Starting phenix.real_space_refine on Sun Aug 9 09:40:15 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ryb_54374/08_2026/9ryb_54374.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ryb_54374/08_2026/9ryb_54374.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.33 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9ryb_54374/08_2026/9ryb_54374.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ryb_54374/08_2026/9ryb_54374.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9ryb_54374/08_2026/9ryb_54374.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ryb_54374/08_2026/9ryb_54374.map" } resolution = 2.33 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.052 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: 8 Type Number sf(0) Gaussians K 1 8.98 5 Zn 8 6.06 5 P 56 5.49 5 Mg 1 5.21 5 S 182 5.16 5 C 20241 2.51 5 N 5638 2.21 5 O 6962 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 33089 Number of models: 1 Model: "" Number of chains: 32 Chain: "A" Number of atoms: 10999 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1397, 10999 Classifications: {'peptide': 1397} Link IDs: {'PCIS': 1, 'PTRANS': 63, 'TRANS': 1332} Chain breaks: 7 Chain: "B" Number of atoms: 9268 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1164, 9268 Classifications: {'peptide': 1164} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 49, 'TRANS': 1113} Chain breaks: 4 Chain: "C" Number of atoms: 2095 Number of conformers: 1 Conformer: "" Number of residues, atoms: 266, 2095 Classifications: {'peptide': 266} Link IDs: {'PTRANS': 11, 'TRANS': 254} Chain: "D" Number of atoms: 1327 Number of conformers: 1 Conformer: "" Number of residues, atoms: 167, 1327 Classifications: {'peptide': 167} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 164} Chain breaks: 2 Chain: "E" Number of atoms: 1744 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1744 Classifications: {'peptide': 213} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 200} Chain: "F" Number of atoms: 670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 670 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 6, 'TRANS': 76} Chain: "G" Number of atoms: 1340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1340 Classifications: {'peptide': 171} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 162} Chain: "H" Number of atoms: 1077 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 1077 Classifications: {'peptide': 134} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 129} Chain breaks: 1 Chain: "I" Number of atoms: 926 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 926 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 5, 'TRANS': 108} Chain: "J" Number of atoms: 532 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 532 Classifications: {'peptide': 65} Link IDs: {'PTRANS': 2, 'TRANS': 62} Chain: "K" Number of atoms: 904 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 904 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 5, 'TRANS': 106} Chain: "L" Number of atoms: 359 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 359 Classifications: {'peptide': 45} Modifications used: {'COO': 1} Link IDs: {'TRANS': 44} Chain: "N" Number of atoms: 334 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 334 Classifications: {'DNA': 16} Link IDs: {'rna3p': 15} Chain: "R" Number of atoms: 246 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 246 Classifications: {'RNA': 11} Modifications used: {'rna3p_pur': 10, 'rna3p_pyr': 1} Link IDs: {'rna3p': 10} Chain: "T" Number of atoms: 537 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 537 Classifications: {'DNA': 27} Link IDs: {'rna3p': 26} Chain: "A" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' K': 1, ' MG': 1, ' ZN': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 10 Unusual residues: {' ZN': 1, 'DPO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 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} Chain: "A" Number of atoms: 267 Number of conformers: 1 Conformer: "" Number of residues, atoms: 267, 267 Classifications: {'water': 267} Link IDs: {None: 266} Chain: "B" Number of atoms: 232 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 232 Classifications: {'water': 232} Link IDs: {None: 231} Chain: "C" Number of atoms: 68 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 68 Classifications: {'water': 68} Link IDs: {None: 67} Chain: "E" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 22 Classifications: {'water': 22} Link IDs: {None: 21} Chain: "F" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 15 Classifications: {'water': 15} Link IDs: {None: 14} Chain: "H" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 10 Classifications: {'water': 10} Link IDs: {None: 9} Chain: "J" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 18 Classifications: {'water': 18} Link IDs: {None: 17} Chain: "K" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 30 Classifications: {'water': 30} Link IDs: {None: 29} Chain: "L" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "R" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 22 Classifications: {'water': 22} Link IDs: {None: 21} Chain: "T" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 24 Classifications: {'water': 24} Link IDs: {None: 23} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 457 SG CYS A 67 57.672 85.268 75.125 1.00103.98 S ATOM 479 SG CYS A 70 57.241 81.968 77.041 1.00102.41 S ATOM 532 SG CYS A 77 60.736 83.560 76.519 1.00 94.81 S ATOM 762 SG CYS A 107 74.434 73.964 31.631 1.00117.65 S ATOM 786 SG CYS A 110 71.539 71.520 31.906 1.00118.46 S ATOM 1091 SG CYS A 148 74.695 70.644 29.876 1.00136.36 S ATOM 1190 SG CYS A 167 72.270 73.224 28.578 1.00138.64 S ATOM 19773 SG CYS B1163 58.865 69.145 67.129 1.00 91.19 S ATOM 19791 SG CYS B1166 61.368 71.249 65.265 1.00 92.95 S ATOM 19916 SG CYS B1182 58.005 72.671 66.501 1.00 97.18 S ATOM 19935 SG CYS B1185 58.209 70.294 63.459 1.00103.28 S ATOM 20923 SG CYS C 86 86.734 95.313 138.128 1.00125.32 S ATOM 20940 SG CYS C 88 85.257 97.758 135.613 1.00138.86 S ATOM 20973 SG CYS C 92 87.054 99.055 138.640 1.00117.01 S ATOM 20996 SG CYS C 95 89.007 97.309 135.807 1.00104.83 S ATOM 28581 SG CYS I 7 133.984 104.507 22.028 1.00237.06 S ATOM 28606 SG CYS I 10 130.471 105.471 22.764 1.00229.45 S ATOM 28772 SG CYS I 29 131.162 101.880 21.465 1.00230.57 S ATOM 28796 SG CYS I 32 131.551 104.853 19.179 1.00231.53 S ATOM 29123 SG CYS I 75 159.058 95.448 58.531 1.00226.68 S ATOM 29145 SG CYS I 78 161.110 98.648 59.223 1.00231.23 S ATOM 29361 SG CYS I 103 157.467 98.428 60.280 1.00219.55 S ATOM 29381 SG CYS I 106 158.473 98.696 56.613 1.00230.59 S ATOM 29500 SG CYS J 7 116.316 95.838 119.573 1.00 78.53 S ATOM 29523 SG CYS J 10 116.715 94.131 122.931 1.00 78.93 S ATOM 29803 SG CYS J 45 119.221 93.476 120.016 1.00 80.02 S ATOM 29809 SG CYS J 46 119.092 96.789 122.000 1.00 80.75 S ATOM 30932 SG CYS L 31 91.076 127.803 102.661 1.00166.25 S ATOM 30952 SG CYS L 34 91.957 130.586 105.131 1.00168.35 S ATOM 31056 SG CYS L 48 88.642 130.589 103.233 1.00165.63 S ATOM 31079 SG CYS L 51 91.932 131.336 101.427 1.00170.77 S Time building chain proxies: 7.70, per 1000 atoms: 0.23 Number of scatterers: 33089 At special positions: 0 Unit cell: (172.425, 155.1, 159.225, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Zn 8 29.99 K 1 19.00 S 182 16.00 P 56 15.00 Mg 1 11.99 O 6962 8.00 N 5638 7.00 C 20241 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: 2.95 Conformation dependent library (CDL) restraints added in 1.4 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1802 " pdb="ZN ZN A1802 " - pdb=" NE2 HIS A 80 " pdb="ZN ZN A1802 " - pdb=" SG CYS A 67 " pdb="ZN ZN A1802 " - pdb=" SG CYS A 77 " pdb="ZN ZN A1802 " - pdb=" SG CYS A 70 " pdb=" ZN A1803 " pdb="ZN ZN A1803 " - pdb=" SG CYS A 148 " pdb="ZN ZN A1803 " - pdb=" SG CYS A 167 " pdb="ZN ZN A1803 " - pdb=" SG CYS A 107 " pdb="ZN ZN A1803 " - pdb=" SG CYS A 110 " pdb=" ZN B1302 " pdb="ZN ZN B1302 " - pdb=" SG CYS B1166 " pdb="ZN ZN B1302 " - pdb=" SG CYS B1163 " pdb="ZN ZN B1302 " - pdb=" SG CYS B1182 " pdb="ZN ZN B1302 " - pdb=" SG CYS B1185 " pdb=" ZN C 401 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 88 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 92 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 86 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 95 " pdb=" ZN I 201 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 32 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 7 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 10 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 29 " pdb=" ZN I 202 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 106 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 78 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 103 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 75 " pdb=" ZN J 101 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 10 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 7 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 46 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 45 " pdb=" ZN L 101 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 48 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 34 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 51 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 31 " Number of angles added : 45 7758 Ramachandran restraints generated. 3879 Oldfield, 0 Emsley, 3879 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7388 Finding SS restraints... Secondary structure from input PDB file: 143 helices and 47 sheets defined 38.6% alpha, 19.9% beta 27 base pairs and 45 stacking pairs defined. Time for finding SS restraints: 4.70 Creating SS restraints... Processing helix chain 'A' and resid 23 through 31 Processing helix chain 'A' and resid 55 through 59 Processing helix chain 'A' and resid 95 through 104 Processing helix chain 'A' and resid 119 through 127 Processing helix chain 'A' and resid 130 through 143 Processing helix chain 'A' and resid 203 through 213 Processing helix chain 'A' and resid 215 through 222 Processing helix chain 'A' and resid 230 through 233 Processing helix chain 'A' and resid 260 through 283 removed outlier: 3.681A pdb=" N GLY A 283 " --> pdb=" O LEU A 279 " (cutoff:3.500A) Processing helix chain 'A' and resid 288 through 305 Processing helix chain 'A' and resid 324 through 330 Processing helix chain 'A' and resid 334 through 340 Processing helix chain 'A' and resid 368 through 374 Processing helix chain 'A' and resid 384 through 395 Processing helix chain 'A' and resid 451 through 453 No H-bonds generated for 'chain 'A' and resid 451 through 453' Processing helix chain 'A' and resid 474 through 479 removed outlier: 3.609A pdb=" N TYR A 478 " --> pdb=" O VAL A 474 " (cutoff:3.500A) Processing helix chain 'A' and resid 494 through 505 Processing helix chain 'A' and resid 506 through 510 Processing helix chain 'A' and resid 524 through 535 removed outlier: 3.575A pdb=" N ARG A 532 " --> pdb=" O LEU A 528 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LYS A 533 " --> pdb=" O CYS A 529 " (cutoff:3.500A) Processing helix chain 'A' and resid 542 through 552 Processing helix chain 'A' and resid 574 through 582 removed outlier: 3.556A pdb=" N VAL A 580 " --> pdb=" O GLN A 576 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N ALA A 581 " --> pdb=" O ILE A 577 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ILE A 582 " --> pdb=" O LEU A 578 " (cutoff:3.500A) Processing helix chain 'A' and resid 618 through 623 Processing helix chain 'A' and resid 628 through 638 Processing helix chain 'A' and resid 638 through 661 removed outlier: 3.564A pdb=" N HIS A 659 " --> pdb=" O PHE A 655 " (cutoff:3.500A) Processing helix chain 'A' and resid 665 through 670 Processing helix chain 'A' and resid 672 through 700 Processing helix chain 'A' and resid 709 through 737 Processing helix chain 'A' and resid 741 through 749 Processing helix chain 'A' and resid 754 through 763 Processing helix chain 'A' and resid 809 through 845 removed outlier: 3.566A pdb=" N GLU A 822 " --> pdb=" O MET A 818 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N GLY A 823 " --> pdb=" O GLY A 819 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N THR A 831 " --> pdb=" O THR A 827 " (cutoff:3.500A) removed outlier: 5.269A pdb=" N ALA A 832 " --> pdb=" O ALA A 828 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N GLU A 833 " --> pdb=" O VAL A 829 " (cutoff:3.500A) Processing helix chain 'A' and resid 867 through 871 Processing helix chain 'A' and resid 874 through 876 No H-bonds generated for 'chain 'A' and resid 874 through 876' Processing helix chain 'A' and resid 889 through 898 Processing helix chain 'A' and resid 909 through 913 removed outlier: 3.570A pdb=" N LEU A 913 " --> pdb=" O PRO A 910 " (cutoff:3.500A) Processing helix chain 'A' and resid 915 through 920 removed outlier: 3.547A pdb=" N LEU A 920 " --> pdb=" O GLY A 916 " (cutoff:3.500A) Processing helix chain 'A' and resid 923 through 947 Processing helix chain 'A' and resid 959 through 972 removed outlier: 3.521A pdb=" N ILE A 963 " --> pdb=" O ASN A 959 " (cutoff:3.500A) Processing helix chain 'A' and resid 982 through 994 removed outlier: 3.676A pdb=" N GLN A 994 " --> pdb=" O VAL A 990 " (cutoff:3.500A) Processing helix chain 'A' and resid 995 through 997 No H-bonds generated for 'chain 'A' and resid 995 through 997' Processing helix chain 'A' and resid 1004 through 1015 removed outlier: 3.537A pdb=" N VAL A1015 " --> pdb=" O GLN A1011 " (cutoff:3.500A) Processing helix chain 'A' and resid 1015 through 1026 Processing helix chain 'A' and resid 1027 through 1034 Processing helix chain 'A' and resid 1038 through 1057 removed outlier: 3.635A pdb=" N VAL A1057 " --> pdb=" O PHE A1053 " (cutoff:3.500A) Processing helix chain 'A' and resid 1063 through 1078 Proline residue: A1075 - end of helix Processing helix chain 'A' and resid 1097 through 1107 Processing helix chain 'A' and resid 1130 through 1139 Processing helix chain 'A' and resid 1166 through 1175 removed outlier: 3.548A pdb=" N SER A1175 " --> pdb=" O GLN A1171 " (cutoff:3.500A) Processing helix chain 'A' and resid 1178 through 1187 removed outlier: 4.060A pdb=" N ASP A1186 " --> pdb=" O GLU A1182 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N GLN A1187 " --> pdb=" O GLN A1183 " (cutoff:3.500A) Processing helix chain 'A' and resid 1198 through 1206 Processing helix chain 'A' and resid 1208 through 1220 Processing helix chain 'A' and resid 1257 through 1271 removed outlier: 3.862A pdb=" N ILE A1271 " --> pdb=" O MET A1267 " (cutoff:3.500A) Processing helix chain 'A' and resid 1312 through 1317 Processing helix chain 'A' and resid 1331 through 1340 Processing helix chain 'A' and resid 1340 through 1357 Processing helix chain 'A' and resid 1364 through 1377 removed outlier: 4.027A pdb=" N MET A1368 " --> pdb=" O ASN A1364 " (cutoff:3.500A) Processing helix chain 'A' and resid 1395 through 1401 Processing helix chain 'A' and resid 1404 through 1416 Processing helix chain 'A' and resid 1423 through 1431 removed outlier: 3.630A pdb=" N ASN A1427 " --> pdb=" O GLY A1423 " (cutoff:3.500A) Processing helix chain 'A' and resid 1436 through 1439 Processing helix chain 'A' and resid 1446 through 1452 removed outlier: 4.204A pdb=" N LYS A1452 " --> pdb=" O GLU A1448 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 37 removed outlier: 3.713A pdb=" N VAL B 33 " --> pdb=" O ASP B 29 " (cutoff:3.500A) Processing helix chain 'B' and resid 44 through 66 removed outlier: 4.553A pdb=" N LEU B 59 " --> pdb=" O VAL B 55 " (cutoff:3.500A) removed outlier: 5.692A pdb=" N GLN B 60 " --> pdb=" O ASP B 56 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ASP B 61 " --> pdb=" O TYR B 57 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N ASP B 66 " --> pdb=" O ILE B 62 " (cutoff:3.500A) Processing helix chain 'B' and resid 79 through 82 Processing helix chain 'B' and resid 113 through 121 Processing helix chain 'B' and resid 158 through 162 removed outlier: 5.439A pdb=" N GLU B 161 " --> pdb=" O ASP B 158 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N SER B 162 " --> pdb=" O ASP B 159 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 158 through 162' Processing helix chain 'B' and resid 185 through 192 Processing helix chain 'B' and resid 282 through 290 Processing helix chain 'B' and resid 293 through 303 removed outlier: 3.643A pdb=" N TYR B 303 " --> pdb=" O GLU B 299 " (cutoff:3.500A) Processing helix chain 'B' and resid 307 through 321 removed outlier: 4.119A pdb=" N LEU B 311 " --> pdb=" O ASP B 307 " (cutoff:3.500A) Proline residue: B 316 - end of helix Processing helix chain 'B' and resid 326 through 338 Processing helix chain 'B' and resid 344 through 359 Processing helix chain 'B' and resid 370 through 390 Processing helix chain 'B' and resid 400 through 402 No H-bonds generated for 'chain 'B' and resid 400 through 402' Processing helix chain 'B' and resid 408 through 438 removed outlier: 3.523A pdb=" N GLU B 438 " --> pdb=" O ARG B 434 " (cutoff:3.500A) Processing helix chain 'B' and resid 443 through 448 Processing helix chain 'B' and resid 450 through 464 Processing helix chain 'B' and resid 487 through 495 Processing helix chain 'B' and resid 509 through 513 Processing helix chain 'B' and resid 515 through 519 Processing helix chain 'B' and resid 551 through 561 Processing helix chain 'B' and resid 567 through 569 No H-bonds generated for 'chain 'B' and resid 567 through 569' Processing helix chain 'B' and resid 592 through 607 Processing helix chain 'B' and resid 654 through 667 Processing helix chain 'B' and resid 680 through 687 Processing helix chain 'B' and resid 696 through 701 removed outlier: 3.725A pdb=" N ILE B 701 " --> pdb=" O GLU B 698 " (cutoff:3.500A) Processing helix chain 'B' and resid 706 through 710 Processing helix chain 'B' and resid 744 through 749 Processing helix chain 'B' and resid 752 through 756 Processing helix chain 'B' and resid 758 through 762 Processing helix chain 'B' and resid 763 through 774 Processing helix chain 'B' and resid 775 through 777 No H-bonds generated for 'chain 'B' and resid 775 through 777' Processing helix chain 'B' and resid 784 through 788 Processing helix chain 'B' and resid 808 through 813 Processing helix chain 'B' and resid 843 through 848 Processing helix chain 'B' and resid 995 through 999 Processing helix chain 'B' and resid 1014 through 1017 Processing helix chain 'B' and resid 1022 through 1039 removed outlier: 3.870A pdb=" N LEU B1026 " --> pdb=" O THR B1022 " (cutoff:3.500A) Processing helix chain 'B' and resid 1051 through 1062 removed outlier: 3.637A pdb=" N HIS B1062 " --> pdb=" O LEU B1058 " (cutoff:3.500A) Processing helix chain 'B' and resid 1098 through 1102 Processing helix chain 'B' and resid 1131 through 1142 Processing helix chain 'B' and resid 1143 through 1153 Processing helix chain 'B' and resid 1197 through 1210 Processing helix chain 'C' and resid 26 through 40 Processing helix chain 'C' and resid 59 through 69 Processing helix chain 'C' and resid 76 through 80 Processing helix chain 'C' and resid 82 through 86 Processing helix chain 'C' and resid 116 through 118 No H-bonds generated for 'chain 'C' and resid 116 through 118' Processing helix chain 'C' and resid 167 through 171 Processing helix chain 'C' and resid 196 through 201 Processing helix chain 'C' and resid 204 through 210 removed outlier: 3.754A pdb=" N GLU C 208 " --> pdb=" O LYS C 205 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N GLU C 210 " --> pdb=" O CYS C 207 " (cutoff:3.500A) Processing helix chain 'C' and resid 239 through 266 removed outlier: 3.557A pdb=" N ASP C 266 " --> pdb=" O LEU C 262 " (cutoff:3.500A) Processing helix chain 'D' and resid 51 through 73 Processing helix chain 'D' and resid 118 through 125 Processing helix chain 'D' and resid 139 through 151 Processing helix chain 'D' and resid 156 through 171 removed outlier: 4.170A pdb=" N VAL D 160 " --> pdb=" O ASP D 156 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N THR D 170 " --> pdb=" O LEU D 166 " (cutoff:3.500A) Processing helix chain 'D' and resid 173 through 181 removed outlier: 3.643A pdb=" N GLY D 181 " --> pdb=" O VAL D 177 " (cutoff:3.500A) Processing helix chain 'D' and resid 187 through 195 Processing helix chain 'D' and resid 196 through 199 removed outlier: 3.599A pdb=" N ASN D 199 " --> pdb=" O PRO D 196 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 196 through 199' Processing helix chain 'D' and resid 203 through 218 Processing helix chain 