Starting phenix.real_space_refine on Thu Oct 29 21:32:26 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9g23_50962/10_2026/9g23_50962.cif Found real_map, /net/cci-nas-00/data/ceres_data/9g23_50962/10_2026/9g23_50962.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9g23_50962/10_2026/9g23_50962.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9g23_50962/10_2026/9g23_50962.map" model { file = "/net/cci-nas-00/data/ceres_data/9g23_50962/10_2026/9g23_50962.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9g23_50962/10_2026/9g23_50962.cif" } resolution = 3.4 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= 0.003 sd= 0.130 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 6 6.06 5 P 74 5.49 5 Mg 1 5.21 5 S 167 5.16 5 C 21355 2.51 5 N 5929 2.21 5 O 6605 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 34137 Number of models: 1 Model: "" Number of chains: 22 Chain: "A" Number of atoms: 11664 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1478, 11664 Classifications: {'peptide': 1478} Link IDs: {'PCIS': 4, 'PTRANS': 55, 'TRANS': 1418} Chain breaks: 5 Chain: "B" Number of atoms: 9274 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1168, 9274 Classifications: {'peptide': 1168} Link IDs: {'PTRANS': 59, 'TRANS': 1108} Chain breaks: 2 Chain: "C" Number of atoms: 2461 Number of conformers: 1 Conformer: "" Number of residues, atoms: 310, 2461 Classifications: {'peptide': 310} Link IDs: {'PTRANS': 19, 'TRANS': 290} 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: 1734 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1734 Classifications: {'peptide': 212} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 199} Chain: "F" Number of atoms: 827 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 827 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 7, 'TRANS': 93} Chain: "G" Number of atoms: 1258 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1258 Classifications: {'peptide': 162} Link IDs: {'PTRANS': 9, 'TRANS': 152} Chain breaks: 1 Chain: "H" Number of atoms: 1060 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1060 Classifications: {'peptide': 132} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 127} 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: 766 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 766 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 3, 'TRANS': 94} Chain: "L" Number of atoms: 352 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 352 Classifications: {'peptide': 44} Modifications used: {'COO': 1} Link IDs: {'TRANS': 43} Chain: "M" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 816 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 5, 'TRANS': 97} Chain: "N" Number of atoms: 921 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 921 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 8, 'TRANS': 107} Chain breaks: 4 Chain: "R" Number of atoms: 239 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 239 Classifications: {'RNA': 11} Modifications used: {'rna2p_pyr': 1, 'rna3p_pur': 8, 'rna3p_pyr': 2} Link IDs: {'rna2p': 1, 'rna3p': 9} Chain: "S" Number of atoms: 526 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 526 Classifications: {'DNA': 26} Link IDs: {'rna3p': 25} Chain breaks: 1 Chain: "T" Number of atoms: 686 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 686 Classifications: {'DNA': 34} Link IDs: {'rna3p': 33} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' ZN': 1, 'APC': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "I" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "J" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 461 SG CYS A 62 53.723 85.462 86.547 1.00 90.94 S ATOM 480 SG CYS A 65 53.562 89.113 87.610 1.00 90.16 S ATOM 535 SG CYS A 72 56.516 87.910 85.457 1.00 92.82 S ATOM 781 SG CYS A 102 82.584 65.464 123.582 1.00125.28 S ATOM 806 SG CYS A 105 81.712 68.218 126.016 1.00131.06 S ATOM 1583 SG CYS A 233 85.309 67.518 125.243 1.00125.49 S ATOM 1605 SG CYS A 236 83.303 64.940 127.258 1.00135.33 S ATOM 20293 SG CYS B1104 61.275 94.943 101.862 1.00 84.24 S ATOM 20319 SG CYS B1107 61.461 91.741 103.661 1.00 86.50 S ATOM 20466 SG CYS B1128 59.026 92.125 100.546 1.00 91.56 S ATOM 20494 SG CYS B1131 58.474 93.680 104.055 1.00 98.12 S ATOM 28808 SG CYS I 10 126.400 27.688 82.433 1.00140.43 S ATOM 28830 SG CYS I 13 123.068 29.040 81.085 1.00143.82 S ATOM 28950 SG CYS I 30 123.213 27.547 84.556 1.00150.04 S ATOM 28971 SG CYS I 33 123.583 25.377 81.372 1.00153.99 S ATOM 29278 SG CYS J 7 96.320 105.073 30.627 1.00 62.52 S ATOM 29301 SG CYS J 10 96.151 108.680 29.304 1.00 63.07 S ATOM 29581 SG CYS J 45 99.474 107.117 30.549 1.00 63.98 S ATOM 29587 SG CYS J 46 97.753 106.257 27.222 1.00 61.85 S ATOM 30602 SG CYS L 31 70.107 69.379 32.535 1.00 82.53 S ATOM 30622 SG CYS L 34 69.978 68.556 28.848 1.00 89.65 S ATOM 30726 SG CYS L 48 66.870 68.075 30.946 1.00100.35 S ATOM 30749 SG CYS L 51 69.865 65.758 31.413 1.00101.01 S Time building chain proxies: 6.92, per 1000 atoms: 0.20 Number of scatterers: 34137 At special positions: 0 Unit cell: (165.426, 169.614, 152.862, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 6 29.99 S 167 16.00 P 74 15.00 Mg 1 11.99 O 6605 8.00 N 5929 7.00 C 21355 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=0, symmetry=0 Time building additional restraints: 2.99 Conformation dependent library (CDL) restraints added in 1.1 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1701 " pdb="ZN ZN A1701 " - pdb=" NE2 HIS A 75 " pdb="ZN ZN A1701 " - pdb=" SG CYS A 65 " pdb="ZN ZN A1701 " - pdb=" SG CYS A 62 " pdb="ZN ZN A1701 " - pdb=" SG CYS A 72 " pdb=" ZN A1702 " pdb="ZN ZN A1702 " - pdb=" SG CYS A 105 " pdb="ZN ZN A1702 " - pdb=" SG CYS A 102 " pdb="ZN ZN A1702 " - pdb=" SG CYS A 233 " pdb="ZN ZN A1702 " - pdb=" SG CYS A 236 " pdb=" ZN B3001 " pdb="ZN ZN B3001 " - pdb=" SG CYS B1104 " pdb="ZN ZN B3001 " - pdb=" SG CYS B1131 " pdb="ZN ZN B3001 " - pdb=" SG CYS B1107 " pdb="ZN ZN B3001 " - pdb=" SG CYS B1128 " pdb=" ZN I3001 " pdb="ZN ZN I3001 " - pdb=" SG CYS I 13 " pdb="ZN ZN I3001 " - pdb=" SG CYS I 33 " pdb="ZN ZN I3001 " - pdb=" SG CYS I 10 " pdb="ZN ZN I3001 " - pdb=" SG CYS I 30 " pdb=" ZN J3001 " pdb="ZN ZN J3001 " - pdb=" SG CYS J 10 " pdb="ZN ZN J3001 " - pdb=" SG CYS J 46 " pdb="ZN ZN J3001 " - pdb=" SG CYS J 45 " pdb="ZN ZN J3001 " - pdb=" SG CYS J 7 " pdb=" ZN L3001 " pdb="ZN ZN L3001 " - pdb=" SG CYS L 34 " pdb="ZN ZN L3001 " - pdb=" SG CYS L 31 " pdb="ZN ZN L3001 " - pdb=" SG CYS L 48 " pdb="ZN ZN L3001 " - pdb=" SG CYS L 51 " Number of angles added : 33 8122 Ramachandran restraints generated. 4061 Oldfield, 0 Emsley, 4061 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7728 Finding SS restraints... Secondary structure from input PDB file: 147 helices and 51 sheets defined 37.6% alpha, 18.3% beta 28 base pairs and 45 stacking pairs defined. Time for finding SS restraints: 4.18 Creating SS restraints... Processing helix chain 'A' and resid 20 through 28 removed outlier: 3.590A pdb=" N ILE A 24 " --> pdb=" O THR A 20 " (cutoff:3.500A) Processing helix chain 'A' and resid 51 through 55 removed outlier: 3.750A pdb=" N GLY A 55 " --> pdb=" O LEU A 52 " (cutoff:3.500A) Processing helix chain 'A' and resid 90 through 99 Processing helix chain 'A' and resid 111 through 127 removed outlier: 3.778A pdb=" N TYR A 127 " --> pdb=" O ARG A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 136 Processing helix chain 'A' and resid 176 through 199 removed outlier: 3.955A pdb=" N GLU A 180 " --> pdb=" O THR A 176 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ASP A 199 " --> pdb=" O LYS A 195 " (cutoff:3.500A) Processing helix chain 'A' and resid 209 through 230 removed outlier: 3.859A pdb=" N ARG A 230 " --> pdb=" O LYS A 226 " (cutoff:3.500A) Processing helix chain 'A' and resid 259 through 268 removed outlier: 4.251A pdb=" N ASN A 263 " --> pdb=" O LYS A 259 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N ASN A 264 " --> pdb=" O GLN A 260 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N ARG A 265 " --> pdb=" O ILE A 261 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N VAL A 266 " --> pdb=" O THR A 262 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N LYS A 267 " --> pdb=" O ASN A 263 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N GLY A 268 " --> pdb=" O ASN A 264 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 259 through 268' Processing helix chain 'A' and resid 316 through 331 Processing helix chain 'A' and resid 331 through 339 removed outlier: 4.300A pdb=" N TYR A 337 " --> pdb=" O CYS A 333 " (cutoff:3.500A) Processing helix chain 'A' and resid 380 through 409 Processing helix chain 'A' and resid 412 through 439 removed outlier: 3.717A pdb=" N ARG A 416 " --> pdb=" O SER A 412 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N ILE A 419 " --> pdb=" O ASP A 415 " (cutoff:3.500A) Processing helix chain 'A' and resid 456 through 460 Processing helix chain 'A' and resid 465 through 471 Processing helix chain 'A' and resid 498 through 503 Processing helix chain 'A' and resid 515 through 526 Processing helix chain 'A' and resid 550 through 560 Processing helix chain 'A' and resid 596 through 598 No H-bonds generated for 'chain 'A' and resid 596 through 598' Processing helix chain 'A' and resid 620 through 625 Processing helix chain 'A' and resid 640 through 648 Processing helix chain 'A' and resid 652 through 657 removed outlier: 3.560A pdb=" N TYR A 657 " --> pdb=" O ASP A 654 " (cutoff:3.500A) Processing helix chain 'A' and resid 671 through 682 removed outlier: 3.755A pdb=" N SER A 675 " --> pdb=" O GLN A 671 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N SER A 682 " --> pdb=" O VAL A 678 " (cutoff:3.500A) Processing helix chain 'A' and resid 688 through 698 Processing helix chain 'A' and resid 728 through 740 Processing helix chain 'A' and resid 792 through 824 Proline residue: A 803 - end of helix removed outlier: 3.679A pdb=" N ALA A 806 " --> pdb=" O GLY A 802 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ALA A 823 " --> pdb=" O ASN A 819 " (cutoff:3.500A) Processing helix chain 'A' and resid 830 through 834 removed outlier: 3.507A pdb=" N ARG A 834 " --> pdb=" O ASP A 831 " (cutoff:3.500A) Processing helix chain 'A' and resid 836 through 848 Processing helix chain 'A' and resid 849 through 851 No H-bonds generated for 'chain 'A' and resid 849 through 851' Processing helix chain 'A' and resid 852 through 862 Processing helix chain 'A' and resid 872 through 885 Processing helix chain 'A' and resid 886 through 912 removed outlier: 3.579A pdb=" N GLY A 890 " --> pdb=" O ASN A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 923 through 931 Processing helix chain 'A' and resid 936 through 945 Processing helix chain 'A' and resid 976 through 980 removed outlier: 3.841A pdb=" N GLY A 980 " --> pdb=" O MET A 977 " (cutoff:3.500A) Processing helix chain 'A' and resid 991 through 1028 removed outlier: 3.879A pdb=" N THR A1013 " --> pdb=" O THR A1009 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N SER A1014 " --> pdb=" O ALA A1010 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N GLY A1017 " --> pdb=" O THR A1013 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N TYR A1018 " --> pdb=" O SER A1014 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N LEU A1019 " --> pdb=" O ARG A1015 " (cutoff:3.500A) Processing helix chain 'A' and resid 1065 through 1072 Processing helix chain 'A' and resid 1072 through 1081 Processing helix chain 'A' and resid 1082 through 1085 Processing helix chain 'A' and resid 1091 through 1108 removed outlier: 3.850A pdb=" N LEU A1095 " --> pdb=" O VAL A1091 " (cutoff:3.500A) Processing helix chain 'A' and resid 1122 through 1127 removed outlier: 4.075A pdb=" N LYS A1126 " --> pdb=" O PRO A1122 " (cutoff:3.500A) Processing helix chain 'A' and resid 1137 through 1151 Processing helix chain 'A' and resid 1162 through 1177 Processing helix chain 'A' and resid 1184 through 1195 Processing helix chain 'A' and resid 1196 through 1200 Processing helix chain 'A' and resid 1218 through 1226 Processing helix chain 'A' and resid 1251 through 1259 Processing helix chain 'A' and resid 1298 through 1306 removed outlier: 4.571A pdb=" N GLU A1304 " --> pdb=" O ASN A1300 " (cutoff:3.500A) Processing helix chain 'A' and resid 1309 through 1338 removed outlier: 5.484A pdb=" N ILE A1322 " --> pdb=" O SER A1318 " (cutoff:3.500A) removed outlier: 4.821A pdb=" N HIS A1323 " --> pdb=" O ASN A1319 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ALA A1327 " --> pdb=" O HIS A1323 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ARG A1338 " --> pdb=" O LYS A1334 " (cutoff:3.500A) Processing helix chain 'A' and resid 1434 through 1438 removed outlier: 4.262A pdb=" N ASN A1437 " --> pdb=" O GLU A1434 " (cutoff:3.500A) Processing helix chain 'A' and resid 1440 through 1454 Processing helix chain 'A' and resid 1486 through 1496 removed outlier: 3.695A pdb=" N GLU A1491 " --> pdb=" O ASN A1487 " (cutoff:3.500A) Processing helix chain 'A' and resid 1525 through 1532 removed outlier: 4.113A pdb=" N MET A1529 " --> pdb=" O ASN A1525 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N ASP A1531 " --> pdb=" O GLN A1527 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N GLN A1532 " --> pdb=" O ALA A1528 " (cutoff:3.500A) Processing helix chain 'A' and resid 1537 through 1541 removed outlier: 3.877A pdb=" N ILE A1541 " --> pdb=" O VAL A1538 " (cutoff:3.500A) Processing helix chain 'A' and resid 1546 through 1554 Processing helix chain 'A' and resid 1554 through 1573 removed outlier: 3.595A pdb=" N VAL A1569 " --> pdb=" O GLU A1565 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N PHE A1570 " --> pdb=" O ILE A1566 " (cutoff:3.500A) Processing helix chain 'A' and resid 1578 through 1590 removed outlier: 3.819A pdb=" N LEU A1582 " --> pdb=" O SER A1578 " (cutoff:3.500A) Processing helix chain 'A' and resid 1599 through 1603 Processing helix chain 'A' and resid 1608 through 1616 removed outlier: 4.310A pdb=" N LYS A1612 " --> pdb=" O SER A1608 " (cutoff:3.500A) Processing helix chain 'A' and resid 1617 through 1627 Processing helix chain 'A' and resid 1636 through 1644 Processing helix chain 'A' and resid 1649 through 1652 removed outlier: 3.845A pdb=" N GLY A1652 " --> pdb=" O VAL A1649 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1649 through 1652' Processing helix chain 'B' and resid 17 through 27 Processing helix chain 'B' and resid 35 through 42 removed outlier: 3.731A pdb=" N GLN B 39 " --> pdb=" O PHE B 35 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N VAL B 42 " --> pdb=" O LEU B 38 " (cutoff:3.500A) Processing helix chain 'B' and resid 42 through 52 removed outlier: 3.797A pdb=" N LEU B 52 " --> pdb=" O SER B 48 " (cutoff:3.500A) Processing helix chain 'B' and resid 55 through 58 removed outlier: 3.526A pdb=" N GLY B 58 " --> pdb=" O GLY B 55 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 55 through 58' Processing helix chain 'B' and resid 59 through 69 removed outlier: 3.919A pdb=" N GLY B 69 " --> pdb=" O VAL B 65 " (cutoff:3.500A) Processing helix chain 'B' and resid 122 through 130 Processing helix chain 'B' and resid 176 through 183 Processing helix chain 'B' and resid 219 through 224 removed outlier: 4.387A pdb=" N ALA B 223 " --> pdb=" O ARG B 219 " (cutoff:3.500A) Processing helix chain 'B' and resid 273 through 281 removed outlier: 4.395A 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 334 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 386 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 405 through 434 Processing helix chain 'B' and resid 442 through 451 Processing helix chain 'B' and resid 456 through 468 Processing helix chain 'B' and resid 492 through 500 removed outlier: 3.893A pdb=" N PHE B 500 " --> pdb=" O PHE B 496 " (cutoff:3.500A) Processing helix chain 'B' and resid 506 through 511 removed outlier: 4.173A pdb=" N GLN B 511 " --> pdb=" O PHE B 508 " (cutoff:3.500A) Processing helix chain 'B' and resid 514 through 518 removed outlier: 3.792A pdb=" N VAL B 517 " --> pdb=" O THR B 514 " (cutoff:3.500A) Processing helix chain 'B' and resid 521 through 525 Processing helix chain 'B' and resid 560 through 568 removed outlier: 3.529A pdb=" N SER B 567 " --> pdb=" O SER B 563 " (cutoff:3.500A) Processing helix chain 'B' and resid 597 through 614 Processing helix chain 'B' and resid 657 through 659 No H-bonds generated for 'chain 