc_final: 0.9117 (p) REVERT: B 1073 GLU cc_start: 0.7962 (tp30) cc_final: 0.7722 (tp30) REVERT: B 1074 MET cc_start: 0.8226 (ttm) cc_final: 0.7863 (ttp) REVERT: B 1075 GLU cc_start: 0.8577 (mp0) cc_final: 0.8166 (mm-30) REVERT: B 1086 PHE cc_start: 0.7584 (m-80) cc_final: 0.7092 (m-80) REVERT: B 1098 TYR cc_start: 0.8722 (t80) cc_final: 0.7742 (t80) REVERT: B 1111 LEU cc_start: 0.9376 (tp) cc_final: 0.9147 (tt) REVERT: C 71 MET cc_start: 0.9242 (mtp) cc_final: 0.8509 (mmm) REVERT: C 88 ASN cc_start: 0.8255 (t0) cc_final: 0.7983 (t0) REVERT: C 95 GLU cc_start: 0.8356 (mm-30) cc_final: 0.7389 (mm-30) REVERT: C 247 PHE cc_start: 0.9058 (t80) cc_final: 0.8745 (t80) REVERT: D 25 THR cc_start: 0.9120 (p) cc_final: 0.8612 (p) REVERT: D 91 ARG cc_start: 0.9402 (ptp90) cc_final: 0.9020 (ptp-170) REVERT: E 116 ILE cc_start: 0.9097 (pt) cc_final: 0.8818 (pt) REVERT: E 140 LEU cc_start: 0.9312 (mm) cc_final: 0.9040 (mm) REVERT: E 215 MET cc_start: 0.8752 (mmt) cc_final: 0.8536 (mmp) REVERT: F 74 ILE cc_start: 0.9392 (mm) cc_final: 0.9107 (tp) REVERT: F 90 ARG cc_start: 0.9407 (ptm-80) cc_final: 0.9129 (ttp80) REVERT: F 103 MET cc_start: 0.9120 (mmt) cc_final: 0.8718 (mmp) REVERT: F 122 MET cc_start: 0.9159 (mtp) cc_final: 0.8803 (mtp) REVERT: F 127 GLU cc_start: 0.8680 (mp0) cc_final: 0.8445 (mp0) REVERT: F 136 ARG cc_start: 0.8034 (mtt180) cc_final: 0.7805 (mtt180) REVERT: G 43 ILE cc_start: 0.9009 (pt) cc_final: 0.8577 (mm) REVERT: G 45 LEU cc_start: 0.9148 (pp) cc_final: 0.8934 (pp) REVERT: G 75 ASN cc_start: 0.9225 (p0) cc_final: 0.8619 (t0) REVERT: G 98 GLU cc_start: 0.8512 (mm-30) cc_final: 0.8142 (mp0) REVERT: G 119 HIS cc_start: 0.7652 (t-90) cc_final: 0.7348 (t-90) REVERT: H 102 TYR cc_start: 0.8758 (p90) cc_final: 0.8208 (p90) REVERT: H 118 PHE cc_start: 0.8695 (m-80) cc_final: 0.8087 (m-80) REVERT: I 60 LEU cc_start: 0.9556 (mm) cc_final: 0.9028 (mm) REVERT: I 64 LYS cc_start: 0.9344 (mtpp) cc_final: 0.8806 (mtpp) REVERT: J 6 ARG cc_start: 0.8415 (mtt90) cc_final: 0.8090 (mtt90) REVERT: J 28 ASP cc_start: 0.8922 (t70) cc_final: 0.8421 (t0) REVERT: J 49 MET cc_start: 0.9361 (tpp) cc_final: 0.8453 (tpp) REVERT: J 58 GLU cc_start: 0.9189 (tp30) cc_final: 0.8905 (tm-30) REVERT: K 46 LYS cc_start: 0.7769 (tptt) cc_final: 0.7206 (tppt) REVERT: K 67 GLU cc_start: 0.8769 (tm-30) cc_final: 0.8323 (tm-30) REVERT: K 125 MET cc_start: 0.8752 (mtt) cc_final: 0.8265 (mmm) REVERT: L 53 HIS cc_start: 0.8816 (t-90) cc_final: 0.8065 (t-90) REVERT: L 68 GLU cc_start: 0.7137 (tm-30) cc_final: 0.6515 (tm-30) REVERT: M 12 ILE cc_start: 0.8823 (mm) cc_final: 0.8617 (mm) REVERT: M 26 PHE cc_start: 0.8278 (m-10) cc_final: 0.7373 (m-10) REVERT: M 30 PHE cc_start: 0.9229 (t80) cc_final: 0.9008 (t80) REVERT: M 38 PHE cc_start: 0.9033 (m-80) cc_final: 0.8665 (m-80) REVERT: M 41 TYR cc_start: 0.8609 (m-80) cc_final: 0.8313 (m-80) REVERT: M 61 GLU cc_start: 0.9141 (mp0) cc_final: 0.8316 (tm-30) REVERT: M 91 TYR cc_start: 0.8726 (m-80) cc_final: 0.8523 (m-80) REVERT: M 92 LYS cc_start: 0.8263 (ttpt) cc_final: 0.7964 (ttpt) REVERT: N 29 PHE cc_start: 0.8910 (m-80) cc_final: 0.8170 (m-80) REVERT: N 80 MET cc_start: 0.8933 (tpt) cc_final: 0.8672 (ptm) REVERT: N 107 MET cc_start: 0.9160 (tmm) cc_final: 0.8683 (mmt) REVERT: N 119 LEU cc_start: 0.8925 (mm) cc_final: 0.8454 (tp) REVERT: O 293 TYR cc_start: 0.8436 (t80) cc_final: 0.8070 (t80) REVERT: O 463 LEU cc_start: 0.9094 (pt) cc_final: 0.8728 (mm) REVERT: O 467 PHE cc_start: 0.9557 (m-80) cc_final: 0.9206 (m-80) REVERT: O 471 MET cc_start: 0.5448 (mtm) cc_final: 0.2978 (mmm) REVERT: O 537 PHE cc_start: 0.9468 (p90) cc_final: 0.8734 (p90) REVERT: O 538 LEU cc_start: 0.9617 (mp) cc_final: 0.9258 (mt) REVERT: P 238 HIS cc_start: 0.9369 (m-70) cc_final: 0.9123 (m90) REVERT: P 258 MET cc_start: 0.8936 (ptt) cc_final: 0.8370 (ptt) REVERT: P 304 LEU cc_start: 0.8446 (mp) cc_final: 0.7964 (mp) REVERT: P 376 GLU cc_start: 0.9505 (mp0) cc_final: 0.8904 (tp30) REVERT: P 