'E' and resid 4 through 26 Processing helix chain 'E' and resid 31 through 36 Processing helix chain 'E' and resid 38 through 46 Processing helix chain 'E' and resid 65 through 72 Processing helix chain 'E' and resid 91 through 103 removed outlier: 3.749A pdb=" N THR E 95 " --> pdb=" O LYS E 91 " (cutoff:3.500A) Processing helix chain 'E' and resid 117 through 124 Processing helix chain 'E' and resid 143 through 147 Processing helix chain 'E' and resid 157 through 169 Processing helix chain 'E' and resid 171 through 175 Processing helix chain 'E' and resid 182 through 189 Processing helix chain 'F' and resid 86 through 103 Processing helix chain 'F' and resid 116 through 127 Processing helix chain 'G' and resid 14 through 18 Processing helix chain 'G' and resid 21 through 32 Processing helix chain 'G' and resid 50 through 54 Processing helix chain 'G' and resid 112 through 115 Processing helix chain 'H' and resid 88 through 93 Processing helix chain 'J' and resid 17 through 27 Processing helix chain 'J' and resid 31 through 39 Processing helix chain 'J' and resid 43 through 52 Processing helix chain 'J' and resid 56 through 61 Processing helix chain 'K' and resid 5 through 10 Processing helix chain 'K' and resid 39 through 51 removed outlier: 3.926A pdb=" N LEU K 45 " --> pdb=" O THR K 41 " (cutoff:3.500A) Processing helix chain 'K' and resid 82 through 111 removed outlier: 3.603A pdb=" N LEU K 111 " --> pdb=" O THR K 107 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 1418 through 1419 Processing sheet with id=AA2, first strand: chain 'A' and resid 82 through 91 removed outlier: 6.871A pdb=" N THR A 237 " --> pdb=" O LEU A 86 " (cutoff:3.500A) removed outlier: 10.608A pdb=" N LYS A 88 " --> pdb=" O ILE A 235 " (cutoff:3.500A) removed outlier: 10.014A pdb=" N ILE A 235 " --> pdb=" O LYS A 88 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 173 through 177 removed outlier: 4.727A pdb=" N LEU A 181 " --> pdb=" O LEU A 202 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 343 through 345 removed outlier: 3.725A pdb=" N LEU B1128 " --> pdb=" O VAL A 345 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 1104 through 1106 Processing sheet with id=AA6, first strand: chain 'A' and resid 375 through 379 removed outlier: 3.718A pdb=" N TYR A 404 " --> pdb=" O GLU A 433 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N HIS A 435 " --> pdb=" O ALA A 402 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N ALA A 402 " --> pdb=" O HIS A 435 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 512 through 513 Processing sheet with id=AA8, first strand: chain 'A' and resid 540 through 541 Processing sheet with id=AA9, first strand: chain 'A' and resid 588 through 590 removed outlier: 6.925A pdb=" N LEU A 606 " --> pdb=" O ILE A 613 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 766 through 767 Processing sheet with id=AB2, first strand: chain 'A' and resid 849 through 850 removed outlier: 6.741A pdb=" N THR A 856 " --> pdb=" O ILE A 864 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 878 through 882 Processing sheet with id=AB4, first strand: chain 'A' and resid 1282 through 1292 removed outlier: 3.730A pdb=" N LEU A1116 " --> pdb=" O THR A1308 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 1141 through 1142 removed outlier: 7.097A pdb=" N THR A1141 " --> pdb=" O LEU A1273 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 1224 through 1228 removed outlier: 6.497A pdb=" N LEU A1192 " --> pdb=" O ILE A1152 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N ILE A1152 " --> pdb=" O LEU A1192 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N ARG A1194 " --> pdb=" O SER A1150 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N SER A1150 " --> pdb=" O ARG A1194 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N GLU A1196 " --> pdb=" O ILE A1148 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N TYR I 44 " --> pdb=" O ILE A1152 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 48 through 49 removed outlier: 4.490A pdb=" N ILE D 48 " --> pdb=" O ILE G 4 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N ARG G 75 " --> pdb=" O LEU G 49 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N CYS G 47 " --> pdb=" O VAL G 77 " (cutoff:3.500A) removed outlier: 7.225A pdb=" N PHE G 79 " --> pdb=" O ILE G 45 " (cutoff:3.500A) removed outlier: 5.805A pdb=" N ILE G 45 " --> pdb=" O PHE G 79 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 143 through 147 removed outlier: 5.361A pdb=" N VAL A1443 " --> pdb=" O ILE G 61 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLY G 59 " --> pdb=" O ILE A1445 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 69 through 73 removed outlier: 5.047A pdb=" N ASP B 131 " --> pdb=" O GLY B 93 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N ILE B 95 " --> pdb=" O PHE B 129 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N PHE B 129 " --> pdb=" O ILE B 95 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N VAL B 97 " --> pdb=" O GLY B 127 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N GLY B 127 " --> pdb=" O VAL B 97 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N ALA B 153 " --> pdb=" O THR B 136 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N GLU B 138 " --> pdb=" O LEU B 151 " (cutoff:3.500A) removed outlier: 5.294A pdb=" N LEU B 151 " --> pdb=" O GLU B 138 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 69 through 73 removed outlier: 5.047A pdb=" N ASP B 131 " --> pdb=" O GLY B 93 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N ILE B 95 " --> pdb=" O PHE B 129 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N PHE B 129 " --> pdb=" O ILE B 95 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N VAL B 97 " --> pdb=" O GLY B 127 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N GLY B 127 " --> pdb=" O VAL B 97 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N GLY B 168 " --> pdb=" O LEU B 128 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N VAL B 130 " --> pdb=" O PHE B 166 " (cutoff:3.500A) removed outlier: 5.543A pdb=" N PHE B 166 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N VAL B 132 " --> pdb=" O LYS B 164 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N LYS B 164 " --> pdb=" O VAL B 132 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 101 through 103 Processing sheet with id=AC3, first strand: chain 'B' and resid 203 through 205 Processing sheet with id=AC4, first strand: chain 'B' and resid 404 through 407 Processing sheet with id=AC5, first strand: chain 'B' and resid 224 through 227 removed outlier: 3.724A pdb=" N HIS B 236 " --> pdb=" O LEU B 258 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N GLN B 255 " --> pdb=" O THR B 272 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 544 through 545 Processing sheet with id=AC7, first strand: chain 'B' and resid 650 through 651 removed outlier: 3.721A pdb=" N GLU B 650 " --> pdb=" O GLU B 641 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 564 through 565 removed outlier: 5.452A pdb=" N TRP B 586 " --> pdb=" O VAL B 582 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N VAL B 582 " --> pdb=" O TRP B 586 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N GLY B 588 " --> pdb=" O VAL B 580 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N ARG B 579 " --> pdb=" O LEU B 624 " (cutoff:3.500A) removed outlier: 7.538A pdb=" N ILE B 626 " --> pdb=" O ARG B 579 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N PHE B 581 " --> pdb=" O ILE B 626 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 792 through 796 removed outlier: 6.949A pdb=" N PHE B 963 " --> pdb=" O VAL B 954 " (cutoff:3.500A) removed outlier: 4.922A pdb=" N VAL B 954 " --> pdb=" O PHE B 963 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N LYS B 965 " --> pdb=" O VAL B 952 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N VAL B 952 " --> pdb=" O LYS B 965 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N ARG B 967 " --> pdb=" O ASP B 950 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N THR B 971 " --> pdb=" O ASN B 946 " (cutoff:3.500A) removed outlier: 8.694A pdb=" N ASN B 946 " --> pdb=" O THR B 971 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 792 through 796 removed outlier: 6.949A pdb=" N PHE B 963 " --> pdb=" O VAL B 954 " (cutoff:3.500A) removed outlier: 4.922A pdb=" N VAL B 954 " --> pdb=" O PHE B 963 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N LYS B 965 " --> pdb=" O VAL B 952 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N VAL B 952 " --> pdb=" O LYS B 965 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N ARG B 967 " --> pdb=" O ASP B 950 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N THR B 971 " --> pdb=" O ASN B 946 " (cutoff:3.500A) removed outlier: 8.694A pdb=" N ASN B 946 " --> pdb=" O THR B 971 " (cutoff:3.500A) removed outlier: 5.153A pdb=" N VAL B 952 " --> pdb=" O LYS L 58 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 804 through 805 Processing sheet with id=AD3, first strand: chain 'B' and resid 1069 through 1070 removed outlier: 7.166A pdb=" N MET B 839 " --> pdb=" O GLY B 991 " (cutoff:3.500A) removed outlier: 6.099A pdb=" N THR B 993 " --> pdb=" O MET B 839 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N MET B 841 " --> pdb=" O THR B 993 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N PHE B1086 " --> pdb=" O ILE B 827 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 873 through 874 Processing sheet with id=AD5, first strand: chain 'B' and resid 1001 through 1002 Processing sheet with id=AD6, first strand: chain 'B' and resid 1158 through 1163 Processing sheet with id=AD7, first strand: chain 'B' and resid 1172 through 1174 Processing sheet with id=AD8, first strand: chain 'C' and resid 7 through 13 removed outlier: 5.383A pdb=" N VAL C 8 " --> pdb=" O SER C 23 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N SER C 23 " --> pdb=" O VAL C 8 " (cutoff:3.500A) removed outlier: 5.659A pdb=" N ILE C 10 " --> pdb=" O ILE C 21 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N ILE C 21 " --> pdb=" O ILE C 10 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N ALA C 175 " --> pdb=" O GLU C 233 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 119 through 120 removed outlier: 6.804A pdb=" N GLU C 152 " --> pdb=" O ASN C 54 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N ASN C 54 " --> pdb=" O GLU C 152 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N LYS C 154 " --> pdb=" O GLU C 52 " (cutoff:3.500A) removed outlier: 5.956A pdb=" N LYS C 160 " --> pdb=" O ILE C 46 " (cutoff:3.500A) removed outlier: 5.467A pdb=" N ILE C 46 " --> pdb=" O LYS C 160 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N GLY C 162 " --> pdb=" O LEU C 44 " (cutoff:3.500A) removed outlier: 5.315A pdb=" N LEU C 44 " --> pdb=" O GLY C 162 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N VAL L 65 " --> pdb=" O VAL C 51 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 111 through 114 removed outlier: 6.318A pdb=" N THR C 111 " --> pdb=" O LYS C 146 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N LYS C 146 " --> pdb=" O THR C 111 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N VAL C 113 " --> pdb=" O ILE C 144 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'D' and resid 36 through 38 Processing sheet with id=AE3, first strand: chain 'E' and resid 47 through 48 removed outlier: 4.986A pdb=" N ARG E 52 " --> pdb=" O ASP E 48 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'E' and resid 60 through 62 removed outlier: 6.398A pdb=" N TRP E 79 " --> pdb=" O ILE E 109 " (cutoff:3.500A) removed outlier: 7.561A pdb=" N VAL E 111 " --> pdb=" O TRP E 79 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N GLU E 81 " --> pdb=" O VAL E 111 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'E' and resid 152 through 155 removed outlier: 3.651A pdb=" N LYS E 152 " --> pdb=" O ILE E 199 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'G' and resid 86 through 95 removed outlier: 7.233A pdb=" N GLU G 100 " --> pdb=" O VAL G 92 " (cutoff:3.500A) removed outlier: 4.938A pdb=" N CYS G 94 " --> pdb=" O GLY G 98 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N GLY G 98 " --> pdb=" O CYS G 94 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N PHE G 99 " --> pdb=" O VAL G 110 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N VAL G 110 " --> pdb=" O PHE G 99 " (cutoff:3.500A) removed outlier: 7.296A pdb=" N LYS G 107 " --> pdb=" O ALA G 159 " (cutoff:3.500A) removed outlier: 7.506A pdb=" N GLY G 161 " --> pdb=" O LYS G 107 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N PHE G 109 " --> pdb=" O GLY G 161 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N HIS G 158 " --> pdb=" O CYS G 150 " (cutoff:3.500A) removed outlier: 5.294A pdb=" N CYS G 150 " --> pdb=" O HIS G 158 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N ILE G 160 " --> pdb=" O GLU G 148 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'G' and resid 120 through 122 removed outlier: 3.902A pdb=" N THR G 120 " --> pdb=" O GLN G 131 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'H' and resid 4 through 16 removed outlier: 6.565A pdb=" N GLU H 27 " --> pdb=" O SER H 13 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N VAL H 15 " --> pdb=" O ARG H 25 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N ARG H 25 " --> pdb=" O VAL H 15 " (cutoff:3.500A) removed outlier: 5.355A pdb=" N LEU H 122 " --> pdb=" O ASP H 41 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N LYS H 103 " --> pdb=" O TYR H 115 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N SER H 117 " --> pdb=" O ALA H 101 " (cutoff:3.500A) removed outlier: 5.681A pdb=" N ALA H 101 " --> pdb=" O SER H 117 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N LEU H 55 " --> pdb=" O ILE H 9 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N ILE H 9 " --> pdb=" O LEU H 55 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N VAL H 57 " --> pdb=" O ASP H 7 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N ASP H 7 " --> pdb=" O VAL H 57 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N ILE H 59 " --> pdb=" O LEU H 5 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'I' and resid 15 through 18 Processing sheet with id=AF1, first strand: chain 'I' and resid 70 through 71 removed outlier: 3.691A pdb=" N ASN I 83 " --> pdb=" O SER I 71 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'K' and resid 19 through 24 removed outlier: 4.592A pdb=" N ALA K 30 " --> pdb=" O ASP K 24 " (cutoff:3.500A) 1369 hydrogen bonds defined for protein. 3768 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 71 hydrogen bonds 142 hydrogen bond angles 0 basepair planarities 27 basepair parallelities 45 stacking parallelities Total time for adding SS restraints: 11.13 Time building geometry restraints manager: 3.89 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.46: 17586 1.46 - 1.71: 15174 1.71 - 1.96: 295 1.96 - 2.20: 1 2.20 - 2.45: 4 Bond restraints: 33060 Sorted by residual: bond pdb=" O4 DPO B1301 " pdb=" P2 DPO B1301 " ideal model delta sigma weight residual 2.766 1.647 1.119 2.00e-02 2.50e+03 3.13e+03 bond pdb=" O4 DPO B1301 " pdb=" P1 DPO B1301 " ideal model delta sigma weight residual 2.409 1.648 0.761 2.00e-02 2.50e+03 1.45e+03 bond pdb=" CD2 PHE D 70 " pdb=" CE2 PHE D 70 " ideal model delta sigma weight residual 1.382 2.449 -1.067 3.00e-02 1.11e+03 1.27e+03 bond pdb=" CA THR D 133 " pdb=" CB THR D 133 " ideal model delta sigma weight residual 1.529 2.071 -0.542 1.58e-02 4.01e+03 1.18e+03 bond pdb=" CD1 PHE D 70 " pdb=" CE1 PHE D 70 " ideal model delta sigma weight residual 1.382 2.354 -0.972 3.00e-02 1.11e+03 1.05e+03 ... (remaining 33055 not shown) Histogram of bond angle deviations from ideal: 0.00 - 16.06: 44859 16.06 - 32.13: 6 32.13 - 48.19: 2 48.19 - 64.26: 0 64.26 - 80.32: 2 Bond angle restraints: 44869 Sorted by residual: angle pdb=" O4 DPO B1301 " pdb=" P2 DPO B1301 " pdb=" O6 DPO B1301 " ideal model delta sigma weight residual 29.11 109.43 -80.32 3.00e+00 1.11e-01 7.17e+02 angle pdb=" O1 DPO B1301 " pdb=" P1 DPO B1301 " pdb=" O4 DPO B1301 " ideal model delta sigma weight residual 31.14 109.75 -78.61 3.00e+00 1.11e-01 6.87e+02 angle pdb=" CA THR D 133 " pdb=" CB THR D 133 " pdb=" CG2 THR D 133 " ideal model delta sigma weight residual 110.50 134.89 -24.39 1.70e+00 3.46e-01 2.06e+02 angle pdb=" P1 DPO B1301 " pdb=" O4 DPO B1301 " pdb=" P2 DPO B1301 " ideal model delta sigma weight residual 81.07 123.75 -42.68 3.00e+00 1.11e-01 2.02e+02 angle pdb=" CA THR D 133 " pdb=" CB THR D 133 " pdb=" OG1 THR D 133 " ideal model delta sigma weight residual 109.60 127.02 -17.42 1.50e+00 4.44e-01 1.35e+02 ... (remaining 44864 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.62: 19059 23.62 - 47.24: 816 47.24 - 70.86: 223 70.86 - 94.48: 21 94.48 - 118.10: 1 Dihedral angle restraints: 20120 sinusoidal: 8713 harmonic: 11407 Sorted by residual: dihedral pdb=" C THR D 133 " pdb=" N THR D 133 " pdb=" CA THR D 133 " pdb=" CB THR D 133 " ideal model delta harmonic sigma weight residual -122.00 -139.23 17.23 0 2.50e+00 1.60e-01 4.75e+01 dihedral pdb=" N THR D 133 " pdb=" C THR D 133 " pdb=" CA THR D 133 " pdb=" CB THR D 133 " ideal model delta harmonic sigma weight residual 123.40 136.90 -13.50 0 2.50e+00 1.60e-01 2.92e+01 dihedral pdb=" CA THR A 69 " pdb=" C THR A 69 " pdb=" N CYS A 70 " pdb=" CA CYS A 70 " ideal model delta harmonic sigma weight residual 180.00 157.44 22.56 0 5.00e+00 4.00e-02 2.04e+01 ... (remaining 20117 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.109: 4917 0.109 - 0.218: 132 0.218 - 0.327: 0 0.327 - 0.436: 0 0.436 - 0.544: 1 Chirality restraints: 5050 Sorted by residual: chirality pdb=" CB THR D 133 " pdb=" CA THR D 133 " pdb=" OG1 THR D 133 " pdb=" CG2 THR D 133 " both_signs ideal model delta sigma weight residual False 2.55 2.01 0.54 2.00e-01 2.50e+01 7.41e+00 chirality pdb=" CA ILE A1436 " pdb=" N ILE A1436 " pdb=" C ILE A1436 " pdb=" CB ILE A1436 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.17 2.00e-01 2.50e+01 7.16e-01 chirality pdb=" C3' G R 9 " pdb=" C4' G R 9 " pdb=" O3' G R 9 " pdb=" C2' G R 9 " both_signs ideal model delta sigma weight residual False -2.48 -2.31 -0.17 2.00e-01 2.50e+01 6.81e-01 ... (remaining 5047 not shown) Planarity restraints: 5623 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE D 70 " 0.010 2.00e-02 2.50e+03 3.81e-02 2.54e+01 pdb=" CG PHE D 70 " 0.014 2.00e-02 2.50e+03 pdb=" CD1 PHE D 70 " -0.047 2.00e-02 2.50e+03 pdb=" CD2 PHE D 70 " 0.032 2.00e-02 2.50e+03 pdb=" CE1 PHE D 70 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 PHE D 70 " -0.063 2.00e-02 2.50e+03 pdb=" CZ PHE D 70 " 0.050 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR D 133 " 0.014 2.00e-02 2.50e+03 2.76e-02 7.61e+00 pdb=" C THR D 133 " -0.048 2.00e-02 2.50e+03 pdb=" O THR D 133 " 0.018 2.00e-02 2.50e+03 pdb=" N THR D 134 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DG N 70 " 0.014 2.00e-02 2.50e+03 1.06e-02 3.38e+00 pdb=" N9 DG N 70 " -0.005 2.00e-02 2.50e+03 pdb=" C8 DG N 70 " -0.005 2.00e-02 2.50e+03 pdb=" N7 DG N 70 " -0.001 2.00e-02 2.50e+03 pdb=" C5 DG N 70 " -0.003 2.00e-02 2.50e+03 pdb=" C6 DG N 70 " -0.012 2.00e-02 2.50e+03 pdb=" O6 DG N 70 " 0.014 2.00e-02 2.50e+03 pdb=" N1 DG N 70 " 0.014 2.00e-02 2.50e+03 pdb=" C2 DG N 70 " -0.023 2.00e-02 2.50e+03 pdb=" N2 DG N 70 " 0.006 2.00e-02 2.50e+03 pdb=" N3 DG N 70 " 0.003 2.00e-02 2.50e+03 pdb=" C4 DG N 70 " -0.000 2.00e-02 2.50e+03 ... (remaining 5620 not shown) Histogram of nonbonded interaction distances: 1.97 - 2.61: 513 2.61 - 3.24: 31850 3.24 - 3.87: 69885 3.87 - 4.51: 96286 4.51 - 5.14: 146300 Nonbonded interactions: 344834 Sorted by model distance: nonbonded pdb=" OD1 ASP A 481 " pdb="MG MG A1801 " model vdw 1.974 2.170 nonbonded pdb="MG MG A1801 " pdb=" O HOH A1914 " model vdw 1.981 2.170 nonbonded pdb=" O LYS B 801 " pdb=" OG1 THR J 52 " model vdw 2.080 3.040 nonbonded pdb=" OD1 ASP A 485 " pdb="MG MG A1801 " model vdw 2.095 2.170 nonbonded pdb="MG MG A1801 " pdb=" O HOH R 101 " model vdw 2.163 2.170 ... (remaining 344829 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: 7.240 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.040 Extract box with map and model: 0.910 Check model and map are aligned: 0.130 Set scattering table: 0.140 Process input model: 43.930 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: 0.010 Load rotamer database and sin/cos tables:7.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 59.