'B' and resid 657 through 659' Processing helix chain 'B' and resid 665 through 670 removed outlier: 3.701A pdb=" N VAL B 670 " --> pdb=" O PRO B 666 " (cutoff:3.500A) Processing helix chain 'B' and resid 677 through 681 removed outlier: 3.641A pdb=" N ILE B 681 " --> pdb=" O PRO B 678 " (cutoff:3.500A) Processing helix chain 'B' and resid 692 through 697 removed outlier: 3.516A pdb=" N ASN B 695 " --> pdb=" O THR B 692 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ILE B 696 " --> pdb=" O PRO B 693 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LEU B 697 " --> pdb=" O THR B 694 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 692 through 697' Processing helix chain 'B' and resid 706 through 710 removed outlier: 3.804A pdb=" N ASN B 710 " --> pdb=" O SER B 707 " (cutoff:3.500A) Processing helix chain 'B' and resid 711 through 722 removed outlier: 3.728A pdb=" N TYR B 717 " --> pdb=" O PRO B 713 " (cutoff:3.500A) Processing helix chain 'B' and resid 732 through 736 removed outlier: 3.698A pdb=" N ARG B 736 " --> pdb=" O LEU B 733 " (cutoff:3.500A) Processing helix chain 'B' and resid 755 through 760 removed outlier: 3.702A pdb=" N ASP B 759 " --> pdb=" O ASN B 755 " (cutoff:3.500A) Processing helix chain 'B' and resid 761 through 765 removed outlier: 3.632A pdb=" N ASN B 764 " --> pdb=" O GLY B 761 " (cutoff:3.500A) Processing helix chain 'B' and resid 791 through 795 Processing helix chain 'B' and resid 833 through 839 removed outlier: 3.520A pdb=" N TRP B 836 " --> pdb=" O PRO B 833 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N LYS B 839 " --> pdb=" O TRP B 836 " (cutoff:3.500A) Processing helix chain 'B' and resid 952 through 958 removed outlier: 4.658A pdb=" N SER B 956 " --> pdb=" O HIS B 952 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ARG B 957 " --> pdb=" O ALA B 953 " (cutoff:3.500A) Processing helix chain 'B' and resid 959 through 976 removed outlier: 3.869A pdb=" N PHE B 963 " --> pdb=" O THR B 959 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LEU B 967 " --> pdb=" O PHE B 963 " (cutoff:3.500A) Processing helix chain 'B' and resid 991 through 1004 removed outlier: 3.727A pdb=" N GLN B 999 " --> pdb=" O TYR B 995 " (cutoff:3.500A) Processing helix chain 'B' and resid 1039 through 1043 Processing helix chain 'B' and resid 1072 through 1082 Processing helix chain 'B' and resid 1084 through 1093 removed outlier: 3.603A pdb=" N LEU B1088 " --> pdb=" O THR B1084 " (cutoff:3.500A) Processing helix chain 'B' and resid 1180 through 1192 Processing helix chain 'C' and resid 32 through 40 Processing helix chain 'C' and resid 60 through 74 removed outlier: 3.713A pdb=" N ALA C 66 " --> pdb=" O SER C 62 " (cutoff:3.500A) Processing helix chain 'C' and resid 93 through 103 Processing helix chain 'C' and resid 109 through 113 removed outlier: 3.805A pdb=" N LEU C 113 " --> pdb=" O PRO C 110 " (cutoff:3.500A) Processing helix chain 'C' and resid 121 through 126 removed outlier: 4.000A pdb=" N PHE C 126 " --> pdb=" O ASP C 122 " (cutoff:3.500A) 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 174 through 179 Processing helix chain 'C' and resid 216 through 220 Processing helix chain 'C' and resid 241 through 250 removed outlier: 3.783A pdb=" N ARG C 245 " --> pdb=" O GLY C 241 " (cutoff:3.500A) Processing helix chain 'C' and resid 278 through 282 Processing helix chain 'C' and resid 309 through 331 Processing helix chain 'D' and resid 36 through 44 removed outlier: 4.785A pdb=" N SER D 42 " --> pdb=" O GLN D 38 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N ILE D 44 " --> pdb=" O LEU D 40 " (cutoff:3.500A) Processing helix chain 'E' and resid 5 through 27 Processing helix chain 'E' and resid 38 through 46 Processing helix chain 'E' and resid 65 through 72 Processing helix chain 'E' and resid 89 through 103 removed outlier: 3.773A pdb=" N PHE E 96 " --> pdb=" O THR E 92 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N GLN E 101 " --> pdb=" O VAL E 97 " (cutoff:3.500A) Processing helix chain 'E' and resid 117 through 124 removed outlier: 3.724A pdb=" N MET E 121 " --> pdb=" O THR E 117 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LYS E 122 " --> pdb=" O PRO E 118 " (cutoff:3.500A) Processing helix chain 'E' and resid 125 through 127 No H-bonds generated for 'chain 'E' and resid 125 through 127' 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 removed outlier: 3.997A pdb=" N LEU E 175 " --> pdb=" O GLU E 172 " (cutoff:3.500A) Processing helix chain 'E' and resid 182 through 189 Processing helix chain 'F' and resid 55 through 73 removed outlier: 3.592A pdb=" N GLN F 59 " --> pdb=" O PRO F 55 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N HIS F 61 " --> pdb=" O ASP F 57 " (cutoff:3.500A) Processing helix chain 'F' and resid 75 through 79 removed outlier: 3.899A pdb=" N ARG F 79 " --> pdb=" O LYS F 76 " (cutoff:3.500A) Processing helix chain 'F' and resid 86 through 103 Processing helix chain 'F' and resid 116 through 128 Processing helix chain 'G' and resid 56 through 65 Processing helix chain 'G' and resid 65 through 70 removed outlier: 3.648A pdb=" N LEU G 69 " --> pdb=" O HIS G 65 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N VAL G 70 " --> pdb=" O LEU G 66 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 65 through 70' Processing helix chain 'G' and resid 149 through 152 Processing helix chain 'H' and resid 88 through 92 removed outlier: 3.536A pdb=" N ASP H 92 " --> pdb=" O LEU H 89 " (cutoff:3.500A) Processing helix chain 'H' and resid 128 through 133 removed outlier: 3.715A pdb=" N ASN H 133 " --> pdb=" O TYR H 129 " (cutoff:3.500A) Processing helix chain 'I' and resid 19 through 23 removed outlier: 3.635A pdb=" N VAL I 23 " --> pdb=" O PRO I 20 " (cutoff:3.500A) Processing helix chain 'I' and resid 58 through 65 removed outlier: 3.608A pdb=" N ALA I 62 " --> pdb=" O SER I 58 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LYS I 63 " --> pdb=" O SER I 59 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N SER I 65 " --> pdb=" O ARG I 61 " (cutoff:3.500A) 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: 3.927A pdb=" N MET J 49 " --> pdb=" O CYS J 45 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ILE J 50 " --> pdb=" O CYS J 46 " (cutoff:3.500A) Processing helix chain 'J' and resid 56 through 61 Processing helix chain 'K' and resid 70 through 82 removed outlier: 3.608A pdb=" N LYS K 82 " --> pdb=" O TYR K 78 " (cutoff:3.500A) Processing helix chain 'K' and resid 112 through 142 Processing helix chain 'M' and resid 67 through 72 removed outlier: 4.152A pdb=" N ALA M 72 " --> pdb=" O SER M 68 " (cutoff:3.500A) Processing helix chain 'M' and resid 103 through 107 removed outlier: 3.930A pdb=" N ASN M 107 " --> pdb=" O LYS M 103 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 103 through 107' Processing helix chain 'N' and resid 149 through 154 Processing sheet with id=AA1, first strand: chain 'A' and resid 1631 through 1632 removed outlier: 6.698A pdb=" N ASN B1199 " --> pdb=" O THR A 12 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N VAL A 14 " --> pdb=" O ARG B1197 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N ARG B1197 " --> pdb=" O VAL A 14 " (cutoff:3.500A) removed outlier: 4.786A pdb=" N PHE A 16 " --> pdb=" O ARG B1195 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N ARG B1195 " --> pdb=" O PHE A 16 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 77 through 86 removed outlier: 10.968A pdb=" N LEU A 81 " --> pdb=" O VAL A 361 " (cutoff:3.500A) removed outlier: 10.968A pdb=" N VAL A 361 " --> pdb=" O LEU A 81 " (cutoff:3.500A) removed outlier: 10.388A pdb=" N VAL A 83 " --> pdb=" O VAL A 359 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N VAL A 359 " --> pdb=" O VAL A 83 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 242 through 246 removed outlier: 3.990A pdb=" N LYS A 250 " --> pdb=" O ASP A 246 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 371 through 372 Processing sheet with id=AA5, first strand: chain 'A' and resid 475 through 476 removed outlier: 3.914A pdb=" N ILE B1069 " --> pdb=" O VAL A 476 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 1045 through 1047 removed outlier: 3.897A pdb=" N SER A 482 " --> pdb=" O MET A 633 " (cutoff:3.500A) removed outlier: 5.671A pdb=" N ILE A 495 " --> pdb=" O ARG A 606 " (cutoff:3.500A) removed outlier: 7.342A pdb=" N LEU A 614 " --> pdb=" O ARG A 481 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N VAL A 483 " --> pdb=" O LEU A 614 " (cutoff:3.500A) removed outlier: 7.309A pdb=" N LEU A 616 " --> pdb=" O VAL A 483 " (cutoff:3.500A) removed outlier: 6.141A pdb=" N SER A 485 " --> pdb=" O LEU A 616 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 506 through 510 removed outlier: 4.358A pdb=" N GLN A 535 " --> pdb=" O TYR A 578 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N HIS A 580 " --> pdb=" O ALA A 533 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N ALA A 533 " --> pdb=" O HIS A 580 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 686 through 687 Processing sheet with id=AA9, first strand: chain 'A' and resid 719 through 721 removed outlier: 6.790A pdb=" N VAL H 96 " --> pdb=" O PHE A 720 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 750 through 752 removed outlier: 6.290A pdb=" N LEU A 770 " --> pdb=" O LEU A 777 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 826 through 827 removed outlier: 4.247A pdb=" N TYR B1027 " --> pdb=" O VAL B 775 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 1026 through 1035 current: chain 'B' and resid 787 through 790 removed outlier: 7.630A pdb=" N MET B 787 " --> pdb=" O SER B 928 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N LYS B 930 " --> pdb=" O MET B 787 " (cutoff:3.500A) removed outlier: 7.207A pdb=" N ILE B 789 " --> pdb=" O LYS B 930 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 917 through 919 removed outlier: 4.247A pdb=" N TYR B1027 " --> pdb=" O VAL B 775 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 1031 through 1032 Processing sheet with id=AB5, first strand: chain 'A' and resid 1507 through 1508 removed outlier: 3.712A pdb=" N THR A1521 " --> pdb=" O MET A1238 " (cutoff:3.500A) removed outlier: 4.842A pdb=" N MET A1238 " --> pdb=" O THR A1521 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 1261 through 1262 removed outlier: 6.875A pdb=" N VAL A1261 " --> pdb=" O ILE A1498 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 1471 through 1473 removed outlier: 3.686A pdb=" N ILE A1292 " --> pdb=" O PHE A1472 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N THR A1275 " --> pdb=" O SER A1289 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N HIS A1293 " --> pdb=" O ILE A1271 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LYS A1269 " --> pdb=" O ARG A1295 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 29 through 30 removed outlier: 3.526A pdb=" N LYS G 106 " --> pdb=" O PHE G 115 " (cutoff:3.500A) removed outlier: 7.224A pdb=" N TRP G 117 " --> pdb=" O LEU G 104 " (cutoff:3.500A) removed outlier: 9.269A pdb=" N LEU G 104 " --> pdb=" O TRP G 117 " (cutoff:3.500A) removed outlier: 5.012A pdb=" N VAL A1656 " --> pdb=" O ILE G 107 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 29 through 30 removed outlier: 7.044A pdb=" N TRP G 117 " --> pdb=" O LYS G 88 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N LYS G 88 " --> pdb=" O TRP G 117 " (cutoff:3.500A) removed outlier: 5.927A pdb=" N HIS G 119 " --> pdb=" O GLY G 86 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N GLY G 86 " --> pdb=" O HIS G 119 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N ASN G 121 " --> pdb=" O TYR G 84 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N TYR G 84 " --> pdb=" O ASN G 121 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N TYR G 123 " --> pdb=" O LEU G 82 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 71 through 74 removed outlier: 4.616A pdb=" N GLN B 101 " --> pdb=" O LYS B 140 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N LYS B 142 " --> pdb=" O VAL B 99 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N VAL B 99 " --> pdb=" O LYS B 142 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 71 through 74 removed outlier: 5.309A pdb=" N GLY B 135 " --> pdb=" O GLY B 160 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N GLY B 160 " --> pdb=" O GLY B 135 " (cutoff:3.500A) removed outlier: 5.295A pdb=" N LEU B 137 " --> pdb=" O CYS B 158 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLU B 154 " --> pdb=" O LEU B 141 " (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 Processing sheet with id=AC6, first strand: chain 'B' and resid 215 through 216 removed outlier: 3.754A pdb=" N THR B 244 " --> pdb=" O ARG B 240 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N THR B 259 " --> pdb=" O HIS B 251 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 550 through 551 Processing sheet with id=AC8, first strand: chain 'B' and resid 550 through 551 Processing sheet with id=AC9, first strand: chain 'B' and resid 571 through 572 removed outlier: 5.861A pdb=" N ILE B 592 " --> pdb=" O ILE B 588 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N ILE B 588 " --> pdb=" O ILE B 592 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 740 through 744 removed outlier: 7.668A pdb=" N THR B 900 " --> pdb=" O LEU B 887 " (cutoff:3.500A) removed outlier: 5.203A pdb=" N LEU B 887 " --> pdb=" O THR B 900 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N SER B 902 " --> pdb=" O VAL B 885 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N VAL B 885 " --> pdb=" O SER B 902 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N LYS B 904 " --> pdb=" O GLU B 883 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 740 through 744 removed outlier: 7.668A pdb=" N THR B 900 " --> pdb=" O LEU B 887 " (cutoff:3.500A) removed outlier: 5.203A pdb=" N LEU B 887 " --> pdb=" O THR B 900 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N SER B 902 " --> pdb=" O VAL B 885 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N VAL B 885 " --> pdb=" O SER B 902 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N LYS B 904 " --> pdb=" O GLU B 883 " (cutoff:3.500A) removed outlier: 5.319A 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 823 through 825 removed outlier: 3.856A pdb=" N CYS B 859 " --> pdb=" O LYS B 872 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ASP B 863 " --> pdb=" O LYS B 868 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N LYS B 868 " --> pdb=" O ASP B 863 " (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 1133 through 1134 Processing sheet with id=AD8, first strand: chain 'C' and resid 41 through 42 removed outlier: 3.670A pdb=" N GLU C 41 " --> pdb=" O ILE C 57 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N THR C 224 " --> pdb=" O GLU C 303 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 41 through 42 removed outlier: 3.670A pdb=" N GLU C 41 " --> pdb=" O ILE C 57 " (cutoff:3.500A) removed outlier: 10.005A pdb=" N ARG C 293 " --> pdb=" O ASN C 234 " (cutoff:3.500A) removed outlier: 9.058A pdb=" N ASN C 234 " --> pdb=" O ARG C 293 " (cutoff:3.500A) removed outlier: 9.594A pdb=" N ARG C 295 " --> pdb=" O GLN C 232 " (cutoff:3.500A) removed outlier: 11.160A pdb=" N GLN C 232 " --> pdb=" O ARG C 295 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N HIS C 297 " --> pdb=" O LEU C 230 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 77 through 88 removed outlier: 5.329A pdb=" N VAL C 78 " --> pdb=" O GLY C 211 " (cutoff:3.500A) removed outlier: 7.156A pdb=" N GLY C 211 " --> pdb=" O VAL C 78 " (cutoff:3.500A) removed outlier: 5.658A pdb=" N ALA C 80 " --> pdb=" O ILE C 209 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N ILE C 209 " --> pdb=" O ALA C 80 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N SER C 203 " --> pdb=" O PHE C 86 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N ASN C 88 " --> pdb=" O GLU C 201 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N GLU C 201 " --> pdb=" O ASN C 88 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N VAL C 133 " --> pdb=" O GLU C 170 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 141 through 142 Processing sheet with id=AE3, first strand: chain 'C' and resid 161 through 163 Processing sheet with id=AE4, first strand: chain 'C' and resid 256 through 258 Processing sheet with id=AE5, first strand: chain 'E' and resid 