Starting phenix.real_space_refine on Sun Aug 9 09:41:18 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9sbn_54732/08_2026/9sbn_54732.cif Found real_map, /net/cci-nas-00/data/ceres_data/9sbn_54732/08_2026/9sbn_54732.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.95 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9sbn_54732/08_2026/9sbn_54732.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9sbn_54732/08_2026/9sbn_54732.map" model { file = "/net/cci-nas-00/data/ceres_data/9sbn_54732/08_2026/9sbn_54732.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9sbn_54732/08_2026/9sbn_54732.cif" } resolution = 3.95 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= 0.023 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 8 6.06 5 P 96 5.49 5 Mg 1 5.21 5 S 182 5.16 5 C 20457 2.51 5 N 5734 2.21 5 O 6423 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.05s 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: 32901 Number of models: 1 Model: "" Number of chains: 21 Chain: "A" Number of atoms: 10859 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1379, 10859 Classifications: {'peptide': 1379} Link IDs: {'PCIS': 1, 'PTRANS': 61, 'TRANS': 1316} Chain breaks: 8 Chain: "B" Number of atoms: 9155 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1150, 9155 Classifications: {'peptide': 1150} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 48, 'TRANS': 1100} Chain breaks: 6 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: 909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 909 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 5, 'TRANS': 106} 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: 825 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 825 Classifications: {'DNA': 40} Link IDs: {'rna3p': 39} Chain breaks: 1 Chain: "R" Number of atoms: 197 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 197 Classifications: {'RNA': 9} Modifications used: {'rna3p_pur': 6, 'rna3p_pyr': 2} Link IDs: {'rna3p': 8} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "T" Number of atoms: 886 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 886 Classifications: {'DNA': 44} Link IDs: {'rna3p': 43} Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 14 Unusual residues: {' ZN': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 49 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ATP:plan-1': 1, 'ATP:plan-2': 1} Unresolved non-hydrogen planarities: 13 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} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 457 SG CYS A 67 108.099 70.064 95.382 1.00235.93 S ATOM 479 SG CYS A 70 107.808 66.798 93.374 1.00228.70 S ATOM 532 SG CYS A 77 105.239 69.572 92.914 1.00207.14 S ATOM 762 SG CYS A 107 83.003 75.521 135.382 1.00250.85 S ATOM 786 SG CYS A 110 84.581 72.454 136.680 1.00234.60 S ATOM 1091 SG CYS A 148 80.965 73.046 137.526 1.00287.30 S ATOM 1105 SG CYS A 167 83.614 75.411 139.042 1.00275.49 S ATOM 19520 SG CYS B1163 99.826 57.730 104.829 1.00227.42 S ATOM 19538 SG CYS B1166 98.184 61.139 104.978 1.00230.11 S ATOM 19663 SG CYS B1182 101.967 60.871 104.736 1.00224.54 S ATOM 19682 SG CYS B1185 100.157 59.941 107.953 1.00248.96 S ATOM 20670 SG CYS C 86 94.370 75.523 26.847 1.00286.05 S ATOM 20687 SG CYS C 88 96.526 77.973 28.678 1.00290.95 S ATOM 20720 SG CYS C 92 95.378 78.849 25.233 1.00244.03 S ATOM 20743 SG CYS C 95 92.861 78.826 28.088 1.00260.56 S ATOM 28328 SG CYS I 7 38.392 128.019 126.155 1.00402.18 S ATOM 28353 SG CYS I 10 42.131 127.788 126.186 1.00403.96 S ATOM 28519 SG CYS I 29 40.142 124.843 127.646 1.00415.38 S ATOM 28543 SG CYS I 32 40.221 128.143 129.450 1.00412.68 S ATOM 28870 SG CYS I 75 17.150 120.687 87.119 1.00421.56 S ATOM 28892 SG CYS I 78 17.441 124.203 86.024 1.00420.90 S ATOM 29108 SG CYS I 103 20.398 121.829 85.472 1.00416.16 S ATOM 29128 SG CYS I 106 19.463 122.970 89.011 1.00410.62 S ATOM 29230 SG CYS J 7 65.100 91.504 38.130 1.00184.83 S ATOM 29253 SG CYS J 10 65.154 89.542 34.860 1.00204.77 S ATOM 29533 SG CYS J 45 61.876 90.639 36.477 1.00193.85 S ATOM 29539 SG CYS J 46 64.110 93.108 34.677 1.00229.23 S ATOM 30662 SG CYS L 31 97.989 115.270 55.119 1.00347.00 S ATOM 30682 SG CYS L 34 99.209 117.021 51.964 1.00331.16 S ATOM 30786 SG CYS L 48 101.668 115.800 54.577 1.00344.76 S ATOM 30809 SG CYS L 51 99.581 118.826 55.300 1.00342.17 S Time building chain proxies: 7.54, per 1000 atoms: 0.23 Number of scatterers: 32901 At special positions: 0 Unit cell: (154.505, 157.769, 183.883, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 8 29.99 S 182 16.00 P 96 15.00 Mg 1 11.99 O 6423 8.00 N 5734 7.00 C 20457 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: 3.41 Conformation dependent library (CDL) restraints added in 1.3 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 77 " pdb="ZN ZN A1802 " - pdb=" SG CYS A 70 " pdb="ZN ZN A1802 " - pdb=" SG CYS A 67 " pdb=" ZN A1803 " pdb="ZN ZN A1803 " - pdb=" SG CYS A 107 " pdb="ZN ZN A1803 " - pdb=" SG CYS A 110 " pdb="ZN ZN A1803 " - pdb=" SG CYS A 167 " pdb="ZN ZN A1803 " - pdb=" SG CYS A 148 " pdb=" ZN B1302 " pdb="ZN ZN B1302 " - pdb=" SG CYS B1166 " pdb="ZN ZN B1302 " - pdb=" SG CYS B1182 " pdb="ZN ZN B1302 " - pdb=" SG CYS B1185 " pdb="ZN ZN B1302 " - pdb=" SG CYS B1163 " 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 10 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 7 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 29 " pdb=" ZN I 202 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 75 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 78 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 106 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 103 " pdb=" ZN J 101 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 45 " 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 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 7678 Ramachandran restraints generated. 3839 Oldfield, 0 Emsley, 3839 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7320 Finding SS restraints... Secondary structure from input PDB file: 145 helices and 47 sheets defined 39.7% alpha, 20.3% beta 37 base pairs and 74 stacking pairs defined. Time for finding SS restraints: 4.21 Creating SS restraints... Processing helix chain 'A' and resid 23 through 31 Processing helix chain 'A' and resid 92 through 94 No H-bonds generated for 'chain 'A' and resid 92 through 94' Processing helix chain 'A' and resid 95 through 106 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 removed outlier: 3.653A pdb=" N HIS A 213 " --> pdb=" O ASN A 209 " (cutoff:3.500A) Processing helix chain 'A' and resid 215 through 222 removed outlier: 3.536A pdb=" N PHE A 219 " --> pdb=" O SER A 215 " (cutoff:3.500A) Processing helix chain 'A' and resid 230 through 235 Processing helix chain 'A' and resid 243 through 247 Processing helix chain 'A' and resid 260 through 283 removed outlier: 3.518A 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: 3.708A 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 507 through 510 Processing helix chain 'A' and resid 524 through 536 removed outlier: 3.649A pdb=" N LEU A 528 " --> pdb=" O VAL A 524 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ARG A 532 " --> pdb=" O LEU A 528 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LYS A 533 " --> pdb=" O CYS A 529 " (cutoff:3.500A) Processing helix chain 'A' and resid 542 through 553 Processing helix chain 'A' and resid 574 through 582 removed outlier: 4.062A pdb=" N VAL A 580 " --> pdb=" O GLN A 576 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N ALA A 581 " --> pdb=" O ILE A 577 " (cutoff:3.500A) removed outlier: 3.597A 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 637 Processing helix chain 'A' and resid 638 through 659 removed outlier: 3.502A pdb=" N HIS A 659 " --> pdb=" O PHE A 655 " (cutoff:3.500A) Processing helix chain 'A' and resid 665 through 670 removed outlier: 3.574A pdb=" N ILE A 670 " --> pdb=" O GLY A 667 " (cutoff:3.500A) Processing helix chain 'A' and resid 672 through 701 removed outlier: 4.323A pdb=" N ASN A 700 " --> pdb=" O GLU A 696 " (cutoff:3.500A) Processing helix chain 'A' and resid 710 through 737 Processing helix chain 'A' and resid 741 through 750 Processing helix chain 'A' and resid 754 through 763 removed outlier: 3.603A pdb=" N ILE A 758 " --> pdb=" O SER A 754 " (cutoff:3.500A) Processing helix chain 'A' and resid 809 through 845 removed outlier: 3.548A pdb=" N GLU A 822 " --> pdb=" O MET A 818 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N GLY A 823 " --> pdb=" O GLY A 819 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N THR A 831 " --> pdb=" O THR A 827 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N ALA A 832 " --> pdb=" O ALA A 828 " (cutoff:3.500A) removed outlier: 4.041A 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 Processing helix chain 'A' and resid 915 through 920 removed outlier: 3.725A 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: 3.568A pdb=" N ILE A 963 " --> pdb=" O ASN A 959 " (cutoff:3.500A) Processing helix chain 'A' and resid 982 through 995 removed outlier: 3.556A pdb=" N GLU A 995 " --> pdb=" O LYS A 991 " (cutoff:3.500A) Processing helix chain 'A' and resid 1004 through 1015 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: 3.543A pdb=" N VAL A1057 " --> pdb=" O PHE A1053 " (cutoff:3.500A) Processing helix chain 'A' and resid 1063 through 1079 Proline residue: A1075 - end of helix Processing helix chain 'A' and resid 1096 through 1107 Processing helix chain 'A' and resid 1130 through 1139 Processing