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6626 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 : 0.014 1.119 33092 Z= 0.605 Angle : 0.844 80.321 44914 Z= 0.403 Chirality : 0.044 0.544 5050 Planarity : 0.004 0.044 5623 Dihedral : 13.962 118.100 12732 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.86 % Favored : 97.06 % Rotamer: Outliers : 3.67 % Allowed : 5.52 % Favored : 90.81 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 2.37 % 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: 0.43 (0.14), residues: 3879 helix: 1.11 (0.14), residues: 1326 sheet: 0.26 (0.20), residues: 642 loop : -0.21 (0.15), residues: 1911 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG J 48 TYR 0.011 0.001 TYR A1349 PHE 0.063 0.002 PHE D 70 TRP 0.011 0.001 TRP B 31 HIS 0.007 0.001 HIS A 659 Details of bonding type rmsd/Z covalent geometry : bond 0.01426 / 0.60 (33060) covalent geometry : angle 0.84148 / 0.40 (44869) hydrogen bonds : bond 0.16970 / 11.26 ( 1408) hydrogen bonds : angle 6.50817 / 4.54 ( 3910) metal coordination : bond 0.00262 / 0.16 ( 32) metal coordination : angle 2.18764 / 1.42 ( 45) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7758 Ramachandran restraints generated. 3879 Oldfield, 0 Emsley, 3879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7758 Ramachandran restraints generated. 3879 Oldfield, 0 Emsley, 3879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 695 residues out of total 3459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 568 time to evaluate : 1.308 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 PHE cc_start: 0.7571 (OUTLIER) cc_final: 0.6170 (t80) REVERT: A 41 MET cc_start: 0.5241 (mmt) cc_final: 0.4419 (mpt) REVERT: A 50 ILE cc_start: 0.7730 (OUTLIER) cc_final: 0.7241 (tp) REVERT: A 68 GLN cc_start: 0.6573 (tt0) cc_final: 0.5406 (mp-120) REVERT: A 74 MET cc_start: 0.7443 (mtt) cc_final: 0.7093 (mmt) REVERT: A 75 ASN cc_start: 0.7536 (t0) cc_final: 0.7285 (t0) REVERT: A 88 LYS cc_start: 0.7000 (mttt) cc_final: 0.6639 (mttp) REVERT: A 129 LYS cc_start: 0.6701 (mtpt) cc_final: 0.5731 (ptmm) REVERT: A 170 THR cc_start: 0.7211 (m) cc_final: 0.6735 (t) REVERT: A 175 ARG cc_start: 0.6775 (ttp80) cc_final: 0.6277 (mtp-110) REVERT: A 180 LYS cc_start: 0.7416 (mtmt) cc_final: 0.6737 (mttp) REVERT: A 280 GLU cc_start: 0.6641 (mt-10) cc_final: 0.6372 (mt-10) REVERT: A 390 GLN cc_start: 0.5694 (tp40) cc_final: 0.5481 (tp40) REVERT: A 393 ARG cc_start: 0.6012 (ttm110) cc_final: 0.5565 (mmt90) REVERT: A 398 GLU cc_start: 0.6108 (tt0) cc_final: 0.5442 (tm-30) REVERT: A 437 MET cc_start: 0.6484 (ptt) cc_final: 0.6070 (mtp) REVERT: A 455 MET cc_start: 0.7948 (ttm) cc_final: 0.7699 (ttt) REVERT: A 472 LEU cc_start: 0.6333 (OUTLIER) cc_final: 0.6050 (mt) REVERT: A 494 SER cc_start: 0.6896 (m) cc_final: 0.6226 (t) REVERT: A 496 GLU cc_start: 0.6045 (tt0) cc_final: 0.4534 (tp30) REVERT: A 497 THR cc_start: 0.7108 (m) cc_final: 0.6699 (p) REVERT: A 589 GLN cc_start: 0.7735 (tt0) cc_final: 0.7445 (tt0) REVERT: A 620 LYS cc_start: 0.6846 (mtpt) cc_final: 0.6487 (mtmt) REVERT: A 644 LYS cc_start: 0.6180 (mttt) cc_final: 0.5504 (mmmt) REVERT: A 685 GLU cc_start: 0.5772 (mt-10) cc_final: 0.4999 (tm-30) REVERT: A 688 LYS cc_start: 0.6540 (mmtt) cc_final: 0.6213 (tptt) REVERT: A 696 GLU cc_start: 0.6085 (tm-30) cc_final: 0.5706 (tm-30) REVERT: A 712 GLU cc_start: 0.6024 (tt0) cc_final: 0.4884 (tm-30) REVERT: A 720 ARG cc_start: 0.6054 (ttp80) cc_final: 0.5765 (ttm110) REVERT: A 724 GLU cc_start: 0.6123 (mt-10) cc_final: 0.4935 (mm-30) REVERT: A 734 GLU cc_start: 0.5979 (tt0) cc_final: 0.5464 (tm-30) REVERT: A 771 GLU cc_start: 0.7180 (mt-10) cc_final: 0.6768 (mt-10) REVERT: A 822 GLU cc_start: 0.6498 (OUTLIER) cc_final: 0.6004 (mt-10) REVERT: A 833 GLU cc_start: 0.6700 (OUTLIER) cc_final: 0.6000 (mt-10) REVERT: A 838 GLN cc_start: 0.6767 (OUTLIER) cc_final: 0.6507 (tp40) REVERT: A 889 SER cc_start: 0.6859 (t) cc_final: 0.6557 (p) REVERT: A 890 ASP cc_start: 0.6083 (OUTLIER) cc_final: 0.5849 (m-30) REVERT: A 912 LEU cc_start: 0.6474 (OUTLIER) cc_final: 0.6221 (pp) REVERT: A 924 LYS cc_start: 0.5756 (OUTLIER) cc_final: 0.5213 (mmtm) REVERT: A 931 GLU cc_start: 0.5470 (tt0) cc_final: 0.5005 (mm-30) REVERT: A 961 ARG cc_start: 0.5539 (mmt90) cc_final: 0.4971 (mtm180) REVERT: A 969 GLN cc_start: 0.6396 (mm110) cc_final: 0.5382 (tp40) REVERT: A 1005 GLU cc_start: 0.6164 (tp30) cc_final: 0.5960 (mm-30) REVERT: A 1012 ARG cc_start: 0.5644 (ptp90) cc_final: 0.5356 (mtt90) REVERT: A 1036 ARG cc_start: 0.6955 (mtt-85) cc_final: 0.6699 (mtp180) REVERT: A 1062 GLU cc_start: 0.6514 (tp30) cc_final: 0.6060 (tp30) REVERT: A 1077 THR cc_start: 0.7076 (m) cc_final: 0.6774 (p) REVERT: A 1135 ARG cc_start: 0.6069 (ttt180) cc_final: 0.5325 (ttt180) REVERT: A 1285 MET cc_start: 0.6873 (mmt) cc_final: 0.6637 (mmm) REVERT: A 1304 TRP cc_start: 0.7170 (m100) cc_final: 0.6898 (m100) REVERT: A 1315 GLU cc_start: 0.6442 (tt0) cc_final: 0.6204 (mt-10) REVERT: A 1407 GLU cc_start: 0.5550 (mp0) cc_final: 0.5035 (mp0) REVERT: A 1420 ASP cc_start: 0.6375 (t0) cc_final: 0.6171 (t0) REVERT: B 21 GLU cc_start: 0.6632 (pt0) cc_final: 0.6096 (mt-10) REVERT: B 43 LEU cc_start: 0.7957 (mt) cc_final: 0.7572 (mm) REVERT: B 101 MET cc_start: 0.6975 (mtt) cc_final: 0.6668 (mtt) REVERT: B 115 GLN cc_start: 0.5154 (tp40) cc_final: 0.4815 (tm-30) REVERT: B 191 LYS cc_start: 0.6566 (mttt) cc_final: 0.6326 (mtmt) REVERT: B 199 MET cc_start: 0.6698 (mmt) cc_final: 0.4917 (pmm) REVERT: B 222 ILE cc_start: 0.6329 (mt) cc_final: 0.5933 (mm) REVERT: B 241 ARG cc_start: 0.6357 (mtt180) cc_final: 0.5761 (mtm-85) REVERT: B 357 GLN cc_start: 0.7415 (tt0) cc_final: 0.6947 (tt0) REVERT: B 359 GLU cc_start: 0.7319 (mp0) cc_final: 0.7034 (mm-30) REVERT: B 393 LYS cc_start: 0.6633 (ttpt) cc_final: 0.5752 (mmtm) REVERT: B 398 ARG cc_start: 0.6742 (mtt-85) cc_final: 0.6057 (ttp-170) REVERT: B 422 LYS cc_start: 0.5866 (mmtm) cc_final: 0.4851 (tmmm) REVERT: B 423 LYS cc_start: 0.6421 (tttp) cc_final: 0.5932 (ttmm) REVERT: B 451 LYS cc_start: 0.6487 (mtmt) cc_final: 0.5731 (tmtt) REVERT: B 468 GLU cc_start: 0.6560 (mp0) cc_final: 0.5499 (mm-30) REVERT: B 531 GLN cc_start: 0.7003 (pm20) cc_final: 0.6646 (pp30) REVERT: B 598 GLU cc_start: 0.6812 (tp30) cc_final: 0.6596 (mm-30) REVERT: B 603 LEU cc_start: 0.7183 (OUTLIER) cc_final: 0.6977 (mt) REVERT: B 621 GLU cc_start: 0.6626 (tp30) cc_final: 0.6091 (mm-30) REVERT: B 622 LYS cc_start: 0.6425 (mtmt) cc_final: 0.5830 (mttp) REVERT: B 637 LEU cc_start: 0.7082 (OUTLIER) cc_final: 0.6674 (pp) REVERT: B 641 GLU cc_start: 0.7233 (tt0) cc_final: 0.6246 (tp30) REVERT: B 665 GLU cc_start: 0.6530 (tt0) cc_final: 0.6278 (tt0) REVERT: B 727 LYS cc_start: 0.6656 (mttp) cc_final: 0.6095 (mtmt) REVERT: B 873 THR cc_start: 0.5427 (m) cc_final: 0.4845 (t) REVERT: B 880 THR cc_start: 0.6270 (OUTLIER) cc_final: 0.6029 (p) REVERT: B 889 THR cc_start: 0.7064 (m) cc_final: 0.6486 (t) REVERT: B 896 ASP cc_start: 0.5484 (t0) cc_final: 0.5218 (p0) REVERT: B 946 ASN cc_start: 0.5677 (OUTLIER) cc_final: 0.5426 (p0) REVERT: B 962 LYS cc_start: 0.6216 (tttt) cc_final: 0.5410 (ttmm) REVERT: B 1057 LYS cc_start: 0.6334 (mttt) cc_final: 0.5854 (tttm) REVERT: B 1112 GLN cc_start: 0.6987 (mt0) cc_final: 0.6665 (mt0) REVERT: B 1124 ARG cc_start: 0.6145 (mtm-85) cc_final: 0.5519 (mtp85) REVERT: B 1188 LYS cc_start: 0.7314 (mtmm) cc_final: 0.7028 (mttt) REVERT: B 1219 ASP cc_start: 0.6918 (OUTLIER) cc_final: 0.6435 (p0) REVERT: C 12 GLU cc_start: 0.6552 (mt-10) cc_final: 0.5464 (tm-30) REVERT: C 19 ASP cc_start: 0.7365 (t0) cc_final: 0.7014 (t70) REVERT: C 40 GLU cc_start: 0.7345 (OUTLIER) cc_final: 0.6998 (mt-10) REVERT: C 50 GLU cc_start: 0.6134 (mt-10) cc_final: 0.5831 (mt-10) REVERT: C 81 GLU cc_start: 0.6355 (tt0) cc_final: 0.5949 (mt-10) REVERT: C 93 ASP cc_start: 0.6571 (m-30) cc_final: 0.6282 (m-30) REVERT: C 94 LYS cc_start: 0.6737 (mtmt) cc_final: 0.6491 (mtmm) REVERT: C 100 THR cc_start: 0.7391 (m) cc_final: 0.6914 (p) REVERT: C 106 GLU cc_start: 0.6832 (mt-10) cc_final: 0.6027 (mm-30) REVERT: C 129 ILE cc_start: 0.6688 (tt) cc_final: 0.6422 (tp) REVERT: C 152 GLU cc_start: 0.7032 (tt0) cc_final: 0.5843 (tm-30) REVERT: C 154 LYS cc_start: 0.6760 (ttpp) cc_final: 0.6205 (tttp) REVERT: C 179 GLU cc_start: 0.6926 (tt0) cc_final: 0.6352 (tm-30) REVERT: C 199 LYS cc_start: 0.6431 (ttmt) cc_final: 0.6032 (mtmt) REVERT: C 224 GLN cc_start: 0.6006 (mt0) cc_final: 0.5730 (mm110) REVERT: E 33 GLU cc_start: 0.7318 (tt0) cc_final: 0.6928 (tm-30) REVERT: E 40 GLU cc_start: 0.5986 (mp0) cc_final: 0.5388 (mm-30) REVERT: E 57 MET cc_start: 0.6703 (mtm) cc_final: 0.6450 (mmm) REVERT: E 78 LEU cc_start: 0.7900 (OUTLIER) cc_final: 0.7691 (tt) REVERT: E 113 GLN cc_start: 0.6832 (OUTLIER) cc_final: 0.5946 (mp10) REVERT: E 162 ARG cc_start: 0.5874 (mtp-110) cc_final: 0.5534 (ttp-110) REVERT: E 192 ARG cc_start: 0.6951 (ttt180) cc_final: 0.6355 (ttp80) REVERT: F 112 GLU cc_start: 0.6857 (OUTLIER) cc_final: 0.6416 (mt-10) REVERT: F 119 ARG cc_start: 0.5592 (tpp80) cc_final: 0.5313 (mmm160) REVERT: F 128 LYS cc_start: 0.6608 (mmtp) cc_final: 0.6245 (mmmm) REVERT: F 129 LYS cc_start: 0.7433 (mmtm) cc_final: 0.7089 (mmtm) REVERT: F 149 GLU cc_start: 0.6488 (tt0) cc_final: 0.5924 (pm20) REVERT: G 77 VAL cc_start: 0.4850 (OUTLIER) cc_final: 0.4586 (t) REVERT: H 128 ASN cc_start: 0.6913 (t0) cc_final: 0.6573 (t0) REVERT: H 129 TYR cc_start: 0.6722 (p90) cc_final: 0.6254 (p90) REVERT: H 145 ARG cc_start: 0.7728 (ptt-90) cc_final: 0.7453 (ptp90) REVERT: I 51 ASN cc_start: 0.4013 (OUTLIER) cc_final: 0.2625 (p0) REVERT: I 70 ARG cc_start: 0.4041 (mtt90) cc_final: 0.3834 (mtt90) REVERT: I 90 GLN cc_start: 0.4870 (mm110) cc_final: 0.4489 (mt0) REVERT: J 19 GLU cc_start: 0.6435 (mm-30) cc_final: 0.6187 (mt-10) REVERT: J 26 GLN cc_start: 0.6430 (tt0) cc_final: 0.6025 (mp10) REVERT: K 20 LYS cc_start: 0.6945 (tttp) cc_final: 0.6364 (ttpm) REVERT: K 54 ARG cc_start: 0.6298 (mtm180) cc_final: 0.5993 (mmp80) REVERT: K 55 LYS cc_start: 0.7049 (mttm) cc_final: 0.6825 (mttp) REVERT: K 102 LYS cc_start: 0.6329 (ttpt) cc_final: 0.5838 (ttpt) outliers start: 127 outliers final: 42 residues processed: 670 average time/residue: 0.7975 time to fit residues: 630.3912 Evaluate side-chains 520 residues out of total 3459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 458 time to evaluate : 1.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 THR Chi-restraints excluded: chain A residue 22 PHE Chi-restraints excluded: chain A residue 50 ILE Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 169 ASN Chi-restraints excluded: chain A residue 380 VAL Chi-restraints excluded: chain A residue 472 LEU Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 703 THR Chi-restraints excluded: chain A residue 822 GLU Chi-restraints excluded: chain A residue 833 GLU Chi-restraints excluded: chain A residue 838 GLN Chi-restraints excluded: chain A residue 890 ASP Chi-restraints excluded: chain A residue 907 THR Chi-restraints excluded: chain A residue 912 LEU Chi-restraints excluded: chain A residue 924 LYS Chi-restraints excluded: chain A residue 1113 THR Chi-restraints excluded: chain A residue 1128 GLN Chi-restraints excluded: chain A residue 1231 ASP Chi-restraints excluded: chain A residue 1438 THR Chi-restraints excluded: chain B residue 58 THR Chi-restraints excluded: chain B residue 77 HIS Chi-restraints excluded: chain B residue 103 ASN Chi-restraints excluded: chain B residue 245 GLU Chi-restraints excluded: chain B residue 298 LEU Chi-restraints excluded: chain B residue 343 ILE Chi-restraints excluded: chain B residue 498 THR Chi-restraints excluded: chain B residue 547 VAL Chi-restraints excluded: chain B residue 603 LEU Chi-restraints excluded: chain B residue 637 LEU Chi-restraints excluded: chain B residue 880 THR Chi-restraints excluded: chain B residue 903 VAL Chi-restraints excluded: chain B residue 936 ASP Chi-restraints excluded: chain B residue 946 ASN Chi-restraints excluded: chain B residue 955 THR Chi-restraints excluded: chain B residue 1150 ARG Chi-restraints excluded: chain B residue 1160 VAL Chi-restraints excluded: chain B residue 1219 ASP Chi-restraints excluded: chain B residue 1223 ASP Chi-restraints excluded: chain C residue 18 VAL Chi-restraints excluded: chain C residue 25 VAL Chi-restraints excluded: chain C residue 40 GLU Chi-restraints excluded: chain C residue 43 THR Chi-restraints excluded: chain C residue 53 THR Chi-restraints excluded: chain C residue 189 THR Chi-restraints excluded: chain D residue 133 THR Chi-restraints excluded: chain D residue 170 THR Chi-restraints excluded: chain D residue 176 GLU Chi-restraints excluded: chain D residue 221 TYR Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain E residue 113 GLN Chi-restraints excluded: chain E residue 196 VAL Chi-restraints excluded: chain F residue 77 ASP Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 112 GLU Chi-restraints excluded: chain F residue 133 VAL Chi-restraints excluded: chain G residue 50 ASP Chi-restraints excluded: chain G residue 77 VAL Chi-restraints excluded: chain G residue 92 VAL Chi-restraints excluded: chain I residue 48 LEU Chi-restraints excluded: chain I residue 51 ASN Chi-restraints excluded: chain K residue 31 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 197 optimal weight: 9.9990 chunk 388 optimal weight: 40.0000 chunk 215 optimal weight: 0.8980 chunk 20 optimal weight: 3.9990 chunk 132 optimal weight: 5.9990 chunk 261 optimal weight: 3.9990 chunk 248 optimal weight: 5.9990 chunk 207 optimal weight: 4.9990 chunk 155 optimal weight: 4.9990 chunk 244 optimal weight: 1.9990 chunk 183 optimal weight: 3.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 118 HIS A 287 HIS A 316 GLN A 425 GLN A 427 GLN A 445 ASN A 515 GLN A 626 ASN A 631 HIS A 717 ASN A 723 ASN A 736 ASN A 786 HIS A 877 HIS A1033 GLN A1052 GLN ** A1188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1278 ASN B 76 GLN B 110 HIS B 121 ASN B 350 GLN B 357 GLN B 395 GLN B 415 GLN B 443 ASN B 572 HIS B 740 HIS B 878 GLN B 881 ASN ** B 957 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 984 HIS B 986 GLN B1025 HIS B1076 HIS B1178 ASN B1193 GLN C 264 GLN ** D 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 157 GLN E 8 ASN E 101 GLN E 179 GLN G 57 GLN H 33 GLN H 83 GLN H 131 ASN H 134 ASN I 89 GLN L 53 HIS Total number of N/Q/H flips: 47 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4080 r_free = 0.4080 target = 0.188824 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.136411 restraints weight = 27624.440| |-----------------------------------------------------------------------------| r_work (start): 0.3520 rms_B_bonded: 2.49 r_work: 0.2951 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.2951 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8811 moved from start: 0.1247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.013 1.065 33092 Z= 0.499 Angle : 0.718 24.399 44914 Z= 0.386 Chirality : 0.050 0.559 5050 Planarity : 0.006 0.075 5623 Dihedral : 13.331 123.236 4997 Min Nonbonded Distance : 1.882 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.76 % Favored : 96.18 % Rotamer: Outliers : 3.61 % Allowed : 8.73 % Favored : 87.66 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 2.37 % 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: 0.24 (0.13), residues: 3879 helix: 0.98 (0.14), residues: 1345 sheet: 0.10 (0.20), residues: 607 loop : -0.33 (0.14), residues: 1927 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 123 TYR 0.022 0.002 TYR B 486 PHE 0.064 0.003 PHE D 70 TRP 0.018 0.002 TRP B 31 HIS 0.012 0.002 HIS A 287 Details of bonding type rmsd/Z covalent geometry : bond 0.01298 / 0.50 (33060) covalent geometry : angle 0.70969 / 0.39 (44869) hydrogen bonds : bond 0.06196 / 4.03 ( 1408) hydrogen bonds : angle 5.29146 / 3.70 ( 3910) metal coordination : bond 0.00488 / 0.33 ( 32) metal coordination : angle 3.56077 / 2.26 ( 45) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7758 Ramachandran restraints generated. 3879 Oldfield, 0 Emsley, 3879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7758 Ramachandran restraints generated. 3879 Oldfield, 0 Emsley, 3879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 579 residues out of total 3459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 454 time to evaluate : 1.263 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 PHE cc_start: 0.8985 (OUTLIER) cc_final: 0.7944 (t80) REVERT: A 41 MET cc_start: 0.5904 (mmt) cc_final: 0.5681 (mmm) REVERT: A 50 ILE cc_start: 0.8587 (OUTLIER) cc_final: 0.8131 (tp) REVERT: A 68 GLN cc_start: 0.6669 (tt0) cc_final: 0.6059 (mp-120) REVERT: A 123 ARG cc_start: 0.7477 (mtt90) cc_final: 0.6949 (mtm110) REVERT: A 129 LYS cc_start: 0.7830 (mtpt) cc_final: 0.7239 (ptmm) REVERT: A 170 THR cc_start: 0.7650 (m) cc_final: 0.7301 (t) REVERT: A 175 ARG cc_start: 0.7621 (ttp80) cc_final: 0.7354 (mtp-110) REVERT: A 180 LYS cc_start: 0.8322 (mtmt) cc_final: 0.7895 (mttp) REVERT: A 261 ASP cc_start: 0.8438 (m-30) cc_final: 0.8020 (m-30) REVERT: A 280 GLU cc_start: 0.7087 (mt-10) cc_final: 0.6737 (mt-10) REVERT: A 333 GLU cc_start: 0.8487 (OUTLIER) cc_final: 0.7964 (mm-30) REVERT: A 398 GLU cc_start: 0.7759 (tt0) cc_final: 0.7554 (tm-30) REVERT: A 472 LEU cc_start: 0.8990 (OUTLIER) cc_final: 0.8536 (mt) REVERT: A 598 LEU cc_start: 0.8044 (OUTLIER) cc_final: 0.7819 (tp) REVERT: A 644 LYS cc_start: 0.8554 (mttt) cc_final: 0.8296 (mmmt) REVERT: A 685 GLU cc_start: 0.7832 (mt-10) cc_final: 0.7340 (tm-30) REVERT: A 696 GLU cc_start: 0.7769 (tm-30) cc_final: 0.7485 (tm-30) REVERT: A 712 GLU cc_start: 0.7350 (tt0) cc_final: 0.6295 (tm-30) REVERT: A 734 GLU cc_start: 0.7844 (tt0) cc_final: 0.7628 (tm-30) REVERT: A 822 GLU cc_start: 0.8262 (OUTLIER) cc_final: 0.7980 (mt-10) REVERT: A 889 SER cc_start: 0.8147 (t) cc_final: 0.7942 (p) REVERT: A 912 LEU cc_start: 0.7561 (OUTLIER) cc_final: 0.7330 (pp) REVERT: A 924 LYS cc_start: 0.6441 (OUTLIER) cc_final: 0.5869 (mmtm) REVERT: A 931 GLU cc_start: 0.7322 (tt0) cc_final: 0.7052 (mm-30) REVERT: A 961 ARG cc_start: 0.7369 (mmt90) cc_final: 0.7105 (mtm180) REVERT: A 969 GLN cc_start: 0.7477 (mm110) cc_final: 0.6838 (tp40) REVERT: A 1062 GLU cc_start: 0.8673 (tp30) cc_final: 0.8448 (tp30) REVERT: A 1132 LYS cc_start: 0.7217 (OUTLIER) cc_final: 0.6869 (mtmt) REVERT: A 1135 ARG cc_start: 0.6889 (ttt180) cc_final: 0.5991 (ttt180) REVERT: A 1304 TRP cc_start: 0.7492 (m100) cc_final: 0.7165 (m100) REVERT: A 1407 GLU cc_start: 0.8326 (mp0) cc_final: 0.8043 (mp0) REVERT: A 1444 MET cc_start: 0.8705 (OUTLIER) cc_final: 0.7283 (mtm) REVERT: B 21 GLU cc_start: 0.7926 (pt0) cc_final: 0.7567 (mt-10) REVERT: B 46 GLN cc_start: 0.8164 (mp-120) cc_final: 0.7550 (pm20) REVERT: B 199 MET cc_start: 0.8374 (mmt) cc_final: 0.7601 (pmm) REVERT: B 357 GLN cc_start: 0.8109 (tt0) cc_final: 0.7653 (tt0) REVERT: B 393 LYS cc_start: 0.7647 (ttpt) cc_final: 0.6966 (mmtp) REVERT: B 398 ARG cc_start: 0.7885 (mtt-85) cc_final: 0.7445 (ttp-170) REVERT: B 422 LYS cc_start: 0.7629 (mmtm) cc_final: 0.7048 (mttp) REVERT: B 423 LYS cc_start: 0.8412 (tttp) cc_final: 0.8005 (ttmm) REVERT: B 451 LYS cc_start: 0.7960 (mtmt) cc_final: 0.7672 (tmtt) REVERT: B 468 GLU cc_start: 0.7591 (mp0) cc_final: 0.7014 (mm-30) REVERT: B 595 ARG cc_start: 0.7869 (ttt180) cc_final: 0.7657 (mpp-170) REVERT: B 621 GLU cc_start: 0.7941 (tp30) cc_final: 0.7672 (mm-30) REVERT: B 622 LYS cc_start: 0.8018 (mtmt) cc_final: 0.7681 (mttp) REVERT: B 650 GLU cc_start: 0.6830 (OUTLIER) cc_final: 0.6231 (tm-30) REVERT: B 665 GLU cc_start: 0.7985 (tt0) cc_final: 0.7714 (tt0) REVERT: B 696 GLU cc_start: 0.8305 (OUTLIER) cc_final: 0.7956 (tp30) REVERT: B 727 LYS cc_start: 0.8696 (mttp) cc_final: 0.8336 (mttm) REVERT: B 873 THR cc_start: 0.7382 (m) cc_final: 0.7119 (t) REVERT: B 889 THR cc_start: 0.8085 (m) cc_final: 0.7840 (t) REVERT: B 1057 LYS cc_start: 0.8723 (mttt) cc_final: 0.8451 (mmtm) REVERT: B 1124 ARG cc_start: 0.8038 (mtm-85) cc_final: 0.7655 (mtp85) REVERT: B 1219 ASP cc_start: 0.8637 (OUTLIER) cc_final: 0.8120 (p0) REVERT: C 12 GLU cc_start: 0.8269 (mt-10) cc_final: 0.7866 (tm-30) REVERT: C 106 GLU cc_start: 0.8101 (mt-10) cc_final: 0.7842 (mm-30) REVERT: C 152 GLU cc_start: 0.8737 (tt0) cc_final: 0.8418 (tm-30) REVERT: D 1 MET cc_start: 0.2303 (pmm) cc_final: 0.2057 (pmt) REVERT: E 33 GLU cc_start: 0.7648 (tt0) cc_final: 0.7389 (tm-30) REVERT: E 40 GLU cc_start: 0.6357 (mp0) cc_final: 0.5676 (mm-30) REVERT: E 57 MET cc_start: 0.7198 (mtm) cc_final: 0.6830 (mmm) REVERT: E 78 LEU cc_start: 0.8753 (OUTLIER) cc_final: 0.8478 (tt) REVERT: F 103 MET cc_start: 0.8358 (OUTLIER) cc_final: 0.8091 (mtp) REVERT: F 112 GLU cc_start: 0.7286 (OUTLIER) cc_final: 0.6993 (mt-10) REVERT: F 123 LYS cc_start: 0.8800 (tttm) cc_final: 0.8560 (tttt) REVERT: F 149 GLU cc_start: 0.8253 (tt0) cc_final: 0.8025 (pm20) REVERT: H 129 TYR cc_start: 0.7866 (p90) cc_final: 0.7609 (p90) REVERT: I 90 GLN cc_start: 0.6562 (mm110) cc_final: 0.6093 (mt0) REVERT: K 20 LYS cc_start: 0.8872 (tttp) cc_final: 0.8662 (ttpm) outliers start: 125 outliers final: 63 residues processed: 545 average time/residue: 0.8050 time to fit residues: 516.2926 Evaluate side-chains 503 residues out of total 3459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 424 time to evaluate : 1.