60 through 62 removed outlier: 6.425A pdb=" N TRP E 79 " --> pdb=" O ILE E 109 " (cutoff:3.500A) removed outlier: 7.850A pdb=" N VAL E 111 " --> pdb=" O TRP E 79 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N GLU E 81 " --> pdb=" O VAL E 111 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N GLY E 108 " --> pdb=" O GLU E 133 " (cutoff:3.500A) removed outlier: 7.740A pdb=" N PHE E 135 " --> pdb=" O GLY E 108 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N PHE E 110 " --> pdb=" O PHE E 135 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'E' and resid 152 through 155 removed outlier: 4.159A pdb=" N LYS E 152 " --> pdb=" O ILE E 199 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N MET E 215 " --> pdb=" O ILE E 178 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'G' and resid 145 through 148 removed outlier: 7.262A pdb=" N GLY G 146 " --> pdb=" O PHE G 138 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N LEU G 133 " --> pdb=" O PHE G 231 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N PHE G 231 " --> pdb=" O LEU G 133 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N GLY G 135 " --> pdb=" O LEU G 229 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N LEU G 229 " --> pdb=" O GLY G 135 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'G' and resid 235 through 237 Processing sheet with id=AE9, first strand: chain 'H' and resid 14 through 16 removed outlier: 3.832A pdb=" N LEU H 38 " --> pdb=" O ALA H 28 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'H' and resid 100 through 106 removed outlier: 5.375A pdb=" N ALA H 101 " --> pdb=" O SER H 117 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N SER H 117 " --> pdb=" O ALA H 101 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N LYS H 103 " --> pdb=" O TYR H 115 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'I' and resid 27 through 29 Processing sheet with id=AF3, first strand: chain 'K' and resid 47 through 49 removed outlier: 6.732A pdb=" N ASN K 102 " --> pdb=" O TYR K 91 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N TYR K 91 " --> pdb=" O ASN K 102 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N ARG K 104 " --> pdb=" O CYS K 89 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N CYS K 89 " --> pdb=" O ARG K 104 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N GLN K 106 " --> pdb=" O GLU K 87 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'N' and resid 30 through 31 removed outlier: 4.219A pdb=" N ALA M 22 " --> pdb=" O LEU N 110 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N VAL M 23 " --> pdb=" O LEU M 96 " (cutoff:3.500A) removed outlier: 7.588A pdb=" N SER M 98 " --> pdb=" O VAL M 23 " (cutoff:3.500A) removed outlier: 6.103A pdb=" N SER M 25 " --> pdb=" O SER M 98 " (cutoff:3.500A) removed outlier: 7.729A pdb=" N VAL M 100 " --> pdb=" O SER M 25 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'M' and resid 90 through 92 removed outlier: 5.924A pdb=" N LEU N 55 " --> pdb=" O PHE N 137 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'N' and resid 81 through 82 removed outlier: 4.068A pdb=" N ILE N 82 " --> pdb=" O HIS N 85 " (cutoff:3.500A) 1294 hydrogen bonds defined for protein. 3588 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 70 hydrogen bonds 140 hydrogen bond angles 0 basepair planarities 28 basepair parallelities 45 stacking parallelities Total time for adding SS restraints: 8.85 Time building geometry restraints manager: 3.91 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.36: 11223 1.36 - 1.50: 9287 1.50 - 1.64: 14159 1.64 - 1.78: 18 1.78 - 1.93: 253 Bond restraints: 34940 Sorted by residual: bond pdb=" C1' APC B3002 " pdb=" C2' APC B3002 " ideal model delta sigma weight residual 1.531 1.345 0.186 1.20e-02 6.94e+03 2.40e+02 bond pdb=" C1' APC B3002 " pdb=" O4' APC B3002 " ideal model delta sigma weight residual 1.416 1.607 -0.191 1.30e-02 5.92e+03 2.15e+02 bond pdb=" C4' APC B3002 " pdb=" O4' APC B3002 " ideal model delta sigma weight residual 1.444 1.301 0.143 1.10e-02 8.26e+03 1.68e+02 bond pdb=" C6 APC B3002 " pdb=" N6 APC B3002 " ideal model delta sigma weight residual 1.337 1.446 -0.109 1.10e-02 8.26e+03 9.90e+01 bond pdb=" C2' APC B3002 " pdb=" O2' APC B3002 " ideal model delta sigma weight residual 1.423 1.500 -0.077 1.30e-02 5.92e+03 3.53e+01 ... (remaining 34935 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.36: 47376 3.36 - 6.72: 124 6.72 - 10.07: 11 10.07 - 13.43: 2 13.43 - 16.79: 1 Bond angle restraints: 47514 Sorted by residual: angle pdb=" C5 APC B3002 " pdb=" C4 APC B3002 " pdb=" N3 APC B3002 " ideal model delta sigma weight residual 126.80 117.31 9.49 1.00e+00 1.00e+00 9.01e+01 angle pdb=" N3 APC B3002 " pdb=" C4 APC B3002 " pdb=" N9 APC B3002 " ideal model delta sigma weight residual 127.04 136.27 -9.23 1.15e+00 7.59e-01 6.47e+01 angle pdb=" N1 APC B3002 " pdb=" C2 APC B3002 " pdb=" N3 APC B3002 " ideal model delta sigma weight residual 128.69 121.63 7.06 1.00e+00 1.00e+00 4.98e+01 angle pdb=" PB APC B3002 " pdb=" O3B APC B3002 " pdb=" PG APC B3002 " ideal model delta sigma weight residual 106.84 123.63 -16.79 3.00e+00 1.11e-01 3.13e+01 angle pdb=" C5 APC B3002 " pdb=" N7 APC B3002 " pdb=" C8 APC B3002 " ideal model delta sigma weight residual 103.68 108.54 -4.86 1.00e+00 1.00e+00 2.36e+01 ... (remaining 47509 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.97: 19823 32.97 - 65.93: 1245 65.93 - 98.90: 80 98.90 - 131.86: 0 131.86 - 164.83: 5 Dihedral angle restraints: 21153 sinusoidal: 9186 harmonic: 11967 Sorted by residual: dihedral pdb=" CA PHE A 628 " pdb=" C PHE A 628 " pdb=" N ASP A 629 " pdb=" CA ASP A 629 " ideal model delta harmonic sigma weight residual -180.00 -139.67 -40.33 0 5.00e+00 4.00e-02 6.50e+01 dihedral pdb=" CA ASP A 629 " pdb=" C ASP A 629 " pdb=" N GLY A 630 " pdb=" CA GLY A 630 " ideal model delta harmonic sigma weight residual -180.00 -153.37 -26.63 0 5.00e+00 4.00e-02 2.84e+01 dihedral pdb=" O1A APC B3002 " pdb=" C3A APC B3002 " pdb=" PA APC B3002 " pdb=" PB APC B3002 " ideal model delta sinusoidal sigma weight residual 59.99 -135.18 -164.83 1 3.00e+01 1.11e-03 2.10e+01 ... (remaining 21150 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 4271 0.050 - 0.100: 821 0.100 - 0.149: 219 0.149 - 0.199: 1 0.199 - 0.249: 2 Chirality restraints: 5314 Sorted by residual: chirality pdb=" C2' APC B3002 " pdb=" C1' APC B3002 " pdb=" C3' APC B3002 " pdb=" O2' APC B3002 " both_signs ideal model delta sigma weight residual False -2.68 -2.43 -0.25 2.00e-01 2.50e+01 1.55e+00 chirality pdb=" C3' 3DR T 17 " pdb=" C4' 3DR T 17 " pdb=" O3' 3DR T 17 " pdb=" C2' 3DR T 17 " both_signs ideal model delta sigma weight residual False -2.70 -2.47 -0.22 2.00e-01 2.50e+01 1.23e+00 chirality pdb=" CB ILE D 22 " pdb=" CA ILE D 22 " pdb=" CG1 ILE D 22 " pdb=" CG2 ILE D 22 " both_signs ideal model delta sigma weight residual False 2.64 2.49 0.16 2.00e-01 2.50e+01 6.28e-01 ... (remaining 5311 not shown) Planarity restraints: 5889 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL A 451 " 0.050 5.00e-02 4.00e+02 7.25e-02 8.41e+00 pdb=" N PRO A 452 " -0.125 5.00e-02 4.00e+02 pdb=" CA PRO A 452 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO A 452 " 0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR E 117 " 0.045 5.00e-02 4.00e+02 6.53e-02 6.82e+00 pdb=" N PRO E 118 " -0.113 5.00e-02 4.00e+02 pdb=" CA PRO E 118 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO E 118 " 0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE C 251 " -0.029 5.00e-02 4.00e+02 4.35e-02 3.03e+00 pdb=" N PRO C 252 " 0.075 5.00e-02 4.00e+02 pdb=" CA PRO C 252 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO C 252 " -0.024 5.00e-02 4.00e+02 ... (remaining 5886 not shown) Histogram of nonbonded interaction distances: 1.73 - 2.36: 80 2.36 - 3.00: 17646 3.00 - 3.63: 50924 3.63 - 4.27: 79693 4.27 - 4.90: 134851 Nonbonded interactions: 283194 Sorted by model distance: nonbonded pdb=" OD1 ASP A 631 " pdb=" O3' G R 12 " model vdw 1.730 3.040 nonbonded pdb=" N ASP A 627 " pdb="MG MG A1703 " model vdw 1.905 2.250 nonbonded pdb=" OD1 ASP A 627 " pdb="MG MG A1703 " model vdw 1.933 2.170 nonbonded pdb=" OD2 ASP B 843 " pdb=" OH TYR L 29 " model vdw 2.144 3.040 nonbonded pdb=" OG1 THR B 694 " pdb=" ND2 ASN B 702 " model vdw 2.184 3.120 ... (remaining 283189 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.570 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: 0.020 Extract box with map and model: 0.660 Check model and map are aligned: 0.090 Set scattering table: 0.050 Process input model: 39.180 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7717 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 : 0.004 0.191 34964 Z= 0.244 Angle : 0.564 16.790 47547 Z= 0.339 Chirality : 0.042 0.249 5314 Planarity : 0.004 0.073 5889 Dihedral : 19.464 164.827 13425 Min Nonbonded Distance : 1.730 Molprobity Statistics. All-atom Clashscore : 9.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 0.33 % Allowed : 33.03 % Favored : 66.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.13 (0.13), residues: 4061 helix: 1.17 (0.15), residues: 1289 sheet: -1.01 (0.21), residues: 619 loop : -0.51 (0.14), residues: 2153 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 174 TYR 0.015 0.001 TYR A1302 PHE 0.015 0.001 PHE A 628 TRP 0.008 0.001 TRP F 146 HIS 0.005 0.001 HIS F 61 Details of bonding type rmsd/Z covalent geometry : bond 0.00373 / 0.24 (34940) covalent geometry : angle 0.55762 / 0.34 (47514) hydrogen bonds : bond 0.16711 / 11.20 ( 1313) hydrogen bonds : angle 6.84308 / 4.85 ( 3728) metal coordination : bond 0.00553 / 0.39 ( 24) metal coordination : angle 3.14466 / 1.81 ( 33) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8122 Ramachandran restraints generated. 4061 Oldfield, 0 Emsley, 4061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8122 Ramachandran restraints generated. 4061 Oldfield, 0 Emsley, 4061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 457 residues out of total 3639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 445 time to evaluate : 1.369 Fit side-chains REVERT: A 589 MET cc_start: 0.8193 (mmm) cc_final: 0.7525 (tpp) REVERT: A 1573 TYR cc_start: 0.8628 (m-80) cc_final: 0.8382 (m-80) outliers start: 12 outliers final: 7 residues processed: 451 average time/residue: 0.2238 time to fit residues: 159.9717 Evaluate side-chains 434 residues out of total 3639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 427 time to evaluate : 1.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain A residue 627 ASP Chi-restraints excluded: chain A residue 646 GLU Chi-restraints excluded: chain A residue 737 LEU Chi-restraints excluded: chain B residue 1049 THR Chi-restraints excluded: chain E residue 124 VAL Chi-restraints excluded: chain I residue 53 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 411 random chunks: [197, 388, 215, 20, 132, 261, 248, 207, 401, 155, 244] chunk 197 optimal weight: 4.9990 chunk 388 optimal weight: 20.0000 chunk 215 optimal weight: 4.9990 chunk 20 optimal weight: 10.0000 chunk 132 optimal weight: 10.0000 chunk 261 optimal weight: 1.9990 chunk 248 optimal weight: 0.8980 chunk 207 optimal weight: 0.9990 chunk 401 optimal weight: 30.0000 chunk 155 optimal weight: 0.9990 chunk 244 optimal weight: 3.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 106 HIS A 107 HIS A 221 HIS A 384 GLN A 525 ASN ** A 617 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 748 ASN A 863 ASN A 939 ASN A 942 GLN A1072 ASN A1237 GLN A1320 GLN ** A1461 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1532 GLN B 27 ASN B 101 GLN B 257 GLN ** B 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 325 GLN B 422 GLN B 469 ASN ** B 492 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 600 GLN B 702 ASN B 735 HIS B1100 GLN B1165 ASN ** C 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 335 GLN D 23 HIS D 26 GLN D 81 ASN E 61 GLN E 153 HIS G 32 ASN G 36 ASN I 21 ASN K 95 HIS K 102 ASN M 89 GLN N 132 GLN Total number of N/Q/H flips: 37 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.164801 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.124492 restraints weight = 40499.448| |-----------------------------------------------------------------------------| r_work (start): 0.3368 rms_B_bonded: 1.91 r_work: 0.3072 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3072 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8403 moved from start: 0.0605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 34964 Z= 0.157 Angle : 0.558 10.510 47547 Z= 0.295 Chirality : 0.043 0.306 5314 Planarity : 0.004 0.066 5889 Dihedral : 13.143 158.429 5319 Min Nonbonded Distance : 1.880 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 3.52 % Allowed : 29.95 % Favored : 66.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.60 % 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: -0.06 (0.13), residues: 4061 helix: 1.22 (0.15), residues: 1308 sheet: -0.93 (0.21), residues: 616 loop : -0.50 (0.14), residues: 2137 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 174 TYR 0.017 0.001 TYR A1302 PHE 0.022 0.001 PHE A 628 TRP 0.016 0.001 TRP B 143 HIS 0.005 0.001 HIS B 824 Details of bonding type rmsd/Z covalent geometry : bond 0.00358 / 0.16 (34940) covalent geometry : angle 0.55020 / 0.29 (47514) hydrogen bonds : bond 0.04387 / 2.92 ( 1313) hydrogen bonds : angle 5.15071 / 3.64 ( 3728) metal coordination : bond 0.00734 / 0.50 ( 24) metal coordination : angle 3.60354 / 2.27 ( 33) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8122 Ramachandran restraints generated. 4061 Oldfield, 0 Emsley, 4061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8122 Ramachandran restraints generated. 4061 Oldfield, 0 Emsley, 4061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 584 residues out of total 3639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 128 poor density : 456 time to evaluate : 1.316 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 59 ARG cc_start: 0.7467 (OUTLIER) cc_final: 0.7061 (ttp-170) REVERT: A 405 LYS cc_start: 0.5749 (mmtm) cc_final: 0.5523 (tppt) REVERT: A 1116 GLN cc_start: 0.7501 (mt0) cc_final: 0.7088 (mt0) REVERT: A 1532 GLN cc_start: 0.8410 (OUTLIER) cc_final: 0.8198 (mp-120) REVERT: B 215 MET cc_start: 0.8778 (ptp) cc_final: 0.8442 (mtm) REVERT: B 477 ASP cc_start: 0.7675 (OUTLIER) cc_final: 0.7060 (t70) REVERT: B 824 HIS cc_start: 0.7564 (OUTLIER) cc_final: 0.6595 (m-70) REVERT: B 883 GLU cc_start: 0.8368 (OUTLIER) cc_final: 0.8095 (tp30) REVERT: B 1192 MET cc_start: 0.8560 (ttm) cc_final: 0.8359 (mtp) REVERT: C 201 GLU cc_start: 0.8307 (pt0) cc_final: 0.8092 (pt0) REVERT: E 20 LYS cc_start: 0.8338 (mmtt) cc_final: 0.7997 (mmtt) outliers start: 128 outliers final: 64 residues processed: 550 average time/residue: 0.2257 time to fit residues: 200.5201 Evaluate side-chains 504 residues out of total 3639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 435 time to evaluate : 1.