helix chain 'A' and resid 1143 through 1145 No H-bonds generated for 'chain 'A' and resid 1143 through 1145' Processing helix chain 'A' and resid 1166 through 1174 removed outlier: 3.515A pdb=" N ILE A1170 " --> pdb=" O ASP A1166 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N PHE A1174 " --> pdb=" O ILE A1170 " (cutoff:3.500A) Processing helix chain 'A' and resid 1198 through 1206 Processing helix chain 'A' and resid 1208 through 1221 Processing helix chain 'A' and resid 1257 through 1270 Processing helix chain 'A' and resid 1312 through 1317 removed outlier: 3.655A pdb=" N MET A1317 " --> pdb=" O LEU A1313 " (cutoff:3.500A) Processing helix chain 'A' and resid 1331 through 1340 Processing helix chain 'A' and resid 1340 through 1357 Processing helix chain 'A' and resid 1358 through 1360 No H-bonds generated for 'chain 'A' and resid 1358 through 1360' Processing helix chain 'A' and resid 1364 through 1375 removed outlier: 4.052A 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: 3.600A pdb=" N ASN A1427 " --> pdb=" O GLY A1423 " (cutoff:3.500A) Processing helix chain 'A' and resid 1446 through 1452 removed outlier: 3.524A pdb=" N LEU A1450 " --> pdb=" O ASP A1446 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 37 removed outlier: 4.195A pdb=" N VAL B 33 " --> pdb=" O ASP B 29 " (cutoff:3.500A) Processing helix chain 'B' and resid 44 through 66 removed outlier: 3.688A pdb=" N LEU B 48 " --> pdb=" O VAL B 44 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N LEU B 59 " --> pdb=" O VAL B 55 " (cutoff:3.500A) removed outlier: 5.620A pdb=" N GLN B 60 " --> pdb=" O ASP B 56 " (cutoff:3.500A) removed outlier: 4.482A 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 120 Processing helix chain 'B' and resid 158 through 160 No H-bonds generated for 'chain 'B' and resid 158 through 160' 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 302 removed outlier: 3.759A pdb=" N ILE B 297 " --> pdb=" O PRO B 293 " (cutoff:3.500A) Processing helix chain 'B' and resid 308 through 322 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 removed outlier: 3.591A pdb=" N ARG B 348 " --> pdb=" O LYS B 344 " (cutoff:3.500A) 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: 3.561A pdb=" N LEU B 412 " --> pdb=" O LEU B 408 " (cutoff:3.500A) removed outlier: 3.506A 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 removed outlier: 3.806A pdb=" N THR B 454 " --> pdb=" O ALA B 450 " (cutoff:3.500A) Processing helix chain 'B' and resid 487 through 496 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 565 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: 3.688A 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 775 removed outlier: 3.945A pdb=" N LYS B 775 " --> pdb=" O SER B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 782 through 788 removed outlier: 3.806A pdb=" N TYR B 785 " --> pdb=" O LEU B 782 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N ASN B 786 " --> pdb=" O THR B 783 " (cutoff:3.500A) Processing helix chain 'B' and resid 806 through 812 removed outlier: 3.510A pdb=" N GLU B 810 " --> pdb=" O ARG B 807 " (cutoff:3.500A) Processing helix chain 'B' and resid 843 through 849 Processing helix chain 'B' and resid 1015 through 1021 removed outlier: 4.374A pdb=" N SER B1019 " --> pdb=" O HIS B1015 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ARG B1020 " --> pdb=" O ALA B1016 " (cutoff:3.500A) Processing helix chain 'B' and resid 1022 through 1039 removed outlier: 3.809A pdb=" N LEU B1026 " --> pdb=" O THR B1022 " (cutoff:3.500A) Processing helix chain 'B' and resid 1051 through 1062 removed outlier: 3.717A pdb=" N GLU B1061 " --> pdb=" O LYS B1057 " (cutoff:3.500A) removed outlier: 3.926A 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 39 removed outlier: 3.502A pdb=" N ALA C 30 " --> pdb=" O ASP C 26 " (cutoff:3.500A) Processing helix chain 'C' and resid 59 through 69 removed outlier: 3.576A pdb=" N LEU C 69 " --> pdb=" O HIS C 65 " (cutoff:3.500A) Processing helix chain 'C' and resid 76 through 80 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 206 through 210 Processing helix chain 'C' and resid 239 through 266 Processing helix chain 'D' and resid 30 through 34 removed outlier: 3.606A pdb=" N GLN D 34 " --> pdb=" O GLN D 31 " (cutoff:3.500A) Processing helix chain 'D' and resid 51 through 73 Processing helix chain 'D' and resid 118 through 134 removed outlier: 3.580A pdb=" N GLN D 132 " --> pdb=" O VAL D 128 " (cutoff:3.500A) Processing helix chain 'D' and resid 138 through 151 Processing helix chain 'D' and resid 156 through 171 removed outlier: 3.740A pdb=" N VAL D 160 " --> pdb=" O ASP D 156 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N THR D 170 " --> pdb=" O LEU D 166 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N GLY D 171 " --> pdb=" O LEU D 167 " (cutoff:3.500A) Processing helix chain 'D' and resid 173 through 183 removed outlier: 3.771A 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: 3.628A 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 55 through 59 removed outlier: 3.513A pdb=" N SER E 59 " --> pdb=" O LYS E 56 " (cutoff:3.500A) Processing helix chain 'E' and resid 65 through 72 Processing helix chain 'E' and resid 91 through 104 removed outlier: 3.707A pdb=" N THR E 95 " --> pdb=" O LYS E 91 " (cutoff:3.500A) Processing helix chain 'E' and resid 117 through 124 removed outlier: 3.769A pdb=" N MET E 121 " --> pdb=" O THR E 117 " (cutoff:3.500A) Processing helix chain 'E' and resid 138 through 141 Processing helix chain 'E' and resid 143 through 147 Processing helix chain 'E' and resid 157 through 169 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 128 Processing helix chain 'G' and resid 14 through 18 Processing helix chain 'G' and resid 21 through 35 removed outlier: 3.748A pdb=" N GLU G 35 " --> pdb=" O LEU G 31 " (cutoff:3.500A) Processing helix chain 'G' and resid 113 through 115 No H-bonds generated for 'chain 'G' and resid 113 through 115' Processing helix chain 'H' and resid 45 through 47 No H-bonds generated for 'chain 'H' and resid 45 through 47' Processing helix chain 'H' and resid 88 through 93 Processing helix chain 'H' and resid 129 through 133 Processing helix chain 'I' and resid 59 through 65 removed outlier: 4.327A pdb=" N GLY I 63 " --> pdb=" O GLN I 60 " (cutoff:3.500A) Processing helix chain 'J' and resid 14 through 16 No H-bonds generated for 'chain 'J' and resid 14 through 16' Processing helix chain 'J' and resid 17 through 27 Processing helix chain 'J' and resid 31 through 39 Processing helix chain 'J' and resid 43 through 53 removed outlier: 3.591A pdb=" N ARG J 47 " --> pdb=" O ARG J 43 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N HIS J 53 " --> pdb=" O MET J 49 " (cutoff:3.500A) Processing helix chain 'J' and resid 56 through 61 removed outlier: 3.651A pdb=" N PHE J 60 " --> pdb=" O LEU J 56 " (cutoff:3.500A) Processing helix chain 'K' and resid 5 through 10 removed outlier: 3.506A pdb=" N PHE K 10 " --> pdb=" O PHE K 7 " (cutoff:3.500A) Processing helix chain 'K' and resid 39 through 52 removed outlier: 4.462A pdb=" N LEU K 45 " --> pdb=" O THR K 41 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ASN K 52 " --> pdb=" O ALA K 48 " (cutoff:3.500A) Processing helix chain 'K' and resid 82 through 112 removed outlier: 3.529A pdb=" N LEU K 111 " --> pdb=" O THR K 107 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N GLN K 112 " --> pdb=" O GLU K 108 " (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 90 removed outlier: 10.044A pdb=" N LEU A 86 " --> pdb=" O PRO A 240 " (cutoff:3.500A) removed outlier: 11.286A pdb=" N LYS A 88 " --> pdb=" O CYS A 238 " (cutoff:3.500A) removed outlier: 7.263A pdb=" N CYS A 238 " --> pdb=" O LYS A 88 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 173 through 177 Processing sheet with id=AA4, first strand: chain 'A' and resid 250 through 252 removed outlier: 3.816A pdb=" N PHE A 252 " --> pdb=" O GLN A 256 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 343 through 344 Processing sheet with id=AA6, first strand: chain 'B' and resid 1104 through 1106 removed outlier: 3.568A pdb=" N THR A 351 " --> pdb=" O MET A 487 " (cutoff:3.500A) removed outlier: 5.980A pdb=" N VAL A 364 " --> pdb=" O LYS A 461 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N ILE A 463 " --> pdb=" O VAL A 364 " (cutoff:3.500A) removed outlier: 5.519A pdb=" N VAL A 366 " --> pdb=" O ILE A 463 " (cutoff:3.500A) removed outlier: 8.439A pdb=" N GLN A 363 " --> pdb=" O ASN A 471 " (cutoff:3.500A) removed outlier: 4.725A pdb=" N ASN A 471 " --> pdb=" O GLN A 363 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LEU A 470 " --> pdb=" O SER A 354 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 375 through 379 removed outlier: 3.577A pdb=" N ARG A 434 " --> pdb=" O TYR A 376 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N TYR A 404 " --> pdb=" O GLU A 433 " (cutoff:3.500A) removed outlier: 5.969A pdb=" N HIS A 435 " --> pdb=" O ALA A 402 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N ALA A 402 " --> pdb=" O HIS A 435 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 512 through 513 Processing sheet with id=AA9, first strand: chain 'A' and resid 540 through 541 Processing sheet with id=AB1, first strand: chain 'A' and resid 588 through 590 removed outlier: 7.177A pdb=" N LEU A 606 " --> pdb=" O ILE A 613 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 766 through 767 Processing sheet with id=AB3, first strand: chain 'A' and resid 849 through 850 removed outlier: 6.740A pdb=" N