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 THR Chi-restraints excluded: chain A residue 22 PHE Chi-restraints excluded: chain A residue 50 ILE Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 333 GLU Chi-restraints excluded: chain A residue 380 VAL Chi-restraints excluded: chain A residue 472 LEU Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 598 LEU Chi-restraints excluded: chain A residue 703 THR Chi-restraints excluded: chain A residue 822 GLU Chi-restraints excluded: chain A residue 833 GLU Chi-restraints excluded: chain A residue 907 THR Chi-restraints excluded: chain A residue 912 LEU Chi-restraints excluded: chain A residue 924 LYS Chi-restraints excluded: chain A residue 983 ILE Chi-restraints excluded: chain A residue 984 LYS Chi-restraints excluded: chain A residue 1112 LYS Chi-restraints excluded: chain A residue 1132 LYS Chi-restraints excluded: chain A residue 1283 VAL Chi-restraints excluded: chain A residue 1322 ILE Chi-restraints excluded: chain A residue 1438 THR Chi-restraints excluded: chain A residue 1444 MET Chi-restraints excluded: chain B residue 58 THR Chi-restraints excluded: chain B residue 77 HIS Chi-restraints excluded: chain B residue 152 ILE Chi-restraints excluded: chain B residue 298 LEU Chi-restraints excluded: chain B residue 305 VAL Chi-restraints excluded: chain B residue 343 ILE Chi-restraints excluded: chain B residue 498 THR Chi-restraints excluded: chain B residue 508 LEU Chi-restraints excluded: chain B residue 547 VAL Chi-restraints excluded: chain B residue 619 ILE Chi-restraints excluded: chain B residue 650 GLU Chi-restraints excluded: chain B residue 696 GLU Chi-restraints excluded: chain B residue 751 VAL Chi-restraints excluded: chain B residue 839 MET Chi-restraints excluded: chain B residue 903 VAL Chi-restraints excluded: chain B residue 908 GLU Chi-restraints excluded: chain B residue 936 ASP Chi-restraints excluded: chain B residue 955 THR Chi-restraints excluded: chain B residue 1150 ARG Chi-restraints excluded: chain B residue 1160 VAL Chi-restraints excluded: chain B residue 1178 ASN Chi-restraints excluded: chain B residue 1219 ASP Chi-restraints excluded: chain C residue 18 VAL Chi-restraints excluded: chain C residue 25 VAL Chi-restraints excluded: chain C residue 43 THR Chi-restraints excluded: chain C residue 53 THR Chi-restraints excluded: chain C residue 56 THR Chi-restraints excluded: chain C residue 102 GLN Chi-restraints excluded: chain C residue 121 VAL Chi-restraints excluded: chain C residue 189 THR Chi-restraints excluded: chain C residue 250 THR Chi-restraints excluded: chain C residue 259 LEU Chi-restraints excluded: chain D residue 38 ILE Chi-restraints excluded: chain D residue 133 THR Chi-restraints excluded: chain D residue 170 THR Chi-restraints excluded: chain D residue 176 GLU Chi-restraints excluded: chain D residue 221 TYR Chi-restraints excluded: chain E residue 48 ASP Chi-restraints excluded: chain E residue 70 SER Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain E residue 207 ARG Chi-restraints excluded: chain F residue 77 ASP Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 103 MET Chi-restraints excluded: chain F residue 108 PHE Chi-restraints excluded: chain F residue 112 GLU Chi-restraints excluded: chain F residue 133 VAL Chi-restraints excluded: chain G residue 50 ASP Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain I residue 48 LEU Chi-restraints excluded: chain I residue 98 VAL Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain K residue 5 ASP Chi-restraints excluded: chain K residue 17 SER Chi-restraints excluded: chain K residue 31 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 304 optimal weight: 4.9990 chunk 239 optimal weight: 0.4980 chunk 7 optimal weight: 4.9990 chunk 249 optimal weight: 5.9990 chunk 222 optimal weight: 9.9990 chunk 13 optimal weight: 5.9990 chunk 81 optimal weight: 1.9990 chunk 240 optimal weight: 0.9990 chunk 318 optimal weight: 0.7980 chunk 322 optimal weight: 0.6980 chunk 382 optimal weight: 0.9980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 390 GLN A 397 ASN A 611 GLN A 626 ASN A 717 ASN A 838 GLN ** A1188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 357 GLN B 363 HIS C 224 GLN C 264 GLN ** D 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 179 GLN H 131 ASN H 134 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4093 r_free = 0.4093 target = 0.189702 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.117872 restraints weight = 27425.739| |-----------------------------------------------------------------------------| r_work (start): 0.3306 rms_B_bonded: 1.70 r_work: 0.3015 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2897 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.2897 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8628 moved from start: 0.1458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 1.065 33092 Z= 0.455 Angle : 0.574 24.416 44914 Z= 0.313 Chirality : 0.044 0.554 5050 Planarity : 0.004 0.043 5623 Dihedral : 13.021 124.065 4959 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.86 % Favored : 97.09 % Rotamer: Outliers : 3.35 % Allowed : 10.52 % Favored : 86.12 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 2.37 % 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: 0.42 (0.13), residues: 3879 helix: 1.24 (0.14), residues: 1350 sheet: 0.12 (0.20), residues: 621 loop : -0.28 (0.14), residues: 1908 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1274 TYR 0.014 0.001 TYR B 486 PHE 0.064 0.002 PHE D 70 TRP 0.013 0.001 TRP B 31 HIS 0.005 0.001 HIS A 659 Details of bonding type rmsd/Z covalent geometry : bond 0.01205 / 0.46 (33060) covalent geometry : angle 0.56700 / 0.31 (44869) hydrogen bonds : bond 0.04770 / 3.07 ( 1408) hydrogen bonds : angle 4.87964 / 3.43 ( 3910) metal coordination : bond 0.00341 / 0.22 ( 32) metal coordination : angle 2.87104 / 1.83 ( 45) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7758 Ramachandran restraints generated. 3879 Oldfield, 0 Emsley, 3879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7758 Ramachandran restraints generated. 3879 Oldfield, 0 Emsley, 3879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 552 residues out of total 3459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 436 time to evaluate : 1.381 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 PHE cc_start: 0.8801 (OUTLIER) cc_final: 0.7925 (t80) REVERT: A 41 MET cc_start: 0.5823 (mmt) cc_final: 0.5433 (mpt) REVERT: A 68 GLN cc_start: 0.6851 (tt0) cc_final: 0.5898 (mp-120) REVERT: A 88 LYS cc_start: 0.7899 (mttp) cc_final: 0.7310 (mttt) REVERT: A 123 ARG cc_start: 0.7192 (OUTLIER) cc_final: 0.6664 (mtm110) REVERT: A 129 LYS cc_start: 0.7574 (mtpt) cc_final: 0.7320 (mptp) REVERT: A 170 THR cc_start: 0.7592 (m) cc_final: 0.7218 (t) REVERT: A 175 ARG cc_start: 0.7584 (ttp80) cc_final: 0.7216 (mtp-110) REVERT: A 180 LYS cc_start: 0.8129 (mtmt) cc_final: 0.7619 (mttp) REVERT: A 261 ASP cc_start: 0.8330 (m-30) cc_final: 0.7920 (m-30) REVERT: A 333 GLU cc_start: 0.8492 (OUTLIER) cc_final: 0.7935 (mm-30) REVERT: A 387 ARG cc_start: 0.7501 (ttp-110) cc_final: 0.7136 (ttp80) REVERT: A 398 GLU cc_start: 0.7504 (tt0) cc_final: 0.7111 (tm-30) REVERT: A 447 GLN cc_start: 0.9192 (OUTLIER) cc_final: 0.8334 (mt0) REVERT: A 472 LEU cc_start: 0.8682 (OUTLIER) cc_final: 0.8146 (mt) REVERT: A 542 GLU cc_start: 0.8967 (OUTLIER) cc_final: 0.8762 (mt-10) REVERT: A 598 LEU cc_start: 0.7851 (OUTLIER) cc_final: 0.7608 (tp) REVERT: A 644 LYS cc_start: 0.8478 (mttt) cc_final: 0.7983 (mmmt) REVERT: A 685 GLU cc_start: 0.7530 (mt-10) cc_final: 0.6782 (tm-30) REVERT: A 696 GLU cc_start: 0.7411 (tm-30) cc_final: 0.7075 (tm-30) REVERT: A 712 GLU cc_start: 0.7030 (tt0) cc_final: 0.5936 (tm-30) REVERT: A 724 GLU cc_start: 0.7875 (mt-10) cc_final: 0.6900 (mm-30) REVERT: A 734 GLU cc_start: 0.7741 (tt0) cc_final: 0.7354 (tm-30) REVERT: A 822 GLU cc_start: 0.8141 (OUTLIER) cc_final: 0.7786 (mt-10) REVERT: A 833 GLU cc_start: 0.7981 (OUTLIER) cc_final: 0.7414 (mm-30) REVERT: A 889 SER cc_start: 0.7951 (t) cc_final: 0.7693 (p) REVERT: A 912 LEU cc_start: 0.7335 (OUTLIER) cc_final: 0.7097 (pp) REVERT: A 924 LYS cc_start: 0.6259 (OUTLIER) cc_final: 0.5615 (mmtm) REVERT: A 931 GLU cc_start: 0.7110 (tt0) cc_final: 0.6647 (mm-30) REVERT: A 961 ARG cc_start: 0.7225 (mmt90) cc_final: 0.6641 (mtm180) REVERT: A 969 GLN cc_start: 0.7154 (mm110) cc_final: 0.6287 (tp40) REVERT: A 1005 GLU cc_start: 0.7961 (OUTLIER) cc_final: 0.7629 (mm-30) REVERT: A 1062 GLU cc_start: 0.8848 (tp30) cc_final: 0.8487 (tp30) REVERT: A 1077 THR cc_start: 0.7611 (m) cc_final: 0.7064 (p) REVERT: A 1135 ARG cc_start: 0.6662 (ttt180) cc_final: 0.5784 (ttt180) REVERT: A 1304 TRP cc_start: 0.7496 (m100) cc_final: 0.7246 (m100) REVERT: A 1398 MET cc_start: 0.8794 (OUTLIER) cc_final: 0.8548 (ttt) REVERT: A 1407 GLU cc_start: 0.8199 (mp0) cc_final: 0.7810 (mp0) REVERT: A 1444 MET cc_start: 0.8473 (OUTLIER) cc_final: 0.6969 (mtm) REVERT: B 21 GLU cc_start: 0.7842 (pt0) cc_final: 0.7323 (mt-10) REVERT: B 46 GLN cc_start: 0.7930 (mp-120) cc_final: 0.7008 (pm20) REVERT: B 199 MET cc_start: 0.8279 (mmt) cc_final: 0.7192 (pmm) REVERT: B 270 LYS cc_start: 0.7006 (mtmp) cc_final: 0.6718 (mtmp) REVERT: B 343 ILE cc_start: 0.6331 (OUTLIER) cc_final: 0.6130 (mm) REVERT: B 357 GLN cc_start: 0.8068 (tt0) cc_final: 0.7703 (tt0) REVERT: B 359 GLU cc_start: 0.7916 (OUTLIER) cc_final: 0.7566 (mp0) REVERT: B 393 LYS cc_start: 0.7547 (ttpt) cc_final: 0.6775 (mmtm) REVERT: B 398 ARG cc_start: 0.7709 (mtt-85) cc_final: 0.7132 (ttp-170) REVERT: B 422 LYS cc_start: 0.7387 (mmtm) cc_final: 0.6352 (tmmm) REVERT: B 423 LYS cc_start: 0.8108 (tttp) cc_final: 0.7611 (ttmm) REVERT: B 451 LYS cc_start: 0.7790 (mtmt) cc_final: 0.7212 (tmtt) REVERT: B 468 GLU cc_start: 0.7530 (mp0) cc_final: 0.6687 (mm-30) REVERT: B 498 THR cc_start: 0.8631 (m) cc_final: 0.8257 (p) REVERT: B 508 LEU cc_start: 0.6834 (OUTLIER) cc_final: 0.6163 (tp) REVERT: B 595 ARG cc_start: 0.7774 (ttt180) cc_final: 0.7274 (mpp-170) REVERT: B 621 GLU cc_start: 0.7769 (tp30) cc_final: 0.7387 (mm-30) REVERT: B 624 LEU cc_start: 0.8852 (OUTLIER) cc_final: 0.8610 (tt) REVERT: B 650 GLU cc_start: 0.6636 (OUTLIER) cc_final: 0.5944 (tm-30) REVERT: B 665 GLU cc_start: 0.7780 (tt0) cc_final: 0.7442 (tt0) REVERT: B 696 GLU cc_start: 0.8190 (OUTLIER) cc_final: 0.7909 (tp30) REVERT: B 727 LYS cc_start: 0.8345 (mttp) cc_final: 0.7901 (mtpm) REVERT: B 862 GLN cc_start: 0.7696 (mt0) cc_final: 0.7488 (mt0) REVERT: B 873 THR cc_start: 0.7044 (m) cc_final: 0.6723 (t) REVERT: B 889 THR cc_start: 0.7984 (m) cc_final: 0.7686 (t) REVERT: B 1057 LYS cc_start: 0.8578 (mttt) cc_final: 0.8266 (mtpm) REVERT: B 1112 GLN cc_start: 0.8857 (mt0) cc_final: 0.8589 (mt0) REVERT: B 1124 ARG cc_start: 0.7973 (mtm-85) cc_final: 0.7400 (mtp85) REVERT: B 1219 ASP cc_start: 0.8530 (OUTLIER) cc_final: 0.8021 (p0) REVERT: C 12 GLU cc_start: 0.8187 (mt-10) cc_final: 0.7508 (tm-30) REVERT: C 102 GLN cc_start: 0.8504 (OUTLIER) cc_final: 0.8129 (mp10) REVERT: C 106 GLU cc_start: 0.8086 (mt-10) cc_final: 0.7593 (mm-30) REVERT: C 152 GLU cc_start: 0.8716 (tt0) cc_final: 0.8181 (tm-30) REVERT: C 160 LYS cc_start: 0.9056 (mttt) cc_final: 0.8845 (mttt) REVERT: C 264 GLN cc_start: 0.7117 (tp40) cc_final: 0.6716 (tp40) REVERT: E 33 GLU cc_start: 0.7647 (tt0) cc_final: 0.7229 (tm-30) REVERT: E 40 GLU cc_start: 0.6295 (mp0) cc_final: 0.5629 (mm-30) REVERT: E 57 MET cc_start: 0.7276 (mtm) cc_final: 0.6806 (mmm) REVERT: E 78 LEU cc_start: 0.8570 (OUTLIER) cc_final: 0.8306 (tt) REVERT: F 103 MET cc_start: 0.8203 (OUTLIER) cc_final: 0.7919 (mtp) REVERT: F 112 GLU cc_start: 0.7229 (OUTLIER) cc_final: 0.6842 (mt-10) REVERT: F 123 LYS cc_start: 0.8366 (tttm) cc_final: 0.8125 (tttt) REVERT: F 149 GLU cc_start: 0.8002 (tt0) cc_final: 0.7440 (pm20) REVERT: G 115 MET cc_start: 0.1633 (mtp) cc_final: 0.1291 (mtp) REVERT: H 129 TYR cc_start: 0.7678 (p90) cc_final: 0.7420 (p90) REVERT: I 1 MET cc_start: 0.4598 (ttt) cc_final: 0.3639 (tmt) REVERT: I 90 GLN cc_start: 0.6304 (mm110) cc_final: 0.5836 (mt0) REVERT: J 26 GLN cc_start: 0.7284 (OUTLIER) cc_final: 0.6062 (mt0) REVERT: J 48 ARG cc_start: 0.8960 (OUTLIER) cc_final: 0.8086 (tmm-80) REVERT: K 20 LYS cc_start: 0.8741 (tttp) cc_final: 0.8400 (ttpm) outliers start: 116 outliers final: 44 residues processed: 514 average time/residue: 0.8439 time to fit residues: 508.6041 Evaluate side-chains 489 residues out of total 3459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 418 time to evaluate : 1.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 THR Chi-restraints excluded: chain A residue 22 PHE Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 123 ARG Chi-restraints excluded: chain A residue 333 GLU Chi-restraints excluded: chain A residue 380 VAL Chi-restraints excluded: chain A residue 447 GLN Chi-restraints excluded: chain A residue 472 LEU Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 542 GLU Chi-restraints excluded: chain A residue 598 LEU Chi-restraints excluded: chain A residue 701 LEU Chi-restraints excluded: chain A residue 703 THR Chi-restraints excluded: chain A residue 727 ASP Chi-restraints excluded: chain A residue 822 GLU Chi-restraints excluded: chain A residue 833 GLU Chi-restraints excluded: chain A residue 834 THR Chi-restraints excluded: chain A residue 907 THR Chi-restraints excluded: chain A residue 912 LEU Chi-restraints excluded: chain A residue 924 LYS Chi-restraints excluded: chain A residue 984 LYS Chi-restraints excluded: chain A residue 1005 GLU Chi-restraints excluded: chain A residue 1398 MET Chi-restraints excluded: chain A residue 1438 THR Chi-restraints excluded: chain A residue 1444 MET Chi-restraints excluded: chain B residue 58 THR Chi-restraints excluded: chain B residue 77 HIS Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 152 ILE Chi-restraints excluded: chain B residue 298 LEU Chi-restraints excluded: chain B residue 343 ILE Chi-restraints excluded: chain B residue 359 GLU Chi-restraints excluded: chain B residue 508 LEU Chi-restraints excluded: chain B residue 541 LEU Chi-restraints excluded: chain B residue 547 VAL Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 624 LEU Chi-restraints excluded: chain B residue 650 GLU Chi-restraints excluded: chain B residue 696 GLU Chi-restraints excluded: chain B residue 903 VAL Chi-restraints excluded: chain B residue 908 GLU Chi-restraints excluded: chain B residue 936 ASP Chi-restraints excluded: chain B residue 1150 ARG Chi-restraints excluded: chain B residue 1160 VAL Chi-restraints excluded: chain B residue 1219 ASP Chi-restraints excluded: chain C residue 18 VAL Chi-restraints excluded: chain C residue 43 THR Chi-restraints excluded: chain C residue 53 THR Chi-restraints excluded: chain C residue 102 GLN Chi-restraints excluded: chain C residue 189 THR Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 133 THR Chi-restraints excluded: chain D residue 170 THR Chi-restraints excluded: chain D residue 221 TYR Chi-restraints excluded: chain E residue 48 ASP Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain E residue 196 VAL Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 103 MET Chi-restraints excluded: chain F residue 108 PHE Chi-restraints excluded: chain F residue 112 GLU Chi-restraints excluded: chain F residue 133 VAL Chi-restraints excluded: chain G residue 50 ASP Chi-restraints excluded: chain G residue 92 VAL Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain I residue 48 LEU Chi-restraints excluded: chain I residue 98 VAL Chi-restraints excluded: chain J residue 26 GLN Chi-restraints excluded: chain J residue 48 ARG Chi-restraints excluded: chain K residue 31 VAL Chi-restraints excluded: chain L residue 27 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 14 optimal weight: 7.9990 chunk 149 optimal weight: 7.9990 chunk 358 optimal weight: 0.5980 chunk 121 optimal weight: 20.0000 chunk 145 optimal weight: 9.9990 chunk 223 optimal weight: 7.9990 chunk 88 optimal weight: 0.5980 chunk 387 optimal weight: 0.8980 chunk 233 optimal weight: 4.9990 chunk 355 optimal weight: 3.9990 chunk 8 optimal weight: 0.6980 overall best weight: 1.3582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 626 ASN A 717 ASN A 838 GLN ** A1188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 17 ASN ** D 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 115 ASN E 179 GLN H 131 ASN H 134 ASN H 139 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4082 r_free = 0.4082 target = 0.188690 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.117080 restraints weight = 27343.647| |-----------------------------------------------------------------------------| r_work (start): 0.3299 rms_B_bonded: 1.62 r_work: 0.3013 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2895 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.2895 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8653 moved from start: 0.1585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 1.065 33092 Z= 0.461 Angle : 0.589 24.416 44914 Z= 0.320 Chirality : 0.045 0.554 5050 Planarity : 0.004 0.043 5623 Dihedral : 12.942 125.538 4949 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.38 % Favored : 96.57 % Rotamer: Outliers : 3.58 % Allowed : 10.81 % Favored : 85.60 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 2.37 % 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: 0.46 (0.13), residues: 3879 helix: 1.31 (0.14), residues: 1349 sheet: 0.10 (0.20), residues: 624 loop : -0.27 (0.14), residues: 1906 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 393 TYR 0.015 0.001 TYR B 486 PHE 0.064 0.002 PHE D 70 TRP 0.014 0.001 TRP B 31 HIS 0.008 0.001 HIS A 399 Details of bonding type rmsd/Z covalent geometry : bond 0.01217 / 0.46 (33060) covalent geometry : angle 0.58240 / 0.32 (44869) hydrogen bonds : bond 0.04798 / 3.09 ( 1408) hydrogen bonds : angle 4.77764 / 3.35 ( 3910) metal coordination : bond 0.00340 / 0.22 ( 32) metal coordination : angle 2.93710 / 1.86 ( 45) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7758 Ramachandran restraints generated. 3879 Oldfield, 0 Emsley, 3879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7758 Ramachandran restraints generated. 