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 ILE Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 59 ARG Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain A residue 106 HIS Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 251 ILE Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain A residue 627 ASP Chi-restraints excluded: chain A residue 727 THR Chi-restraints excluded: chain A residue 737 LEU Chi-restraints excluded: chain A residue 811 SER Chi-restraints excluded: chain A residue 1011 VAL Chi-restraints excluded: chain A residue 1028 GLU Chi-restraints excluded: chain A residue 1089 LEU Chi-restraints excluded: chain A residue 1192 SER Chi-restraints excluded: chain A residue 1200 MET Chi-restraints excluded: chain A residue 1248 ASP Chi-restraints excluded: chain A residue 1474 LEU Chi-restraints excluded: chain A residue 1500 GLN Chi-restraints excluded: chain A residue 1520 VAL Chi-restraints excluded: chain A residue 1532 GLN Chi-restraints excluded: chain A residue 1569 VAL Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain B residue 228 SER Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 274 VAL Chi-restraints excluded: chain B residue 302 LEU Chi-restraints excluded: chain B residue 325 GLN Chi-restraints excluded: chain B residue 425 ILE Chi-restraints excluded: chain B residue 453 VAL Chi-restraints excluded: chain B residue 477 ASP Chi-restraints excluded: chain B residue 487 VAL Chi-restraints excluded: chain B residue 583 LEU Chi-restraints excluded: chain B residue 824 HIS Chi-restraints excluded: chain B residue 883 GLU Chi-restraints excluded: chain B residue 900 THR Chi-restraints excluded: chain B residue 903 ILE Chi-restraints excluded: chain B residue 927 CYS Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1045 GLN Chi-restraints excluded: chain B residue 1049 THR Chi-restraints excluded: chain B residue 1111 LEU Chi-restraints excluded: chain B residue 1185 LEU Chi-restraints excluded: chain C residue 29 ASN Chi-restraints excluded: chain C residue 62 SER Chi-restraints excluded: chain C residue 72 ILE Chi-restraints excluded: chain C residue 224 THR Chi-restraints excluded: chain C residue 334 THR Chi-restraints excluded: chain E residue 22 MET Chi-restraints excluded: chain E residue 61 GLN Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain E residue 124 VAL Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 34 ASP Chi-restraints excluded: chain H residue 36 CYS Chi-restraints excluded: chain H residue 54 SER Chi-restraints excluded: chain H residue 61 SER Chi-restraints excluded: chain I residue 24 LEU Chi-restraints excluded: chain K residue 103 ILE Chi-restraints excluded: chain K residue 129 ASP Chi-restraints excluded: chain K residue 140 LYS Chi-restraints excluded: chain M residue 89 GLN Chi-restraints excluded: chain M residue 97 VAL Chi-restraints excluded: chain N residue 52 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 411 random chunks: [46, 238, 70, 94, 322, 318, 269, 140, 222, 82, 180] chunk 46 optimal weight: 7.9990 chunk 238 optimal weight: 3.9990 chunk 70 optimal weight: 3.9990 chunk 94 optimal weight: 3.9990 chunk 322 optimal weight: 0.0060 chunk 318 optimal weight: 4.9990 chunk 269 optimal weight: 6.9990 chunk 140 optimal weight: 0.2980 chunk 222 optimal weight: 4.9990 chunk 82 optimal weight: 1.9990 chunk 180 optimal weight: 0.0570 overall best weight: 1.2718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 221 HIS A 617 HIS A1072 ASN B 27 ASN ** B 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 325 GLN B 600 GLN B 669 GLN ** C 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 335 GLN D 23 HIS D 26 GLN E 61 GLN M 74 ASN M 89 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.165625 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.125232 restraints weight = 40528.186| |-----------------------------------------------------------------------------| r_work (start): 0.3377 rms_B_bonded: 1.95 r_work: 0.3083 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3083 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8392 moved from start: 0.0767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 34964 Z= 0.131 Angle : 0.529 10.078 47547 Z= 0.278 Chirality : 0.043 0.308 5314 Planarity : 0.003 0.043 5889 Dihedral : 13.096 159.028 5314 Min Nonbonded Distance : 1.895 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 3.82 % Allowed : 29.76 % Favored : 66.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.60 % 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: 0.02 (0.13), residues: 4061 helix: 1.31 (0.15), residues: 1308 sheet: -0.82 (0.22), residues: 603 loop : -0.50 (0.13), residues: 2150 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 174 TYR 0.018 0.001 TYR A1302 PHE 0.017 0.001 PHE A 628 TRP 0.014 0.001 TRP B 143 HIS 0.005 0.001 HIS A 106 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.13 (34940) covalent geometry : angle 0.52148 / 0.28 (47514) hydrogen bonds : bond 0.03900 / 2.59 ( 1313) hydrogen bonds : angle 4.82512 / 3.40 ( 3728) metal coordination : bond 0.00576 / 0.41 ( 24) metal coordination : angle 3.35054 / 2.12 ( 33) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8122 Ramachandran restraints generated. 4061 Oldfield, 0 Emsley, 4061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8122 Ramachandran restraints generated. 4061 Oldfield, 0 Emsley, 4061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 605 residues out of total 3639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 139 poor density : 466 time to evaluate : 1.232 Fit side-chains revert: symmetry clash REVERT: A 59 ARG cc_start: 0.7512 (OUTLIER) cc_final: 0.7116 (ttp-170) REVERT: A 970 LYS cc_start: 0.8147 (OUTLIER) cc_final: 0.7897 (mtmm) REVERT: A 1116 GLN cc_start: 0.7443 (mt0) cc_final: 0.7038 (mt0) REVERT: A 1126 LYS cc_start: 0.8840 (OUTLIER) cc_final: 0.8638 (ptpt) REVERT: A 1133 LEU cc_start: 0.8958 (OUTLIER) cc_final: 0.8393 (tt) REVERT: A 1434 GLU cc_start: 0.4783 (OUTLIER) cc_final: 0.4227 (pt0) REVERT: A 1439 MET cc_start: 0.5640 (ttp) cc_final: 0.5367 (ttm) REVERT: B 215 MET cc_start: 0.8687 (ptp) cc_final: 0.8244 (mtm) REVERT: B 477 ASP cc_start: 0.7633 (OUTLIER) cc_final: 0.7030 (t70) REVERT: B 824 HIS cc_start: 0.7808 (OUTLIER) cc_final: 0.6939 (m-70) REVERT: B 883 GLU cc_start: 0.8347 (OUTLIER) cc_final: 0.8044 (tp30) REVERT: C 43 ASN cc_start: 0.8087 (t0) cc_final: 0.7773 (t0) REVERT: C 245 ARG cc_start: 0.7701 (mpt180) cc_final: 0.7447 (mpt180) REVERT: H 144 ILE cc_start: 0.9140 (OUTLIER) cc_final: 0.8916 (mt) REVERT: K 48 LYS cc_start: 0.8719 (ttmt) cc_final: 0.8174 (ttpt) outliers start: 139 outliers final: 81 residues processed: 568 average time/residue: 0.2186 time to fit residues: 199.9240 Evaluate side-chains 527 residues out of total 3639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 437 time to evaluate : 1.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 ILE Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 59 ARG Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 251 ILE Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 357 MET Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain A residue 419 ILE Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 632 GLU Chi-restraints excluded: chain A residue 727 THR Chi-restraints excluded: chain A residue 737 LEU Chi-restraints excluded: chain A residue 970 LYS Chi-restraints excluded: chain A residue 990 ILE Chi-restraints excluded: chain A residue 1019 LEU Chi-restraints excluded: chain A residue 1028 GLU Chi-restraints excluded: chain A residue 1030 VAL Chi-restraints excluded: chain A residue 1035 ASP Chi-restraints excluded: chain A residue 1089 LEU Chi-restraints excluded: chain A residue 1126 LYS Chi-restraints excluded: chain A residue 1133 LEU Chi-restraints excluded: chain A residue 1139 ASN Chi-restraints excluded: chain A residue 1192 SER Chi-restraints excluded: chain A residue 1248 ASP Chi-restraints excluded: chain A residue 1289 SER Chi-restraints excluded: chain A residue 1323 HIS Chi-restraints excluded: chain A residue 1434 GLU Chi-restraints excluded: chain A residue 1474 LEU Chi-restraints excluded: chain A residue 1500 GLN Chi-restraints excluded: chain A residue 1520 VAL Chi-restraints excluded: chain A residue 1532 GLN Chi-restraints excluded: chain A residue 1649 VAL Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain B residue 228 SER Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 274 VAL Chi-restraints excluded: chain B residue 302 LEU Chi-restraints excluded: chain B residue 425 ILE Chi-restraints excluded: chain B residue 453 VAL Chi-restraints excluded: chain B residue 477 ASP Chi-restraints excluded: chain B residue 487 VAL Chi-restraints excluded: chain B residue 583 LEU Chi-restraints excluded: chain B residue 752 VAL Chi-restraints excluded: chain B residue 769 PHE Chi-restraints excluded: chain B residue 824 HIS Chi-restraints excluded: chain B residue 883 GLU Chi-restraints excluded: chain B residue 900 THR Chi-restraints excluded: chain B residue 903 ILE Chi-restraints excluded: chain B residue 944 GLN Chi-restraints excluded: chain B residue 982 THR Chi-restraints excluded: chain B residue 990 ASP Chi-restraints excluded: chain B residue 1045 GLN Chi-restraints excluded: chain B residue 1049 THR Chi-restraints excluded: chain B residue 1110 ILE Chi-restraints excluded: chain B residue 1111 LEU Chi-restraints excluded: chain B residue 1185 LEU Chi-restraints excluded: chain C residue 29 ASN Chi-restraints excluded: chain C residue 62 SER Chi-restraints excluded: chain C residue 72 ILE Chi-restraints excluded: chain C residue 224 THR Chi-restraints excluded: chain C residue 334 THR Chi-restraints excluded: chain D residue 31 VAL Chi-restraints excluded: chain E residue 22 MET Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain E residue 124 VAL Chi-restraints excluded: chain E residue 215 MET Chi-restraints excluded: chain G residue 245 VAL Chi-restraints excluded: chain H residue 8 ASP Chi-restraints excluded: chain H residue 34 ASP Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 100 THR Chi-restraints excluded: chain H residue 143 LEU Chi-restraints excluded: chain H residue 144 ILE Chi-restraints excluded: chain I residue 24 LEU Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain K residue 51 THR Chi-restraints excluded: chain K residue 87 GLU Chi-restraints excluded: chain K residue 103 ILE Chi-restraints excluded: chain K residue 129 ASP Chi-restraints excluded: chain K residue 140 LYS Chi-restraints excluded: chain L residue 35 SER Chi-restraints excluded: chain M residue 87 SER Chi-restraints excluded: chain M residue 97 VAL Chi-restraints excluded: chain N residue 52 GLN Chi-restraints excluded: chain N residue 53 VAL Chi-restraints excluded: chain N residue 65 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 411 random chunks: [299, 194, 401, 397, 392, 372, 368, 379, 26, 157, 271] chunk 299 optimal weight: 1.9990 chunk 194 optimal weight: 2.9990 chunk 401 optimal weight: 30.0000 chunk 397 optimal weight: 30.0000 chunk 392 optimal weight: 7.9990 chunk 372 optimal weight: 6.9990 chunk 368 optimal weight: 6.9990 chunk 379 optimal weight: 0.6980 chunk 26 optimal weight: 6.9990 chunk 157 optimal weight: 0.0470 chunk 271 optimal weight: 0.8980 overall best weight: 1.3282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 221 HIS A 671 GLN ** B 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 400 GLN B 422 GLN ** B 492 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 93 GLN C 335 GLN D 23 HIS D 26 GLN F 61 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.165776 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.125436 restraints weight = 40268.619| |-----------------------------------------------------------------------------| r_work (start): 0.3378 rms_B_bonded: 1.96 r_work: 0.3087 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8388 moved from start: 0.0913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 34964 Z= 0.129 Angle : 0.520 9.817 47547 Z= 0.272 Chirality : 0.043 0.308 5314 Planarity : 0.003 0.043 5889 Dihedral : 13.049 157.636 5312 Min Nonbonded Distance : 1.890 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 3.98 % Allowed : 29.32 % Favored : 66.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.60 % 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: 0.05 (0.13), residues: 4061 helix: 1.34 (0.15), residues: 1309 sheet: -0.82 (0.22), residues: 603 loop : -0.48 (0.13), residues: 2149 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG L 54 TYR 0.017 0.001 TYR A1302 PHE 0.016 0.001 PHE A 628 TRP 0.014 0.001 TRP B 143 HIS 0.005 0.001 HIS A 221 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.13 (34940) covalent geometry : angle 0.51320 / 0.27 (47514) hydrogen bonds : bond 0.03653 / 2.41 ( 1313) hydrogen bonds : angle 4.64101 / 3.28 ( 3728) metal coordination : bond 0.00609 / 0.42 ( 24) metal coordination : angle 3.22219 / 2.02 ( 33) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8122 Ramachandran restraints generated. 4061 Oldfield, 0 Emsley, 4061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8122 Ramachandran restraints generated. 4061 Oldfield, 0 Emsley, 4061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 601 residues out of total 3639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 145 poor density : 456 time to evaluate : 1.315 Fit side-chains REVERT: A 59 ARG cc_start: 0.7522 (OUTLIER) cc_final: 0.7129 (ttp-170) REVERT: A 589 MET cc_start: 0.8000 (mmm) cc_final: 0.7772 (mmm) REVERT: A 970 LYS cc_start: 0.8137 (OUTLIER) cc_final: 0.7885 (mtmm) REVERT: A 1116 GLN cc_start: 0.7570 (mt0) cc_final: 0.7269 (mt0) REVERT: A 1126 LYS cc_start: 0.8836 (OUTLIER) cc_final: 0.8632 (ptpt) REVERT: A 1133 LEU cc_start: 0.8974 (OUTLIER) cc_final: 0.8394 (tt) REVERT: A 1434 GLU cc_start: 0.4722 (OUTLIER) cc_final: 0.4162 (pt0) REVERT: A 1439 MET cc_start: 0.5476 (ttp) cc_final: 0.5275 (ttm) REVERT: B 215 MET cc_start: 0.8709 (ptp) cc_final: 0.8236 (mtm) REVERT: B 477 ASP cc_start: 0.7637 (OUTLIER) cc_final: 0.7030 (t70) REVERT: B 762 MET cc_start: 0.8650 (mmt) cc_final: 0.8385 (mmt) REVERT: B 835 GLU cc_start: 0.7426 (OUTLIER) cc_final: 0.7189 (mt-10) REVERT: B 867 ASN cc_start: 0.8253 (OUTLIER) cc_final: 0.8023 (m110) REVERT: B 883 GLU cc_start: 0.8356 (OUTLIER) cc_final: 0.8042 (tp30) REVERT: C 43 ASN cc_start: 0.7993 (t0) cc_final: 0.7694 (t0) REVERT: E 20 LYS cc_start: 0.8349 (mmtt) cc_final: 0.7996 (mmtt) REVERT: H 144 ILE cc_start: 0.9135 (OUTLIER) cc_final: 0.8889 (mt) REVERT: L 60 ARG cc_start: 0.8493 (OUTLIER) cc_final: 0.7649 (ttt180) outliers start: 145 outliers final: 93 residues processed: 562 average time/residue: 0.2195 time to fit residues: 197.9946 Evaluate side-chains 544 residues out of total 3639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 440 time to evaluate : 1.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 ILE Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 59 ARG Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 251 ILE Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 313 THR Chi-restraints excluded: chain A residue 357 MET Chi-restraints excluded: chain A residue 393 SER Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 581 ILE Chi-restraints excluded: chain A residue 727 THR Chi-restraints excluded: chain A residue 737 LEU Chi-restraints excluded: chain A residue 811 SER Chi-restraints excluded: chain A residue 970 LYS Chi-restraints excluded: chain A residue 990 ILE Chi-restraints excluded: chain A residue 1011 VAL Chi-restraints excluded: chain A residue 1019 LEU Chi-restraints excluded: chain A residue 1028 GLU Chi-restraints excluded: chain A residue 1030 VAL Chi-restraints excluded: chain A residue 1035 ASP Chi-restraints excluded: chain A residue 1089 LEU Chi-restraints excluded: chain A residue 1126 LYS Chi-restraints excluded: chain A residue 1133 LEU Chi-restraints excluded: chain A residue 1139 ASN Chi-restraints excluded: chain A residue 1192 SER Chi-restraints excluded: chain A residue 1248 ASP Chi-restraints excluded: chain A residue 1261 VAL Chi-restraints excluded: chain A residue 1289 SER Chi-restraints excluded: chain A residue 1323 HIS Chi-restraints excluded: chain A residue 1434 GLU Chi-restraints excluded: chain A residue 1474 LEU Chi-restraints excluded: chain A residue 1500 GLN Chi-restraints excluded: chain A residue 1520 VAL Chi-restraints excluded: chain A residue 1649 VAL Chi-restraints excluded: chain B residue 68 ILE Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain B residue 228 SER Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain B residue 271 VAL Chi-restraints excluded: chain B residue 274 VAL Chi-restraints excluded: chain B residue 302 LEU Chi-restraints excluded: chain B residue 359 LEU Chi-restraints excluded: chain B residue 425 ILE Chi-restraints excluded: chain B residue 453 VAL Chi-restraints excluded: chain B residue 477 ASP Chi-restraints excluded: chain B residue 487 VAL Chi-restraints excluded: chain B residue 583 LEU Chi-restraints excluded: chain B residue 752 VAL Chi-restraints excluded: chain B residue 773 VAL Chi-restraints excluded: chain B residue 835 GLU Chi-restraints excluded: chain B residue 867 ASN Chi-restraints excluded: chain B residue 883 GLU Chi-restraints excluded: chain B residue 900 THR Chi-restraints excluded: chain B residue 903 ILE Chi-restraints excluded: chain B residue 941 THR Chi-restraints excluded: chain B residue 944 GLN Chi-restraints excluded: chain B residue 982 THR Chi-restraints excluded: chain B residue 990 ASP Chi-restraints excluded: chain B residue 1046 VAL Chi-restraints excluded: chain B residue 1079 LEU Chi-restraints excluded: chain B residue 1110 ILE Chi-restraints excluded: chain B residue 1111 LEU Chi-restraints excluded: chain B residue 1185 LEU Chi-restraints excluded: chain C residue 29 ASN Chi-restraints excluded: chain C residue 62 SER Chi-restraints excluded: chain C residue 72 ILE Chi-restraints excluded: chain C residue 224 THR Chi-restraints excluded: chain C residue 331 CYS Chi-restraints excluded: chain C residue 334 THR Chi-restraints excluded: chain E residue 22 MET Chi-restraints excluded: chain E residue 65 THR Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain E residue 124 VAL Chi-restraints excluded: chain E residue 215 MET Chi-restraints excluded: chain G residue 147 LEU Chi-restraints excluded: chain G residue 245 VAL Chi-restraints excluded: chain H residue 34 ASP Chi-restraints excluded: chain H residue 54 SER Chi-restraints excluded: chain H residue 61 SER Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 100 THR Chi-restraints excluded: chain H residue 143 LEU Chi-restraints excluded: chain H residue 144 ILE Chi-restraints excluded: chain I residue 24 LEU Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain K residue 51 THR Chi-restraints excluded: chain K residue 103 ILE Chi-restraints excluded: chain K residue 129 ASP Chi-restraints excluded: chain K residue 140 LYS Chi-restraints excluded: chain L residue 60 ARG Chi-restraints excluded: chain M residue 37 THR Chi-restraints excluded: chain M residue 97 VAL Chi-restraints excluded: chain N residue 52 GLN Chi-restraints excluded: chain N residue 53 VAL Chi-restraints excluded: chain N residue 57 LYS Chi-restraints excluded: chain N residue 65 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 411 random chunks: [297, 306, 116, 359, 91, 265, 403, 364, 10, 25, 122] chunk 297 optimal weight: 5.9990 chunk 306 optimal weight: 9.9990 chunk 116 optimal weight: 8.9990 chunk 359 optimal weight: 1.9990 chunk 91 optimal weight: 0.8980 chunk 265 optimal weight: 0.7980 chunk 403 optimal weight: 8.9990 chunk 364 optimal weight: 10.0000 chunk 10 optimal weight: 7.9990 chunk 25 optimal weight: 4.9990 chunk 122 optimal weight: 9.9990 overall best weight: 2.