THR A 856 " --> pdb=" O ILE A 864 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 878 through 882 Processing sheet with id=AB5, first strand: chain 'A' and resid 1282 through 1292 removed outlier: 3.551A pdb=" N VAL A1283 " --> pdb=" O GLU A1307 " (cutoff:3.500A) removed outlier: 8.124A pdb=" N TRP A1304 " --> pdb=" O LEU A1120 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N LEU A1120 " --> pdb=" O TRP A1304 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N THR A1308 " --> pdb=" O LEU A1116 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N LEU A1116 " --> pdb=" O THR A1308 " (cutoff:3.500A) removed outlier: 11.098A pdb=" N THR A1117 " --> pdb=" O THR A1325 " (cutoff:3.500A) removed outlier: 8.785A pdb=" N THR A1325 " --> pdb=" O THR A1117 " (cutoff:3.500A) removed outlier: 4.832A pdb=" N TYR A1119 " --> pdb=" O ASP A1323 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 1224 through 1228 removed outlier: 4.415A pdb=" N LEU A1236 " --> pdb=" O LEU A1197 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N VAL A1242 " --> pdb=" O TRP A1191 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N TRP A1191 " --> pdb=" O VAL A1242 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N LEU A1192 " --> pdb=" O ILE A1152 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N ILE A1152 " --> pdb=" O LEU A1192 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N ARG A1194 " --> pdb=" O SER A1150 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N SER A1150 " --> pdb=" O ARG A1194 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N GLU A1196 " --> pdb=" O ILE A1148 " (cutoff:3.500A) removed outlier: 4.073A 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 50 removed outlier: 4.240A pdb=" N ILE D 48 " --> pdb=" O ILE G 4 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N PHE G 2 " --> pdb=" O LEU D 50 " (cutoff:3.500A) removed outlier: 5.398A pdb=" N VAL A1443 " --> pdb=" O ILE G 61 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 48 through 50 removed outlier: 4.240A pdb=" N ILE D 48 " --> pdb=" O ILE G 4 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N PHE G 2 " --> pdb=" O LEU D 50 " (cutoff:3.500A) removed outlier: 7.712A pdb=" N ARG G 75 " --> pdb=" O VAL G 48 " (cutoff:3.500A) removed outlier: 5.395A pdb=" N VAL G 48 " --> pdb=" O ARG G 75 " (cutoff:3.500A) removed outlier: 7.125A pdb=" N VAL G 77 " --> pdb=" O LEU G 46 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 69 through 71 removed outlier: 5.045A pdb=" N ARG B 86 " --> pdb=" O ALA B 139 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N ALA B 139 " --> pdb=" O ARG B 86 " (cutoff:3.500A) removed outlier: 5.215A pdb=" N TYR B 88 " --> pdb=" O TYR B 137 " (cutoff:3.500A) removed outlier: 7.130A pdb=" N TYR B 137 " --> pdb=" O TYR B 88 " (cutoff:3.500A) removed outlier: 5.115A pdb=" N ILE B 90 " --> pdb=" O ARG B 135 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N ARG B 135 " --> pdb=" O ILE B 90 " (cutoff:3.500A) removed outlier: 5.018A pdb=" N PHE B 92 " --> pdb=" O LYS B 133 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N LYS B 133 " --> pdb=" O PHE B 92 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N LYS B 94 " --> pdb=" O ASP B 131 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N THR B 98 " --> pdb=" O GLY B 127 " (cutoff:3.500A) removed outlier: 4.891A pdb=" N GLY B 127 " --> pdb=" O THR B 98 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N SER B 125 " --> pdb=" O PRO B 100 " (cutoff:3.500A) removed outlier: 8.213A pdb=" N VAL B 132 " --> pdb=" O SER B 156 " (cutoff:3.500A) removed outlier: 5.780A pdb=" N SER B 156 " --> pdb=" O VAL B 132 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N LYS B 134 " --> pdb=" O GLU B 154 " (cutoff:3.500A) removed outlier: 5.023A pdb=" N GLU B 154 " --> pdb=" O LYS B 134 " (cutoff:3.500A) removed outlier: 8.073A pdb=" N THR B 136 " --> pdb=" O ILE B 152 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ILE B 152 " --> pdb=" O THR B 136 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 109 through 111 removed outlier: 5.045A pdb=" N ARG B 86 " --> pdb=" O ALA B 139 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N ALA B 139 " --> pdb=" O ARG B 86 " (cutoff:3.500A) removed outlier: 5.215A pdb=" N TYR B 88 " --> pdb=" O TYR B 137 " (cutoff:3.500A) removed outlier: 7.130A pdb=" N TYR B 137 " --> pdb=" O TYR B 88 " (cutoff:3.500A) removed outlier: 5.115A pdb=" N ILE B 90 " --> pdb=" O ARG B 135 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N ARG B 135 " --> pdb=" O ILE B 90 " (cutoff:3.500A) removed outlier: 5.018A pdb=" N PHE B 92 " --> pdb=" O LYS B 133 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N LYS B 133 " --> pdb=" O PHE B 92 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N LYS B 94 " --> pdb=" O ASP B 131 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N THR B 98 " --> pdb=" O GLY B 127 " (cutoff:3.500A) removed outlier: 4.891A pdb=" N GLY B 127 " --> pdb=" O THR B 98 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N SER B 125 " --> pdb=" O PRO B 100 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N GLY B 168 " --> pdb=" O LEU B 128 " (cutoff:3.500A) removed outlier: 7.070A pdb=" N VAL B 130 " --> pdb=" O PHE B 166 " (cutoff:3.500A) removed outlier: 5.965A pdb=" N PHE B 166 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 7.548A pdb=" N VAL B 132 " --> pdb=" O LYS B 164 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N LYS B 164 " --> pdb=" O VAL B 132 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 203 through 205 Processing sheet with id=AC3, first strand: chain 'B' and resid 404 through 407 removed outlier: 6.114A pdb=" N ALA B 214 " --> pdb=" O ASN B 499 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 224 through 227 removed outlier: 4.280A pdb=" N HIS B 236 " --> pdb=" O LEU B 258 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N GLN B 255 " --> pdb=" O THR B 272 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 544 through 545 Processing sheet with id=AC6, first strand: chain 'B' and resid 585 through 590 removed outlier: 5.144A pdb=" N TRP B 586 " --> pdb=" O VAL B 582 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N VAL B 582 " --> pdb=" O TRP B 586 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N GLY B 588 " --> pdb=" O VAL B 580 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 640 through 641 Processing sheet with id=AC8, first strand: chain 'B' and resid 703 through 704 Processing sheet with id=AC9, first strand: chain 'B' and resid 792 through 796 removed outlier: 3.742A pdb=" N SER B 853 " --> pdb=" O LYS B 972 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N PHE B 963 " --> pdb=" O VAL B 954 " (cutoff:3.500A) removed outlier: 4.815A pdb=" N VAL B 954 " --> pdb=" O PHE B 963 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N LYS B 965 " --> pdb=" O VAL B 952 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N VAL B 952 " --> pdb=" O LYS B 965 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N ARG B 967 " --> pdb=" O ASP B 950 " (cutoff:3.500A) removed outlier: 6.053A pdb=" N THR B 971 " --> pdb=" O ASN B 946 " (cutoff:3.500A) removed outlier: 7.979A 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: 3.742A pdb=" N SER B 853 " --> pdb=" O LYS B 972 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N PHE B 963 " --> pdb=" O VAL B 954 " (cutoff:3.500A) removed outlier: 4.815A pdb=" N VAL B 954 " --> pdb=" O PHE B 963 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N LYS B 965 " --> pdb=" O VAL B 952 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N VAL B 952 " --> pdb=" O LYS B 965 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N ARG B 967 " --> pdb=" O ASP B 950 " (cutoff:3.500A) removed outlier: 6.053A pdb=" N THR B 971 " --> pdb=" O ASN B 946 " (cutoff:3.500A) removed outlier: 7.979A pdb=" N ASN B 946 " --> pdb=" O THR B 971 " (cutoff:3.500A) removed outlier: 5.224A pdb=" N VAL B 952 " --> pdb=" O LYS L 58 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N LEU L 27 " --> pdb=" O LEU L 40 " (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: 7.117A pdb=" N MET B 839 " --> pdb=" O GLY B 991 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N THR B 993 " --> pdb=" O MET B 839 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N MET B 841 " --> pdb=" O THR B 993 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ILE B1012 " --> pdb=" O ALA B 826 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N PHE B1086 " --> pdb=" O ILE B 827 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 910 through 912 removed outlier: 3.539A pdb=" N ILE B 912 " --> pdb=" O THR B 939 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 1158 through 1163 Processing sheet with id=AD6, first strand: chain 'B' and resid 1172 through 1174 Processing sheet with id=AD7, first strand: chain 'C' and resid 7 through 13 removed outlier: 5.294A pdb=" N VAL C 8 " --> pdb=" O SER C 23 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N SER C 23 " --> pdb=" O VAL C 8 " (cutoff:3.500A) removed outlier: 5.543A pdb=" N ILE C 10 " --> pdb=" O ILE C 21 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N ILE C 21 " --> pdb=" O ILE C 10 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ASN C 231 " --> pdb=" O GLU C 177 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N ALA C 175 " --> pdb=" O GLU C 233 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 119 through 120 removed outlier: 6.837A pdb=" N GLU C 152 " --> pdb=" O ASN C 54 