3879 Oldfield, 0 Emsley, 3879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 545 residues out of total 3459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 421 time to evaluate : 1.296 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 PHE cc_start: 0.8836 (OUTLIER) cc_final: 0.7832 (t80) REVERT: A 41 MET cc_start: 0.5947 (mmt) cc_final: 0.5546 (mpt) REVERT: A 66 LYS cc_start: 0.7358 (mttm) cc_final: 0.6994 (mptm) REVERT: A 68 GLN cc_start: 0.6748 (tt0) cc_final: 0.5848 (mp-120) REVERT: A 88 LYS cc_start: 0.7895 (mttp) cc_final: 0.7410 (mttt) REVERT: A 123 ARG cc_start: 0.7236 (OUTLIER) cc_final: 0.6627 (mtm110) REVERT: A 129 LYS cc_start: 0.7569 (mtpt) cc_final: 0.7330 (mptp) REVERT: A 175 ARG cc_start: 0.7587 (ttp80) cc_final: 0.7236 (mtp-110) REVERT: A 180 LYS cc_start: 0.8116 (mtmt) cc_final: 0.7606 (mttp) REVERT: A 261 ASP cc_start: 0.8322 (m-30) cc_final: 0.7911 (m-30) REVERT: A 387 ARG cc_start: 0.7495 (ttp-110) cc_final: 0.7139 (ttp80) REVERT: A 398 GLU cc_start: 0.7512 (tt0) cc_final: 0.7144 (tm-30) REVERT: A 447 GLN cc_start: 0.9194 (OUTLIER) cc_final: 0.8301 (mt0) REVERT: A 472 LEU cc_start: 0.8750 (OUTLIER) cc_final: 0.8216 (mt) REVERT: A 598 LEU cc_start: 0.7869 (OUTLIER) cc_final: 0.7645 (tp) REVERT: A 644 LYS cc_start: 0.8477 (mttt) cc_final: 0.7983 (mmmt) REVERT: A 685 GLU cc_start: 0.7465 (mt-10) cc_final: 0.6762 (tm-30) REVERT: A 696 GLU cc_start: 0.7381 (tm-30) cc_final: 0.6790 (mt-10) REVERT: A 712 GLU cc_start: 0.7033 (tt0) cc_final: 0.5931 (tm-30) REVERT: A 734 GLU cc_start: 0.7739 (tt0) cc_final: 0.7359 (tm-30) REVERT: A 822 GLU cc_start: 0.8131 (OUTLIER) cc_final: 0.7762 (mt-10) REVERT: A 833 GLU cc_start: 0.7915 (OUTLIER) cc_final: 0.7350 (mm-30) REVERT: A 889 SER cc_start: 0.7974 (t) cc_final: 0.7755 (p) REVERT: A 924 LYS cc_start: 0.6335 (OUTLIER) cc_final: 0.5690 (mmtm) REVERT: A 931 GLU cc_start: 0.7073 (tt0) cc_final: 0.6623 (mm-30) REVERT: A 961 ARG cc_start: 0.7245 (mmt90) cc_final: 0.6681 (mtm180) REVERT: A 969 GLN cc_start: 0.7292 (mm110) cc_final: 0.6420 (tp40) REVERT: A 1062 GLU cc_start: 0.8844 (tp30) cc_final: 0.8560 (tp30) REVERT: A 1077 THR cc_start: 0.7775 (m) cc_final: 0.7284 (p) REVERT: A 1132 LYS cc_start: 0.7122 (OUTLIER) cc_final: 0.6726 (mtmt) REVERT: A 1135 ARG cc_start: 0.6675 (ttt180) cc_final: 0.5790 (ttt180) REVERT: A 1304 TRP cc_start: 0.7515 (m100) cc_final: 0.7224 (m100) REVERT: A 1398 MET cc_start: 0.8889 (OUTLIER) cc_final: 0.8669 (ttt) REVERT: A 1407 GLU cc_start: 0.8213 (mp0) cc_final: 0.7813 (mp0) REVERT: A 1444 MET cc_start: 0.8487 (OUTLIER) cc_final: 0.6997 (mtm) REVERT: B 21 GLU cc_start: 0.7838 (pt0) cc_final: 0.7332 (mt-10) REVERT: B 46 GLN cc_start: 0.7972 (OUTLIER) cc_final: 0.7059 (pm20) REVERT: B 199 MET cc_start: 0.8281 (mmt) cc_final: 0.7234 (pmm) REVERT: B 270 LYS cc_start: 0.6982 (mtmp) cc_final: 0.6681 (mtmp) REVERT: B 357 GLN cc_start: 0.8119 (tt0) cc_final: 0.7767 (tt0) REVERT: B 359 GLU cc_start: 0.7918 (OUTLIER) cc_final: 0.7577 (mp0) REVERT: B 393 LYS cc_start: 0.7554 (ttpt) cc_final: 0.6783 (mmtm) REVERT: B 398 ARG cc_start: 0.7689 (mtt-85) cc_final: 0.7160 (ttp-170) REVERT: B 422 LYS cc_start: 0.7397 (mmtm) cc_final: 0.6360 (tmmm) REVERT: B 423 LYS cc_start: 0.8107 (tttp) cc_final: 0.7602 (ttmm) REVERT: B 451 LYS cc_start: 0.7791 (mtmt) cc_final: 0.7247 (tmtt) REVERT: B 468 GLU cc_start: 0.7549 (mp0) cc_final: 0.6713 (mm-30) REVERT: B 508 LEU cc_start: 0.6852 (OUTLIER) cc_final: 0.6174 (tp) REVERT: B 595 ARG cc_start: 0.7775 (ttt180) cc_final: 0.7233 (mpp-170) REVERT: B 621 GLU cc_start: 0.7754 (tp30) cc_final: 0.7443 (mm-30) REVERT: B 650 GLU cc_start: 0.6730 (OUTLIER) cc_final: 0.6124 (tm-30) REVERT: B 665 GLU cc_start: 0.7817 (tt0) cc_final: 0.7522 (tt0) REVERT: B 696 GLU cc_start: 0.8201 (OUTLIER) cc_final: 0.7951 (tp30) REVERT: B 727 LYS cc_start: 0.8374 (mttp) cc_final: 0.7914 (mttm) REVERT: B 862 GLN cc_start: 0.7702 (mt0) cc_final: 0.7497 (mt0) REVERT: B 873 THR cc_start: 0.7062 (m) cc_final: 0.6773 (t) REVERT: B 889 THR cc_start: 0.7972 (m) cc_final: 0.7681 (t) REVERT: B 1057 LYS cc_start: 0.8606 (mttt) cc_final: 0.8099 (mmtm) REVERT: B 1112 GLN cc_start: 0.8867 (mt0) cc_final: 0.8616 (mt0) REVERT: B 1124 ARG cc_start: 0.7959 (mtm-85) cc_final: 0.7386 (mtp85) REVERT: B 1219 ASP cc_start: 0.8522 (OUTLIER) cc_final: 0.7979 (p0) REVERT: C 12 GLU cc_start: 0.8176 (mt-10) cc_final: 0.7509 (tm-30) REVERT: C 102 GLN cc_start: 0.8509 (OUTLIER) cc_final: 0.8157 (mp10) REVERT: C 106 GLU cc_start: 0.8065 (mt-10) cc_final: 0.7614 (mm-30) REVERT: C 152 GLU cc_start: 0.8711 (tt0) cc_final: 0.8190 (tm-30) REVERT: E 33 GLU cc_start: 0.7649 (tt0) cc_final: 0.7226 (tm-30) REVERT: E 40 GLU cc_start: 0.6352 (mp0) cc_final: 0.5669 (mm-30) REVERT: E 57 MET cc_start: 0.7222 (mtm) cc_final: 0.6745 (mmm) REVERT: E 78 LEU cc_start: 0.8548 (OUTLIER) cc_final: 0.8286 (tt) REVERT: F 103 MET cc_start: 0.8188 (mtp) cc_final: 0.7811 (mtp) REVERT: F 112 GLU cc_start: 0.7196 (OUTLIER) cc_final: 0.6957 (mt-10) REVERT: F 149 GLU cc_start: 0.8083 (tt0) cc_final: 0.7605 (pm20) REVERT: G 115 MET cc_start: 0.1551 (mtp) cc_final: 0.1212 (mtp) REVERT: H 129 TYR cc_start: 0.7636 (p90) cc_final: 0.7433 (p90) REVERT: I 1 MET cc_start: 0.4615 (ttt) cc_final: 0.3629 (tmt) REVERT: J 26 GLN cc_start: 0.7354 (OUTLIER) cc_final: 0.6218 (mt0) REVERT: K 20 LYS cc_start: 0.8751 (tttp) cc_final: 0.8413 (ttpm) outliers start: 124 outliers final: 62 residues processed: 507 average time/residue: 0.7975 time to fit residues: 476.4511 Evaluate side-chains 492 residues out of total 3459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 409 time to evaluate : 1.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 THR Chi-restraints excluded: chain A residue 22 PHE Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 123 ARG Chi-restraints excluded: chain A residue 380 VAL Chi-restraints excluded: chain A residue 447 GLN Chi-restraints excluded: chain A residue 472 LEU Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 598 LEU Chi-restraints excluded: chain A residue 701 LEU Chi-restraints excluded: chain A residue 703 THR Chi-restraints excluded: chain A residue 727 ASP Chi-restraints excluded: chain A residue 822 GLU Chi-restraints excluded: chain A residue 833 GLU Chi-restraints excluded: chain A residue 834 THR Chi-restraints excluded: chain A residue 885 THR Chi-restraints excluded: chain A residue 907 THR Chi-restraints excluded: chain A residue 924 LYS Chi-restraints excluded: chain A residue 1112 LYS Chi-restraints excluded: chain A residue 1128 GLN Chi-restraints excluded: chain A residue 1132 LYS Chi-restraints excluded: chain A residue 1283 VAL Chi-restraints excluded: chain A residue 1322 ILE Chi-restraints excluded: chain A residue 1398 MET Chi-restraints excluded: chain A residue 1438 THR Chi-restraints excluded: chain A residue 1444 MET Chi-restraints excluded: chain B residue 46 GLN Chi-restraints excluded: chain B residue 58 THR Chi-restraints excluded: chain B residue 77 HIS Chi-restraints excluded: chain B residue 298 LEU Chi-restraints excluded: chain B residue 305 VAL Chi-restraints excluded: chain B residue 359 GLU Chi-restraints excluded: chain B residue 487 THR Chi-restraints excluded: chain B residue 498 THR Chi-restraints excluded: chain B residue 508 LEU Chi-restraints excluded: chain B residue 541 LEU Chi-restraints excluded: chain B residue 547 VAL Chi-restraints excluded: chain B residue 650 GLU Chi-restraints excluded: chain B residue 696 GLU Chi-restraints excluded: chain B residue 839 MET Chi-restraints excluded: chain B residue 903 VAL Chi-restraints excluded: chain B residue 908 GLU Chi-restraints excluded: chain B residue 936 ASP Chi-restraints excluded: chain B residue 955 THR Chi-restraints excluded: chain B residue 1150 ARG Chi-restraints excluded: chain B residue 1160 VAL Chi-restraints excluded: chain B residue 1219 ASP Chi-restraints excluded: chain C residue 18 VAL Chi-restraints excluded: chain C residue 25 VAL Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 43 THR Chi-restraints excluded: chain C residue 53 THR Chi-restraints excluded: chain C residue 56 THR Chi-restraints excluded: chain C residue 102 GLN Chi-restraints excluded: chain C residue 189 THR Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 38 ILE Chi-restraints excluded: chain D residue 133 THR Chi-restraints excluded: chain D residue 170 THR Chi-restraints excluded: chain D residue 221 TYR Chi-restraints excluded: chain E residue 31 THR Chi-restraints excluded: chain E residue 48 ASP Chi-restraints excluded: chain E residue 70 SER Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain E residue 152 LYS Chi-restraints excluded: chain E residue 196 VAL Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 108 PHE Chi-restraints excluded: chain F residue 112 GLU Chi-restraints excluded: chain F residue 133 VAL Chi-restraints excluded: chain G residue 50 ASP Chi-restraints excluded: chain G residue 86 VAL Chi-restraints excluded: chain G residue 92 VAL Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain I residue 48 LEU Chi-restraints excluded: chain I residue 87 GLN Chi-restraints excluded: chain I residue 98 VAL Chi-restraints excluded: chain J residue 26 GLN Chi-restraints excluded: chain K residue 5 ASP Chi-restraints excluded: chain K residue 17 SER Chi-restraints excluded: chain K residue 31 VAL Chi-restraints excluded: chain K residue 55 LYS Chi-restraints excluded: chain L residue 27 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 172 optimal weight: 4.9990 chunk 2 optimal weight: 5.9990 chunk 353 optimal weight: 6.9990 chunk 89 optimal weight: 6.9990 chunk 282 optimal weight: 20.0000 chunk 269 optimal weight: 3.9990 chunk 82 optimal weight: 3.9990 chunk 154 optimal weight: 2.9990 chunk 217 optimal weight: 7.9990 chunk 61 optimal weight: 3.9990 chunk 297 optimal weight: 7.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 626 ASN A 736 ASN A 838 GLN A1188 GLN B 357 GLN C 131 HIS ** D 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 179 GLN H 131 ASN H 134 ASN I 46 HIS I 114 GLN L 66 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.187211 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.134701 restraints weight = 27337.553| |-----------------------------------------------------------------------------| r_work (start): 0.3518 rms_B_bonded: 2.47 r_work: 0.2950 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.2950 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8824 moved from start: 0.1730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.014 1.062 33092 Z= 0.527 Angle : 0.742 24.367 44914 Z= 0.397 Chirality : 0.053 0.556 5050 Planarity : 0.006 0.088 5623 Dihedral : 13.144 125.376 4945 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.07 % Favored : 95.88 % Rotamer: Outliers : 3.93 % Allowed : 11.22 % Favored : 84.85 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 2.37 % 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: 0.21 (0.13), residues: 3879 helix: 0.98 (0.14), residues: 1351 sheet: 0.05 (0.20), residues: 614 loop : -0.37 (0.14), residues: 1914 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 485 TYR 0.026 0.003 TYR B 486 PHE 0.062 0.003 PHE D 70 TRP 0.019 0.003 TRP B 31 HIS 0.010 0.002 HIS A 659 Details of bonding type rmsd/Z covalent geometry : bond 0.01363 / 0.53 (33060) covalent geometry : angle 0.73354 / 0.40 (44869) hydrogen bonds : bond 0.06186 / 4.03 ( 1408) hydrogen bonds : angle 5.04130 / 3.53 ( 3910) metal coordination : bond 0.00596 / 0.42 ( 32) metal coordination : angle 3.63045 / 2.31 ( 45) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7758 Ramachandran restraints generated. 3879 Oldfield, 0 Emsley, 3879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7758 Ramachandran restraints generated. 3879 Oldfield, 0 Emsley, 3879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 553 residues out of total 3459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 136 poor density : 417 time to evaluate : 1.300 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 PHE cc_start: 0.8987 (OUTLIER) cc_final: 0.7838 (t80) REVERT: A 36 ARG cc_start: 0.7763 (OUTLIER) cc_final: 0.7424 (mtt-85) REVERT: A 41 MET cc_start: 0.6295 (mmt) cc_final: 0.5761 (mpp) REVERT: A 68 GLN cc_start: 0.6764 (tt0) cc_final: 0.6132 (mp-120) REVERT: A 88 LYS cc_start: 0.8076 (mttp) cc_final: 0.7650 (mttt) REVERT: A 123 ARG cc_start: 0.7576 (OUTLIER) cc_final: 0.6949 (mtt90) REVERT: A 175 ARG cc_start: 0.7651 (ttp80) cc_final: 0.7224 (mtp85) REVERT: A 180 LYS cc_start: 0.8370 (mtmt) cc_final: 0.7939 (mttp) REVERT: A 333 GLU cc_start: 0.8502 (OUTLIER) cc_final: 0.7990 (mm-30) REVERT: A 398 GLU cc_start: 0.7786 (tt0) cc_final: 0.7572 (tm-30) REVERT: A 447 GLN cc_start: 0.9154 (OUTLIER) cc_final: 0.8277 (mt0) REVERT: A 472 LEU cc_start: 0.9024 (OUTLIER) cc_final: 0.8573 (mt) REVERT: A 598 LEU cc_start: 0.8167 (OUTLIER) cc_final: 0.7966 (tp) REVERT: A 644 LYS cc_start: 0.8617 (mttt) cc_final: 0.8267 (tptm) REVERT: A 685 GLU cc_start: 0.7897 (mt-10) cc_final: 0.7415 (tm-30) REVERT: A 696 GLU cc_start: 0.7741 (tm-30) cc_final: 0.7395 (tm-30) REVERT: A 712 GLU cc_start: 0.7464 (tt0) cc_final: 0.6429 (tm-30) REVERT: A 734 GLU cc_start: 0.7893 (tt0) cc_final: 0.7673 (tm-30) REVERT: A 822 GLU cc_start: 0.8310 (OUTLIER) cc_final: 0.8017 (mt-10) REVERT: A 833 GLU cc_start: 0.7995 (OUTLIER) cc_final: 0.7655 (mm-30) REVERT: A 898 ARG cc_start: 0.8191 (OUTLIER) cc_final: 0.7662 (tmt-80) REVERT: A 912 LEU cc_start: 0.7626 (OUTLIER) cc_final: 0.7399 (pp) REVERT: A 924 LYS cc_start: 0.6575 (OUTLIER) cc_final: 0.5996 (mmtm) REVERT: A 931 GLU cc_start: 0.7342 (tt0) cc_final: 0.7088 (mm-30) REVERT: A 961 ARG cc_start: 0.7443 (mmt90) cc_final: 0.7150 (mtm180) REVERT: A 969 GLN cc_start: 0.7489 (mm110) cc_final: 0.6862 (tp40) REVERT: A 1062 GLU cc_start: 0.8663 (tp30) cc_final: 0.8455 (tp30) REVERT: A 1077 THR cc_start: 0.8024 (m) cc_final: 0.7779 (p) REVERT: A 1135 ARG cc_start: 0.6959 (ttt180) cc_final: 0.6073 (ttt180) REVERT: A 1304 TRP cc_start: 0.7658 (m100) cc_final: 0.7302 (m100) REVERT: A 1366 ARG cc_start: 0.8461 (OUTLIER) cc_final: 0.7769 (mtt90) REVERT: A 1407 GLU cc_start: 0.8360 (mp0) cc_final: 0.8047 (mp0) REVERT: A 1444 MET cc_start: 0.8717 (OUTLIER) cc_final: 0.7275 (mtm) REVERT: B 21 GLU cc_start: 0.7961 (pt0) cc_final: 0.7617 (mt-10) REVERT: B 46 GLN cc_start: 0.8163 (OUTLIER) cc_final: 0.7530 (pm20) REVERT: B 270 LYS cc_start: 0.7248 (mtmp) cc_final: 0.6935 (mtmp) REVERT: B 357 GLN cc_start: 0.8286 (tt0) cc_final: 0.7957 (tt0) REVERT: B 393 LYS cc_start: 0.7750 (ttpt) cc_final: 0.6979 (mmtp) REVERT: B 398 ARG cc_start: 0.7892 (mtt-85) cc_final: 0.7512 (ttp-170) REVERT: B 422 LYS cc_start: 0.7693 (mmtm) cc_final: 0.7114 (mttp) REVERT: B 423 LYS cc_start: 0.8440 (tttp) cc_final: 0.8027 (ttmm) REVERT: B 451 LYS cc_start: 0.7957 (mtmt) cc_final: 0.7685 (tmtt) REVERT: B 468 GLU cc_start: 0.7627 (mp0) cc_final: 0.7034 (mm-30) REVERT: B 595 ARG cc_start: 0.7964 (ttt180) cc_final: 0.7730 (mpp-170) REVERT: B 621 GLU cc_start: 0.8000 (tp30) cc_final: 0.7635 (mm-30) REVERT: B 624 LEU cc_start: 0.9038 (OUTLIER) cc_final: 0.8650 (tt) REVERT: B 650 GLU cc_start: 0.6908 (OUTLIER) cc_final: 0.6482 (tm-30) REVERT: B 665 GLU cc_start: 0.8010 (tt0) cc_final: 0.7705 (tt0) REVERT: B 696 GLU cc_start: 0.8331 (OUTLIER) cc_final: 0.8040 (tp30) REVERT: B 727 LYS cc_start: 0.8718 (mttp) cc_final: 0.8355 (mttm) REVERT: B 873 THR cc_start: 0.7471 (m) cc_final: 0.7142 (t) REVERT: B 889 THR cc_start: 0.8111 (m) cc_final: 0.7879 (t) REVERT: B 1057 LYS cc_start: 0.8756 (mttt) cc_final: 0.8466 (mmtm) REVERT: B 1124 ARG cc_start: 0.8103 (mtm-85) cc_final: 0.7691 (mtp85) REVERT: B 1219 ASP cc_start: 0.8616 (OUTLIER) cc_final: 0.8107 (p0) REVERT: C 12 GLU cc_start: 0.8318 (mt-10) cc_final: 0.7844 (tm-30) REVERT: C 106 GLU cc_start: 0.8032 (mt-10) cc_final: 0.7810 (mm-30) REVERT: C 152 GLU cc_start: 0.8760 (tt0) cc_final: 0.8422 (tm-30) REVERT: E 33 GLU cc_start: 0.7670 (tt0) cc_final: 0.7423 (tm-30) REVERT: E 40 GLU cc_start: 0.6481 (mp0) cc_final: 0.5716 (mm-30) REVERT: E 57 MET cc_start: 0.7204 (mtm) cc_final: 0.6806 (mmm) REVERT: E 78 LEU cc_start: 0.8809 (OUTLIER) cc_final: 0.8558 (tt) REVERT: F 112 GLU cc_start: 0.7377 (OUTLIER) cc_final: 0.7095 (mt-10) REVERT: F 123 LYS cc_start: 0.8816 (tttm) cc_final: 0.8572 (tttt) REVERT: F 149 GLU cc_start: 0.8279 (tt0) cc_final: 0.8041 (pm20) REVERT: G 115 MET cc_start: 0.1381 (mtp) cc_final: 0.1004 (mtp) REVERT: I 1 MET cc_start: 0.4706 (ttt) cc_final: 0.3709 (tmt) REVERT: J 26 GLN cc_start: 0.7557 (OUTLIER) cc_final: 0.6288 (mt0) REVERT: J 48 ARG cc_start: 0.9051 (OUTLIER) cc_final: 0.8176 (tmm-80) REVERT: K 55 LYS cc_start: 0.9173 (OUTLIER) cc_final: 0.8834 (mtmp) outliers start: 136 outliers final: 77 residues processed: 512 average time/residue: 0.7610 time to fit residues: 459.8151 Evaluate side-chains 513 residues out of total 3459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 412 time to evaluate : 1.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 THR Chi-restraints excluded: chain A residue 22 PHE Chi-restraints excluded: chain A residue 36 ARG Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 123 ARG Chi-restraints excluded: chain A residue 169 ASN Chi-restraints excluded: chain A residue 291 GLU Chi-restraints excluded: chain A residue 333 GLU Chi-restraints excluded: chain A residue 380 VAL Chi-restraints excluded: chain A residue 447 GLN Chi-restraints excluded: chain A residue 472 LEU Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 501 LEU Chi-restraints excluded: chain A residue 598 LEU Chi-restraints excluded: chain A residue 701 LEU Chi-restraints excluded: chain A residue 703 THR Chi-restraints excluded: chain A residue 727 ASP Chi-restraints excluded: chain A residue 822 GLU Chi-restraints excluded: chain A residue 833 GLU Chi-restraints excluded: chain A residue 834 THR Chi-restraints excluded: chain A residue 885 THR Chi-restraints excluded: chain A residue 898 ARG Chi-restraints excluded: chain A residue 907 THR Chi-restraints excluded: chain A residue 912 LEU Chi-restraints excluded: chain A residue 919 ILE Chi-restraints excluded: chain A residue 924 LYS Chi-restraints excluded: chain A residue 1043 ASP Chi-restraints excluded: chain A residue 1112 LYS Chi-restraints excluded: chain A residue 1283 VAL Chi-restraints excluded: chain A residue 1322 ILE Chi-restraints excluded: chain A residue 1355 VAL Chi-restraints excluded: chain A residue 1366 ARG Chi-restraints excluded: chain A residue 1438 THR Chi-restraints excluded: chain A residue 1444 MET Chi-restraints excluded: chain B residue 46 GLN Chi-restraints excluded: chain B residue 58 THR Chi-restraints excluded: chain B residue 77 HIS Chi-restraints excluded: chain B residue 103 ASN Chi-restraints excluded: chain B residue 152 ILE Chi-restraints excluded: chain B residue 298 LEU Chi-restraints excluded: chain B residue 305 VAL Chi-restraints excluded: chain B residue 487 THR Chi-restraints excluded: chain B residue 498 THR Chi-restraints excluded: chain B residue 508 LEU Chi-restraints excluded: chain B residue 541 LEU Chi-restraints excluded: chain B residue 547 VAL Chi-restraints excluded: chain B residue 624 LEU Chi-restraints excluded: chain B residue 650 GLU Chi-restraints excluded: chain B residue 696 GLU Chi-restraints excluded: chain B residue 751 VAL Chi-restraints excluded: chain B residue 839 MET Chi-restraints excluded: chain B residue 903 VAL Chi-restraints excluded: chain B residue 936 ASP Chi-restraints excluded: chain B residue 955 THR Chi-restraints excluded: chain B residue 1150 ARG Chi-restraints excluded: chain B residue 1160 VAL Chi-restraints excluded: chain B residue 1219 ASP Chi-restraints excluded: chain C residue 18 VAL Chi-restraints excluded: chain C residue 25 VAL Chi-restraints excluded: chain C residue 43 THR Chi-restraints excluded: chain C residue 53 THR Chi-restraints excluded: chain C residue 56 THR Chi-restraints excluded: chain C residue 136 ASP Chi-restraints excluded: chain C residue 189 THR Chi-restraints excluded: chain C residue 205 LYS Chi-restraints excluded: chain C residue 250 THR Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 38 ILE Chi-restraints excluded: chain D residue 133 THR Chi-restraints excluded: chain D residue 170 THR Chi-restraints excluded: chain D residue 221 TYR Chi-restraints excluded: chain E residue 31 THR Chi-restraints excluded: chain E residue 48 ASP Chi-restraints excluded: chain E residue 70 SER Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain E residue 115 ASN Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain E residue 152 LYS Chi-restraints excluded: chain E residue 196 VAL Chi-restraints excluded: chain E residue 207 ARG Chi-restraints excluded: chain F residue 77 ASP Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 108 PHE Chi-restraints excluded: chain F residue 112 GLU Chi-restraints excluded: chain F residue 133 VAL Chi-restraints excluded: chain G residue 50 ASP Chi-restraints excluded: chain G residue 86 VAL Chi-restraints excluded: chain G residue 92 VAL Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain I residue 48 LEU Chi-restraints excluded: chain I residue 61 ASP Chi-restraints excluded: chain I residue 87 GLN Chi-restraints excluded: chain I residue 98 VAL Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain J residue 26 GLN Chi-restraints excluded: chain J residue 48 ARG Chi-restraints excluded: chain K residue 5 ASP Chi-restraints excluded: chain K residue 17 SER Chi-restraints excluded: chain K residue 31 VAL Chi-restraints excluded: chain K residue 55 LYS Chi-restraints excluded: chain L residue 27 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 4 optimal weight: 2.9990 chunk 279 optimal weight: 0.5980 chunk 49 optimal weight: 1.9990 chunk 184 optimal weight: 0.3980 chunk 224 optimal weight: 0.9990 chunk 190 optimal weight: 0.6980 chunk 381 optimal weight: 1.9990 chunk 138 optimal weight: 1.9990 chunk 28 optimal weight: 0.9990 chunk 244 optimal weight: 0.8980 chunk 340 optimal weight: 3.