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 221 HIS A1128 ASN ** B 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 325 GLN B 422 GLN ** B 492 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 335 GLN D 23 HIS D 26 GLN F 61 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.162976 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.122096 restraints weight = 40519.273| |-----------------------------------------------------------------------------| r_work (start): 0.3333 rms_B_bonded: 1.99 r_work: 0.3040 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.2902 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.2902 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8503 moved from start: 0.1006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 34964 Z= 0.213 Angle : 0.579 11.707 47547 Z= 0.300 Chirality : 0.045 0.303 5314 Planarity : 0.004 0.043 5889 Dihedral : 13.077 155.999 5311 Min Nonbonded Distance : 1.884 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 4.84 % Allowed : 28.74 % Favored : 66.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.60 % 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: -0.13 (0.13), residues: 4061 helix: 1.16 (0.15), residues: 1311 sheet: -0.92 (0.21), residues: 613 loop : -0.56 (0.13), residues: 2137 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 174 TYR 0.019 0.002 TYR C 227 PHE 0.018 0.001 PHE A 628 TRP 0.013 0.001 TRP B 143 HIS 0.007 0.001 HIS A 798 Details of bonding type rmsd/Z covalent geometry : bond 0.00506 / 0.21 (34940) covalent geometry : angle 0.57002 / 0.30 (47514) hydrogen bonds : bond 0.04101 / 2.72 ( 1313) hydrogen bonds : angle 4.72406 / 3.34 ( 3728) metal coordination : bond 0.01082 / 0.72 ( 24) metal coordination : angle 3.93908 / 2.49 ( 33) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8122 Ramachandran restraints generated. 4061 Oldfield, 0 Emsley, 4061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8122 Ramachandran restraints generated. 4061 Oldfield, 0 Emsley, 4061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 629 residues out of total 3639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 176 poor density : 453 time to evaluate : 1.302 Fit side-chains revert: symmetry clash REVERT: A 59 ARG cc_start: 0.7665 (OUTLIER) cc_final: 0.7238 (ttp-170) REVERT: A 366 ARG cc_start: 0.8531 (OUTLIER) cc_final: 0.8226 (ttt90) REVERT: A 589 MET cc_start: 0.8272 (mmm) cc_final: 0.8018 (mmm) REVERT: A 970 LYS cc_start: 0.8327 (OUTLIER) cc_final: 0.8044 (mtmm) REVERT: A 1116 GLN cc_start: 0.7663 (mt0) cc_final: 0.7345 (mt0) REVERT: A 1133 LEU cc_start: 0.9177 (OUTLIER) cc_final: 0.8574 (tt) REVERT: A 1222 LEU cc_start: 0.9116 (OUTLIER) cc_final: 0.8763 (mm) REVERT: A 1434 GLU cc_start: 0.4768 (OUTLIER) cc_final: 0.4331 (pt0) REVERT: B 614 GLU cc_start: 0.8094 (OUTLIER) cc_final: 0.7589 (pt0) REVERT: B 835 GLU cc_start: 0.7739 (OUTLIER) cc_final: 0.7528 (mt-10) REVERT: B 867 ASN cc_start: 0.8236 (OUTLIER) cc_final: 0.8023 (m110) REVERT: B 883 GLU cc_start: 0.8572 (OUTLIER) cc_final: 0.8313 (tp30) REVERT: C 43 ASN cc_start: 0.8190 (t0) cc_final: 0.7852 (t0) REVERT: D 45 ASP cc_start: 0.3382 (OUTLIER) cc_final: 0.2930 (t0) REVERT: G 226 ASP cc_start: 0.0425 (OUTLIER) cc_final: 0.0206 (t0) REVERT: H 126 GLU cc_start: 0.8692 (tt0) cc_final: 0.8479 (tt0) REVERT: H 144 ILE cc_start: 0.9264 (OUTLIER) cc_final: 0.9041 (mt) outliers start: 176 outliers final: 124 residues processed: 588 average time/residue: 0.2171 time to fit residues: 206.4486 Evaluate side-chains 562 residues out of total 3639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 137 poor density : 425 time to evaluate : 1.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 ILE Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 59 ARG Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 251 ILE Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 313 THR Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain A residue 357 MET Chi-restraints excluded: chain A residue 366 ARG Chi-restraints excluded: chain A residue 393 SER Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain A residue 419 ILE Chi-restraints excluded: chain A residue 428 VAL Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain A residue 581 ILE Chi-restraints excluded: chain A residue 727 THR Chi-restraints excluded: chain A residue 737 LEU Chi-restraints excluded: chain A residue 909 SER Chi-restraints excluded: chain A residue 961 VAL Chi-restraints excluded: chain A residue 970 LYS Chi-restraints excluded: chain A residue 990 ILE Chi-restraints excluded: chain A residue 1011 VAL Chi-restraints excluded: chain A residue 1028 GLU Chi-restraints excluded: chain A residue 1030 VAL Chi-restraints excluded: chain A residue 1035 ASP Chi-restraints excluded: chain A residue 1083 SER Chi-restraints excluded: chain A residue 1133 LEU Chi-restraints excluded: chain A residue 1139 ASN Chi-restraints excluded: chain A residue 1192 SER Chi-restraints excluded: chain A residue 1200 MET Chi-restraints excluded: chain A residue 1222 LEU Chi-restraints excluded: chain A residue 1248 ASP Chi-restraints excluded: chain A residue 1253 THR Chi-restraints excluded: chain A residue 1261 VAL Chi-restraints excluded: chain A residue 1289 SER Chi-restraints excluded: chain A residue 1323 HIS Chi-restraints excluded: chain A residue 1434 GLU Chi-restraints excluded: chain A residue 1474 LEU Chi-restraints excluded: chain A residue 1500 GLN Chi-restraints excluded: chain A residue 1520 VAL Chi-restraints excluded: chain A residue 1649 VAL Chi-restraints excluded: chain B residue 68 ILE Chi-restraints excluded: chain B residue 93 ASN Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain B residue 207 ILE Chi-restraints excluded: chain B residue 217 ILE Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain B residue 271 VAL Chi-restraints excluded: chain B residue 274 VAL Chi-restraints excluded: chain B residue 281 CYS Chi-restraints excluded: chain B residue 302 LEU Chi-restraints excluded: chain B residue 325 GLN Chi-restraints excluded: chain B residue 359 LEU Chi-restraints excluded: chain B residue 360 VAL Chi-restraints excluded: chain B residue 425 ILE Chi-restraints excluded: chain B residue 453 VAL Chi-restraints excluded: chain B residue 487 VAL Chi-restraints excluded: chain B residue 533 THR Chi-restraints excluded: chain B residue 537 SER Chi-restraints excluded: chain B residue 583 LEU Chi-restraints excluded: chain B residue 614 GLU Chi-restraints excluded: chain B residue 689 VAL Chi-restraints excluded: chain B residue 721 MET Chi-restraints excluded: chain B residue 752 VAL Chi-restraints excluded: chain B residue 773 VAL Chi-restraints excluded: chain B residue 831 GLU Chi-restraints excluded: chain B residue 835 GLU Chi-restraints excluded: chain B residue 867 ASN Chi-restraints excluded: chain B residue 883 GLU Chi-restraints excluded: chain B residue 900 THR Chi-restraints excluded: chain B residue 902 SER Chi-restraints excluded: chain B residue 903 ILE Chi-restraints excluded: chain B residue 941 THR Chi-restraints excluded: chain B residue 944 GLN Chi-restraints excluded: chain B residue 982 THR Chi-restraints excluded: chain B residue 1045 GLN Chi-restraints excluded: chain B residue 1046 VAL Chi-restraints excluded: chain B residue 1049 THR Chi-restraints excluded: chain B residue 1079 LEU Chi-restraints excluded: chain B residue 1085 SER Chi-restraints excluded: chain B residue 1099 THR Chi-restraints excluded: chain B residue 1110 ILE Chi-restraints excluded: chain B residue 1111 LEU Chi-restraints excluded: chain B residue 1120 ILE Chi-restraints excluded: chain B residue 1185 LEU Chi-restraints excluded: chain C residue 29 ASN Chi-restraints excluded: chain C residue 62 SER Chi-restraints excluded: chain C residue 208 CYS Chi-restraints excluded: chain C residue 224 THR Chi-restraints excluded: chain C residue 331 CYS Chi-restraints excluded: chain C residue 334 THR Chi-restraints excluded: chain D residue 31 VAL Chi-restraints excluded: chain D residue 45 ASP Chi-restraints excluded: chain D residue 86 ILE Chi-restraints excluded: chain D residue 92 ILE Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain E residue 116 ILE Chi-restraints excluded: chain E residue 124 VAL Chi-restraints excluded: chain E residue 196 VAL Chi-restraints excluded: chain E residue 215 MET Chi-restraints excluded: chain G residue 80 VAL Chi-restraints excluded: chain G residue 100 THR Chi-restraints excluded: chain G residue 108 THR Chi-restraints excluded: chain G residue 124 VAL Chi-restraints excluded: chain G residue 147 LEU Chi-restraints excluded: chain G residue 226 ASP Chi-restraints excluded: chain G residue 237 HIS Chi-restraints excluded: chain G residue 245 VAL Chi-restraints excluded: chain H residue 8 ASP Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 54 SER Chi-restraints excluded: chain H residue 61 SER Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 143 LEU Chi-restraints excluded: chain H residue 144 ILE Chi-restraints excluded: chain I residue 24 LEU Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain K residue 51 THR Chi-restraints excluded: chain K residue 103 ILE Chi-restraints excluded: chain K residue 140 LYS Chi-restraints excluded: chain L residue 35 SER Chi-restraints excluded: chain M residue 37 THR Chi-restraints excluded: chain M residue 78 VAL Chi-restraints excluded: chain M residue 97 VAL Chi-restraints excluded: chain N residue 52 GLN Chi-restraints excluded: chain N residue 53 VAL Chi-restraints excluded: chain N residue 57 LYS Chi-restraints excluded: chain N residue 65 SER Chi-restraints excluded: chain N residue 160 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 411 random chunks: [163, 103, 319, 44, 208, 8, 333, 259, 294, 20, 320] chunk 163 optimal weight: 0.8980 chunk 103 optimal weight: 0.9990 chunk 319 optimal weight: 5.9990 chunk 44 optimal weight: 5.9990 chunk 208 optimal weight: 3.9990 chunk 8 optimal weight: 0.0870 chunk 333 optimal weight: 5.9990 chunk 259 optimal weight: 4.9990 chunk 294 optimal weight: 0.6980 chunk 20 optimal weight: 3.9990 chunk 320 optimal weight: 8.9990 overall best weight: 1.3362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 221 HIS ** B 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 325 GLN ** B 492 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 335 GLN D 23 HIS D 26 GLN F 61 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.165070 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.124656 restraints weight = 40299.172| |-----------------------------------------------------------------------------| r_work (start): 0.3368 rms_B_bonded: 1.93 r_work: 0.3089 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2951 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.2951 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8467 moved from start: 0.1035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 34964 Z= 0.132 Angle : 0.533 10.500 47547 Z= 0.279 Chirality : 0.043 0.302 5314 Planarity : 0.003 0.044 5889 Dihedral : 13.054 156.412 5311 Min Nonbonded Distance : 1.892 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 4.20 % Allowed : 29.32 % Favored : 66.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.60 % 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: -0.02 (0.13), residues: 4061 helix: 1.28 (0.15), residues: 1310 sheet: -0.89 (0.21), residues: 610 loop : -0.50 (0.13), residues: 2141 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 174 TYR 0.018 0.001 TYR A1302 PHE 0.021 0.001 PHE B 301 TRP 0.012 0.001 TRP B 143 HIS 0.005 0.001 HIS F 61 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.13 (34940) covalent geometry : angle 0.52545 / 0.28 (47514) hydrogen bonds : bond 0.03687 / 2.43 ( 1313) hydrogen bonds : angle 4.59160 / 3.24 ( 3728) metal coordination : bond 0.00632 / 0.44 ( 24) metal coordination : angle 3.47348 / 2.17 ( 33) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8122 Ramachandran restraints generated. 4061 Oldfield, 0 Emsley, 4061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8122 Ramachandran restraints generated. 4061 Oldfield, 0 Emsley, 4061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 611 residues out of total 3639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 153 poor density : 458 time to evaluate : 1.373 Fit side-chains revert: symmetry clash REVERT: A 59 ARG cc_start: 0.7631 (OUTLIER) cc_final: 0.7214 (ttp-170) REVERT: A 403 LEU cc_start: 0.5735 (tp) cc_final: 0.5512 (tp) REVERT: A 429 THR cc_start: 0.8644 (OUTLIER) cc_final: 0.8406 (t) REVERT: A 589 MET cc_start: 0.8147 (mmm) cc_final: 0.7864 (mmm) REVERT: A 970 LYS cc_start: 0.8238 (OUTLIER) cc_final: 0.7984 (mtmm) REVERT: A 1116 GLN cc_start: 0.7659 (mt0) cc_final: 0.7369 (mt0) REVERT: A 1133 LEU cc_start: 0.9112 (OUTLIER) cc_final: 0.8563 (tt) REVERT: A 1173 LYS cc_start: 0.8081 (OUTLIER) cc_final: 0.7721 (tttp) REVERT: A 1222 LEU cc_start: 0.9115 (OUTLIER) cc_final: 0.8744 (mm) REVERT: A 1223 ARG cc_start: 0.8426 (mtp-110) cc_final: 0.8086 (mtp-110) REVERT: A 1238 MET cc_start: 0.8432 (OUTLIER) cc_final: 0.8179 (mtm) REVERT: A 1434 GLU cc_start: 0.4804 (OUTLIER) cc_final: 0.4353 (pt0) REVERT: A 1439 MET cc_start: 0.5415 (ttp) cc_final: 0.5072 (ttm) REVERT: B 215 MET cc_start: 0.8790 (ptp) cc_final: 0.8441 (mtm) REVERT: B 762 MET cc_start: 0.8844 (mmt) cc_final: 0.8569 (mmt) REVERT: B 835 GLU cc_start: 0.7682 (OUTLIER) cc_final: 0.7475 (mt-10) REVERT: B 851 TYR cc_start: 0.9077 (t80) cc_final: 0.8683 (t80) REVERT: B 867 ASN cc_start: 0.8272 (OUTLIER) cc_final: 0.8055 (m110) REVERT: B 883 GLU cc_start: 0.8534 (OUTLIER) cc_final: 0.8261 (tp30) REVERT: C 43 ASN cc_start: 0.8174 (t0) cc_final: 0.7843 (t0) REVERT: D 45 ASP cc_start: 0.3697 (OUTLIER) cc_final: 0.3431 (t0) REVERT: E 20 LYS cc_start: 0.8459 (mmtt) cc_final: 0.8131 (mmtt) REVERT: E 33 GLU cc_start: 0.7834 (OUTLIER) cc_final: 0.6690 (mp0) REVERT: G 226 ASP cc_start: 0.0397 (OUTLIER) cc_final: 0.0177 (t0) REVERT: H 144 ILE cc_start: 0.9212 (OUTLIER) cc_final: 0.8960 (mt) outliers start: 153 outliers final: 95 residues processed: 574 average time/residue: 0.2147 time to fit residues: 199.4338 Evaluate side-chains 545 residues out of total 3639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 435 time to evaluate : 1.