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N ASN C 54 " --> pdb=" O GLU C 152 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N LYS C 154 " --> pdb=" O GLU C 52 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N GLU C 52 " --> pdb=" O LYS C 154 " (cutoff:3.500A) removed outlier: 6.129A pdb=" N LYS C 160 " --> pdb=" O ILE C 46 " (cutoff:3.500A) removed outlier: 5.267A pdb=" N ILE C 46 " --> pdb=" O LYS C 160 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N GLY C 162 " --> pdb=" O LEU C 44 " (cutoff:3.500A) removed outlier: 5.032A pdb=" N LEU C 44 " --> pdb=" O GLY C 162 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N VAL L 65 " --> pdb=" O VAL C 51 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 111 through 114 Processing sheet with id=AE1, first strand: chain 'D' and resid 36 through 38 Processing sheet with id=AE2, first strand: chain 'E' and resid 47 through 48 removed outlier: 4.822A pdb=" N ARG E 52 " --> pdb=" O ASP E 48 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'E' and resid 60 through 62 removed outlier: 6.368A pdb=" N TRP E 79 " --> pdb=" O ILE E 109 " (cutoff:3.500A) removed outlier: 7.850A pdb=" N VAL E 111 " --> pdb=" O TRP E 79 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N GLU E 81 " --> pdb=" O VAL E 111 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'E' and resid 152 through 155 removed outlier: 3.950A pdb=" N LYS E 152 " --> pdb=" O ILE E 199 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'G' and resid 86 through 87 removed outlier: 6.171A pdb=" N ILE G 160 " --> pdb=" O GLU G 148 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N CYS G 150 " --> pdb=" O HIS G 158 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N HIS G 158 " --> pdb=" O CYS G 150 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N LYS G 107 " --> pdb=" O ILE G 157 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ALA G 159 " --> pdb=" O LYS G 107 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N THR G 111 " --> pdb=" O GLY G 161 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N GLY G 98 " --> pdb=" O CYS G 94 " (cutoff:3.500A) removed outlier: 5.286A pdb=" N CYS G 94 " --> pdb=" O GLY G 98 " (cutoff:3.500A) removed outlier: 7.696A pdb=" N GLU G 100 " --> pdb=" O VAL G 92 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N VAL G 92 " --> pdb=" O GLU G 100 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'G' and resid 86 through 87 Processing sheet with id=AE7, first strand: chain 'G' and resid 120 through 122 removed outlier: 3.617A pdb=" N TYR G 130 " --> pdb=" O ILE G 137 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'H' and resid 4 through 16 removed outlier: 5.905A pdb=" N VAL H 12 " --> pdb=" O ALA H 29 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N ALA H 29 " --> pdb=" O VAL H 12 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLU H 14 " --> pdb=" O GLU H 27 " (cutoff:3.500A) removed outlier: 5.807A pdb=" N LEU H 122 " --> pdb=" O ASP H 41 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LYS H 103 " --> pdb=" O TYR H 115 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N SER H 117 " --> pdb=" O ALA H 101 " (cutoff:3.500A) removed outlier: 5.763A pdb=" N ALA H 101 " --> pdb=" O SER H 117 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N LEU H 55 " --> pdb=" O ILE H 9 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N ILE H 9 " --> pdb=" O LEU H 55 " (cutoff:3.500A) removed outlier: 7.130A pdb=" N VAL H 57 " --> pdb=" O ASP H 7 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N ASP H 7 " --> pdb=" O VAL H 57 " (cutoff:3.500A) removed outlier: 6.566A 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 19 removed outlier: 3.814A pdb=" N PHE I 27 " --> pdb=" O GLU I 36 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N GLU I 36 " --> pdb=" O PHE I 27 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'I' and resid 70 through 71 removed outlier: 4.093A 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 23 1353 hydrogen bonds defined for protein. 3699 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 96 hydrogen bonds 192 hydrogen bond angles 0 basepair planarities 37 basepair parallelities 74 stacking parallelities Total time for adding SS restraints: 10.80 Time building geometry restraints manager: 4.37 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 10497 1.34 - 1.46: 5617 1.46 - 1.58: 17081 1.58 - 1.70: 187 1.70 - 1.82: 292 Bond restraints: 33674 Sorted by residual: bond pdb=" C1' DC T 22 " pdb=" N1 DC T 22 " ideal model delta sigma weight residual 1.468 1.556 -0.088 1.40e-02 5.10e+03 3.98e+01 bond pdb=" C1' DC T 21 " pdb=" N1 DC T 21 " ideal model delta sigma weight residual 1.468 1.556 -0.088 1.40e-02 5.10e+03 3.98e+01 bond pdb=" C1' DT T 30 " pdb=" N1 DT T 30 " ideal model delta sigma weight residual 1.468 1.556 -0.088 1.40e-02 5.10e+03 3.97e+01 bond pdb=" O5' ATP B1301 " pdb=" PA ATP B1301 " ideal model delta sigma weight residual 1.579 1.510 0.069 1.10e-02 8.26e+03 3.96e+01 bond pdb=" C1' DC T 32 " pdb=" N1 DC T 32 " ideal model delta sigma weight residual 1.468 1.556 -0.088 1.40e-02 5.10e+03 3.95e+01 ... (remaining 33669 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.19: 45646 3.19 - 6.39: 169 6.39 - 9.58: 37 9.58 - 12.78: 2 12.78 - 15.97: 2 Bond angle restraints: 45856 Sorted by residual: angle pdb=" PB ATP B1301 " pdb=" O3B ATP B1301 " pdb=" PG ATP B1301 " ideal model delta sigma weight residual 139.87 123.90 15.97 1.00e+00 1.00e+00 2.55e+02 angle pdb=" PA ATP B1301 " pdb=" O3A ATP B1301 " pdb=" PB ATP B1301 " ideal model delta sigma weight residual 136.83 123.88 12.95 1.00e+00 1.00e+00 1.68e+02 angle pdb=" O3A ATP B1301 " pdb=" PB ATP B1301 " pdb=" O3B ATP B1301 " ideal model delta sigma weight residual 101.57 109.71 -8.14 1.54e+00 4.24e-01 2.81e+01 angle pdb=" O2G ATP B1301 " pdb=" PG ATP B1301 " pdb=" O3B ATP B1301 " ideal model delta sigma weight residual 104.48 109.58 -5.10 1.14e+00 7.76e-01 2.02e+01 angle pdb=" O3B ATP B1301 " pdb=" PG ATP B1301 " pdb=" O3G ATP B1301 " ideal model delta sigma weight residual 104.48 109.43 -4.95 1.14e+00 7.76e-01 1.90e+01 ... (remaining 45851 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.66: 19719 33.66 - 67.32: 581 67.32 - 100.98: 43 100.98 - 134.63: 3 134.63 - 168.29: 2 Dihedral angle restraints: 20348 sinusoidal: 9046 harmonic: 11302 Sorted by residual: 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 180.00 153.98 26.02 0 5.00e+00 4.00e-02 2.71e+01 dihedral pdb=" CA THR A 709 " pdb=" C THR A 709 " pdb=" N LEU A 710 " pdb=" CA LEU A 710 " ideal model delta harmonic sigma weight residual 180.00 -159.93 -20.07 0 5.00e+00 4.00e-02 1.61e+01 dihedral pdb=" CA MET A 708 " pdb=" C MET A 708 " pdb=" N THR A 709 " pdb=" CA THR A 709 " ideal model delta harmonic sigma weight residual -180.00 -160.09 -19.91 0 5.00e+00 4.00e-02 1.59e+01 ... (remaining 20345 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 3513 0.034 - 0.068: 1071 0.068 - 0.102: 395 0.102 - 0.137: 171 0.137 - 0.171: 6 Chirality restraints: 5156 Sorted by residual: chirality pdb=" C2' G R 9 " pdb=" C3' G R 9 " pdb=" O2' G R 9 " pdb=" C1' G R 9 " both_signs ideal model delta sigma weight residual False -2.62 -2.79 0.17 2.00e-01 2.50e+01 7.29e-01 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 2.59 -0.16 2.00e-01 2.50e+01 6.50e-01 chirality pdb=" C3' DC T 38 " pdb=" C4' DC T 38 " pdb=" O3' DC T 38 " pdb=" C2' DC T 38 " both_signs ideal model delta sigma weight residual False -2.73 -2.57 -0.16 2.00e-01 2.50e+01 6.29e-01 ... (remaining 5153 not shown) Planarity restraints: 5608 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL A1098 " 0.032 5.00e-02 4.00e+02 4.87e-02 3.79e+00 pdb=" N PRO A1099 " -0.084 5.00e-02 4.00e+02 pdb=" CA PRO A1099 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO A1099 " 0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA A1434 " -0.031 5.00e-02 4.00e+02 4.63e-02 3.43e+00 pdb=" N PRO A1435 " 0.080 5.00e-02 4.00e+02 pdb=" CA PRO A1435 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO A1435 " -0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' DC T 38 " 0.010 2.00e-02 2.50e+03 1.16e-02 3.04e+00 pdb=" N1 DC T 38 " -0.011 2.00e-02 2.50e+03 pdb=" C2 DC T 38 " 0.024 2.00e-02 2.50e+03 pdb=" O2 DC T 38 " -0.016 2.00e-02 2.50e+03 pdb=" N3 DC T 38 " -0.006 2.00e-02 2.50e+03 pdb=" C4 DC T 38 " 0.009 2.00e-02 2.50e+03 pdb=" N4 DC T 38 " -0.000 2.00e-02 2.50e+03 pdb=" C5 DC T 38 " -0.005 2.00e-02 2.50e+03 pdb=" C6 DC T 38 " -0.006 2.00e-02 2.50e+03 ... (remaining 5605 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.59: 389 2.59 - 3.17: 28153 3.17 - 3.74: 52952 3.74 - 4.32: 71924 4.32 - 4.90: 116405 Nonbonded interactions: 269823 Sorted by model distance: nonbonded pdb=" OD1 ASP A 481 " pdb="MG MG A1801 " model vdw 2.009 2.170 nonbonded pdb=" O THR B 680 " pdb=" OG SER B 683 " model vdw 2.168 3.040 nonbonded pdb=" O ILE B1103 " pdb=" NH1 ARG B1122 " model vdw 2.179 3.120 nonbonded pdb=" O LEU D 148 " pdb=" OG SER D 152 " model vdw 2.182 3.040 nonbonded pdb=" OG SER A 23 " pdb=" OE1 GLU A 25 " model vdw 2.199 3.040 ... (remaining 269818 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.190 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 0.560 Check model and map are aligned: 0.110 Set scattering table: 0.090 Process input model: 42.600 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8299 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.119 33706 Z= 0.265 Angle : 0.598 15.974 45901 Z= 0.396 Chirality : 0.041 0.171 5156 Planarity : 0.003 0.049 5608 Dihedral : 14.814 168.294 13028 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 10.34 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.88 % Favored : 96.07 % Rotamer: Outliers : 0.00 % Allowed : 0.15 % Favored : 99.