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 397 ASN A 626 ASN A 838 GLN B 357 GLN ** D 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 179 GLN H 131 ASN L 66 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4084 r_free = 0.4084 target = 0.188897 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.116515 restraints weight = 27341.552| |-----------------------------------------------------------------------------| r_work (start): 0.3290 rms_B_bonded: 1.67 r_work: 0.3016 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2895 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.2895 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8648 moved from start: 0.1735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 1.064 33092 Z= 0.456 Angle : 0.577 24.416 44914 Z= 0.313 Chirality : 0.044 0.553 5050 Planarity : 0.004 0.044 5623 Dihedral : 12.941 125.631 4945 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.25 % Favored : 96.70 % Rotamer: Outliers : 3.12 % Allowed : 12.26 % Favored : 84.62 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 2.37 % 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: 0.41 (0.13), residues: 3879 helix: 1.26 (0.14), residues: 1355 sheet: 0.09 (0.20), residues: 622 loop : -0.32 (0.14), residues: 1902 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 393 TYR 0.015 0.001 TYR B 486 PHE 0.064 0.002 PHE D 70 TRP 0.014 0.001 TRP B 31 HIS 0.005 0.001 HIS E 99 Details of bonding type rmsd/Z covalent geometry : bond 0.01207 / 0.46 (33060) covalent geometry : angle 0.57009 / 0.31 (44869) hydrogen bonds : bond 0.04538 / 2.92 ( 1408) hydrogen bonds : angle 4.68791 / 3.29 ( 3910) metal coordination : bond 0.00340 / 0.23 ( 32) metal coordination : angle 2.91750 / 1.87 ( 45) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7758 Ramachandran restraints generated. 3879 Oldfield, 0 Emsley, 3879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7758 Ramachandran restraints generated. 3879 Oldfield, 0 Emsley, 3879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 527 residues out of total 3459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 419 time to evaluate : 1.269 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 PHE cc_start: 0.8843 (OUTLIER) cc_final: 0.7838 (t80) REVERT: A 36 ARG cc_start: 0.7574 (OUTLIER) cc_final: 0.7222 (mtt-85) REVERT: A 41 MET cc_start: 0.5995 (mmt) cc_final: 0.5430 (mpp) REVERT: A 68 GLN cc_start: 0.6816 (tt0) cc_final: 0.5877 (mp-120) REVERT: A 88 LYS cc_start: 0.7872 (mttp) cc_final: 0.7400 (mttt) REVERT: A 123 ARG cc_start: 0.7241 (OUTLIER) cc_final: 0.6592 (mtm110) REVERT: A 170 THR cc_start: 0.7603 (m) cc_final: 0.7233 (t) REVERT: A 175 ARG cc_start: 0.7600 (ttp80) cc_final: 0.7010 (mtp85) REVERT: A 180 LYS cc_start: 0.8136 (mtmt) cc_final: 0.7610 (mttp) REVERT: A 333 GLU cc_start: 0.8495 (OUTLIER) cc_final: 0.7920 (mm-30) REVERT: A 390 GLN cc_start: 0.7711 (tp40) cc_final: 0.7498 (tp40) REVERT: A 398 GLU cc_start: 0.7543 (tt0) cc_final: 0.7163 (tm-30) REVERT: A 447 GLN cc_start: 0.9185 (OUTLIER) cc_final: 0.8294 (mt0) REVERT: A 472 LEU cc_start: 0.8711 (OUTLIER) cc_final: 0.8174 (mt) REVERT: A 644 LYS cc_start: 0.8472 (mttt) cc_final: 0.7974 (mmmt) REVERT: A 685 GLU cc_start: 0.7530 (mt-10) cc_final: 0.6806 (tm-30) REVERT: A 696 GLU cc_start: 0.7358 (tm-30) cc_final: 0.6963 (tm-30) REVERT: A 712 GLU cc_start: 0.7052 (tt0) cc_final: 0.5916 (tm-30) REVERT: A 734 GLU cc_start: 0.7744 (tt0) cc_final: 0.7342 (tm-30) REVERT: A 822 GLU cc_start: 0.8187 (OUTLIER) cc_final: 0.7804 (mt-10) REVERT: A 833 GLU cc_start: 0.7887 (mt-10) cc_final: 0.7324 (tp30) REVERT: A 845 LEU cc_start: 0.7459 (OUTLIER) cc_final: 0.7108 (mt) REVERT: A 898 ARG cc_start: 0.8002 (OUTLIER) cc_final: 0.7395 (tmt-80) REVERT: A 912 LEU cc_start: 0.7303 (OUTLIER) cc_final: 0.6992 (pp) REVERT: A 924 LYS cc_start: 0.6335 (OUTLIER) cc_final: 0.5710 (mmtm) REVERT: A 931 GLU cc_start: 0.7049 (tt0) cc_final: 0.6580 (mm-30) REVERT: A 961 ARG cc_start: 0.7263 (mmt90) cc_final: 0.6741 (mtm180) REVERT: A 969 GLN cc_start: 0.7167 (mm110) cc_final: 0.6310 (tp40) REVERT: A 1005 GLU cc_start: 0.7979 (OUTLIER) cc_final: 0.7643 (mm-30) REVERT: A 1062 GLU cc_start: 0.8812 (tp30) cc_final: 0.8472 (tp30) REVERT: A 1077 THR cc_start: 0.7697 (m) cc_final: 0.7239 (p) REVERT: A 1135 ARG cc_start: 0.6686 (ttt180) cc_final: 0.5733 (ttt180) REVERT: A 1304 TRP cc_start: 0.7541 (m100) cc_final: 0.7204 (m100) REVERT: A 1407 GLU cc_start: 0.8216 (mp0) cc_final: 0.7830 (mp0) REVERT: A 1444 MET cc_start: 0.8475 (OUTLIER) cc_final: 0.7017 (mtm) REVERT: B 21 GLU cc_start: 0.7834 (pt0) cc_final: 0.7345 (mt-10) REVERT: B 46 GLN cc_start: 0.7964 (OUTLIER) cc_final: 0.7063 (pm20) REVERT: B 199 MET cc_start: 0.8222 (mmt) cc_final: 0.7174 (pmm) REVERT: B 270 LYS cc_start: 0.7014 (mtmp) cc_final: 0.6696 (mtmp) REVERT: B 357 GLN cc_start: 0.8100 (tt0) cc_final: 0.7682 (tt0) REVERT: B 393 LYS cc_start: 0.7591 (ttpt) cc_final: 0.6704 (mmtp) REVERT: B 398 ARG cc_start: 0.7762 (mtt-85) cc_final: 0.7208 (ttp-170) REVERT: B 422 LYS cc_start: 0.7414 (mmtm) cc_final: 0.6348 (tmmm) REVERT: B 423 LYS cc_start: 0.8077 (tttp) cc_final: 0.7581 (ttmm) REVERT: B 451 LYS cc_start: 0.7770 (mtmt) cc_final: 0.7239 (tmtt) REVERT: B 468 GLU cc_start: 0.7563 (mp0) cc_final: 0.6748 (mm-30) REVERT: B 498 THR cc_start: 0.8619 (m) cc_final: 0.8264 (p) REVERT: B 508 LEU cc_start: 0.6850 (OUTLIER) cc_final: 0.6179 (tp) REVERT: B 595 ARG cc_start: 0.7784 (ttt180) cc_final: 0.7282 (mpp-170) REVERT: B 621 GLU cc_start: 0.7832 (tp30) cc_final: 0.7533 (mm-30) REVERT: B 624 LEU cc_start: 0.8914 (OUTLIER) cc_final: 0.8517 (tt) REVERT: B 650 GLU cc_start: 0.6696 (OUTLIER) cc_final: 0.6282 (tm-30) REVERT: B 665 GLU cc_start: 0.7810 (tt0) cc_final: 0.7465 (tt0) REVERT: B 696 GLU cc_start: 0.8189 (OUTLIER) cc_final: 0.7967 (tp30) REVERT: B 727 LYS cc_start: 0.8371 (mttp) cc_final: 0.7900 (mttm) REVERT: B 873 THR cc_start: 0.7116 (m) cc_final: 0.6764 (t) REVERT: B 889 THR cc_start: 0.7963 (m) cc_final: 0.7670 (t) REVERT: B 1057 LYS cc_start: 0.8604 (mttt) cc_final: 0.8294 (mtpm) REVERT: B 1124 ARG cc_start: 0.8046 (mtm-85) cc_final: 0.7470 (mtp85) REVERT: B 1189 ILE cc_start: 0.8404 (OUTLIER) cc_final: 0.8105 (pp) REVERT: B 1219 ASP cc_start: 0.8504 (OUTLIER) cc_final: 0.8032 (p0) REVERT: C 12 GLU cc_start: 0.8178 (mt-10) cc_final: 0.7471 (tm-30) REVERT: C 102 GLN cc_start: 0.8457 (OUTLIER) cc_final: 0.8118 (mp10) REVERT: C 106 GLU cc_start: 0.8077 (mt-10) cc_final: 0.7602 (mm-30) REVERT: C 152 GLU cc_start: 0.8729 (tt0) cc_final: 0.8198 (tm-30) REVERT: C 264 GLN cc_start: 0.7160 (tp40) cc_final: 0.6749 (tp40) REVERT: D 47 LEU cc_start: 0.3057 (tp) cc_final: 0.2831 (mt) REVERT: E 33 GLU cc_start: 0.7714 (tt0) cc_final: 0.7264 (tm-30) REVERT: E 40 GLU cc_start: 0.6415 (mp0) cc_final: 0.5735 (mm-30) REVERT: E 57 MET cc_start: 0.7274 (mtm) cc_final: 0.6681 (mmm) REVERT: E 78 LEU cc_start: 0.8554 (OUTLIER) cc_final: 0.8308 (tt) REVERT: E 94 LYS cc_start: 0.7138 (mmmt) cc_final: 0.6902 (mmmt) REVERT: F 103 MET cc_start: 0.8221 (mtp) cc_final: 0.7777 (mtp) REVERT: F 112 GLU cc_start: 0.7253 (OUTLIER) cc_final: 0.6970 (mt-10) REVERT: F 149 GLU cc_start: 0.8066 (tt0) cc_final: 0.7524 (pm20) REVERT: G 1 MET cc_start: 0.0960 (OUTLIER) cc_final: 0.0744 (ptm) REVERT: G 115 MET cc_start: 0.1531 (mtp) cc_final: 0.1171 (mtp) REVERT: I 1 MET cc_start: 0.4631 (ttt) cc_final: 0.3700 (tmt) REVERT: J 48 ARG cc_start: 0.8957 (OUTLIER) cc_final: 0.8091 (tmm-80) REVERT: K 55 LYS cc_start: 0.9088 (OUTLIER) cc_final: 0.8652 (mtmp) outliers start: 108 outliers final: 55 residues processed: 496 average time/residue: 0.7873 time to fit residues: 460.1923 Evaluate side-chains 493 residues out of total 3459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 412 time to evaluate : 1.068 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 THR Chi-restraints excluded: chain A residue 22 PHE Chi-restraints excluded: chain A residue 36 ARG Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 123 ARG Chi-restraints excluded: chain A residue 291 GLU Chi-restraints excluded: chain A residue 333 GLU Chi-restraints excluded: chain A residue 380 VAL Chi-restraints excluded: chain A residue 447 GLN Chi-restraints excluded: chain A residue 472 LEU Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 701 LEU Chi-restraints excluded: chain A residue 703 THR Chi-restraints excluded: chain A residue 727 ASP Chi-restraints excluded: chain A residue 822 GLU Chi-restraints excluded: chain A residue 834 THR Chi-restraints excluded: chain A residue 845 LEU Chi-restraints excluded: chain A residue 898 ARG Chi-restraints excluded: chain A residue 907 THR Chi-restraints excluded: chain A residue 912 LEU Chi-restraints excluded: chain A residue 924 LYS Chi-restraints excluded: chain A residue 998 LEU Chi-restraints excluded: chain A residue 1005 GLU Chi-restraints excluded: chain A residue 1283 VAL Chi-restraints excluded: chain A residue 1438 THR Chi-restraints excluded: chain A residue 1444 MET Chi-restraints excluded: chain B residue 46 GLN Chi-restraints excluded: chain B residue 58 THR Chi-restraints excluded: chain B residue 77 HIS Chi-restraints excluded: chain B residue 298 LEU Chi-restraints excluded: chain B residue 305 VAL Chi-restraints excluded: chain B residue 487 THR Chi-restraints excluded: chain B residue 508 LEU Chi-restraints excluded: chain B residue 541 LEU Chi-restraints excluded: chain B residue 547 VAL Chi-restraints excluded: chain B residue 624 LEU Chi-restraints excluded: chain B residue 650 GLU Chi-restraints excluded: chain B residue 696 GLU Chi-restraints excluded: chain B residue 839 MET Chi-restraints excluded: chain B residue 903 VAL Chi-restraints excluded: chain B residue 955 THR Chi-restraints excluded: chain B residue 1150 ARG Chi-restraints excluded: chain B residue 1160 VAL Chi-restraints excluded: chain B residue 1189 ILE Chi-restraints excluded: chain B residue 1219 ASP Chi-restraints excluded: chain C residue 18 VAL Chi-restraints excluded: chain C residue 25 VAL Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 43 THR Chi-restraints excluded: chain C residue 53 THR Chi-restraints excluded: chain C residue 56 THR Chi-restraints excluded: chain C residue 102 GLN Chi-restraints excluded: chain C residue 189 THR Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 133 THR Chi-restraints excluded: chain D residue 170 THR Chi-restraints excluded: chain D residue 221 TYR Chi-restraints excluded: chain E residue 31 THR Chi-restraints excluded: chain E residue 48 ASP Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain E residue 98 ILE Chi-restraints excluded: chain E residue 115 ASN Chi-restraints excluded: chain E residue 152 LYS Chi-restraints excluded: chain E residue 196 VAL Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 112 GLU Chi-restraints excluded: chain F residue 133 VAL Chi-restraints excluded: chain G residue 1 MET Chi-restraints excluded: chain G residue 50 ASP Chi-restraints excluded: chain G residue 86 VAL Chi-restraints excluded: chain G residue 92 VAL Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain I residue 48 LEU Chi-restraints excluded: chain I residue 61 ASP Chi-restraints excluded: chain I residue 87 GLN Chi-restraints excluded: chain I residue 98 VAL Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain J residue 48 ARG Chi-restraints excluded: chain K residue 31 VAL Chi-restraints excluded: chain K residue 55 LYS Chi-restraints excluded: chain L residue 27 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 27 optimal weight: 8.9990 chunk 212 optimal weight: 3.9990 chunk 381 optimal weight: 0.9990 chunk 230 optimal weight: 0.5980 chunk 382 optimal weight: 0.8980 chunk 208 optimal weight: 1.9990 chunk 231 optimal weight: 4.9990 chunk 365 optimal weight: 20.0000 chunk 286 optimal weight: 8.9990 chunk 71 optimal weight: 0.8980 chunk 177 optimal weight: 4.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 626 ASN A 838 GLN C 24 ASN ** D 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 115 ASN E 179 GLN H 131 ASN H 134 ASN I 90 GLN L 66 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4084 r_free = 0.4084 target = 0.188826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.116814 restraints weight = 27423.381| |-----------------------------------------------------------------------------| r_work (start): 0.3293 rms_B_bonded: 1.68 r_work: 0.3008 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2892 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.2892 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8659 moved from start: 0.1797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 1.064 33092 Z= 0.457 Angle : 0.577 24.415 44914 Z= 0.313 Chirality : 0.044 0.552 5050 Planarity : 0.004 0.043 5623 Dihedral : 12.826 127.179 4940 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.51 % Favored : 96.44 % Rotamer: Outliers : 3.24 % Allowed : 12.40 % Favored : 84.36 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 2.37 % 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: 0.50 (0.13), residues: 3879 helix: 1.34 (0.14), residues: 1357 sheet: 0.13 (0.20), residues: 618 loop : -0.26 (0.14), residues: 1904 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A1366 TYR 0.015 0.001 TYR B 486 PHE 0.063 0.002 PHE D 70 TRP 0.014 0.001 TRP B 31 HIS 0.009 0.001 HIS A1173 Details of bonding type rmsd/Z covalent geometry : bond 0.01210 / 0.46 (33060) covalent geometry : angle 0.57032 / 0.31 (44869) hydrogen bonds : bond 0.04514 / 2.90 ( 1408) hydrogen bonds : angle 4.61495 / 3.24 ( 3910) metal coordination : bond 0.00313 / 0.21 ( 32) metal coordination : angle 2.82449 / 1.79 ( 45) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7758 Ramachandran restraints generated. 3879 Oldfield, 0 Emsley, 3879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7758 Ramachandran restraints generated. 3879 Oldfield, 0 Emsley, 3879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 524 residues out of total 3459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 412 time to evaluate : 1.306 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 PHE cc_start: 0.8822 (OUTLIER) cc_final: 0.7943 (t80) REVERT: A 36 ARG cc_start: 0.7601 (OUTLIER) cc_final: 0.7245 (mtt-85) REVERT: A 41 MET cc_start: 0.6028 (mmt) cc_final: 0.5474 (mpp) REVERT: A 68 GLN cc_start: 0.6830 (tt0) cc_final: 0.5938 (mp-120) REVERT: A 88 LYS cc_start: 0.7886 (mttp) cc_final: 0.7362 (mttt) REVERT: A 123 ARG cc_start: 0.7349 (OUTLIER) cc_final: 0.6724 (mtm110) REVERT: A 170 THR cc_start: 0.7607 (m) cc_final: 0.7242 (t) REVERT: A 175 ARG cc_start: 0.7591 (ttp80) cc_final: 0.6915 (mtp85) REVERT: A 180 LYS cc_start: 0.8199 (mtmt) cc_final: 0.7693 (mttp) REVERT: A 398 GLU cc_start: 0.7574 (tt0) cc_final: 0.7187 (tm-30) REVERT: A 447 GLN cc_start: 0.9204 (OUTLIER) cc_final: 0.8316 (mt0) REVERT: A 472 LEU cc_start: 0.8748 (OUTLIER) cc_final: 0.8210 (mt) REVERT: A 644 LYS cc_start: 0.8514 (mttt) cc_final: 0.8015 (mmmt) REVERT: A 685 GLU cc_start: 0.7546 (mt-10) cc_final: 0.6811 (tm-30) REVERT: A 696 GLU cc_start: 0.7410 (tm-30) cc_final: 0.7021 (tm-30) REVERT: A 712 GLU cc_start: 0.7123 (tt0) cc_final: 0.5984 (tm-30) REVERT: A 734 GLU cc_start: 0.7752 (tt0) cc_final: 0.7347 (tm-30) REVERT: A 822 GLU cc_start: 0.8208 (OUTLIER) cc_final: 0.7828 (mt-10) REVERT: A 833 GLU cc_start: 0.7849 (mt-10) cc_final: 0.7293 (tp30) REVERT: A 845 LEU cc_start: 0.7479 (OUTLIER) cc_final: 0.7111 (mt) REVERT: A 898 ARG cc_start: 0.8039 (OUTLIER) cc_final: 0.7432 (tmt-80) REVERT: A 912 LEU cc_start: 0.7343 (OUTLIER) cc_final: 0.7053 (pp) REVERT: A 924 LYS cc_start: 0.6321 (OUTLIER) cc_final: 0.5682 (mmtm) REVERT: A 931 GLU cc_start: 0.7179 (tt0) cc_final: 0.6723 (mm-30) REVERT: A 961 ARG cc_start: 0.7269 (mmt90) cc_final: 0.6776 (mtm180) REVERT: A 969 GLN cc_start: 0.7308 (mm110) cc_final: 0.6447 (tp40) REVERT: A 1005 GLU cc_start: 0.8025 (OUTLIER) cc_final: 0.7668 (mm-30) REVERT: A 1062 GLU cc_start: 0.8800 (tp30) cc_final: 0.8469 (tp30) REVERT: A 1077 THR cc_start: 0.7685 (m) cc_final: 0.7226 (p) REVERT: A 1132 LYS cc_start: 0.7130 (OUTLIER) cc_final: 0.6721 (mtmt) REVERT: A 1135 ARG cc_start: 0.6719 (ttt180) cc_final: 0.5766 (ttt180) REVERT: A 1304 TRP cc_start: 0.7556 (m100) cc_final: 0.7225 (m100) REVERT: A 1407 GLU cc_start: 0.8229 (mp0) cc_final: 0.7841 (mp0) REVERT: A 1444 MET cc_start: 0.8513 (OUTLIER) cc_final: 0.7025 (mtm) REVERT: B 21 GLU cc_start: 0.7872 (pt0) cc_final: 0.7387 (mt-10) REVERT: B 46 GLN cc_start: 0.7996 (OUTLIER) cc_final: 0.7104 (pm20) REVERT: B 199 MET cc_start: 0.8266 (mmt) cc_final: 0.7258 (pmm) REVERT: B 357 GLN cc_start: 0.8168 (tt0) cc_final: 0.7828 (tt0) REVERT: B 393 LYS cc_start: 0.7585 (ttpt) cc_final: 0.6724 (mmtp) REVERT: B 398 ARG cc_start: 0.7764 (mtt-85) cc_final: 0.7217 (ttp-170) REVERT: B 422 LYS cc_start: 0.7457 (mmtm) cc_final: 0.6422 (tmmm) REVERT: B 423 LYS cc_start: 0.8125 (tttp) cc_final: 0.7632 (ttmm) REVERT: B 451 LYS cc_start: 0.7809 (mtmt) cc_final: 0.7255 (tmtt) REVERT: B 468 GLU cc_start: 0.7591 (mp0) cc_final: 0.6761 (mm-30) REVERT: B 498 THR cc_start: 0.8640 (OUTLIER) cc_final: 0.8295 (p) REVERT: B 508 LEU cc_start: 0.6821 (OUTLIER) cc_final: 0.6148 (tp) REVERT: B 595 ARG cc_start: 0.7766 (ttt180) cc_final: 0.7328 (mpp-170) REVERT: B 621 GLU cc_start: 0.7864 (tp30) cc_final: 0.7577 (mm-30) REVERT: B 624 LEU cc_start: 0.8923 (OUTLIER) cc_final: 0.8535 (tt) REVERT: B 650 GLU cc_start: 0.6729 (OUTLIER) cc_final: 0.6327 (tm-30) REVERT: B 665 GLU cc_start: 0.7841 (tt0) cc_final: 0.7497 (tt0) REVERT: B 696 GLU cc_start: 0.8219 (OUTLIER) cc_final: 0.7985 (tp30) REVERT: B 727 LYS cc_start: 0.8358 (mttp) cc_final: 0.7886 (mttm) REVERT: B 873 THR cc_start: 0.7107 (m) cc_final: 0.6811 (t) REVERT: B 889 THR cc_start: 0.7896 (m) cc_final: 0.7628 (t) REVERT: B 1057 LYS cc_start: 0.8631 (mttt) cc_final: 0.8326 (mtpm) REVERT: B 1124 ARG cc_start: 0.8082 (mtm-85) cc_final: 0.7504 (mtp85) REVERT: B 1189 ILE cc_start: 0.8411 (OUTLIER) cc_final: 0.8117 (pp) REVERT: B 1219 ASP cc_start: 0.8540 (OUTLIER) cc_final: 0.8022 (p0) REVERT: C 12 GLU cc_start: 0.8188 (mt-10) cc_final: 0.7486 (tm-30) REVERT: C 102 GLN cc_start: 0.8454 (OUTLIER) cc_final: 0.8124 (mp10) REVERT: C 106 GLU cc_start: 0.8122 (mt-10) cc_final: 0.7625 (mm-30) REVERT: C 152 GLU cc_start: 0.8734 (tt0) cc_final: 0.8209 (tm-30) REVERT: C 264 GLN cc_start: 0.7167 (tp40) cc_final: 0.6762 (tp40) REVERT: D 47 LEU cc_start: 0.3165 (tp) cc_final: 0.2933 (mt) REVERT: E 33 GLU cc_start: 0.7721 (tt0) cc_final: 0.7290 (tm-30) REVERT: E 40 GLU cc_start: 0.6369 (mp0) cc_final: 0.5683 (mm-30) REVERT: E 57 MET cc_start: 0.7251 (mtm) cc_final: 0.6657 (mmm) REVERT: E 78 LEU cc_start: 0.8586 (OUTLIER) cc_final: 0.8321 (tt) REVERT: E 94 LYS cc_start: 0.7166 (mmmt) cc_final: 0.6925 (mmmt) REVERT: F 103 MET cc_start: 0.8236 (mtp) cc_final: 0.7770 (mtp) REVERT: F 112 GLU cc_start: 0.7253 (OUTLIER) cc_final: 0.6969 (mt-10) REVERT: F 123 LYS cc_start: 0.8457 (tttm) cc_final: 0.8160 (tttt) REVERT: F 149 GLU cc_start: 0.8130 (tt0) cc_final: 0.7671 (pm20) REVERT: G 1 MET cc_start: 0.0923 (OUTLIER) cc_final: 0.0696 (ptm) REVERT: G 115 MET cc_start: 0.1503 (mtp) cc_final: 0.1123 (mtp) REVERT: I 1 MET cc_start: 0.4629 (ttt) cc_final: 0.3732 (tmt) REVERT: J 26 GLN cc_start: 0.7356 (OUTLIER) cc_final: 0.6155 (mt0) REVERT: J 48 ARG cc_start: 0.8999 (OUTLIER) cc_final: 0.8075 (tmm-80) REVERT: K 55 LYS cc_start: 0.9081 (OUTLIER) cc_final: 0.8561 (mtmp) outliers start: 112 outliers final: 65 residues processed: 490 average time/residue: 0.7807 time to fit residues: 449.9851 Evaluate side-chains 500 residues out of total 3459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 407 time to evaluate : 1.