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 59 ARG Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 251 ILE Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 313 THR Chi-restraints excluded: chain A residue 357 MET Chi-restraints excluded: chain A residue 393 SER Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain A residue 428 VAL Chi-restraints excluded: chain A residue 429 THR Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain A residue 581 ILE Chi-restraints excluded: chain A residue 909 SER Chi-restraints excluded: chain A residue 961 VAL Chi-restraints excluded: chain A residue 970 LYS Chi-restraints excluded: chain A residue 990 ILE Chi-restraints excluded: chain A residue 1028 GLU Chi-restraints excluded: chain A residue 1030 VAL Chi-restraints excluded: chain A residue 1035 ASP Chi-restraints excluded: chain A residue 1133 LEU Chi-restraints excluded: chain A residue 1139 ASN Chi-restraints excluded: chain A residue 1173 LYS Chi-restraints excluded: chain A residue 1192 SER Chi-restraints excluded: chain A residue 1200 MET Chi-restraints excluded: chain A residue 1222 LEU Chi-restraints excluded: chain A residue 1238 MET Chi-restraints excluded: chain A residue 1248 ASP Chi-restraints excluded: chain A residue 1253 THR Chi-restraints excluded: chain A residue 1261 VAL Chi-restraints excluded: chain A residue 1289 SER Chi-restraints excluded: chain A residue 1434 GLU Chi-restraints excluded: chain A residue 1474 LEU Chi-restraints excluded: chain A residue 1500 GLN Chi-restraints excluded: chain A residue 1520 VAL Chi-restraints excluded: chain A residue 1649 VAL Chi-restraints excluded: chain B residue 68 ILE Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain B residue 207 ILE Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain B residue 274 VAL Chi-restraints excluded: chain B residue 359 LEU Chi-restraints excluded: chain B residue 425 ILE Chi-restraints excluded: chain B residue 453 VAL Chi-restraints excluded: chain B residue 487 VAL Chi-restraints excluded: chain B residue 752 VAL Chi-restraints excluded: chain B residue 773 VAL Chi-restraints excluded: chain B residue 831 GLU Chi-restraints excluded: chain B residue 835 GLU Chi-restraints excluded: chain B residue 867 ASN Chi-restraints excluded: chain B residue 883 GLU Chi-restraints excluded: chain B residue 900 THR Chi-restraints excluded: chain B residue 903 ILE Chi-restraints excluded: chain B residue 927 CYS Chi-restraints excluded: chain B residue 941 THR Chi-restraints excluded: chain B residue 944 GLN Chi-restraints excluded: chain B residue 982 THR Chi-restraints excluded: chain B residue 990 ASP Chi-restraints excluded: chain B residue 1045 GLN Chi-restraints excluded: chain B residue 1049 THR Chi-restraints excluded: chain B residue 1079 LEU Chi-restraints excluded: chain B residue 1110 ILE Chi-restraints excluded: chain B residue 1111 LEU Chi-restraints excluded: chain B residue 1120 ILE Chi-restraints excluded: chain B residue 1185 LEU Chi-restraints excluded: chain C residue 29 ASN Chi-restraints excluded: chain C residue 62 SER Chi-restraints excluded: chain C residue 72 ILE Chi-restraints excluded: chain C residue 208 CYS Chi-restraints excluded: chain C residue 224 THR Chi-restraints excluded: chain C residue 331 CYS Chi-restraints excluded: chain C residue 334 THR Chi-restraints excluded: chain D residue 45 ASP Chi-restraints excluded: chain D residue 86 ILE Chi-restraints excluded: chain E residue 22 MET Chi-restraints excluded: chain E residue 33 GLU Chi-restraints excluded: chain E residue 65 THR Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain E residue 124 VAL Chi-restraints excluded: chain E residue 215 MET Chi-restraints excluded: chain G residue 80 VAL Chi-restraints excluded: chain G residue 108 THR Chi-restraints excluded: chain G residue 124 VAL Chi-restraints excluded: chain G residue 147 LEU Chi-restraints excluded: chain G residue 226 ASP Chi-restraints excluded: chain G residue 237 HIS Chi-restraints excluded: chain G residue 245 VAL Chi-restraints excluded: chain H residue 8 ASP Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 54 SER Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 143 LEU Chi-restraints excluded: chain H residue 144 ILE Chi-restraints excluded: chain I residue 24 LEU Chi-restraints excluded: chain J residue 12 LYS Chi-restraints excluded: chain K residue 51 THR Chi-restraints excluded: chain K residue 103 ILE Chi-restraints excluded: chain K residue 140 LYS Chi-restraints excluded: chain L residue 35 SER Chi-restraints excluded: chain M residue 78 VAL Chi-restraints excluded: chain N residue 25 ILE Chi-restraints excluded: chain N residue 52 GLN Chi-restraints excluded: chain N residue 53 VAL Chi-restraints excluded: chain N residue 65 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 411 random chunks: [28, 355, 45, 154, 270, 106, 389, 200, 78, 152, 138] chunk 28 optimal weight: 6.9990 chunk 355 optimal weight: 7.9990 chunk 45 optimal weight: 3.9990 chunk 154 optimal weight: 9.9990 chunk 270 optimal weight: 5.9990 chunk 106 optimal weight: 8.9990 chunk 389 optimal weight: 10.0000 chunk 200 optimal weight: 10.0000 chunk 78 optimal weight: 10.0000 chunk 152 optimal weight: 0.9980 chunk 138 optimal weight: 0.9980 overall best weight: 3.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 221 HIS B 27 ASN B 182 GLN ** B 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 325 GLN C 335 GLN D 23 HIS D 26 GLN F 61 HIS H 11 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.161204 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.120822 restraints weight = 40609.548| |-----------------------------------------------------------------------------| r_work (start): 0.3312 rms_B_bonded: 1.97 r_work: 0.3031 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2899 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.2899 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8513 moved from start: 0.1159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 34964 Z= 0.263 Angle : 0.626 14.009 47547 Z= 0.322 Chirality : 0.047 0.298 5314 Planarity : 0.004 0.043 5889 Dihedral : 13.147 154.190 5309 Min Nonbonded Distance : 1.846 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 4.56 % Allowed : 29.10 % Favored : 66.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.60 % 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: -0.31 (0.13), residues: 4061 helix: 0.98 (0.14), residues: 1317 sheet: -0.98 (0.21), residues: 601 loop : -0.67 (0.13), residues: 2143 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 305 TYR 0.021 0.002 TYR C 227 PHE 0.018 0.002 PHE A 628 TRP 0.013 0.001 TRP B 143 HIS 0.008 0.001 HIS A 798 Details of bonding type rmsd/Z covalent geometry : bond 0.00630 / 0.26 (34940) covalent geometry : angle 0.61402 / 0.32 (47514) hydrogen bonds : bond 0.04365 / 2.90 ( 1313) hydrogen bonds : angle 4.78804 / 3.39 ( 3728) metal coordination : bond 0.01548 / 1.08 ( 24) metal coordination : angle 4.75041 / 2.87 ( 33) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8122 Ramachandran restraints generated. 4061 Oldfield, 0 Emsley, 4061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8122 Ramachandran restraints generated. 4061 Oldfield, 0 Emsley, 4061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 601 residues out of total 3639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 166 poor density : 435 time to evaluate : 1.064 Fit side-chains revert: symmetry clash REVERT: A 59 ARG cc_start: 0.7577 (OUTLIER) cc_final: 0.7146 (ttp-170) REVERT: A 403 LEU cc_start: 0.5762 (tp) cc_final: 0.5528 (tp) REVERT: A 429 THR cc_start: 0.8739 (OUTLIER) cc_final: 0.8476 (t) REVERT: A 589 MET cc_start: 0.8253 (mmm) cc_final: 0.7932 (mmm) REVERT: A 1173 LYS cc_start: 0.8100 (OUTLIER) cc_final: 0.7687 (tttp) REVERT: A 1222 LEU cc_start: 0.9113 (OUTLIER) cc_final: 0.8767 (mm) REVERT: A 1434 GLU cc_start: 0.4835 (OUTLIER) cc_final: 0.4379 (pt0) REVERT: A 1439 MET cc_start: 0.5462 (ttp) cc_final: 0.5224 (ttm) REVERT: B 215 MET cc_start: 0.8886 (ptp) cc_final: 0.8587 (mtm) REVERT: B 835 GLU cc_start: 0.7661 (OUTLIER) cc_final: 0.7461 (mt-10) REVERT: B 867 ASN cc_start: 0.8284 (OUTLIER) cc_final: 0.8080 (m110) REVERT: B 883 GLU cc_start: 0.8563 (OUTLIER) cc_final: 0.8311 (tp30) REVERT: C 43 ASN cc_start: 0.8282 (t0) cc_final: 0.7983 (t0) REVERT: D 45 ASP cc_start: 0.3230 (OUTLIER) cc_final: 0.2992 (t0) REVERT: E 20 LYS cc_start: 0.8473 (mmtt) cc_final: 0.8142 (mmtt) REVERT: E 33 GLU cc_start: 0.7809 (OUTLIER) cc_final: 0.6730 (mp0) REVERT: G 229 LEU cc_start: 0.2158 (OUTLIER) cc_final: 0.1740 (tp) REVERT: H 126 GLU cc_start: 0.8664 (tt0) cc_final: 0.8426 (tt0) REVERT: H 144 ILE cc_start: 0.9252 (OUTLIER) cc_final: 0.9044 (mt) REVERT: K 59 THR cc_start: 0.8859 (OUTLIER) cc_final: 0.8609 (m) outliers start: 166 outliers final: 124 residues processed: 569 average time/residue: 0.2184 time to fit residues: 201.8150 Evaluate side-chains 562 residues out of total 3639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 137 poor density : 425 time to evaluate : 1.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 59 ARG Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 251 ILE Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 313 THR Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain A residue 357 MET Chi-restraints excluded: chain A residue 393 SER Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain A residue 419 ILE Chi-restraints excluded: chain A residue 428 VAL Chi-restraints excluded: chain A residue 429 THR Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain A residue 581 ILE Chi-restraints excluded: chain A residue 703 GLU Chi-restraints excluded: chain A residue 780 ILE Chi-restraints excluded: chain A residue 909 SER Chi-restraints excluded: chain A residue 961 VAL Chi-restraints excluded: chain A residue 990 ILE Chi-restraints excluded: chain A residue 1011 VAL Chi-restraints excluded: chain A residue 1028 GLU Chi-restraints excluded: chain A residue 1030 VAL Chi-restraints excluded: chain A residue 1035 ASP Chi-restraints excluded: chain A residue 1083 SER Chi-restraints excluded: chain A residue 1139 ASN Chi-restraints excluded: chain A residue 1173 LYS Chi-restraints excluded: chain A residue 1185 VAL Chi-restraints excluded: chain A residue 1192 SER Chi-restraints excluded: chain A residue 1200 MET Chi-restraints excluded: chain A residue 1216 THR Chi-restraints excluded: chain A residue 1222 LEU Chi-restraints excluded: chain A residue 1248 ASP Chi-restraints excluded: chain A residue 1253 THR Chi-restraints excluded: chain A residue 1289 SER Chi-restraints excluded: chain A residue 1434 GLU Chi-restraints excluded: chain A residue 1474 LEU Chi-restraints excluded: chain A residue 1500 GLN Chi-restraints excluded: chain A residue 1520 VAL Chi-restraints excluded: chain A residue 1649 VAL Chi-restraints excluded: chain B residue 68 ILE Chi-restraints excluded: chain B residue 73 ILE Chi-restraints excluded: chain B residue 93 ASN Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain B residue 207 ILE Chi-restraints excluded: chain B residue 217 ILE Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain B residue 271 VAL Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 274 VAL Chi-restraints excluded: chain B residue 281 CYS Chi-restraints excluded: chain B residue 325 GLN Chi-restraints excluded: chain B residue 359 LEU Chi-restraints excluded: chain B residue 360 VAL Chi-restraints excluded: chain B residue 453 VAL Chi-restraints excluded: chain B residue 487 VAL Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 533 THR Chi-restraints excluded: chain B residue 537 SER Chi-restraints excluded: chain B residue 689 VAL Chi-restraints excluded: chain B residue 721 MET Chi-restraints excluded: chain B residue 752 VAL Chi-restraints excluded: chain B residue 773 VAL Chi-restraints excluded: chain B residue 835 GLU Chi-restraints excluded: chain B residue 867 ASN Chi-restraints excluded: chain B residue 883 GLU Chi-restraints excluded: chain B residue 900 THR Chi-restraints excluded: chain B residue 902 SER Chi-restraints excluded: chain B residue 903 ILE Chi-restraints excluded: chain B residue 927 CYS Chi-restraints excluded: chain B residue 941 THR Chi-restraints excluded: chain B residue 944 GLN Chi-restraints excluded: chain B residue 982 THR Chi-restraints excluded: chain B residue 1045 GLN Chi-restraints excluded: chain B residue 1046 VAL Chi-restraints excluded: chain B residue 1049 THR Chi-restraints excluded: chain B residue 1079 LEU Chi-restraints excluded: chain B residue 1085 SER Chi-restraints excluded: chain B residue 1110 ILE Chi-restraints excluded: chain B residue 1111 LEU Chi-restraints excluded: chain B residue 1120 ILE Chi-restraints excluded: chain B residue 1200 VAL Chi-restraints excluded: chain C residue 29 ASN Chi-restraints excluded: chain C residue 62 SER Chi-restraints excluded: chain C residue 141 THR Chi-restraints excluded: chain C residue 208 CYS Chi-restraints excluded: chain C residue 224 THR Chi-restraints excluded: chain C residue 331 CYS Chi-restraints excluded: chain C residue 334 THR Chi-restraints excluded: chain D residue 45 ASP Chi-restraints excluded: chain D residue 86 ILE Chi-restraints excluded: chain D residue 92 ILE Chi-restraints excluded: chain E residue 33 GLU Chi-restraints excluded: chain E residue 65 THR Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain E residue 116 ILE Chi-restraints excluded: chain E residue 124 VAL Chi-restraints excluded: chain E residue 196 VAL Chi-restraints excluded: chain G residue 80 VAL Chi-restraints excluded: chain G residue 108 THR Chi-restraints excluded: chain G residue 124 VAL Chi-restraints excluded: chain G residue 147 LEU Chi-restraints excluded: chain G residue 229 LEU Chi-restraints excluded: chain G residue 237 HIS Chi-restraints excluded: chain G residue 245 VAL Chi-restraints excluded: chain H residue 8 ASP Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 32 THR Chi-restraints excluded: chain H residue 42 ILE Chi-restraints excluded: chain H residue 54 SER Chi-restraints excluded: chain H residue 61 SER Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 143 LEU Chi-restraints excluded: chain H residue 144 ILE Chi-restraints excluded: chain I residue 24 LEU Chi-restraints excluded: chain I residue 47 VAL Chi-restraints excluded: chain J residue 12 LYS Chi-restraints excluded: chain K residue 51 THR Chi-restraints excluded: chain K residue 59 THR Chi-restraints excluded: chain K residue 103 ILE Chi-restraints excluded: chain K residue 140 LYS Chi-restraints excluded: chain L residue 35 SER Chi-restraints excluded: chain L residue 53 HIS Chi-restraints excluded: chain M residue 37 THR Chi-restraints excluded: chain M residue 78 VAL Chi-restraints excluded: chain N residue 25 ILE Chi-restraints excluded: chain N residue 52 GLN Chi-restraints excluded: chain N residue 53 VAL Chi-restraints excluded: chain N residue 65 SER Chi-restraints excluded: chain N residue 160 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 411 random chunks: [169, 25, 66, 251, 405, 305, 51, 351, 333, 9, 322] chunk 169 optimal weight: 8.9990 chunk 25 optimal weight: 1.9990 chunk 66 optimal weight: 0.9990 chunk 251 optimal weight: 4.9990 chunk 405 optimal weight: 20.0000 chunk 305 optimal weight: 4.9990 chunk 51 optimal weight: 4.9990 chunk 351 optimal weight: 8.9990 chunk 333 optimal weight: 1.9990 chunk 9 optimal weight: 0.7980 chunk 322 optimal weight: 6.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 221 HIS ** B 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 325 GLN C 335 GLN D 23 HIS D 26 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.163004 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.122091 restraints weight = 40422.060| |-----------------------------------------------------------------------------| r_work (start): 0.3327 rms_B_bonded: 1.95 r_work: 0.3050 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2915 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.2915 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8490 moved from start: 0.1146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 34964 Z= 0.174 Angle : 0.572 12.496 47547 Z= 0.296 Chirality : 0.044 0.296 5314 Planarity : 0.004 0.044 5889 Dihedral : 13.154 154.731 5309 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 4.26 % Allowed : 29.54 % Favored : 66.