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.41 % 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: 0.99 (0.14), residues: 3839 helix: 2.12 (0.15), residues: 1284 sheet: 0.19 (0.22), residues: 592 loop : -0.13 (0.15), residues: 1963 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 969 TYR 0.025 0.001 TYR B 797 PHE 0.014 0.001 PHE I 4 TRP 0.010 0.001 TRP C 170 HIS 0.009 0.001 HIS A1173 Details of bonding type rmsd/Z covalent geometry : bond 0.00382 / 0.26 (33674) covalent geometry : angle 0.59431 / 0.40 (45856) hydrogen bonds : bond 0.18798 / 12.77 ( 1414) hydrogen bonds : angle 6.90158 / 4.93 ( 3891) metal coordination : bond 0.00493 / 0.32 ( 32) metal coordination : angle 2.29802 / 1.60 ( 45) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7678 Ramachandran restraints generated. 3839 Oldfield, 0 Emsley, 3839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7678 Ramachandran restraints generated. 3839 Oldfield, 0 Emsley, 3839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 634 residues out of total 3426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 634 time to evaluate : 1.273 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 MET cc_start: 0.8455 (mtt) cc_final: 0.7925 (mmm) REVERT: A 103 CYS cc_start: 0.9614 (m) cc_final: 0.9380 (m) REVERT: A 146 MET cc_start: 0.9074 (mmm) cc_final: 0.8866 (mmm) REVERT: A 270 LEU cc_start: 0.9410 (mt) cc_final: 0.9149 (tp) REVERT: A 293 GLU cc_start: 0.9544 (tt0) cc_final: 0.9276 (pt0) REVERT: A 346 ASP cc_start: 0.8810 (m-30) cc_final: 0.8587 (m-30) REVERT: A 453 MET cc_start: 0.9466 (mpp) cc_final: 0.9237 (mpp) REVERT: A 496 GLU cc_start: 0.9029 (tt0) cc_final: 0.8333 (tp30) REVERT: A 510 GLN cc_start: 0.9367 (mm-40) cc_final: 0.8952 (mm-40) REVERT: A 511 ILE cc_start: 0.9500 (mt) cc_final: 0.9073 (mm) REVERT: A 521 MET cc_start: 0.9241 (mtt) cc_final: 0.8812 (mtm) REVERT: A 616 VAL cc_start: 0.9038 (t) cc_final: 0.8809 (p) REVERT: A 618 GLU cc_start: 0.9227 (pm20) cc_final: 0.8746 (pm20) REVERT: A 696 GLU cc_start: 0.9388 (tt0) cc_final: 0.8933 (tp30) REVERT: A 727 ASP cc_start: 0.9406 (m-30) cc_final: 0.8947 (t0) REVERT: A 748 MET cc_start: 0.9463 (mtm) cc_final: 0.8805 (mtp) REVERT: A 801 GLU cc_start: 0.9215 (tm-30) cc_final: 0.8801 (tm-30) REVERT: A 838 GLN cc_start: 0.9295 (tp40) cc_final: 0.8955 (tm-30) REVERT: A 873 MET cc_start: 0.9310 (mmt) cc_final: 0.8939 (mmm) REVERT: A 884 ASP cc_start: 0.8857 (m-30) cc_final: 0.8497 (p0) REVERT: A 931 GLU cc_start: 0.9727 (tt0) cc_final: 0.9429 (pt0) REVERT: A 975 HIS cc_start: 0.8800 (m-70) cc_final: 0.8345 (t-90) REVERT: A 1063 MET cc_start: 0.9331 (mmm) cc_final: 0.9113 (mmt) REVERT: A 1207 LEU cc_start: 0.9398 (mt) cc_final: 0.8980 (mp) REVERT: A 1280 GLU cc_start: 0.8799 (mm-30) cc_final: 0.8285 (mp0) REVERT: A 1284 MET cc_start: 0.8821 (ttm) cc_final: 0.8556 (mtt) REVERT: A 1368 MET cc_start: 0.9516 (mtm) cc_final: 0.9135 (mtp) REVERT: A 1373 ASP cc_start: 0.9217 (m-30) cc_final: 0.8934 (m-30) REVERT: A 1454 MET cc_start: 0.8923 (mtp) cc_final: 0.8394 (tmm) REVERT: B 43 LEU cc_start: 0.9704 (mt) cc_final: 0.9473 (mm) REVERT: B 86 ARG cc_start: 0.9423 (mmt90) cc_final: 0.9082 (mmm-85) REVERT: B 101 MET cc_start: 0.9143 (mtt) cc_final: 0.8896 (mtp) REVERT: B 471 LYS cc_start: 0.7176 (mptt) cc_final: 0.6387 (tttp) REVERT: B 563 MET cc_start: 0.9022 (ttp) cc_final: 0.8724 (tpp) REVERT: B 629 ASP cc_start: 0.9107 (t0) cc_final: 0.8696 (p0) REVERT: B 703 ILE cc_start: 0.9703 (mt) cc_final: 0.9238 (tp) REVERT: B 789 MET cc_start: 0.9115 (mmm) cc_final: 0.8734 (mmt) REVERT: B 860 MET cc_start: 0.8967 (ttt) cc_final: 0.8618 (tmm) REVERT: B 893 LEU cc_start: 0.6653 (mt) cc_final: 0.6355 (mt) REVERT: B 942 ARG cc_start: 0.6684 (mtt-85) cc_final: 0.6427 (mtp85) REVERT: B 987 LYS cc_start: 0.8912 (ptpt) cc_final: 0.8646 (ptpp) REVERT: B 1028 GLU cc_start: 0.9515 (tt0) cc_final: 0.9295 (tt0) REVERT: B 1072 MET cc_start: 0.9155 (mmm) cc_final: 0.8377 (mmm) REVERT: B 1095 LEU cc_start: 0.9659 (mt) cc_final: 0.9226 (mp) REVERT: B 1111 MET cc_start: 0.8917 (mmm) cc_final: 0.8470 (mmm) REVERT: B 1206 GLU cc_start: 0.9470 (mt-10) cc_final: 0.9259 (mt-10) REVERT: C 190 ASP cc_start: 0.9385 (t0) cc_final: 0.9114 (t0) REVERT: D 29 LEU cc_start: 0.7200 (mt) cc_final: 0.6660 (mt) REVERT: D 32 GLU cc_start: 0.7967 (mm-30) cc_final: 0.7583 (mt-10) REVERT: D 37 GLN cc_start: 0.6844 (mm-40) cc_final: 0.5579 (pt0) REVERT: D 48 ILE cc_start: 0.7879 (mt) cc_final: 0.7620 (mp) REVERT: D 59 ILE cc_start: 0.8971 (mt) cc_final: 0.8504 (mt) REVERT: E 22 MET cc_start: 0.9444 (ttp) cc_final: 0.9086 (ttm) REVERT: E 32 GLN cc_start: 0.9437 (tt0) cc_final: 0.9159 (tp-100) REVERT: E 58 MET cc_start: 0.9395 (mtp) cc_final: 0.8921 (mtp) REVERT: E 137 GLU cc_start: 0.9494 (tt0) cc_final: 0.9281 (mt-10) REVERT: F 76 LYS cc_start: 0.9498 (tptt) cc_final: 0.9214 (tppt) REVERT: F 87 LYS cc_start: 0.9366 (ptpt) cc_final: 0.9138 (pttp) REVERT: F 96 THR cc_start: 0.9576 (m) cc_final: 0.9287 (p) REVERT: F 116 ASP cc_start: 0.9407 (t70) cc_final: 0.9157 (t70) REVERT: F 130 ILE cc_start: 0.9605 (mt) cc_final: 0.9327 (mt) REVERT: F 144 GLU cc_start: 0.8800 (mt-10) cc_final: 0.8303 (mt-10) REVERT: G 29 LYS cc_start: 0.8992 (tppt) cc_final: 0.8708 (tptp) REVERT: G 46 LEU cc_start: 0.8884 (mt) cc_final: 0.8663 (mt) REVERT: G 50 ASP cc_start: 0.7571 (t0) cc_final: 0.7270 (t0) REVERT: G 102 GLN cc_start: 0.5064 (tp40) cc_final: 0.4671 (pp30) REVERT: G 137 ILE cc_start: 0.7091 (mt) cc_final: 0.6731 (pt) REVERT: H 14 GLU cc_start: 0.8924 (tt0) cc_final: 0.8363 (tm-30) REVERT: H 24 CYS cc_start: 0.9361 (m) cc_final: 0.9091 (m) REVERT: H 105 GLU cc_start: 0.9058 (tt0) cc_final: 0.8439 (tm-30) REVERT: H 107 VAL cc_start: 0.8996 (t) cc_final: 0.8445 (t) REVERT: H 112 ILE cc_start: 0.9290 (pt) cc_final: 0.8446 (pt) REVERT: H 123 MET cc_start: 0.9580 (ttt) cc_final: 0.9175 (tmm) REVERT: H 126 GLU cc_start: 0.9194 (tt0) cc_final: 0.8885 (tp30) REVERT: H 136 LYS cc_start: 0.9175 (mmtp) cc_final: 0.8936 (mptt) REVERT: H 137 GLN cc_start: 0.9433 (tt0) cc_final: 0.8916 (tp40) REVERT: I 64 SER cc_start: 0.9166 (m) cc_final: 0.8678 (p) REVERT: I 104 LEU cc_start: 0.7015 (mt) cc_final: 0.6750 (mt) REVERT: J 12 LYS cc_start: 0.8436 (tttm) cc_final: 0.8110 (ttmm) REVERT: K 52 ASN cc_start: 0.9271 (m-40) cc_final: 0.9065 (m-40) REVERT: K 54 ARG cc_start: 0.9573 (mtm180) cc_final: 0.9023 (mtt-85) REVERT: K 72 LYS cc_start: 0.9471 (mttt) cc_final: 0.9209 (mtpt) REVERT: K 85 ASP cc_start: 0.8878 (m-30) cc_final: 0.8424 (t0) REVERT: K 106 GLU cc_start: 0.9606 (mt-10) cc_final: 0.9249 (mt-10) REVERT: K 108 GLU cc_start: 0.9376 (mm-30) cc_final: 0.8921 (tt0) REVERT: L 27 LEU cc_start: 0.8323 (mm) cc_final: 0.8105 (mt) REVERT: L 47 ARG cc_start: 0.8028 (ptm160) cc_final: 0.7366 (ttt180) REVERT: L 54 ARG cc_start: 0.8133 (mtt-85) cc_final: 0.7705 (mtm-85) REVERT: L 57 LEU cc_start: 0.8808 (mp) cc_final: 0.8536 (mt) REVERT: L 64 LEU cc_start: 0.8453 (tp) cc_final: 0.7760 (tt) outliers start: 0 outliers final: 0 residues processed: 634 average time/residue: 0.2315 time to fit residues: 233.2399 Evaluate side-chains 428 residues out of total 3426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 428 time to evaluate : 1.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 393 random chunks: chunk 197 optimal weight: 10.0000 chunk 388 optimal weight: 5.9990 chunk 215 optimal weight: 5.9990 chunk 20 optimal weight: 3.9990 chunk 132 optimal weight: 9.9990 chunk 261 optimal weight: 8.9990 chunk 248 optimal weight: 0.1980 chunk 207 optimal weight: 8.9990 chunk 155 optimal weight: 0.7980 chunk 244 optimal weight: 5.9990 chunk 183 optimal weight: 1.9990 overall best weight: 2.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 488 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 742 ASN ** A 862 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1270 ASN ** A1432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 46 GLN B 415 GLN B 494 HIS ** B 984 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1015 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 10 ASN G 71 ASN I 46 HIS ** L 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.075041 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2808 r_free = 0.2808 target = 0.051894 restraints weight = 125097.499| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2851 r_free = 0.2851 target = 0.053482 restraints weight = 64927.822| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.2879 r_free = 0.2879 target = 0.054531 restraints weight = 42576.895| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.2897 r_free = 0.2897 target = 0.055198 restraints weight = 32555.403| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2907 r_free = 0.2907 target = 0.055585 restraints weight = 27541.492| |-----------------------------------------------------------------------------| r_work (final): 0.2879 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8541 moved from start: 0.1594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.082 33706 Z= 0.190 Angle : 0.672 23.557 45901 Z= 0.347 Chirality : 0.046 0.234 5156 Planarity : 0.005 0.067 5608 Dihedral : 17.208 164.154 5260 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 10.75 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.17 % Favored : 95.78 % Rotamer: Outliers : 1.37 % Allowed : 7.01 % Favored : 91.