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 THR Chi-restraints excluded: chain A residue 22 PHE Chi-restraints excluded: chain A residue 36 ARG Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 123 ARG Chi-restraints excluded: chain A residue 167 CYS Chi-restraints excluded: chain A residue 291 GLU Chi-restraints excluded: chain A residue 380 VAL Chi-restraints excluded: chain A residue 447 GLN Chi-restraints excluded: chain A residue 472 LEU Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 701 LEU Chi-restraints excluded: chain A residue 703 THR Chi-restraints excluded: chain A residue 727 ASP Chi-restraints excluded: chain A residue 822 GLU Chi-restraints excluded: chain A residue 834 THR Chi-restraints excluded: chain A residue 845 LEU Chi-restraints excluded: chain A residue 885 THR Chi-restraints excluded: chain A residue 898 ARG Chi-restraints excluded: chain A residue 907 THR Chi-restraints excluded: chain A residue 912 LEU Chi-restraints excluded: chain A residue 924 LYS Chi-restraints excluded: chain A residue 998 LEU Chi-restraints excluded: chain A residue 1005 GLU Chi-restraints excluded: chain A residue 1036 ARG Chi-restraints excluded: chain A residue 1112 LYS Chi-restraints excluded: chain A residue 1128 GLN Chi-restraints excluded: chain A residue 1132 LYS Chi-restraints excluded: chain A residue 1283 VAL Chi-restraints excluded: chain A residue 1322 ILE Chi-restraints excluded: chain A residue 1438 THR Chi-restraints excluded: chain A residue 1444 MET Chi-restraints excluded: chain B residue 46 GLN Chi-restraints excluded: chain B residue 58 THR Chi-restraints excluded: chain B residue 77 HIS Chi-restraints excluded: chain B residue 298 LEU Chi-restraints excluded: chain B residue 305 VAL Chi-restraints excluded: chain B residue 487 THR Chi-restraints excluded: chain B residue 498 THR Chi-restraints excluded: chain B residue 508 LEU Chi-restraints excluded: chain B residue 531 GLN Chi-restraints excluded: chain B residue 541 LEU Chi-restraints excluded: chain B residue 547 VAL Chi-restraints excluded: chain B residue 624 LEU Chi-restraints excluded: chain B residue 650 GLU Chi-restraints excluded: chain B residue 696 GLU Chi-restraints excluded: chain B residue 737 THR Chi-restraints excluded: chain B residue 839 MET Chi-restraints excluded: chain B residue 903 VAL Chi-restraints excluded: chain B residue 955 THR Chi-restraints excluded: chain B residue 1150 ARG Chi-restraints excluded: chain B residue 1160 VAL Chi-restraints excluded: chain B residue 1189 ILE Chi-restraints excluded: chain B residue 1219 ASP Chi-restraints excluded: chain C residue 18 VAL Chi-restraints excluded: chain C residue 25 VAL Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 43 THR Chi-restraints excluded: chain C residue 53 THR Chi-restraints excluded: chain C residue 56 THR Chi-restraints excluded: chain C residue 102 GLN Chi-restraints excluded: chain C residue 189 THR Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 38 ILE Chi-restraints excluded: chain D residue 133 THR Chi-restraints excluded: chain D residue 170 THR Chi-restraints excluded: chain D residue 221 TYR Chi-restraints excluded: chain E residue 31 THR Chi-restraints excluded: chain E residue 48 ASP Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain E residue 98 ILE Chi-restraints excluded: chain E residue 115 ASN Chi-restraints excluded: chain E residue 152 LYS Chi-restraints excluded: chain E residue 196 VAL Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 108 PHE Chi-restraints excluded: chain F residue 112 GLU Chi-restraints excluded: chain F residue 133 VAL Chi-restraints excluded: chain G residue 1 MET Chi-restraints excluded: chain G residue 50 ASP Chi-restraints excluded: chain G residue 86 VAL Chi-restraints excluded: chain G residue 92 VAL Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain I residue 48 LEU Chi-restraints excluded: chain I residue 61 ASP Chi-restraints excluded: chain I residue 87 GLN Chi-restraints excluded: chain I residue 98 VAL Chi-restraints excluded: chain J residue 26 GLN Chi-restraints excluded: chain J residue 48 ARG Chi-restraints excluded: chain K residue 5 ASP Chi-restraints excluded: chain K residue 31 VAL Chi-restraints excluded: chain K residue 55 LYS Chi-restraints excluded: chain L residue 27 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 282 optimal weight: 20.0000 chunk 58 optimal weight: 5.9990 chunk 179 optimal weight: 4.9990 chunk 91 optimal weight: 0.7980 chunk 371 optimal weight: 0.7980 chunk 249 optimal weight: 0.0670 chunk 70 optimal weight: 7.9990 chunk 358 optimal weight: 0.7980 chunk 104 optimal weight: 7.9990 chunk 376 optimal weight: 0.9990 chunk 90 optimal weight: 0.9980 overall best weight: 0.6918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 397 ASN A 626 ASN A 838 GLN C 24 ASN ** D 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 179 GLN H 131 ASN H 134 ASN L 66 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.189864 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.118535 restraints weight = 27404.562| |-----------------------------------------------------------------------------| r_work (start): 0.3318 rms_B_bonded: 1.62 r_work: 0.3040 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2921 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.2921 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8612 moved from start: 0.1849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 1.065 33092 Z= 0.452 Angle : 0.554 24.425 44914 Z= 0.301 Chirality : 0.043 0.550 5050 Planarity : 0.004 0.044 5623 Dihedral : 12.754 127.772 4940 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.12 % Favored : 96.83 % Rotamer: Outliers : 2.92 % Allowed : 12.86 % Favored : 84.22 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 2.37 % 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: 0.57 (0.14), residues: 3879 helix: 1.44 (0.14), residues: 1356 sheet: 0.14 (0.20), residues: 618 loop : -0.24 (0.15), residues: 1905 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 393 TYR 0.013 0.001 TYR B 486 PHE 0.063 0.002 PHE D 70 TRP 0.013 0.001 TRP B 31 HIS 0.005 0.001 HIS A 399 Details of bonding type rmsd/Z covalent geometry : bond 0.01199 / 0.45 (33060) covalent geometry : angle 0.54801 / 0.30 (44869) hydrogen bonds : bond 0.04206 / 2.70 ( 1408) hydrogen bonds : angle 4.52075 / 3.18 ( 3910) metal coordination : bond 0.00278 / 0.18 ( 32) metal coordination : angle 2.63327 / 1.68 ( 45) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7758 Ramachandran restraints generated. 3879 Oldfield, 0 Emsley, 3879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7758 Ramachandran restraints generated. 3879 Oldfield, 0 Emsley, 3879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 516 residues out of total 3459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 415 time to evaluate : 1.220 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 PHE cc_start: 0.8783 (OUTLIER) cc_final: 0.7875 (t80) REVERT: A 36 ARG cc_start: 0.7552 (OUTLIER) cc_final: 0.7196 (mtt-85) REVERT: A 41 MET cc_start: 0.6023 (mmt) cc_final: 0.5471 (mpp) REVERT: A 63 ARG cc_start: 0.7119 (ptt90) cc_final: 0.6457 (tmt-80) REVERT: A 66 LYS cc_start: 0.7278 (mttm) cc_final: 0.6950 (mptm) REVERT: A 68 GLN cc_start: 0.6814 (tt0) cc_final: 0.5885 (mp-120) REVERT: A 88 LYS cc_start: 0.7848 (mttp) cc_final: 0.7384 (mttt) REVERT: A 123 ARG cc_start: 0.7245 (OUTLIER) cc_final: 0.6719 (mtm110) REVERT: A 175 ARG cc_start: 0.7576 (ttp80) cc_final: 0.6865 (mtp85) REVERT: A 180 LYS cc_start: 0.8137 (mtmt) cc_final: 0.7624 (mttp) REVERT: A 217 LYS cc_start: 0.7555 (mtpt) cc_final: 0.7288 (ttmm) REVERT: A 390 GLN cc_start: 0.7658 (tp40) cc_final: 0.7328 (tp40) REVERT: A 398 GLU cc_start: 0.7439 (tt0) cc_final: 0.7036 (tm-30) REVERT: A 447 GLN cc_start: 0.9187 (OUTLIER) cc_final: 0.8292 (mt0) REVERT: A 472 LEU cc_start: 0.8668 (OUTLIER) cc_final: 0.8135 (mt) REVERT: A 644 LYS cc_start: 0.8446 (mttt) cc_final: 0.7946 (mmmt) REVERT: A 685 GLU cc_start: 0.7443 (mt-10) cc_final: 0.6745 (tm-30) REVERT: A 696 GLU cc_start: 0.7264 (tm-30) cc_final: 0.6882 (tm-30) REVERT: A 712 GLU cc_start: 0.6999 (tt0) cc_final: 0.5850 (tm-30) REVERT: A 734 GLU cc_start: 0.7677 (tt0) cc_final: 0.7269 (tm-30) REVERT: A 822 GLU cc_start: 0.8149 (OUTLIER) cc_final: 0.7759 (mt-10) REVERT: A 833 GLU cc_start: 0.7788 (mt-10) cc_final: 0.7255 (tp30) REVERT: A 845 LEU cc_start: 0.7366 (OUTLIER) cc_final: 0.7043 (mt) REVERT: A 898 ARG cc_start: 0.7944 (tmt-80) cc_final: 0.7712 (tmt-80) REVERT: A 912 LEU cc_start: 0.7227 (OUTLIER) cc_final: 0.6931 (pp) REVERT: A 924 LYS cc_start: 0.6236 (OUTLIER) cc_final: 0.5600 (mmtm) REVERT: A 931 GLU cc_start: 0.7062 (tt0) cc_final: 0.6613 (mm-30) REVERT: A 961 ARG cc_start: 0.7189 (mmt90) cc_final: 0.6621 (mtm180) REVERT: A 969 GLN cc_start: 0.7353 (mm110) cc_final: 0.6445 (tp40) REVERT: A 1005 GLU cc_start: 0.7948 (OUTLIER) cc_final: 0.7585 (mm-30) REVERT: A 1062 GLU cc_start: 0.8768 (tp30) cc_final: 0.8423 (tp30) REVERT: A 1077 THR cc_start: 0.7629 (m) cc_final: 0.7187 (p) REVERT: A 1132 LYS cc_start: 0.7095 (OUTLIER) cc_final: 0.6743 (mttm) REVERT: A 1135 ARG cc_start: 0.6602 (ttt180) cc_final: 0.5667 (ttt180) REVERT: A 1407 GLU cc_start: 0.8183 (mp0) cc_final: 0.7783 (mp0) REVERT: A 1444 MET cc_start: 0.8449 (OUTLIER) cc_final: 0.6918 (mmm) REVERT: B 21 GLU cc_start: 0.7799 (pt0) cc_final: 0.7327 (mt-10) REVERT: B 46 GLN cc_start: 0.7912 (OUTLIER) cc_final: 0.6995 (pm20) REVERT: B 199 MET cc_start: 0.8236 (mmt) cc_final: 0.7195 (pmm) REVERT: B 357 GLN cc_start: 0.8129 (tt0) cc_final: 0.7824 (tt0) REVERT: B 393 LYS cc_start: 0.7573 (ttpt) cc_final: 0.6697 (mmtp) REVERT: B 398 ARG cc_start: 0.7688 (mtt-85) cc_final: 0.7186 (ttp-170) REVERT: B 422 LYS cc_start: 0.7381 (mmtm) cc_final: 0.6322 (tmmm) REVERT: B 423 LYS cc_start: 0.8037 (tttp) cc_final: 0.7547 (ttmm) REVERT: B 451 LYS cc_start: 0.7719 (mtmt) cc_final: 0.7183 (tmtt) REVERT: B 468 GLU cc_start: 0.7555 (mp0) cc_final: 0.6694 (mm-30) REVERT: B 498 THR cc_start: 0.8565 (m) cc_final: 0.8248 (p) REVERT: B 508 LEU cc_start: 0.6797 (OUTLIER) cc_final: 0.6107 (tp) REVERT: B 595 ARG cc_start: 0.7735 (ttt180) cc_final: 0.7261 (mpp-170) REVERT: B 621 GLU cc_start: 0.7795 (tp30) cc_final: 0.7510 (mm-30) REVERT: B 624 LEU cc_start: 0.8875 (OUTLIER) cc_final: 0.8479 (tt) REVERT: B 650 GLU cc_start: 0.6636 (OUTLIER) cc_final: 0.6222 (tm-30) REVERT: B 665 GLU cc_start: 0.7772 (tt0) cc_final: 0.7474 (tt0) REVERT: B 727 LYS cc_start: 0.8325 (mttp) cc_final: 0.7848 (mttm) REVERT: B 873 THR cc_start: 0.7025 (m) cc_final: 0.6720 (t) REVERT: B 889 THR cc_start: 0.7877 (m) cc_final: 0.7605 (t) REVERT: B 1057 LYS cc_start: 0.8563 (mttt) cc_final: 0.8248 (mtpm) REVERT: B 1124 ARG cc_start: 0.8026 (mtm-85) cc_final: 0.7449 (mtp85) REVERT: B 1189 ILE cc_start: 0.8367 (OUTLIER) cc_final: 0.8081 (pp) REVERT: B 1219 ASP cc_start: 0.8429 (OUTLIER) cc_final: 0.7910 (p0) REVERT: C 12 GLU cc_start: 0.8146 (mt-10) cc_final: 0.7438 (tm-30) REVERT: C 102 GLN cc_start: 0.8419 (OUTLIER) cc_final: 0.8089 (mp10) REVERT: C 106 GLU cc_start: 0.8059 (mt-10) cc_final: 0.7578 (mm-30) REVERT: C 152 GLU cc_start: 0.8693 (tt0) cc_final: 0.8157 (tm-30) REVERT: C 264 GLN cc_start: 0.7098 (tp40) cc_final: 0.6683 (tp40) REVERT: D 47 LEU cc_start: 0.3106 (tp) cc_final: 0.2885 (mt) REVERT: E 33 GLU cc_start: 0.7744 (tt0) cc_final: 0.7281 (tm-30) REVERT: E 40 GLU cc_start: 0.6390 (mp0) cc_final: 0.5709 (mm-30) REVERT: E 57 MET cc_start: 0.7218 (mtm) cc_final: 0.6635 (mmm) REVERT: E 78 LEU cc_start: 0.8542 (OUTLIER) cc_final: 0.8295 (tt) REVERT: E 94 LYS cc_start: 0.7175 (mmmt) cc_final: 0.6938 (mmmt) REVERT: F 103 MET cc_start: 0.8174 (mtp) cc_final: 0.7730 (mtp) REVERT: F 112 GLU cc_start: 0.7270 (OUTLIER) cc_final: 0.7059 (mt-10) REVERT: F 149 GLU cc_start: 0.8021 (tt0) cc_final: 0.7581 (pm20) REVERT: G 115 MET cc_start: 0.1586 (mtp) cc_final: 0.1242 (mtp) REVERT: I 1 MET cc_start: 0.4580 (ttt) cc_final: 0.3691 (tmt) REVERT: J 26 GLN cc_start: 0.7293 (OUTLIER) cc_final: 0.6156 (mt0) REVERT: J 48 ARG cc_start: 0.8942 (OUTLIER) cc_final: 0.8052 (tmm-80) outliers start: 101 outliers final: 61 residues processed: 489 average time/residue: 0.7474 time to fit residues: 430.1771 Evaluate side-chains 495 residues out of total 3459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 411 time to evaluate : 1.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 THR Chi-restraints excluded: chain A residue 22 PHE Chi-restraints excluded: chain A residue 36 ARG Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 123 ARG Chi-restraints excluded: chain A residue 291 GLU Chi-restraints excluded: chain A residue 380 VAL Chi-restraints excluded: chain A residue 447 GLN Chi-restraints excluded: chain A residue 472 LEU Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 701 LEU Chi-restraints excluded: chain A residue 703 THR Chi-restraints excluded: chain A residue 727 ASP Chi-restraints excluded: chain A residue 822 GLU Chi-restraints excluded: chain A residue 834 THR Chi-restraints excluded: chain A residue 845 LEU Chi-restraints excluded: chain A residue 885 THR Chi-restraints excluded: chain A residue 907 THR Chi-restraints excluded: chain A residue 912 LEU Chi-restraints excluded: chain A residue 924 LYS Chi-restraints excluded: chain A residue 998 LEU Chi-restraints excluded: chain A residue 1005 GLU Chi-restraints excluded: chain A residue 1036 ARG Chi-restraints excluded: chain A residue 1132 LYS Chi-restraints excluded: chain A residue 1283 VAL Chi-restraints excluded: chain A residue 1322 ILE Chi-restraints excluded: chain A residue 1438 THR Chi-restraints excluded: chain A residue 1444 MET Chi-restraints excluded: chain B residue 46 GLN Chi-restraints excluded: chain B residue 58 THR Chi-restraints excluded: chain B residue 77 HIS Chi-restraints excluded: chain B residue 298 LEU Chi-restraints excluded: chain B residue 305 VAL Chi-restraints excluded: chain B residue 487 THR Chi-restraints excluded: chain B residue 508 LEU Chi-restraints excluded: chain B residue 531 GLN Chi-restraints excluded: chain B residue 541 LEU Chi-restraints excluded: chain B residue 547 VAL Chi-restraints excluded: chain B residue 624 LEU Chi-restraints excluded: chain B residue 650 GLU Chi-restraints excluded: chain B residue 737 THR Chi-restraints excluded: chain B residue 839 MET Chi-restraints excluded: chain B residue 903 VAL Chi-restraints excluded: chain B residue 955 THR Chi-restraints excluded: chain B residue 1150 ARG Chi-restraints excluded: chain B residue 1160 VAL Chi-restraints excluded: chain B residue 1189 ILE Chi-restraints excluded: chain B residue 1219 ASP Chi-restraints excluded: chain C residue 18 VAL Chi-restraints excluded: chain C residue 25 VAL Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 43 THR Chi-restraints excluded: chain C residue 53 THR Chi-restraints excluded: chain C residue 56 THR Chi-restraints excluded: chain C residue 102 GLN Chi-restraints excluded: chain C residue 189 THR Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 133 THR Chi-restraints excluded: chain D residue 170 THR Chi-restraints excluded: chain D residue 221 TYR Chi-restraints excluded: chain E residue 31 THR Chi-restraints excluded: chain E residue 48 ASP Chi-restraints excluded: chain E residue 70 SER Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain E residue 98 ILE Chi-restraints excluded: chain E residue 196 VAL Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 108 PHE Chi-restraints excluded: chain F residue 112 GLU Chi-restraints excluded: chain F residue 133 VAL Chi-restraints excluded: chain G residue 50 ASP Chi-restraints excluded: chain G residue 86 VAL Chi-restraints excluded: chain G residue 92 VAL Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain I residue 48 LEU Chi-restraints excluded: chain I residue 61 ASP Chi-restraints excluded: chain I residue 98 VAL Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain J residue 26 GLN Chi-restraints excluded: chain J residue 48 ARG Chi-restraints excluded: chain K residue 5 ASP Chi-restraints excluded: chain K residue 31 VAL Chi-restraints excluded: chain K residue 55 LYS Chi-restraints excluded: chain L residue 27 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 337 optimal weight: 4.9990 chunk 67 optimal weight: 6.9990 chunk 382 optimal weight: 3.9990 chunk 374 optimal weight: 6.9990 chunk 160 optimal weight: 8.9990 chunk 117 optimal weight: 1.9990 chunk 221 optimal weight: 0.9980 chunk 378 optimal weight: 1.9990 chunk 192 optimal weight: 7.9990 chunk 230 optimal weight: 2.9990 chunk 99 optimal weight: 2.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 479 ASN A 626 ASN A 838 GLN C 24 ASN ** D 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 179 GLN E 115 ASN E 179 GLN H 131 ASN H 134 ASN L 66 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4083 r_free = 0.4083 target = 0.189206 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.139127 restraints weight = 27169.875| |-----------------------------------------------------------------------------| r_work (start): 0.3557 rms_B_bonded: 2.29 r_work: 0.2975 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.2855 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.2855 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8841 moved from start: 0.1870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.013 1.064 33092 Z= 0.477 Angle : 0.635 24.371 44914 Z= 0.342 Chirality : 0.047 0.546 5050 Planarity : 0.005 0.063 5623 Dihedral : 12.836 127.886 4940 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.61 % Favored : 96.34 % Rotamer: Outliers : 3.09 % Allowed : 12.86 % Favored : 84.04 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 2.37 % 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: 0.44 (0.13), residues: 3879 helix: 1.27 (0.14), residues: 1355 sheet: 0.14 (0.20), residues: 621 loop : -0.30 (0.14), residues: 1903 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 393 TYR 0.019 0.002 TYR B 486 PHE 0.062 0.002 PHE D 70 TRP 0.013 0.002 TRP B 31 HIS 0.009 0.001 HIS A 399 Details of bonding type rmsd/Z covalent geometry : bond 0.01252 / 0.48 (33060) covalent geometry : angle 0.62842 / 0.34 (44869) hydrogen bonds : bond 0.05081 / 3.29 ( 1408) hydrogen bonds : angle 4.69294 / 3.29 ( 3910) metal coordination : bond 0.00390 / 0.27 ( 32) metal coordination : angle 3.03105 / 1.92 ( 45) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7758 Ramachandran restraints generated. 3879 Oldfield, 0 Emsley, 3879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7758 Ramachandran restraints generated. 3879 Oldfield, 0 Emsley, 3879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 516 residues out of total 3459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 409 time to evaluate : 1.264 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 PHE cc_start: 0.8961 (OUTLIER) cc_final: 0.7953 (t80) REVERT: A 36 ARG cc_start: 0.7772 (OUTLIER) cc_final: 0.7422 (mtt-85) REVERT: A 41 MET cc_start: 0.6344 (mmt) cc_final: 0.5936 (mmm) REVERT: A 66 LYS cc_start: 0.7620 (mttm) cc_final: 0.7321 (mptm) REVERT: A 68 GLN cc_start: 0.6808 (tt0) cc_final: 0.5976 (mp-120) REVERT: A 88 LYS cc_start: 0.8024 (mttp) cc_final: 0.7561 (mttt) REVERT: A 123 ARG cc_start: 0.7592 (OUTLIER) cc_final: 0.7012 (mtm110) REVERT: A 175 ARG cc_start: 0.7790 (ttp80) cc_final: 0.7280 (mtp85) REVERT: A 180 LYS cc_start: 0.8344 (mtmt) cc_final: 0.7902 (mttp) REVERT: A 333 GLU cc_start: 0.8611 (OUTLIER) cc_final: 0.8117 (mm-30) REVERT: A 390 GLN cc_start: 0.8037 (tp40) cc_final: 0.7712 (tp-100) REVERT: A 398 GLU cc_start: 0.7810 (tt0) cc_final: 0.7518 (tm-30) REVERT: A 447 GLN cc_start: 0.9218 (OUTLIER) cc_final: 0.8388 (mt0) REVERT: A 472 LEU cc_start: 0.8980 (OUTLIER) cc_final: 0.8455 (mp) REVERT: A 644 LYS cc_start: 0.8709 (mttt) cc_final: 0.8377 (mmmt) REVERT: A 685 GLU cc_start: 0.7919 (mt-10) cc_final: 0.7254 (tm-30) REVERT: A 696 GLU cc_start: 0.7818 (tm-30) cc_final: 0.7471 (tm-30) REVERT: A 712 GLU cc_start: 0.7438 (tt0) cc_final: 0.6368 (tm-30) REVERT: A 734 GLU cc_start: 0.8046 (tt0) cc_final: 0.7735 (tm-30) REVERT: A 822 GLU cc_start: 0.8434 (OUTLIER) cc_final: 0.8155 (mt-10) REVERT: A 833 GLU cc_start: 0.8142 (mt-10) cc_final: 0.7642 (tp30) REVERT: A 845 LEU cc_start: 0.7650 (OUTLIER) cc_final: 0.7261 (mt) REVERT: A 898 ARG cc_start: 0.8218 (OUTLIER) cc_final: 0.7617 (tmt-80) REVERT: A 912 LEU cc_start: 0.7564 (OUTLIER) cc_final: 0.7295 (pp) REVERT: A 924 LYS cc_start: 0.6510 (OUTLIER) cc_final: 0.5895 (mmtm) REVERT: A 931 GLU cc_start: 0.7555 (tt0) cc_final: 0.7118 (mm-30) REVERT: A 961 ARG cc_start: 0.7553 (mmt90) cc_final: 0.7158 (mtm180) REVERT: A 969 GLN cc_start: 0.7586 (mm110) cc_final: 0.6792 (tp40) REVERT: A 1005 GLU cc_start: 0.8339 (OUTLIER) cc_final: 0.8015 (mm-30) REVERT: A 1062 GLU cc_start: 0.8850 (tp30) cc_final: 0.8564 (tp30) REVERT: A 1077 THR cc_start: 0.7945 (m) cc_final: 0.7590 (p) REVERT: A 1135 ARG cc_start: 0.7063 (ttt180) cc_final: 0.6125 (ttt180) REVERT: A 1304 TRP cc_start: 0.7515 (m100) cc_final: 0.7099 (m100) REVERT: A 1407 GLU cc_start: 0.8499 (mp0) cc_final: 0.8175 (mp0) REVERT: A 1444 MET cc_start: 0.8680 (OUTLIER) cc_final: 0.7310 (mtm) REVERT: B 21 GLU cc_start: 0.8130 (pt0) cc_final: 0.7633 (mt-10) REVERT: B 46 GLN cc_start: 0.8229 (OUTLIER) cc_final: 0.7531 (pm20) REVERT: B 199 MET cc_start: 0.8434 (mmt) cc_final: 0.7560 (pmm) REVERT: B 270 LYS cc_start: 0.7323 (mtmp) cc_final: 0.7007 (mtmp) REVERT: B 357 GLN cc_start: 0.8256 (tt0) cc_final: 0.7972 (tt0) REVERT: B 393 LYS cc_start: 0.7766 (ttpt) cc_final: 0.6967 (mmtp) REVERT: B 398 ARG cc_start: 0.7987 (mtt-85) cc_final: 0.7434 (ttp-170) REVERT: B 422 LYS cc_start: 0.7703 (mmtm) cc_final: 0.6731 (tmmm) REVERT: B 423 LYS cc_start: 0.8407 (tttp) cc_final: 0.7970 (ttmm) REVERT: B 451 LYS cc_start: 0.7997 (mtmt) cc_final: 0.7586 (tmtt) REVERT: B 468 GLU cc_start: 0.7813 (mp0) cc_final: 