381 MET cc_start: 0.9353 (mmp) cc_final: 0.8975 (mmm) REVERT: P 413 LEU cc_start: 0.9793 (mt) cc_final: 0.9505 (mt) REVERT: Q 212 HIS cc_start: 0.9401 (m-70) cc_final: 0.8846 (m-70) REVERT: Q 229 TRP cc_start: 0.6374 (t60) cc_final: 0.5721 (t60) REVERT: Q 251 TRP cc_start: 0.6823 (p-90) cc_final: 0.6032 (p-90) REVERT: Q 257 ILE cc_start: 0.9310 (tp) cc_final: 0.8818 (tp) REVERT: Q 274 MET cc_start: 0.9527 (tpt) cc_final: 0.8849 (tpt) REVERT: Q 277 ILE cc_start: 0.9490 (tp) cc_final: 0.8932 (tp) REVERT: Q 278 TYR cc_start: 0.9631 (m-10) cc_final: 0.8985 (m-80) REVERT: Q 365 TRP cc_start: 0.9053 (m100) cc_final: 0.7821 (m100) outliers start: 0 outliers final: 0 residues processed: 864 average time/residue: 0.1609 time to fit residues: 236.3496 Evaluate side-chains 702 residues out of total 4950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 702 time to evaluate : 1.015 ------------------------------------------------------------------------------- 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: 6.9990 chunk 203 optimal weight: 0.9980 chunk 105 optimal weight: 20.0000 chunk 450 optimal weight: 6.9990 chunk 542 optimal weight: 10.0000 chunk 305 optimal weight: 2.9990 chunk 185 optimal weight: 10.0000 chunk 489 optimal weight: 8.9990 chunk 423 optimal weight: 20.0000 chunk 507 optimal weight: 10.0000 chunk 102 optimal weight: 3.9990 overall best weight: 4.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 382 GLN ** A 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 575 HIS B 673 ASN B 764 ASN ** B 824 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 912 GLN B1041 ASN ** 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** ** O 346 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 395 GLN O 454 GLN O 757 GLN ** 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: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.090270 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.070252 restraints weight = 238407.068| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.072104 restraints weight = 130210.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 21)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.073153 restraints weight = 83956.377| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.074016 restraints weight = 62953.042| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 19)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.074464 restraints weight = 50996.986| |-----------------------------------------------------------------------------| r_work (final): 0.3360 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7355 moved from start: 0.6845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.092 47692 Z= 0.201 Angle : 0.861 37.606 64864 Z= 0.426 Chirality : 0.050 0.666 7252 Planarity : 0.007 0.277 7976 Dihedral : 14.227 178.208 7127 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 20.99 Ramachandran Plot: Outliers : 0.57 % Allowed : 7.82 % Favored : 91.61 % Rotamer: Outliers : 0.00 % Allowed : 0.40 % Favored : 99.60 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.65 % Twisted General : 0.11 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.11 (0.11), residues: 5432 helix: 0.37 (0.11), residues: 1960 sheet: -1.01 (0.18), residues: 697 loop : -1.49 (0.12), residues: 2775 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG B 815 TYR 0.049 0.002 TYR P 227 PHE 0.115 0.002 PHE Q 358 TRP 0.048 0.002 TRP N 54 HIS 0.015 0.001 HIS E 147 Details of bonding type rmsd/Z covalent geometry : bond 0.00433 / 0.20 (47647) covalent geometry : angle 0.82724 / 0.42 (64831) hydrogen bonds : bond 0.05140 / 3.44 ( 1994) hydrogen bonds : angle 6.01209 / 4.25 ( 5479) metal coordination : bond 0.01700 / 1.00 ( 24) metal coordination : angle 10.67866 / 6.43 ( 33) Misc. bond : bond 0.01128 / 0.67 ( 21) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8471.15 seconds wall clock time: 147 minutes 5.11 seconds (8825.11 seconds total)