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.41 % 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: 0.70 (0.14), residues: 3839 helix: 1.79 (0.14), residues: 1311 sheet: 0.08 (0.22), residues: 584 loop : -0.29 (0.15), residues: 1944 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG I 30 TYR 0.019 0.001 TYR B 797 PHE 0.018 0.002 PHE K 71 TRP 0.011 0.001 TRP C 201 HIS 0.009 0.001 HIS A1173 Details of bonding type rmsd/Z covalent geometry : bond 0.00412 / 0.19 (33674) covalent geometry : angle 0.65473 / 0.35 (45856) hydrogen bonds : bond 0.04678 / 3.15 ( 1414) hydrogen bonds : angle 5.38142 / 3.88 ( 3891) metal coordination : bond 0.00715 / 0.50 ( 32) metal coordination : angle 4.89379 / 3.05 ( 45) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7678 Ramachandran restraints generated. 3839 Oldfield, 0 Emsley, 3839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7678 Ramachandran restraints generated. 3839 Oldfield, 0 Emsley, 3839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 498 residues out of total 3426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 451 time to evaluate : 1.320 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 MET cc_start: 0.8266 (mtt) cc_final: 0.7727 (mmt) REVERT: A 293 GLU cc_start: 0.9146 (tt0) cc_final: 0.8909 (tp30) REVERT: A 437 MET cc_start: 0.8223 (mtp) cc_final: 0.7923 (mtm) REVERT: A 455 MET cc_start: 0.8745 (tpp) cc_final: 0.8017 (tpp) REVERT: A 496 GLU cc_start: 0.8444 (tt0) cc_final: 0.8166 (tp30) REVERT: A 510 GLN cc_start: 0.9058 (mm-40) cc_final: 0.8641 (mp10) REVERT: A 511 ILE cc_start: 0.9504 (mt) cc_final: 0.9172 (mm) REVERT: A 727 ASP cc_start: 0.9109 (m-30) cc_final: 0.8812 (t0) REVERT: A 748 MET cc_start: 0.8937 (mtm) cc_final: 0.8383 (mtp) REVERT: A 838 GLN cc_start: 0.9365 (tp40) cc_final: 0.8970 (tm-30) REVERT: A 873 MET cc_start: 0.9232 (mmt) cc_final: 0.8938 (mmm) REVERT: A 1063 MET cc_start: 0.9270 (mmm) cc_final: 0.9042 (mmt) REVERT: A 1070 GLN cc_start: 0.9337 (mt0) cc_final: 0.9118 (mt0) REVERT: A 1280 GLU cc_start: 0.8500 (mm-30) cc_final: 0.8108 (mp0) REVERT: A 1368 MET cc_start: 0.9278 (mtm) cc_final: 0.8744 (mtp) REVERT: A 1373 ASP cc_start: 0.8767 (m-30) cc_final: 0.8439 (m-30) REVERT: A 1378 GLN cc_start: 0.8629 (mm-40) cc_final: 0.8171 (tp40) REVERT: B 86 ARG cc_start: 0.9386 (mmt90) cc_final: 0.8948 (mmm-85) REVERT: B 101 MET cc_start: 0.9276 (mtt) cc_final: 0.9065 (mtp) REVERT: B 239 GLU cc_start: 0.8677 (pp20) cc_final: 0.8371 (tm-30) REVERT: B 427 ASP cc_start: 0.8708 (m-30) cc_final: 0.8493 (m-30) REVERT: B 471 LYS cc_start: 0.7436 (mptt) cc_final: 0.6624 (tttp) REVERT: B 552 MET cc_start: 0.8890 (mmp) cc_final: 0.8675 (mmp) REVERT: B 942 ARG cc_start: 0.7403 (mtt-85) cc_final: 0.7063 (mtp85) REVERT: B 987 LYS cc_start: 0.8965 (ptpt) cc_final: 0.8673 (ptpp) REVERT: B 1028 GLU cc_start: 0.9193 (tt0) cc_final: 0.8896 (tt0) REVERT: B 1072 MET cc_start: 0.8949 (mmm) cc_final: 0.8389 (mmm) REVERT: B 1111 MET cc_start: 0.9428 (mmm) cc_final: 0.8923 (mmm) REVERT: B 1210 MET cc_start: 0.8979 (OUTLIER) cc_final: 0.8736 (mmt) REVERT: C 190 ASP cc_start: 0.9052 (t0) cc_final: 0.8758 (t0) REVERT: D 28 GLN cc_start: 0.6825 (tm-30) cc_final: 0.6115 (tm-30) REVERT: E 22 MET cc_start: 0.9317 (ttp) cc_final: 0.8878 (ttm) REVERT: E 25 ASP cc_start: 0.9108 (m-30) cc_final: 0.8672 (m-30) REVERT: E 58 MET cc_start: 0.8905 (mtp) cc_final: 0.8437 (mtp) REVERT: F 96 THR cc_start: 0.9612 (m) cc_final: 0.9395 (p) REVERT: F 144 GLU cc_start: 0.8413 (mt-10) cc_final: 0.8037 (mt-10) REVERT: G 29 LYS cc_start: 0.8997 (tppt) cc_final: 0.8727 (mmmt) REVERT: G 32 GLU cc_start: 0.8464 (mt-10) cc_final: 0.8047 (mt-10) REVERT: G 33 GLU cc_start: 0.8513 (tp30) cc_final: 0.8115 (mm-30) REVERT: G 137 ILE cc_start: 0.7263 (mt) cc_final: 0.6860 (pt) REVERT: G 148 GLU cc_start: 0.8195 (tp30) cc_final: 0.7984 (tm-30) REVERT: H 14 GLU cc_start: 0.8493 (tt0) cc_final: 0.8077 (tm-30) REVERT: H 105 GLU cc_start: 0.8499 (tt0) cc_final: 0.8295 (tm-30) REVERT: H 107 VAL cc_start: 0.9152 (t) cc_final: 0.8461 (t) REVERT: H 112 ILE cc_start: 0.9385 (pt) cc_final: 0.8266 (pt) REVERT: H 139 ASN cc_start: 0.9032 (m-40) cc_final: 0.8819 (m-40) REVERT: H 146 ARG cc_start: 0.8266 (ttp-170) cc_final: 0.7972 (ttp80) REVERT: I 101 PHE cc_start: 0.8686 (m-80) cc_final: 0.8394 (m-80) REVERT: J 12 LYS cc_start: 0.9371 (tttm) cc_final: 0.8961 (ttmm) REVERT: J 26 GLN cc_start: 0.8913 (tm-30) cc_final: 0.8511 (pp30) REVERT: J 27 GLU cc_start: 0.8886 (OUTLIER) cc_final: 0.8616 (pt0) REVERT: J 49 MET cc_start: 0.9338 (mmm) cc_final: 0.8684 (mpp) REVERT: K 5 ASP cc_start: 0.8825 (m-30) cc_final: 0.8562 (m-30) REVERT: K 36 GLU cc_start: 0.8976 (mm-30) cc_final: 0.8683 (mm-30) REVERT: L 67 PHE cc_start: 0.9132 (m-80) cc_final: 0.8749 (m-10) outliers start: 47 outliers final: 21 residues processed: 475 average time/residue: 0.2109 time to fit residues: 165.8069 Evaluate side-chains 389 residues out of total 3426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 366 time to evaluate : 1.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 649 ILE Chi-restraints excluded: chain A residue 716 ASP Chi-restraints excluded: chain A residue 1398 MET Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 322 PHE Chi-restraints excluded: chain B residue 394 ASP Chi-restraints excluded: chain B residue 408 LEU Chi-restraints excluded: chain B residue 616 ILE Chi-restraints excluded: chain B residue 953 LEU Chi-restraints excluded: chain B residue 1093 GLN Chi-restraints excluded: chain B residue 1120 GLU Chi-restraints excluded: chain B residue 1210 MET Chi-restraints excluded: chain C residue 240 VAL Chi-restraints excluded: chain C residue 258 ILE Chi-restraints excluded: chain E residue 175 LEU Chi-restraints excluded: chain F residue 153 VAL Chi-restraints excluded: chain G residue 6 ASP Chi-restraints excluded: chain G residue 10 ASN Chi-restraints excluded: chain G residue 147 ILE Chi-restraints excluded: chain I residue 103 CYS Chi-restraints excluded: chain J residue 27 GLU Chi-restraints excluded: chain J residue 50 ILE Chi-restraints excluded: chain L residue 30 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 393 random chunks: chunk 296 optimal weight: 8.9990 chunk 335 optimal weight: 0.9990 chunk 310 optimal weight: 7.9990 chunk 155 optimal weight: 5.9990 chunk 156 optimal weight: 7.9990 chunk 317 optimal weight: 4.9990 chunk 68 optimal weight: 2.9990 chunk 251 optimal weight: 5.9990 chunk 16 optimal weight: 8.9990 chunk 8 optimal weight: 0.1980 chunk 344 optimal weight: 6.9990 overall best weight: 3.0388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 118 HIS ** A 451 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 488 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 548 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 862 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 415 GLN B 440 HIS B 862 GLN ** B 984 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1015 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 206 ASN G 71 ASN ** L 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.075077 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2776 r_free = 0.2776 target = 0.051768 restraints weight = 127387.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2820 r_free = 0.2820 target = 0.053325 restraints weight = 66202.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.2848 r_free = 0.2848 target = 0.054338 restraints weight = 43462.783| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.2866 r_free = 0.2866 target = 0.054988 restraints weight = 33284.776| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2876 r_free = 0.2876 target = 0.055347 restraints weight = 28212.291| |-----------------------------------------------------------------------------| r_work (final): 0.2855 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8560 moved from start: 0.2025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 33706 Z= 0.201 Angle : 0.641 13.896 45901 Z= 0.332 Chirality : 0.045 0.246 5156 Planarity : 0.004 0.046 5608 Dihedral : 17.132 162.369 5260 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 11.02 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.30 % Favored : 95.65 % Rotamer: Outliers : 1.66 % Allowed : 9.84 % Favored : 88.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.41 % 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: 0.53 (0.14), residues: 3839 helix: 1.63 (0.14), residues: 1325 sheet: -0.02 (0.21), residues: 587 loop : -0.39 (0.15), residues: 1927 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 485 TYR 0.015 0.001 TYR D 147 PHE 0.020 0.001 PHE D 70 TRP 0.010 0.001 TRP C 201 HIS 0.007 0.001 HIS A1173 Details of bonding type rmsd/Z covalent geometry : bond 0.00436 / 0.20 (33674) covalent geometry : angle 0.63002 / 0.33 (45856) hydrogen bonds : bond 0.04156 / 2.80 ( 1414) hydrogen bonds : angle 5.12746 / 3.69 ( 3891) metal coordination : bond 0.00657 / 0.46 ( 32) metal coordination : angle 3.76304 / 2.46 ( 45) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7678 Ramachandran restraints generated. 3839 Oldfield, 0 Emsley, 3839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7678 Ramachandran restraints generated. 