0.6959 (mm-30) REVERT: B 508 LEU cc_start: 0.7087 (OUTLIER) cc_final: 0.6428 (tp) REVERT: B 595 ARG cc_start: 0.8104 (ttt180) cc_final: 0.7630 (mpp-170) REVERT: B 621 GLU cc_start: 0.8023 (tp30) cc_final: 0.7774 (mm-30) REVERT: B 624 LEU cc_start: 0.9036 (OUTLIER) cc_final: 0.8671 (tt) REVERT: B 650 GLU cc_start: 0.6907 (OUTLIER) cc_final: 0.6641 (tm-30) REVERT: B 665 GLU cc_start: 0.8056 (tt0) cc_final: 0.7726 (tt0) REVERT: B 696 GLU cc_start: 0.8472 (OUTLIER) cc_final: 0.8237 (tp30) REVERT: B 708 GLU cc_start: 0.7778 (mp0) cc_final: 0.7561 (mp0) REVERT: B 727 LYS cc_start: 0.8662 (mttp) cc_final: 0.8267 (mttm) REVERT: B 873 THR cc_start: 0.7419 (m) cc_final: 0.7136 (t) REVERT: B 889 THR cc_start: 0.7997 (m) cc_final: 0.7767 (t) REVERT: B 1057 LYS cc_start: 0.8811 (mttt) cc_final: 0.8483 (mmtm) REVERT: B 1124 ARG cc_start: 0.8225 (mtm-85) cc_final: 0.7755 (mtp85) REVERT: B 1189 ILE cc_start: 0.8532 (OUTLIER) cc_final: 0.8265 (pp) REVERT: B 1219 ASP cc_start: 0.8741 (OUTLIER) cc_final: 0.8208 (p0) REVERT: C 12 GLU cc_start: 0.8380 (mt-10) cc_final: 0.7805 (tm-30) REVERT: C 102 GLN cc_start: 0.8581 (mt0) cc_final: 0.8355 (mp10) REVERT: C 106 GLU cc_start: 0.8323 (mt-10) cc_final: 0.7931 (mm-30) REVERT: C 152 GLU cc_start: 0.8887 (tt0) cc_final: 0.8494 (tm-30) REVERT: C 264 GLN cc_start: 0.7483 (tp40) cc_final: 0.6983 (tp40) REVERT: E 33 GLU cc_start: 0.7762 (tt0) cc_final: 0.7377 (tm-30) REVERT: E 40 GLU cc_start: 0.6502 (mp0) cc_final: 0.5806 (mm-30) REVERT: E 57 MET cc_start: 0.7401 (mtm) cc_final: 0.6829 (mmm) REVERT: E 78 LEU cc_start: 0.8740 (OUTLIER) cc_final: 0.8483 (tt) REVERT: E 94 LYS cc_start: 0.7166 (mmmt) cc_final: 0.6965 (mmmt) REVERT: F 103 MET cc_start: 0.8459 (mtp) cc_final: 0.8066 (mtp) REVERT: F 149 GLU cc_start: 0.8389 (tt0) cc_final: 0.8050 (pm20) REVERT: I 1 MET cc_start: 0.4826 (ttt) cc_final: 0.3858 (tmt) REVERT: J 26 GLN cc_start: 0.7601 (OUTLIER) cc_final: 0.6442 (mt0) REVERT: J 48 ARG cc_start: 0.9059 (OUTLIER) cc_final: 0.8179 (tmm-80) REVERT: K 55 LYS cc_start: 0.9190 (OUTLIER) cc_final: 0.8755 (mtmp) outliers start: 107 outliers final: 66 residues processed: 484 average time/residue: 0.7408 time to fit residues: 420.8502 Evaluate side-chains 498 residues out of total 3459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 408 time to evaluate : 0.821 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 THR Chi-restraints excluded: chain A residue 22 PHE Chi-restraints excluded: chain A residue 36 ARG Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 123 ARG Chi-restraints excluded: chain A residue 167 CYS Chi-restraints excluded: chain A residue 291 GLU Chi-restraints excluded: chain A residue 333 GLU Chi-restraints excluded: chain A residue 380 VAL Chi-restraints excluded: chain A residue 447 GLN Chi-restraints excluded: chain A residue 472 LEU Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 701 LEU Chi-restraints excluded: chain A residue 703 THR Chi-restraints excluded: chain A residue 727 ASP Chi-restraints excluded: chain A residue 822 GLU Chi-restraints excluded: chain A residue 834 THR Chi-restraints excluded: chain A residue 845 LEU Chi-restraints excluded: chain A residue 885 THR Chi-restraints excluded: chain A residue 898 ARG Chi-restraints excluded: chain A residue 907 THR Chi-restraints excluded: chain A residue 912 LEU Chi-restraints excluded: chain A residue 924 LYS Chi-restraints excluded: chain A residue 984 LYS Chi-restraints excluded: chain A residue 998 LEU Chi-restraints excluded: chain A residue 1005 GLU Chi-restraints excluded: chain A residue 1036 ARG Chi-restraints excluded: chain A residue 1112 LYS Chi-restraints excluded: chain A residue 1283 VAL Chi-restraints excluded: chain A residue 1322 ILE Chi-restraints excluded: chain A residue 1438 THR Chi-restraints excluded: chain A residue 1444 MET Chi-restraints excluded: chain B residue 46 GLN Chi-restraints excluded: chain B residue 58 THR Chi-restraints excluded: chain B residue 77 HIS Chi-restraints excluded: chain B residue 298 LEU Chi-restraints excluded: chain B residue 305 VAL Chi-restraints excluded: chain B residue 487 THR Chi-restraints excluded: chain B residue 498 THR Chi-restraints excluded: chain B residue 508 LEU Chi-restraints excluded: chain B residue 531 GLN Chi-restraints excluded: chain B residue 547 VAL Chi-restraints excluded: chain B residue 624 LEU Chi-restraints excluded: chain B residue 650 GLU Chi-restraints excluded: chain B residue 696 GLU Chi-restraints excluded: chain B residue 737 THR Chi-restraints excluded: chain B residue 839 MET Chi-restraints excluded: chain B residue 903 VAL Chi-restraints excluded: chain B residue 955 THR Chi-restraints excluded: chain B residue 1150 ARG Chi-restraints excluded: chain B residue 1160 VAL Chi-restraints excluded: chain B residue 1189 ILE Chi-restraints excluded: chain B residue 1219 ASP Chi-restraints excluded: chain C residue 18 VAL Chi-restraints excluded: chain C residue 25 VAL Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 43 THR Chi-restraints excluded: chain C residue 53 THR Chi-restraints excluded: chain C residue 56 THR Chi-restraints excluded: chain C residue 136 ASP Chi-restraints excluded: chain C residue 189 THR Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 38 ILE Chi-restraints excluded: chain D residue 133 THR Chi-restraints excluded: chain D residue 170 THR Chi-restraints excluded: chain D residue 221 TYR Chi-restraints excluded: chain E residue 31 THR Chi-restraints excluded: chain E residue 48 ASP Chi-restraints excluded: chain E residue 70 SER Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain E residue 98 ILE Chi-restraints excluded: chain E residue 115 ASN Chi-restraints excluded: chain E residue 196 VAL Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 108 PHE Chi-restraints excluded: chain F residue 133 VAL Chi-restraints excluded: chain G residue 50 ASP Chi-restraints excluded: chain G residue 86 VAL Chi-restraints excluded: chain G residue 92 VAL Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain I residue 48 LEU Chi-restraints excluded: chain I residue 61 ASP Chi-restraints excluded: chain I residue 98 VAL Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain J residue 26 GLN Chi-restraints excluded: chain J residue 48 ARG Chi-restraints excluded: chain K residue 5 ASP Chi-restraints excluded: chain K residue 31 VAL Chi-restraints excluded: chain K residue 55 LYS Chi-restraints excluded: chain L residue 27 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 356 optimal weight: 20.0000 chunk 292 optimal weight: 0.9990 chunk 150 optimal weight: 6.9990 chunk 129 optimal weight: 3.9990 chunk 380 optimal weight: 6.9990 chunk 367 optimal weight: 0.7980 chunk 332 optimal weight: 0.9980 chunk 70 optimal weight: 6.9990 chunk 308 optimal weight: 8.9990 chunk 323 optimal weight: 3.9990 chunk 283 optimal weight: 7.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 397 ASN A 626 ASN A 736 ASN A 838 GLN C 24 ASN ** D 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 179 GLN H 131 ASN H 134 ASN L 66 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4083 r_free = 0.4083 target = 0.189215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.137193 restraints weight = 27426.068| |-----------------------------------------------------------------------------| r_work (start): 0.3529 rms_B_bonded: 2.29 r_work: 0.2971 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work: 0.2859 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.2859 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8851 moved from start: 0.1894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 1.065 33092 Z= 0.475 Angle : 0.632 24.401 44914 Z= 0.340 Chirality : 0.047 0.549 5050 Planarity : 0.005 0.058 5623 Dihedral : 12.821 127.683 4937 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.53 % Favored : 96.42 % Rotamer: Outliers : 2.83 % Allowed : 13.13 % Favored : 84.04 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 2.37 % 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: 0.39 (0.13), residues: 3879 helix: 1.22 (0.14), residues: 1357 sheet: 0.13 (0.20), residues: 621 loop : -0.33 (0.14), residues: 1901 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 393 TYR 0.019 0.002 TYR B 486 PHE 0.062 0.002 PHE D 70 TRP 0.013 0.002 TRP B 31 HIS 0.009 0.001 HIS A 399 Details of bonding type rmsd/Z covalent geometry : bond 0.01250 / 0.48 (33060) covalent geometry : angle 0.62482 / 0.34 (44869) hydrogen bonds : bond 0.05063 / 3.28 ( 1408) hydrogen bonds : angle 4.70383 / 3.30 ( 3910) metal coordination : bond 0.00390 / 0.27 ( 32) metal coordination : angle 3.07170 / 1.95 ( 45) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7758 Ramachandran restraints generated. 3879 Oldfield, 0 Emsley, 3879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7758 Ramachandran restraints generated. 3879 Oldfield, 0 Emsley, 3879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 507 residues out of total 3459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 409 time to evaluate : 1.334 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 PHE cc_start: 0.8971 (OUTLIER) cc_final: 0.7999 (t80) REVERT: A 36 ARG cc_start: 0.7787 (OUTLIER) cc_final: 0.7437 (mtt-85) REVERT: A 41 MET cc_start: 0.6461 (mmt) cc_final: 0.6065 (mmm) REVERT: A 68 GLN cc_start: 0.6845 (tt0) cc_final: 0.6015 (mp-120) REVERT: A 88 LYS cc_start: 0.8037 (mttp) cc_final: 0.7574 (mttt) REVERT: A 123 ARG cc_start: 0.7617 (OUTLIER) cc_final: 0.7227 (mtm110) REVERT: A 175 ARG cc_start: 0.7776 (ttp80) cc_final: 0.7171 (mtp85) REVERT: A 180 LYS cc_start: 0.8404 (mtmt) cc_final: 0.7984 (mttp) REVERT: A 333 GLU cc_start: 0.8641 (OUTLIER) cc_final: 0.8165 (mm-30) REVERT: A 390 GLN cc_start: 0.8066 (tp40) cc_final: 0.7744 (tp-100) REVERT: A 398 GLU cc_start: 0.7890 (tt0) cc_final: 0.7588 (tm-30) REVERT: A 447 GLN cc_start: 0.9208 (OUTLIER) cc_final: 0.8388 (mt0) REVERT: A 472 LEU cc_start: 0.8961 (OUTLIER) cc_final: 0.8432 (mp) REVERT: A 644 LYS cc_start: 0.8738 (mttt) cc_final: 0.8407 (mmmt) REVERT: A 685 GLU cc_start: 0.7999 (mt-10) cc_final: 0.7334 (tm-30) REVERT: A 696 GLU cc_start: 0.7907 (tm-30) cc_final: 0.7562 (tm-30) REVERT: A 712 GLU cc_start: 0.7521 (tt0) cc_final: 0.6438 (tm-30) REVERT: A 734 GLU cc_start: 0.8126 (tt0) cc_final: 0.7813 (tm-30) REVERT: A 822 GLU cc_start: 0.8457 (OUTLIER) cc_final: 0.8191 (mt-10) REVERT: A 833 GLU cc_start: 0.8154 (mt-10) cc_final: 0.7694 (tp30) REVERT: A 845 LEU cc_start: 0.7640 (OUTLIER) cc_final: 0.7272 (mt) REVERT: A 912 LEU cc_start: 0.7626 (OUTLIER) cc_final: 0.7320 (pp) REVERT: A 924 LYS cc_start: 0.6513 (OUTLIER) cc_final: 0.5899 (mmtm) REVERT: A 931 GLU cc_start: 0.7628 (tt0) cc_final: 0.7201 (mm-30) REVERT: A 961 ARG cc_start: 0.7577 (mmt90) cc_final: 0.7194 (mtm180) REVERT: A 969 GLN cc_start: 0.7642 (mm110) cc_final: 0.6848 (tp40) REVERT: A 1005 GLU cc_start: 0.8365 (OUTLIER) cc_final: 0.8049 (mm-30) REVERT: A 1062 GLU cc_start: 0.8837 (tp30) cc_final: 0.8533 (tp30) REVERT: A 1077 THR cc_start: 0.7953 (m) cc_final: 0.7613 (p) REVERT: A 1135 ARG cc_start: 0.6960 (ttt180) cc_final: 0.6007 (ttt180) REVERT: A 1304 TRP cc_start: 0.7518 (m100) cc_final: 0.7124 (m100) REVERT: A 1407 GLU cc_start: 0.8516 (mp0) cc_final: 0.8205 (mp0) REVERT: A 1444 MET cc_start: 0.8702 (OUTLIER) cc_final: 0.7320 (mtm) REVERT: B 21 GLU cc_start: 0.8138 (pt0) cc_final: 0.7677 (mt-10) REVERT: B 46 GLN cc_start: 0.8234 (OUTLIER) cc_final: 0.7558 (pm20) REVERT: B 199 MET cc_start: 0.8442 (mmt) cc_final: 0.7585 (pmm) REVERT: B 270 LYS cc_start: 0.7289 (mtmp) cc_final: 0.6997 (mtmp) REVERT: B 357 GLN cc_start: 0.8236 (tt0) cc_final: 0.7944 (tt0) REVERT: B 393 LYS cc_start: 0.7822 (ttpt) cc_final: 0.7026 (mmtp) REVERT: B 398 ARG cc_start: 0.7990 (mtt-85) cc_final: 0.7448 (ttp-170) REVERT: B 422 LYS cc_start: 0.7742 (mmtm) cc_final: 0.6796 (tmmm) REVERT: B 423 LYS cc_start: 0.8454 (tttp) cc_final: 0.8036 (ttmm) REVERT: B 451 LYS cc_start: 0.8024 (mtmt) cc_final: 0.7611 (tmtt) REVERT: B 468 GLU cc_start: 0.7827 (mp0) cc_final: 0.7018 (mm-30) REVERT: B 508 LEU cc_start: 0.7106 (OUTLIER) cc_final: 0.6469 (tp) REVERT: B 595 ARG cc_start: 0.8082 (ttt180) cc_final: 0.7693 (mpp-170) REVERT: B 621 GLU cc_start: 0.8078 (tp30) cc_final: 0.7844 (mm-30) REVERT: B 624 LEU cc_start: 0.9041 (OUTLIER) cc_final: 0.8686 (tt) REVERT: B 650 GLU cc_start: 0.6911 (OUTLIER) cc_final: 0.6707 (tm-30) REVERT: B 665 GLU cc_start: 0.8123 (tt0) cc_final: 0.7801 (tt0) REVERT: B 696 GLU cc_start: 0.8483 (OUTLIER) cc_final: 0.8250 (tp30) REVERT: B 708 GLU cc_start: 0.7816 (mp0) cc_final: 0.7601 (mp0) REVERT: B 727 LYS cc_start: 0.8674 (mttp) cc_final: 0.8283 (mttm) REVERT: B 873 THR cc_start: 0.7503 (m) cc_final: 0.7210 (t) REVERT: B 889 THR cc_start: 0.8082 (m) cc_final: 0.7876 (t) REVERT: B 1057 LYS cc_start: 0.8838 (mttt) cc_final: 0.8505 (mmtm) REVERT: B 1124 ARG cc_start: 0.8262 (mtm-85) cc_final: 0.7793 (mtp85) REVERT: B 1219 ASP cc_start: 0.8755 (OUTLIER) cc_final: 0.8244 (p0) REVERT: C 12 GLU cc_start: 0.8439 (mt-10) cc_final: 0.7833 (tm-30) REVERT: C 102 GLN cc_start: 0.8587 (mt0) cc_final: 0.8366 (mp10) REVERT: C 106 GLU cc_start: 0.8367 (mt-10) cc_final: 0.7966 (mm-30) REVERT: C 152 GLU cc_start: 0.8948 (tt0) cc_final: 0.8523 (tm-30) REVERT: C 264 GLN cc_start: 0.7505 (tp40) cc_final: 0.7124 (tp40) REVERT: E 33 GLU cc_start: 0.7784 (tt0) cc_final: 0.7400 (tm-30) REVERT: E 40 GLU cc_start: 0.6510 (mp0) cc_final: 0.5805 (mm-30) REVERT: E 57 MET cc_start: 0.7384 (mtm) cc_final: 0.6808 (mmm) REVERT: E 78 LEU cc_start: 0.8773 (OUTLIER) cc_final: 0.8510 (tt) REVERT: E 94 LYS cc_start: 0.7152 (mmmt) cc_final: 0.6931 (mmmt) REVERT: F 103 MET cc_start: 0.8485 (mtp) cc_final: 0.8094 (mtp) REVERT: F 149 GLU cc_start: 0.8458 (tt0) cc_final: 0.8095 (pm20) REVERT: I 1 MET cc_start: 0.4858 (ttt) cc_final: 0.3880 (tmt) REVERT: J 26 GLN cc_start: 0.7619 (OUTLIER) cc_final: 0.6465 (mt0) REVERT: J 48 ARG cc_start: 0.9034 (OUTLIER) cc_final: 0.8171 (tmm-80) REVERT: K 55 LYS cc_start: 0.9190 (OUTLIER) cc_final: 0.8742 (mtmp) outliers start: 98 outliers final: 67 residues processed: 481 average time/residue: 0.7486 time to fit residues: 423.4596 Evaluate side-chains 495 residues out of total 3459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 406 time to evaluate : 1.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 THR Chi-restraints excluded: chain A residue 22 PHE Chi-restraints excluded: chain A residue 36 ARG Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 123 ARG Chi-restraints excluded: chain A residue 167 CYS Chi-restraints excluded: chain A residue 291 GLU Chi-restraints excluded: chain A residue 333 GLU Chi-restraints excluded: chain A residue 380 VAL Chi-restraints excluded: chain A residue 447 GLN Chi-restraints excluded: chain A residue 472 LEU Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 672 ASP Chi-restraints excluded: chain A residue 701 LEU Chi-restraints excluded: chain A residue 703 THR Chi-restraints excluded: chain A residue 727 ASP Chi-restraints excluded: chain A residue 822 GLU Chi-restraints excluded: chain A residue 834 THR Chi-restraints excluded: chain A residue 845 LEU Chi-restraints excluded: chain A residue 885 THR Chi-restraints excluded: chain A residue 907 THR Chi-restraints excluded: chain A residue 912 LEU Chi-restraints excluded: chain A residue 924 LYS Chi-restraints excluded: chain A residue 984 LYS Chi-restraints excluded: chain A residue 998 LEU Chi-restraints excluded: chain A residue 1005 GLU Chi-restraints excluded: chain A residue 1036 ARG Chi-restraints excluded: chain A residue 1112 LYS Chi-restraints excluded: chain A residue 1283 VAL Chi-restraints excluded: chain A residue 1322 ILE Chi-restraints excluded: chain A residue 1438 THR Chi-restraints excluded: chain A residue 1444 MET Chi-restraints excluded: chain B residue 46 GLN Chi-restraints excluded: chain B residue 58 THR Chi-restraints excluded: chain B residue 77 HIS Chi-restraints excluded: chain B residue 298 LEU Chi-restraints excluded: chain B residue 305 VAL Chi-restraints excluded: chain B residue 487 THR Chi-restraints excluded: chain B residue 498 THR Chi-restraints excluded: chain B residue 508 LEU Chi-restraints excluded: chain B residue 531 GLN Chi-restraints excluded: chain B residue 547 VAL Chi-restraints excluded: chain B residue 624 LEU Chi-restraints excluded: chain B residue 650 GLU Chi-restraints excluded: chain B residue 696 GLU Chi-restraints excluded: chain B residue 737 THR Chi-restraints excluded: chain B residue 751 VAL Chi-restraints excluded: chain B residue 839 MET Chi-restraints excluded: chain B residue 903 VAL Chi-restraints excluded: chain B residue 955 THR Chi-restraints excluded: chain B residue 1150 ARG Chi-restraints excluded: chain B residue 1160 VAL Chi-restraints excluded: chain B residue 1189 ILE Chi-restraints excluded: chain B residue 1219 ASP Chi-restraints excluded: chain C residue 18 VAL Chi-restraints excluded: chain C residue 25 VAL Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 43 THR Chi-restraints excluded: chain C residue 53 THR Chi-restraints excluded: chain C residue 56 THR Chi-restraints excluded: chain C residue 136 ASP Chi-restraints excluded: chain C residue 189 THR Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 38 ILE Chi-restraints excluded: chain D residue 133 THR Chi-restraints excluded: chain D residue 170 THR Chi-restraints excluded: chain D residue 221 TYR Chi-restraints excluded: chain E residue 31 THR Chi-restraints excluded: chain E residue 48 ASP Chi-restraints excluded: chain E residue 70 SER Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain E residue 98 ILE Chi-restraints excluded: chain E residue 196 VAL Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 133 VAL Chi-restraints excluded: chain G residue 50 ASP Chi-restraints excluded: chain G residue 86 VAL Chi-restraints excluded: chain G residue 92 VAL Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain I residue 48 LEU Chi-restraints excluded: chain I residue 61 ASP Chi-restraints excluded: chain I residue 98 VAL Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain J residue 26 GLN Chi-restraints excluded: chain J residue 48 ARG Chi-restraints excluded: chain K residue 5 ASP Chi-restraints excluded: chain K residue 31 VAL Chi-restraints excluded: chain K residue 55 LYS Chi-restraints excluded: chain L residue 27 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 200 optimal weight: 0.9990 chunk 11 optimal weight: 3.9990 chunk 50 optimal weight: 0.7980 chunk 14 optimal weight: 8.9990 chunk 73 optimal weight: 4.9990 chunk 21 optimal weight: 4.9990 chunk 308 optimal weight: 7.9990 chunk 142 optimal weight: 3.9990 chunk 247 optimal weight: 3.9990 chunk 20 optimal weight: 10.0000 chunk 201 optimal weight: 0.8980 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 397 ASN A 626 ASN A 838 GLN B 363 HIS ** D 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 179 GLN H 131 ASN H 134 ASN L 66 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4082 r_free = 0.4082 target = 0.189057 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.137115 restraints weight = 27265.332| |-----------------------------------------------------------------------------| r_work (start): 0.3529 rms_B_bonded: 2.28 r_work: 0.2973 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.2973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8795 moved from start: 0.1931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 1.066 33092 Z= 0.475 Angle : 0.633 24.403 44914 Z= 0.341 Chirality : 0.047 0.548 5050 Planarity : 0.005 0.057 5623 Dihedral : 12.821 127.451 4937 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.63 % Favored : 96.31 % Rotamer: Outliers : 2.83 % Allowed : 13.21 % Favored : 83.95 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 2.37 % 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: 0.36 (0.13), residues: 3879 helix: 1.17 (0.14), residues: 1360 sheet: 0.13 (0.20), residues: 615 loop : -0.34 (0.14), residues: 1904 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 393 TYR 0.018 0.002 TYR B 486 PHE 0.062 0.002 PHE D 70 TRP 0.014 0.002 TRP A 954 HIS 0.008 0.001 HIS A 399 Details of bonding type rmsd/Z covalent geometry : bond 0.01249 / 0.48 (33060) covalent geometry : angle 0.62560 / 0.34 (44869) hydrogen bonds : bond 0.05091 / 3.30 ( 1408) hydrogen bonds : angle 4.72051 / 3.32 ( 3910) metal coordination : bond 0.00389 / 0.27 ( 32) metal coordination : angle 3.09012 / 1.96 ( 45) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 16905.89 seconds wall clock time: 287 minutes 23.09 seconds (17243.09 seconds total)