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.60 % 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: -0.22 (0.13), residues: 4061 helix: 1.09 (0.15), residues: 1310 sheet: -1.00 (0.21), residues: 610 loop : -0.61 (0.13), residues: 2141 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 174 TYR 0.019 0.001 TYR A1302 PHE 0.014 0.001 PHE B 301 TRP 0.012 0.001 TRP B 143 HIS 0.005 0.001 HIS F 61 Details of bonding type rmsd/Z covalent geometry : bond 0.00409 / 0.17 (34940) covalent geometry : angle 0.56032 / 0.30 (47514) hydrogen bonds : bond 0.03974 / 2.63 ( 1313) hydrogen bonds : angle 4.68232 / 3.31 ( 3728) metal coordination : bond 0.01038 / 0.75 ( 24) metal coordination : angle 4.33968 / 2.62 ( 33) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8122 Ramachandran restraints generated. 4061 Oldfield, 0 Emsley, 4061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8122 Ramachandran restraints generated. 4061 Oldfield, 0 Emsley, 4061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 596 residues out of total 3639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 155 poor density : 441 time to evaluate : 1.053 Fit side-chains revert: symmetry clash REVERT: A 59 ARG cc_start: 0.7556 (OUTLIER) cc_final: 0.7113 (ttp-170) REVERT: A 403 LEU cc_start: 0.5808 (tp) cc_final: 0.5602 (tp) REVERT: A 429 THR cc_start: 0.8693 (OUTLIER) cc_final: 0.8427 (t) REVERT: A 589 MET cc_start: 0.8200 (mmm) cc_final: 0.7860 (mmm) REVERT: A 700 ILE cc_start: 0.9243 (OUTLIER) cc_final: 0.9009 (mm) REVERT: A 1173 LYS cc_start: 0.8105 (OUTLIER) cc_final: 0.7703 (tttp) REVERT: A 1222 LEU cc_start: 0.9122 (OUTLIER) cc_final: 0.8778 (mm) REVERT: A 1223 ARG cc_start: 0.8402 (mtp-110) cc_final: 0.8082 (mtp-110) REVERT: A 1434 GLU cc_start: 0.4795 (OUTLIER) cc_final: 0.4351 (pt0) REVERT: A 1439 MET cc_start: 0.5419 (ttp) cc_final: 0.5176 (ttm) REVERT: B 157 ASP cc_start: 0.7935 (OUTLIER) cc_final: 0.7632 (p0) REVERT: B 215 MET cc_start: 0.8862 (ptp) cc_final: 0.8605 (mtm) REVERT: B 762 MET cc_start: 0.8894 (mmt) cc_final: 0.8675 (mmt) REVERT: B 835 GLU cc_start: 0.7630 (OUTLIER) cc_final: 0.7428 (mt-10) REVERT: B 867 ASN cc_start: 0.8279 (OUTLIER) cc_final: 0.8064 (m110) REVERT: B 883 GLU cc_start: 0.8576 (OUTLIER) cc_final: 0.8304 (tp30) REVERT: C 43 ASN cc_start: 0.8232 (t0) cc_final: 0.7902 (t0) REVERT: D 45 ASP cc_start: 0.3659 (OUTLIER) cc_final: 0.3199 (t0) REVERT: D 46 GLU cc_start: 0.4749 (OUTLIER) cc_final: 0.3839 (pm20) REVERT: E 20 LYS cc_start: 0.8462 (mmtt) cc_final: 0.8141 (mmtt) REVERT: E 33 GLU cc_start: 0.7798 (OUTLIER) cc_final: 0.6650 (mp0) REVERT: G 229 LEU cc_start: 0.2169 (OUTLIER) cc_final: 0.1748 (tp) REVERT: H 126 GLU cc_start: 0.8660 (tt0) cc_final: 0.8417 (tt0) REVERT: H 144 ILE cc_start: 0.9236 (OUTLIER) cc_final: 0.9005 (mt) REVERT: K 59 THR cc_start: 0.8885 (OUTLIER) cc_final: 0.8614 (m) outliers start: 155 outliers final: 118 residues processed: 561 average time/residue: 0.2198 time to fit residues: 199.6170 Evaluate side-chains 559 residues out of total 3639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 134 poor density : 425 time to evaluate : 1.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 59 ARG Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 251 ILE Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 313 THR Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain A residue 357 MET Chi-restraints excluded: chain A residue 393 SER Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain A residue 419 ILE Chi-restraints excluded: chain A residue 428 VAL Chi-restraints excluded: chain A residue 429 THR Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain A residue 581 ILE Chi-restraints excluded: chain A residue 594 THR Chi-restraints excluded: chain A residue 646 GLU Chi-restraints excluded: chain A residue 700 ILE Chi-restraints excluded: chain A residue 703 GLU Chi-restraints excluded: chain A residue 780 ILE Chi-restraints excluded: chain A residue 909 SER Chi-restraints excluded: chain A residue 961 VAL Chi-restraints excluded: chain A residue 990 ILE Chi-restraints excluded: chain A residue 1011 VAL Chi-restraints excluded: chain A residue 1028 GLU Chi-restraints excluded: chain A residue 1030 VAL Chi-restraints excluded: chain A residue 1035 ASP Chi-restraints excluded: chain A residue 1083 SER Chi-restraints excluded: chain A residue 1139 ASN Chi-restraints excluded: chain A residue 1173 LYS Chi-restraints excluded: chain A residue 1192 SER Chi-restraints excluded: chain A residue 1200 MET Chi-restraints excluded: chain A residue 1216 THR Chi-restraints excluded: chain A residue 1222 LEU Chi-restraints excluded: chain A residue 1248 ASP Chi-restraints excluded: chain A residue 1253 THR Chi-restraints excluded: chain A residue 1261 VAL Chi-restraints excluded: chain A residue 1289 SER Chi-restraints excluded: chain A residue 1434 GLU Chi-restraints excluded: chain A residue 1474 LEU Chi-restraints excluded: chain A residue 1491 GLU Chi-restraints excluded: chain A residue 1500 GLN Chi-restraints excluded: chain A residue 1520 VAL Chi-restraints excluded: chain A residue 1649 VAL Chi-restraints excluded: chain B residue 68 ILE Chi-restraints excluded: chain B residue 73 ILE Chi-restraints excluded: chain B residue 157 ASP Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain B residue 207 ILE Chi-restraints excluded: chain B residue 217 ILE Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain B residue 271 VAL Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 274 VAL Chi-restraints excluded: chain B residue 325 GLN Chi-restraints excluded: chain B residue 359 LEU Chi-restraints excluded: chain B residue 425 ILE Chi-restraints excluded: chain B residue 453 VAL Chi-restraints excluded: chain B residue 487 VAL Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 537 SER Chi-restraints excluded: chain B residue 583 LEU Chi-restraints excluded: chain B residue 721 MET Chi-restraints excluded: chain B residue 752 VAL Chi-restraints excluded: chain B residue 773 VAL Chi-restraints excluded: chain B residue 831 GLU Chi-restraints excluded: chain B residue 835 GLU Chi-restraints excluded: chain B residue 867 ASN Chi-restraints excluded: chain B residue 883 GLU Chi-restraints excluded: chain B residue 900 THR Chi-restraints excluded: chain B residue 903 ILE Chi-restraints excluded: chain B residue 927 CYS Chi-restraints excluded: chain B residue 941 THR Chi-restraints excluded: chain B residue 944 GLN Chi-restraints excluded: chain B residue 982 THR Chi-restraints excluded: chain B residue 990 ASP Chi-restraints excluded: chain B residue 1045 GLN Chi-restraints excluded: chain B residue 1049 THR Chi-restraints excluded: chain B residue 1079 LEU Chi-restraints excluded: chain B residue 1110 ILE Chi-restraints excluded: chain B residue 1111 LEU Chi-restraints excluded: chain B residue 1120 ILE Chi-restraints excluded: chain C residue 29 ASN Chi-restraints excluded: chain C residue 62 SER Chi-restraints excluded: chain C residue 141 THR Chi-restraints excluded: chain C residue 208 CYS Chi-restraints excluded: chain C residue 224 THR Chi-restraints excluded: chain C residue 331 CYS Chi-restraints excluded: chain C residue 334 THR Chi-restraints excluded: chain D residue 45 ASP Chi-restraints excluded: chain D residue 46 GLU Chi-restraints excluded: chain D residue 86 ILE Chi-restraints excluded: chain D residue 92 ILE Chi-restraints excluded: chain E residue 33 GLU Chi-restraints excluded: chain E residue 65 THR Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain E residue 215 MET Chi-restraints excluded: chain G residue 80 VAL Chi-restraints excluded: chain G residue 108 THR Chi-restraints excluded: chain G residue 124 VAL Chi-restraints excluded: chain G residue 147 LEU Chi-restraints excluded: chain G residue 229 LEU Chi-restraints excluded: chain G residue 237 HIS Chi-restraints excluded: chain G residue 245 VAL Chi-restraints excluded: chain H residue 8 ASP Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 42 ILE Chi-restraints excluded: chain H residue 54 SER Chi-restraints excluded: chain H residue 61 SER Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 143 LEU Chi-restraints excluded: chain H residue 144 ILE Chi-restraints excluded: chain I residue 24 LEU Chi-restraints excluded: chain J residue 12 LYS Chi-restraints excluded: chain K residue 51 THR Chi-restraints excluded: chain K residue 59 THR Chi-restraints excluded: chain K residue 103 ILE Chi-restraints excluded: chain K residue 140 LYS Chi-restraints excluded: chain L residue 35 SER Chi-restraints excluded: chain L residue 53 HIS Chi-restraints excluded: chain M residue 37 THR Chi-restraints excluded: chain M residue 78 VAL Chi-restraints excluded: chain N residue 25 ILE Chi-restraints excluded: chain N residue 52 GLN Chi-restraints excluded: chain N residue 53 VAL Chi-restraints excluded: chain N residue 65 SER Chi-restraints excluded: chain N residue 160 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 411 random chunks: [362, 7, 360, 85, 389, 231, 321, 310, 117, 347, 395] chunk 362 optimal weight: 10.0000 chunk 7 optimal weight: 6.9990 chunk 360 optimal weight: 3.9990 chunk 85 optimal weight: 1.9990 chunk 389 optimal weight: 7.9990 chunk 231 optimal weight: 9.9990 chunk 321 optimal weight: 9.9990 chunk 310 optimal weight: 0.0070 chunk 117 optimal weight: 7.9990 chunk 347 optimal weight: 6.9990 chunk 395 optimal weight: 9.9990 overall best weight: 4.0006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 221 HIS A 560 GLN A1072 ASN A1532 GLN B 27 ASN ** B 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 335 GLN D 23 HIS D 26 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.160677 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.119607 restraints weight = 40615.412| |-----------------------------------------------------------------------------| r_work (start): 0.3300 rms_B_bonded: 1.93 r_work: 0.3011 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2873 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.2873 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8526 moved from start: 0.1253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.062 34964 Z= 0.279 Angle : 0.644 14.344 47547 Z= 0.331 Chirality : 0.047 0.293 5314 Planarity : 0.004 0.043 5889 Dihedral : 13.259 153.105 5308 Min Nonbonded Distance : 1.839 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer: Outliers : 4.37 % Allowed : 29.57 % Favored : 66.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.60 % 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: -0.47 (0.13), residues: 4061 helix: 0.82 (0.14), residues: 1314 sheet: -1.05 (0.21), residues: 600 loop : -0.76 (0.13), residues: 2147 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 305 TYR 0.021 0.002 TYR C 227 PHE 0.018 0.002 PHE B 938 TRP 0.013 0.001 TRP B 143 HIS 0.008 0.001 HIS A 798 Details of bonding type rmsd/Z covalent geometry : bond 0.00667 / 0.28 (34940) covalent geometry : angle 0.63068 / 0.33 (47514) hydrogen bonds : bond 0.04470 / 2.96 ( 1313) hydrogen bonds : angle 4.83136 / 3.42 ( 3728) metal coordination : bond 0.01548 / 1.06 ( 24) metal coordination : angle 4.94467 / 3.00 ( 33) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8122 Ramachandran restraints generated. 4061 Oldfield, 0 Emsley, 4061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8122 Ramachandran restraints generated. 4061 Oldfield, 0 Emsley, 4061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 589 residues out of total 3639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 159 poor density : 430 time to evaluate : 1.239 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 59 ARG cc_start: 0.7620 (OUTLIER) cc_final: 0.7200 (ttp-170) REVERT: A 265 ARG cc_start: 0.7458 (tmt-80) cc_final: 0.7019 (tpt90) REVERT: A 388 LYS cc_start: 0.8839 (tptm) cc_final: 0.8350 (tppt) REVERT: A 429 THR cc_start: 0.8762 (OUTLIER) cc_final: 0.8501 (t) REVERT: A 589 MET cc_start: 0.8379 (mmm) cc_final: 0.8047 (mmm) REVERT: A 1173 LYS cc_start: 0.8162 (OUTLIER) cc_final: 0.7759 (tttp) REVERT: A 1222 LEU cc_start: 0.9135 (OUTLIER) cc_final: 0.8808 (mm) REVERT: A 1434 GLU cc_start: 0.4804 (OUTLIER) cc_final: 0.4401 (pt0) REVERT: B 157 ASP cc_start: 0.8138 (OUTLIER) cc_final: 0.7806 (p0) REVERT: B 215 MET cc_start: 0.8971 (ptp) cc_final: 0.8702 (mtm) REVERT: B 762 MET cc_start: 0.8957 (mmt) cc_final: 0.8666 (mmt) REVERT: B 867 ASN cc_start: 0.8284 (OUTLIER) cc_final: 0.8074 (m110) REVERT: B 883 GLU cc_start: 0.8578 (OUTLIER) cc_final: 0.8330 (tp30) REVERT: D 45 ASP cc_start: 0.3668 (OUTLIER) cc_final: 0.3223 (t0) REVERT: D 46 GLU cc_start: 0.5006 (OUTLIER) cc_final: 0.4255 (pm20) REVERT: E 33 GLU cc_start: 0.7844 (OUTLIER) cc_final: 0.6757 (mp0) REVERT: G 229 LEU cc_start: 0.2170 (OUTLIER) cc_final: 0.1756 (tp) REVERT: H 126 GLU cc_start: 0.8717 (tt0) cc_final: 0.8476 (tt0) REVERT: H 144 ILE cc_start: 0.9271 (OUTLIER) cc_final: 0.9070 (mt) REVERT: K 59 THR cc_start: 0.8916 (OUTLIER) cc_final: 0.8666 (m) outliers start: 159 outliers final: 126 residues processed: 553 average time/residue: 0.2126 time to fit residues: 190.4123 Evaluate side-chains 561 residues out of total 3639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 140 poor density : 421 time to evaluate : 1.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 59 ARG Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain A residue 133 SER Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 251 ILE Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 313 THR Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain A residue 357 MET Chi-restraints excluded: chain A residue 393 SER Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain A residue 419 ILE Chi-restraints excluded: chain A residue 428 VAL Chi-restraints excluded: chain A residue 429 THR Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain A residue 581 ILE Chi-restraints excluded: chain A residue 594 THR Chi-restraints excluded: chain A residue 646 GLU Chi-restraints excluded: chain A residue 703 GLU Chi-restraints excluded: chain A residue 780 ILE Chi-restraints excluded: chain A residue 909 SER Chi-restraints excluded: chain A residue 961 VAL Chi-restraints excluded: chain A residue 990 ILE Chi-restraints excluded: chain A residue 1011 VAL Chi-restraints excluded: chain A residue 1028 GLU Chi-restraints excluded: chain A residue 1030 VAL Chi-restraints excluded: chain A residue 1035 ASP Chi-restraints excluded: chain A residue 1083 SER Chi-restraints excluded: chain A residue 1139 ASN Chi-restraints excluded: chain A residue 1173 LYS Chi-restraints excluded: chain A residue 1192 SER Chi-restraints excluded: chain A residue 1200 MET Chi-restraints excluded: chain A residue 1216 THR Chi-restraints excluded: chain A residue 1222 LEU Chi-restraints excluded: chain A residue 1248 ASP Chi-restraints excluded: chain A residue 1253 THR Chi-restraints excluded: chain A residue 1289 SER Chi-restraints excluded: chain A residue 1434 GLU Chi-restraints excluded: chain A residue 1474 LEU Chi-restraints excluded: chain A residue 1491 GLU Chi-restraints excluded: chain A residue 1518 VAL Chi-restraints excluded: chain A residue 1520 VAL Chi-restraints excluded: chain A residue 1543 SER Chi-restraints excluded: chain A residue 1649 VAL Chi-restraints excluded: chain B residue 27 ASN Chi-restraints excluded: chain B residue 68 ILE Chi-restraints excluded: chain B residue 73 ILE Chi-restraints excluded: chain B residue 93 ASN Chi-restraints excluded: chain B residue 157 ASP Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain B residue 207 ILE Chi-restraints excluded: chain B residue 217 ILE Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain B residue 271 VAL Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 274 VAL Chi-restraints excluded: chain B residue 359 LEU Chi-restraints excluded: chain B residue 453 VAL Chi-restraints excluded: chain B residue 487 VAL Chi-restraints excluded: chain B residue 492 ASN Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 507 SER Chi-restraints excluded: chain B residue 537 SER Chi-restraints excluded: chain B residue 583 LEU Chi-restraints excluded: chain B residue 721 MET Chi-restraints excluded: chain B residue 752 VAL Chi-restraints excluded: chain B residue 758 ASP Chi-restraints excluded: chain B residue 773 VAL Chi-restraints excluded: chain B residue 831 GLU Chi-restraints excluded: chain B residue 867 ASN Chi-restraints excluded: chain B residue 883 GLU Chi-restraints excluded: chain B residue 900 THR Chi-restraints excluded: chain B residue 903 ILE Chi-restraints excluded: chain B residue 927 CYS Chi-restraints