3839 Oldfield, 0 Emsley, 3839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 452 residues out of total 3426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 395 time to evaluate : 1.285 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 MET cc_start: 0.8387 (mtt) cc_final: 0.7793 (mmt) REVERT: A 437 MET cc_start: 0.8235 (mtp) cc_final: 0.7943 (mtm) REVERT: A 455 MET cc_start: 0.8610 (tpp) cc_final: 0.7959 (tpp) REVERT: A 510 GLN cc_start: 0.9185 (mm-40) cc_final: 0.8947 (mp10) REVERT: A 515 GLN cc_start: 0.8875 (tm-30) cc_final: 0.8661 (tm-30) REVERT: A 521 MET cc_start: 0.9147 (mtm) cc_final: 0.8770 (mtm) REVERT: A 727 ASP cc_start: 0.9158 (m-30) cc_final: 0.8804 (t0) REVERT: A 748 MET cc_start: 0.8975 (mtm) cc_final: 0.8654 (mtp) REVERT: A 838 GLN cc_start: 0.9346 (tp40) cc_final: 0.8992 (tm-30) REVERT: A 873 MET cc_start: 0.9268 (mmt) cc_final: 0.8992 (mmm) REVERT: A 975 HIS cc_start: 0.8674 (OUTLIER) cc_final: 0.8069 (t-90) REVERT: A 1063 MET cc_start: 0.9308 (mmm) cc_final: 0.9053 (mmt) REVERT: A 1267 MET cc_start: 0.9009 (mmp) cc_final: 0.8703 (mmp) REVERT: A 1280 GLU cc_start: 0.8431 (mm-30) cc_final: 0.8027 (mp0) REVERT: A 1368 MET cc_start: 0.9288 (mtm) cc_final: 0.8772 (mtp) REVERT: A 1373 ASP cc_start: 0.8768 (m-30) cc_final: 0.8420 (m-30) REVERT: A 1375 MET cc_start: 0.9254 (mtp) cc_final: 0.8990 (mtm) REVERT: A 1378 GLN cc_start: 0.8838 (mm-40) cc_final: 0.8208 (tp40) REVERT: A 1429 ILE cc_start: 0.9604 (mt) cc_final: 0.9393 (mm) REVERT: A 1444 MET cc_start: 0.8684 (OUTLIER) cc_final: 0.8482 (mmt) REVERT: B 86 ARG cc_start: 0.9348 (mmt90) cc_final: 0.8894 (mmm-85) REVERT: B 101 MET cc_start: 0.9273 (mtt) cc_final: 0.9047 (mtp) REVERT: B 322 PHE cc_start: 0.9298 (OUTLIER) cc_final: 0.8830 (t80) REVERT: B 427 ASP cc_start: 0.8736 (m-30) cc_final: 0.8486 (m-30) REVERT: B 471 LYS cc_start: 0.7291 (mptt) cc_final: 0.6507 (tttp) REVERT: B 542 MET cc_start: 0.8505 (mtp) cc_final: 0.7932 (mmm) REVERT: B 860 MET cc_start: 0.8235 (tmm) cc_final: 0.7756 (tmm) REVERT: B 942 ARG cc_start: 0.7486 (mtt-85) cc_final: 0.7133 (mtp85) REVERT: B 1028 GLU cc_start: 0.9158 (tt0) cc_final: 0.8839 (tt0) REVERT: B 1072 MET cc_start: 0.8885 (mmm) cc_final: 0.8380 (mmm) REVERT: B 1111 MET cc_start: 0.9402 (mmm) cc_final: 0.8898 (mmm) REVERT: C 190 ASP cc_start: 0.9116 (t0) cc_final: 0.8750 (t0) REVERT: D 117 GLU cc_start: 0.8345 (OUTLIER) cc_final: 0.7910 (pm20) REVERT: E 22 MET cc_start: 0.9251 (ttp) cc_final: 0.8776 (ttm) REVERT: E 25 ASP cc_start: 0.9116 (m-30) cc_final: 0.8640 (m-30) REVERT: E 32 GLN cc_start: 0.8698 (tp-100) cc_final: 0.7544 (tp-100) REVERT: E 57 MET cc_start: 0.8739 (mtm) cc_final: 0.8430 (ptt) REVERT: E 58 MET cc_start: 0.8918 (mtp) cc_final: 0.8475 (mtp) REVERT: F 96 THR cc_start: 0.9623 (m) cc_final: 0.9385 (p) REVERT: F 124 GLU cc_start: 0.8484 (tt0) cc_final: 0.7974 (tt0) REVERT: F 130 ILE cc_start: 0.9631 (mt) cc_final: 0.9382 (mp) REVERT: F 144 GLU cc_start: 0.8351 (mt-10) cc_final: 0.8022 (mt-10) REVERT: G 21 ARG cc_start: 0.8706 (ttm110) cc_final: 0.8236 (ttm110) REVERT: G 29 LYS cc_start: 0.9004 (tppt) cc_final: 0.8752 (mmmt) REVERT: G 32 GLU cc_start: 0.8509 (mt-10) cc_final: 0.8208 (mt-10) REVERT: G 33 GLU cc_start: 0.8514 (tp30) cc_final: 0.8187 (mm-30) REVERT: G 137 ILE cc_start: 0.7194 (mt) cc_final: 0.6790 (pt) REVERT: H 24 CYS cc_start: 0.9081 (m) cc_final: 0.8746 (m) REVERT: H 105 GLU cc_start: 0.8406 (tt0) cc_final: 0.8178 (tm-30) REVERT: H 107 VAL cc_start: 0.9151 (t) cc_final: 0.8453 (t) REVERT: H 139 ASN cc_start: 0.9026 (m-40) cc_final: 0.8803 (m-40) REVERT: H 146 ARG cc_start: 0.8253 (ttp-170) cc_final: 0.7804 (ttp80) REVERT: I 27 PHE cc_start: 0.8358 (m-80) cc_final: 0.8059 (m-80) REVERT: I 61 ASP cc_start: 0.8183 (t0) cc_final: 0.7904 (t0) REVERT: I 101 PHE cc_start: 0.8714 (m-80) cc_final: 0.8422 (m-80) REVERT: J 12 LYS cc_start: 0.9445 (tttm) cc_final: 0.9005 (ttmm) REVERT: J 27 GLU cc_start: 0.8900 (OUTLIER) cc_final: 0.8453 (pt0) REVERT: J 49 MET cc_start: 0.9404 (mmm) cc_final: 0.8943 (tpp) REVERT: K 36 GLU cc_start: 0.8994 (mm-30) cc_final: 0.8670 (mm-30) REVERT: L 29 TYR cc_start: 0.8942 (m-80) cc_final: 0.8279 (m-10) REVERT: L 54 ARG cc_start: 0.8347 (mtt-85) cc_final: 0.7966 (mtt90) REVERT: L 67 PHE cc_start: 0.9217 (m-80) cc_final: 0.8807 (m-10) outliers start: 57 outliers final: 27 residues processed: 429 average time/residue: 0.2105 time to fit residues: 149.8523 Evaluate side-chains 394 residues out of total 3426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 362 time to evaluate : 1.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 CYS Chi-restraints excluded: chain A residue 649 ILE Chi-restraints excluded: chain A residue 716 ASP Chi-restraints excluded: chain A residue 755 PHE Chi-restraints excluded: chain A residue 975 HIS Chi-restraints excluded: chain A residue 1444 MET Chi-restraints excluded: chain B residue 322 PHE Chi-restraints excluded: chain B residue 386 LEU Chi-restraints excluded: chain B residue 394 ASP Chi-restraints excluded: chain B residue 408 LEU Chi-restraints excluded: chain B residue 616 ILE Chi-restraints excluded: chain B residue 782 LEU Chi-restraints excluded: chain B residue 953 LEU Chi-restraints excluded: chain B residue 1021 MET Chi-restraints excluded: chain B residue 1093 GLN Chi-restraints excluded: chain B residue 1120 GLU Chi-restraints excluded: chain C residue 240 VAL Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain C residue 258 ILE Chi-restraints excluded: chain D residue 117 GLU Chi-restraints excluded: chain D residue 218 GLU Chi-restraints excluded: chain E residue 21 GLU Chi-restraints excluded: chain E residue 83 CYS Chi-restraints excluded: chain E residue 115 ASN Chi-restraints excluded: chain E residue 175 LEU Chi-restraints excluded: chain F residue 153 VAL Chi-restraints excluded: chain G residue 6 ASP Chi-restraints excluded: chain G residue 147 ILE Chi-restraints excluded: chain I residue 104 LEU Chi-restraints excluded: chain J residue 27 GLU Chi-restraints excluded: chain J residue 29 GLU Chi-restraints excluded: chain J residue 50 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 393 random chunks: chunk 294 optimal weight: 10.0000 chunk 183 optimal weight: 6.9990 chunk 368 optimal weight: 1.9990 chunk 123 optimal weight: 3.9990 chunk 281 optimal weight: 20.0000 chunk 133 optimal weight: 8.9990 chunk 44 optimal weight: 2.9990 chunk 268 optimal weight: 6.9990 chunk 75 optimal weight: 8.9990 chunk 56 optimal weight: 7.9990 chunk 226 optimal weight: 6.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 451 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 488 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 862 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 415 GLN ** B 984 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1093 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 188 HIS G 10 ASN G 71 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.072826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.2750 r_free = 0.2750 target = 0.049969 restraints weight = 124947.154| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2791 r_free = 0.2791 target = 0.051410 restraints weight = 67397.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2818 r_free = 0.2818 target = 0.052382 restraints weight = 45496.374| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.2835 r_free = 0.2835 target = 0.052991 restraints weight = 35292.599| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2844 r_free = 0.2844 target = 0.053326 restraints weight = 30180.178| |-----------------------------------------------------------------------------| r_work (final): 0.2821 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8613 moved from start: 0.2297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.082 33706 Z= 0.273 Angle : 0.666 13.048 45901 Z= 0.344 Chirality : 0.045 0.256 5156 Planarity : 0.004 0.046 5608 Dihedral : 17.201 160.298 5260 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 11.46 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.13 % Favored : 94.82 % Rotamer: Outliers : 1.90 % Allowed : 11.24 % Favored : 86.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.41 % 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: 0.37 (0.14), residues: 3839 helix: 1.50 (0.14), residues: 1327 sheet: -0.20 (0.21), residues: 585 loop : -0.45 (0.15), residues: 1927 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B1135 TYR 0.015 0.001 TYR D 147 PHE 0.017 0.002 PHE K 71 TRP 0.010 0.001 TRP C 201 HIS 0.007 0.001 HIS A1173 Details of bonding type rmsd/Z covalent geometry : bond 0.00588 / 0.27 (33674) covalent geometry : angle 0.65538 / 0.34 (45856) hydrogen bonds : bond 0.04066 / 2.72 ( 1414) hydrogen bonds : angle 5.08934 / 3.67 ( 3891) metal coordination : bond 0.00889 / 0.60 ( 32) metal coordination : angle 3.85491 / 2.54 ( 45) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7678 Ramachandran restraints generated. 3839 Oldfield, 0 Emsley, 3839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7678 Ramachandran restraints generated. 