excluded: chain B residue 941 THR Chi-restraints excluded: chain B residue 944 GLN Chi-restraints excluded: chain B residue 982 THR Chi-restraints excluded: chain B residue 1045 GLN Chi-restraints excluded: chain B residue 1049 THR Chi-restraints excluded: chain B residue 1079 LEU Chi-restraints excluded: chain B residue 1085 SER Chi-restraints excluded: chain B residue 1110 ILE Chi-restraints excluded: chain B residue 1111 LEU Chi-restraints excluded: chain B residue 1120 ILE Chi-restraints excluded: chain B residue 1200 VAL Chi-restraints excluded: chain C residue 29 ASN Chi-restraints excluded: chain C residue 62 SER Chi-restraints excluded: chain C residue 141 THR Chi-restraints excluded: chain C residue 208 CYS Chi-restraints excluded: chain C residue 224 THR Chi-restraints excluded: chain C residue 331 CYS Chi-restraints excluded: chain C residue 334 THR Chi-restraints excluded: chain D residue 45 ASP Chi-restraints excluded: chain D residue 46 GLU Chi-restraints excluded: chain D residue 86 ILE Chi-restraints excluded: chain D residue 92 ILE Chi-restraints excluded: chain E residue 9 ILE Chi-restraints excluded: chain E residue 33 GLU Chi-restraints excluded: chain E residue 65 THR Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain E residue 116 ILE Chi-restraints excluded: chain G residue 80 VAL Chi-restraints excluded: chain G residue 108 THR Chi-restraints excluded: chain G residue 124 VAL Chi-restraints excluded: chain G residue 147 LEU Chi-restraints excluded: chain G residue 229 LEU Chi-restraints excluded: chain G residue 237 HIS Chi-restraints excluded: chain G residue 245 VAL Chi-restraints excluded: chain H residue 8 ASP Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 32 THR Chi-restraints excluded: chain H residue 42 ILE Chi-restraints excluded: chain H residue 54 SER Chi-restraints excluded: chain H residue 61 SER Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 143 LEU Chi-restraints excluded: chain H residue 144 ILE Chi-restraints excluded: chain I residue 24 LEU Chi-restraints excluded: chain I residue 47 VAL Chi-restraints excluded: chain J residue 12 LYS Chi-restraints excluded: chain K residue 51 THR Chi-restraints excluded: chain K residue 59 THR Chi-restraints excluded: chain K residue 103 ILE Chi-restraints excluded: chain K residue 140 LYS Chi-restraints excluded: chain L residue 35 SER Chi-restraints excluded: chain L residue 53 HIS Chi-restraints excluded: chain M residue 37 THR Chi-restraints excluded: chain M residue 78 VAL Chi-restraints excluded: chain N residue 25 ILE Chi-restraints excluded: chain N residue 52 GLN Chi-restraints excluded: chain N residue 53 VAL Chi-restraints excluded: chain N residue 65 SER Chi-restraints excluded: chain N residue 124 THR Chi-restraints excluded: chain N residue 160 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 411 random chunks: [360, 32, 101, 67, 40, 34, 227, 347, 78, 1, 305] chunk 360 optimal weight: 10.0000 chunk 32 optimal weight: 8.9990 chunk 101 optimal weight: 9.9990 chunk 67 optimal weight: 4.9990 chunk 40 optimal weight: 0.9980 chunk 34 optimal weight: 9.9990 chunk 227 optimal weight: 9.9990 chunk 347 optimal weight: 0.6980 chunk 78 optimal weight: 9.9990 chunk 1 optimal weight: 3.9990 chunk 305 optimal weight: 3.9990 overall best weight: 2.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 221 HIS A1072 ASN A1116 GLN ** A1461 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 27 ASN ** B 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 325 GLN C 335 GLN D 23 HIS D 26 GLN H 11 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.160878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.119681 restraints weight = 40572.504| |-----------------------------------------------------------------------------| r_work (start): 0.3298 rms_B_bonded: 1.98 r_work: 0.3008 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.2874 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.2874 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8524 moved from start: 0.1263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.109 34964 Z= 0.256 Angle : 0.723 59.200 47547 Z= 0.390 Chirality : 0.046 0.522 5314 Planarity : 0.004 0.047 5889 Dihedral : 13.267 153.120 5308 Min Nonbonded Distance : 1.841 Molprobity Statistics. All-atom Clashscore : 9.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer: Outliers : 4.20 % Allowed : 29.73 % Favored : 66.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.60 % 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: -0.48 (0.13), residues: 4061 helix: 0.83 (0.14), residues: 1313 sheet: -1.06 (0.21), residues: 600 loop : -0.77 (0.13), residues: 2148 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 305 TYR 0.020 0.002 TYR C 227 PHE 0.017 0.002 PHE A 628 TRP 0.012 0.001 TRP B 143 HIS 0.007 0.001 HIS A 798 Details of bonding type rmsd/Z covalent geometry : bond 0.00607 / 0.26 (34940) covalent geometry : angle 0.71133 / 0.39 (47514) hydrogen bonds : bond 0.04434 / 2.93 ( 1313) hydrogen bonds : angle 4.83116 / 3.42 ( 3728) metal coordination : bond 0.01442 / 0.98 ( 24) metal coordination : angle 4.95239 / 3.01 ( 33) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8122 Ramachandran restraints generated. 4061 Oldfield, 0 Emsley, 4061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8122 Ramachandran restraints generated. 4061 Oldfield, 0 Emsley, 4061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 575 residues out of total 3639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 153 poor density : 422 time to evaluate : 1.353 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 59 ARG cc_start: 0.7577 (OUTLIER) cc_final: 0.7141 (ttp-170) REVERT: A 265 ARG cc_start: 0.7463 (tmt-80) cc_final: 0.7026 (tpt90) REVERT: A 388 LYS cc_start: 0.8846 (tptm) cc_final: 0.8360 (tppt) REVERT: A 429 THR cc_start: 0.8758 (OUTLIER) cc_final: 0.8496 (t) REVERT: A 589 MET cc_start: 0.8369 (mmm) cc_final: 0.8027 (mmm) REVERT: A 1173 LYS cc_start: 0.8160 (OUTLIER) cc_final: 0.7758 (tttp) REVERT: A 1222 LEU cc_start: 0.9149 (OUTLIER) cc_final: 0.8819 (mm) REVERT: A 1434 GLU cc_start: 0.4800 (OUTLIER) cc_final: 0.4384 (pt0) REVERT: B 27 ASN cc_start: 0.8267 (OUTLIER) cc_final: 0.8040 (p0) REVERT: B 157 ASP cc_start: 0.8136 (OUTLIER) cc_final: 0.7798 (p0) REVERT: B 215 MET cc_start: 0.8974 (ptp) cc_final: 0.8701 (mtm) REVERT: B 651 ARG cc_start: 0.8909 (OUTLIER) cc_final: 0.8044 (ttp-170) REVERT: B 762 MET cc_start: 0.8941 (mmt) cc_final: 0.8661 (mmt) REVERT: B 835 GLU cc_start: 0.8166 (mt-10) cc_final: 0.7952 (mp0) REVERT: B 867 ASN cc_start: 0.8266 (OUTLIER) cc_final: 0.8060 (m110) REVERT: B 883 GLU cc_start: 0.8613 (OUTLIER) cc_final: 0.8368 (tp30) REVERT: D 45 ASP cc_start: 0.3658 (OUTLIER) cc_final: 0.3217 (t0) REVERT: D 46 GLU cc_start: 0.4988 (OUTLIER) cc_final: 0.4248 (pm20) REVERT: E 33 GLU cc_start: 0.7867 (OUTLIER) cc_final: 0.6749 (mp0) REVERT: G 229 LEU cc_start: 0.2157 (OUTLIER) cc_final: 0.1749 (tp) REVERT: H 126 GLU cc_start: 0.8731 (tt0) cc_final: 0.8492 (tt0) REVERT: H 144 ILE cc_start: 0.9271 (OUTLIER) cc_final: 0.9069 (mt) REVERT: K 59 THR cc_start: 0.8924 (OUTLIER) cc_final: 0.8671 (m) outliers start: 153 outliers final: 132 residues processed: 541 average time/residue: 0.2168 time to fit residues: 189.4300 Evaluate side-chains 567 residues out of total 3639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 148 poor density : 419 time to evaluate : 1.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 59 ARG Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain A residue 133 SER Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 251 ILE Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 313 THR Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain A residue 357 MET Chi-restraints excluded: chain A residue 393 SER Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain A residue 419 ILE Chi-restraints excluded: chain A residue 428 VAL Chi-restraints excluded: chain A residue 429 THR Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain A residue 581 ILE Chi-restraints excluded: chain A residue 594 THR Chi-restraints excluded: chain A residue 646 GLU Chi-restraints excluded: chain A residue 703 GLU Chi-restraints excluded: chain A residue 780 ILE Chi-restraints excluded: chain A residue 909 SER Chi-restraints excluded: chain A residue 961 VAL Chi-restraints excluded: chain A residue 990 ILE Chi-restraints excluded: chain A residue 1011 VAL Chi-restraints excluded: chain A residue 1028 GLU Chi-restraints excluded: chain A residue 1030 VAL Chi-restraints excluded: chain A residue 1035 ASP Chi-restraints excluded: chain A residue 1083 SER Chi-restraints excluded: chain A residue 1139 ASN Chi-restraints excluded: chain A residue 1173 LYS Chi-restraints excluded: chain A residue 1192 SER Chi-restraints excluded: chain A residue 1200 MET Chi-restraints excluded: chain A residue 1216 THR Chi-restraints excluded: chain A residue 1222 LEU Chi-restraints excluded: chain A residue 1248 ASP Chi-restraints excluded: chain A residue 1253 THR Chi-restraints excluded: chain A residue 1289 SER Chi-restraints excluded: chain A residue 1434 GLU Chi-restraints excluded: chain A residue 1474 LEU Chi-restraints excluded: chain A residue 1491 GLU Chi-restraints excluded: chain A residue 1518 VAL Chi-restraints excluded: chain A residue 1520 VAL Chi-restraints excluded: chain A residue 1543 SER Chi-restraints excluded: chain A residue 1613 MET Chi-restraints excluded: chain A residue 1649 VAL Chi-restraints excluded: chain B residue 27 ASN Chi-restraints excluded: chain B residue 68 ILE Chi-restraints excluded: chain B residue 73 ILE Chi-restraints excluded: chain B residue 93 ASN Chi-restraints excluded: chain B residue 157 ASP Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain B residue 207 ILE Chi-restraints excluded: chain B residue 217 ILE Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain B residue 271 VAL Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 274 VAL Chi-restraints excluded: chain B residue 281 CYS Chi-restraints excluded: chain B residue 325 GLN Chi-restraints excluded: chain B residue 359 LEU Chi-restraints excluded: chain B residue 453 VAL Chi-restraints excluded: chain B residue 487 VAL Chi-restraints excluded: chain B residue 492 ASN Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 507 SER Chi-restraints excluded: chain B residue 533 THR Chi-restraints excluded: chain B residue 537 SER Chi-restraints excluded: chain B residue 583 LEU Chi-restraints excluded: chain B residue 651 ARG Chi-restraints excluded: chain B residue 721 MET Chi-restraints excluded: chain B residue 752 VAL Chi-restraints excluded: chain B residue 758 ASP Chi-restraints excluded: chain B residue 773 VAL Chi-restraints excluded: chain B residue 831 GLU Chi-restraints excluded: chain B residue 867 ASN Chi-restraints excluded: chain B residue 883 GLU Chi-restraints excluded: chain B residue 900 THR Chi-restraints excluded: chain B residue 902 SER Chi-restraints excluded: chain B residue 903 ILE Chi-restraints excluded: chain B residue 927 CYS Chi-restraints excluded: chain B residue 941 THR Chi-restraints excluded: chain B residue 944 GLN Chi-restraints excluded: chain B residue 982 THR Chi-restraints excluded: chain B residue 1045 GLN Chi-restraints excluded: chain B residue 1049 THR Chi-restraints excluded: chain B residue 1079 LEU Chi-restraints excluded: chain B residue 1085 SER Chi-restraints excluded: chain B residue 1110 ILE Chi-restraints excluded: chain B residue 1111 LEU Chi-restraints excluded: chain B residue 1120 ILE Chi-restraints excluded: chain B residue 1200 VAL Chi-restraints excluded: chain C residue 29 ASN Chi-restraints excluded: chain C residue 61 THR Chi-restraints excluded: chain C residue 62 SER Chi-restraints excluded: chain C residue 141 THR Chi-restraints excluded: chain C residue 208 CYS Chi-restraints excluded: chain C residue 224 THR Chi-restraints excluded: chain C residue 279 VAL Chi-restraints excluded: chain C residue 331 CYS Chi-restraints excluded: chain C residue 334 THR Chi-restraints excluded: chain D residue 45 ASP Chi-restraints excluded: chain D residue 46 GLU Chi-restraints excluded: chain D residue 86 ILE Chi-restraints excluded: chain D residue 92 ILE Chi-restraints excluded: chain E residue 33 GLU Chi-restraints excluded: chain E residue 65 THR Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain E residue 116 ILE Chi-restraints excluded: chain G residue 80 VAL Chi-restraints excluded: chain G residue 108 THR Chi-restraints excluded: chain G residue 124 VAL Chi-restraints excluded: chain G residue 147 LEU Chi-restraints excluded: chain G residue 229 LEU Chi-restraints excluded: chain G residue 237 HIS Chi-restraints excluded: chain G residue 245 VAL Chi-restraints excluded: chain H residue 8 ASP Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 32 THR Chi-restraints excluded: chain H residue 42 ILE Chi-restraints excluded: chain H residue 54 SER Chi-restraints excluded: chain H residue 61 SER Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 143 LEU Chi-restraints excluded: chain H residue 144 ILE Chi-restraints excluded: chain I residue 24 LEU Chi-restraints excluded: chain I residue 47 VAL Chi-restraints excluded: chain J residue 12 LYS Chi-restraints excluded: chain K residue 51 THR Chi-restraints excluded: chain K residue 59 THR Chi-restraints excluded: chain K residue 103 ILE Chi-restraints excluded: chain K residue 140 LYS Chi-restraints excluded: chain L residue 35 SER Chi-restraints excluded: chain L residue 53 HIS Chi-restraints excluded: chain M residue 37 THR Chi-restraints excluded: chain M residue 78 VAL Chi-restraints excluded: chain M residue 97 VAL Chi-restraints excluded: chain N residue 25 ILE Chi-restraints excluded: chain N residue 52 GLN Chi-restraints excluded: chain N residue 53 VAL Chi-restraints excluded: chain N residue 65 SER Chi-restraints excluded: chain N residue 124 THR Chi-restraints excluded: chain N residue 160 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 411 random chunks: [349, 188, 262, 22, 139, 320, 280, 86, 361, 236, 237] chunk 349 optimal weight: 0.5980 chunk 188 optimal weight: 7.9990 chunk 262 optimal weight: 0.7980 chunk 22 optimal weight: 20.0000 chunk 139 optimal weight: 2.9990 chunk 320 optimal weight: 8.9990 chunk 280 optimal weight: 0.8980 chunk 86 optimal weight: 1.9990 chunk 361 optimal weight: 7.9990 chunk 236 optimal weight: 0.4980 chunk 237 optimal weight: 0.5980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 106 HIS A 221 HIS A1072 ASN ** A1116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1461 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 335 GLN D 23 HIS D 26 GLN H 11 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.160355 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.119546 restraints weight = 40314.555| |-----------------------------------------------------------------------------| r_work (start): 0.3301 rms_B_bonded: 1.96 r_work: 0.3012 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2871 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.2871 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8524 moved from start: 0.1264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.122 34964 Z= 0.256 Angle : 0.663 23.204 47547 Z= 0.350 Chirality : 0.046 0.414 5314 Planarity : 0.004 0.090 5889 Dihedral : 13.267 153.120 5308 Min Nonbonded Distance : 1.841 Molprobity Statistics. All-atom Clashscore : 9.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer: Outliers : 4.09 % Allowed : 29.79 % Favored : 66.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.60 % 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: -0.48 (0.13), residues: 4061 helix: 0.83 (0.14), residues: 1313 sheet: -1.06 (0.21), residues: 600 loop : -0.77 (0.13), residues: 2148 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 305 TYR 0.020 0.002 TYR C 227 PHE 0.017 0.002 PHE A 628 TRP 0.012 0.001 TRP B 143 HIS 0.007 0.001 HIS A 798 Details of bonding type rmsd/Z covalent geometry : bond 0.00606 / 0.26 (34940) covalent geometry : angle 0.65046 / 0.35 (47514) hydrogen bonds : bond 0.04434 / 2.93 ( 1313) hydrogen bonds : angle 4.83116 / 3.42 ( 3728) metal coordination : bond 0.01442 / 0.98 ( 24) metal coordination : angle 4.95239 / 3.01 ( 33) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8710.37 seconds wall clock time: 149 minutes 46.67 seconds (8986.67 seconds total)