3839 Oldfield, 0 Emsley, 3839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 445 residues out of total 3426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 380 time to evaluate : 0.960 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 MET cc_start: 0.8399 (mtt) cc_final: 0.7813 (tpp) REVERT: A 437 MET cc_start: 0.8259 (mtp) cc_final: 0.7927 (mtm) REVERT: A 455 MET cc_start: 0.8511 (tpp) cc_final: 0.7889 (tpp) REVERT: A 510 GLN cc_start: 0.9209 (mm-40) cc_final: 0.8853 (mm-40) REVERT: A 605 MET cc_start: 0.9322 (tpp) cc_final: 0.8952 (tpp) REVERT: A 727 ASP cc_start: 0.9155 (m-30) cc_final: 0.8790 (t0) REVERT: A 838 GLN cc_start: 0.9348 (tp40) cc_final: 0.8925 (tm-30) REVERT: A 873 MET cc_start: 0.9285 (mmt) cc_final: 0.9080 (mmm) REVERT: A 975 HIS cc_start: 0.8670 (OUTLIER) cc_final: 0.8123 (t-90) REVERT: A 1070 GLN cc_start: 0.9390 (mt0) cc_final: 0.9117 (mt0) REVERT: A 1220 PHE cc_start: 0.8684 (OUTLIER) cc_final: 0.8418 (m-10) REVERT: A 1224 LEU cc_start: 0.9164 (tp) cc_final: 0.8453 (mt) REVERT: A 1280 GLU cc_start: 0.8292 (mm-30) cc_final: 0.7984 (mp0) REVERT: A 1368 MET cc_start: 0.9279 (mtm) cc_final: 0.8804 (mtp) REVERT: A 1373 ASP cc_start: 0.8775 (m-30) cc_final: 0.8430 (m-30) REVERT: A 1378 GLN cc_start: 0.8783 (mm-40) cc_final: 0.8356 (tp40) REVERT: B 86 ARG cc_start: 0.9323 (mmt90) cc_final: 0.8860 (mmm-85) REVERT: B 239 GLU cc_start: 0.8660 (pp20) cc_final: 0.8435 (tm-30) REVERT: B 427 ASP cc_start: 0.8752 (m-30) cc_final: 0.8481 (m-30) REVERT: B 471 LYS cc_start: 0.7345 (mptt) cc_final: 0.6543 (tttp) REVERT: B 542 MET cc_start: 0.8615 (mtp) cc_final: 0.8397 (tpp) REVERT: B 942 ARG cc_start: 0.7609 (mtt-85) cc_final: 0.7262 (mtp85) REVERT: B 1028 GLU cc_start: 0.9144 (tt0) cc_final: 0.8850 (tt0) REVERT: B 1072 MET cc_start: 0.8823 (mmm) cc_final: 0.8377 (mmm) REVERT: B 1111 MET cc_start: 0.9357 (mmm) cc_final: 0.8817 (mmm) REVERT: B 1210 MET cc_start: 0.9029 (mmt) cc_final: 0.8699 (mmp) REVERT: C 190 ASP cc_start: 0.9044 (t0) cc_final: 0.8704 (t0) REVERT: E 22 MET cc_start: 0.9241 (ttp) cc_final: 0.8801 (ttm) REVERT: E 25 ASP cc_start: 0.9104 (m-30) cc_final: 0.8651 (m-30) REVERT: E 58 MET cc_start: 0.8844 (mtp) cc_final: 0.8409 (mtp) REVERT: F 85 MET cc_start: 0.9043 (tmm) cc_final: 0.8762 (tmm) REVERT: F 144 GLU cc_start: 0.8376 (mt-10) cc_final: 0.8056 (mt-10) REVERT: G 21 ARG cc_start: 0.8727 (ttm110) cc_final: 0.8387 (ttm110) REVERT: G 29 LYS cc_start: 0.9011 (tppt) cc_final: 0.8514 (mmmt) REVERT: G 33 GLU cc_start: 0.8565 (tp30) cc_final: 0.8322 (mm-30) REVERT: G 137 ILE cc_start: 0.7068 (mt) cc_final: 0.6737 (pt) REVERT: H 24 CYS cc_start: 0.9080 (m) cc_final: 0.8720 (m) REVERT: H 105 GLU cc_start: 0.8460 (tt0) cc_final: 0.8212 (tm-30) REVERT: H 107 VAL cc_start: 0.9169 (t) cc_final: 0.8429 (t) REVERT: H 139 ASN cc_start: 0.8929 (m-40) cc_final: 0.8721 (m-40) REVERT: I 13 MET cc_start: 0.6851 (ppp) cc_final: 0.5988 (ppp) REVERT: I 27 PHE cc_start: 0.8422 (m-80) cc_final: 0.8206 (m-80) REVERT: I 61 ASP cc_start: 0.8222 (t0) cc_final: 0.7985 (t0) REVERT: I 101 PHE cc_start: 0.8671 (m-80) cc_final: 0.8385 (m-80) REVERT: J 12 LYS cc_start: 0.9515 (tttm) cc_final: 0.9059 (ttmm) REVERT: J 26 GLN cc_start: 0.8918 (pp30) cc_final: 0.8659 (pp30) REVERT: J 27 GLU cc_start: 0.8902 (OUTLIER) cc_final: 0.8460 (pt0) REVERT: J 49 MET cc_start: 0.9443 (mmm) cc_final: 0.9125 (tpp) REVERT: K 36 GLU cc_start: 0.8977 (mm-30) cc_final: 0.8705 (mm-30) REVERT: L 67 PHE cc_start: 0.9371 (m-80) cc_final: 0.8924 (m-10) outliers start: 65 outliers final: 37 residues processed: 424 average time/residue: 0.1900 time to fit residues: 134.7609 Evaluate side-chains 391 residues out of total 3426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 351 time to evaluate : 0.992 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 CYS Chi-restraints excluded: chain A residue 131 SER Chi-restraints excluded: chain A residue 268 ASP Chi-restraints excluded: chain A residue 449 SER Chi-restraints excluded: chain A residue 472 LEU Chi-restraints excluded: chain A residue 649 ILE Chi-restraints excluded: chain A residue 658 LEU Chi-restraints excluded: chain A residue 716 ASP Chi-restraints excluded: chain A residue 755 PHE Chi-restraints excluded: chain A residue 824 LEU Chi-restraints excluded: chain A residue 863 VAL Chi-restraints excluded: chain A residue 975 HIS Chi-restraints excluded: chain A residue 1000 LEU Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1101 LEU Chi-restraints excluded: chain A residue 1220 PHE Chi-restraints excluded: chain A residue 1336 MET Chi-restraints excluded: chain B residue 386 LEU Chi-restraints excluded: chain B residue 616 ILE Chi-restraints excluded: chain B residue 782 LEU Chi-restraints excluded: chain B residue 1021 MET Chi-restraints excluded: chain B residue 1093 GLN Chi-restraints excluded: chain B residue 1095 LEU Chi-restraints excluded: chain B residue 1120 GLU Chi-restraints excluded: chain C residue 240 VAL Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain C residue 258 ILE Chi-restraints excluded: chain D residue 218 GLU Chi-restraints excluded: chain E residue 21 GLU Chi-restraints excluded: chain E residue 83 CYS Chi-restraints excluded: chain E residue 115 ASN Chi-restraints excluded: chain E residue 175 LEU Chi-restraints excluded: chain F residue 153 VAL Chi-restraints excluded: chain G residue 10 ASN Chi-restraints excluded: chain G residue 109 PHE Chi-restraints excluded: chain G residue 147 ILE Chi-restraints excluded: chain J residue 3 VAL Chi-restraints excluded: chain J residue 27 GLU Chi-restraints excluded: chain J residue 29 GLU Chi-restraints excluded: chain J residue 50 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 393 random chunks: chunk 293 optimal weight: 0.9980 chunk 31 optimal weight: 0.8980 chunk 289 optimal weight: 9.9990 chunk 331 optimal weight: 0.7980 chunk 237 optimal weight: 10.0000 chunk 16 optimal weight: 0.7980 chunk 55 optimal weight: 4.9990 chunk 74 optimal weight: 5.9990 chunk 44 optimal weight: 5.9990 chunk 193 optimal weight: 3.9990 chunk 41 optimal weight: 0.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 451 HIS ** A 488 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 548 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 862 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1432 GLN ** B 415 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 984 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 100 GLN G 71 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.074690 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2797 r_free = 0.2797 target = 0.051507 restraints weight = 122937.099| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.2839 r_free = 0.2839 target = 0.053071 restraints weight = 64029.928| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.2867 r_free = 0.2867 target = 0.054094 restraints weight = 42330.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.2884 r_free = 0.2884 target = 0.054753 restraints weight = 32568.327| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2894 r_free = 0.2894 target = 0.055106 restraints weight = 27675.305| |-----------------------------------------------------------------------------| r_work (final): 0.2869 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8544 moved from start: 0.2415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 33706 Z= 0.121 Angle : 0.608 13.711 45901 Z= 0.310 Chirality : 0.044 0.253 5156 Planarity : 0.004 0.048 5608 Dihedral : 17.134 161.304 5260 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 9.95 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.04 % Favored : 95.91 % Rotamer: Outliers : 1.40 % Allowed : 12.46 % Favored : 86.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.41 % 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: 0.49 (0.14), residues: 3839 helix: 1.61 (0.15), residues: 1327 sheet: -0.04 (0.21), residues: 591 loop : -0.43 (0.15), residues: 1921 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 335 TYR 0.017 0.001 TYR H 141 PHE 0.017 0.001 PHE D 70 TRP 0.010 0.001 TRP C 201 HIS 0.007 0.001 HIS A1173 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.12 (33674) covalent geometry : angle 0.59401 / 0.31 (45856) hydrogen bonds : bond 0.03566 / 2.39 ( 1414) hydrogen bonds : angle 4.81489 / 3.48 ( 3891) metal coordination : bond 0.01058 / 0.79 ( 32) metal coordination : angle 4.15921 / 2.61 ( 45) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7678 Ramachandran restraints generated. 3839 Oldfield, 0 Emsley, 3839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7678 Ramachandran restraints generated. 3839 Oldfield, 0 Emsley, 3839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 450 residues out of total 3426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 402 time to evaluate : 1.238 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 MET cc_start: 0.8496 (mtt) cc_final: 0.7872 (tpp) REVERT: A 437 MET cc_start: 0.8340 (mtp) cc_final: 0.7956 (mtm) REVERT: A 455 MET cc_start: 0.8405 (tpp) cc_final: 0.7778 (tpp) REVERT: A 510 GLN cc_start: 0.9201 (mm-40) cc_final: 0.8717 (mp10) REVERT: A 727 ASP cc_start: 0.9151 (m-30) cc_final: 0.8775 (t0) REVERT: A 838 GLN cc_start: 0.9300 (tp40) cc_final: 0.8964 (tm-30) REVERT: A 873 MET cc_start: 0.9301 (mmt) cc_final: 0.9062 (mmm) REVERT: A 975 HIS cc_start: 0.8647 (OUTLIER) cc_final: 0.8022 (t-90) REVERT: A 1220 PHE cc_start: 0.8692 (OUTLIER) cc_final: 0.8425 (m-10) REVERT: A 1224 LEU cc_start: 0.9164 (tp) cc_final: 0.8524 (mt) REVERT: A 1280 GLU cc_start: 0.8440 (mm-30) cc_final: 0.8042 (mp0) REVERT: A 1368 MET cc_start: 0.9262 (mtm) cc_final: 0.8730 (mtp) REVERT: A 1373 ASP cc_start: 0.8761 (m-30) cc_final: 0.8355 (m-30) REVERT: A 1378 GLN cc_start: 0.8800 (mm-40) cc_final: 0.8351 (tp40) REVERT: B 86 ARG cc_start: 0.9326 (mmt90) cc_final: 0.8847 (mmm-85) REVERT: B 239 GLU cc_start: 0.8602 (pp20) cc_final: 0.8370 (tm-30) REVERT: B 471 LYS cc_start: 0.7324 (mptt) cc_final: 0.6511 (tttp) REVERT: B 839 MET cc_start: 0.8969 (ptp) cc_final: 0.8765 (pmm) REVERT: B 942 ARG cc_start: 0.7477 (mtt-85) cc_final: 0.7141 (mtp85) REVERT: B 999 MET cc_start: 0.9484 (mmm) cc_final: 0.9050 (mmm) REVERT: B 1028 GLU cc_start: 0.9172 (tt0) cc_final: 0.8849 (tm-30) REVERT: B 1072 MET cc_start: 0.8834 (mmm) cc_final: 0.8378 (mmm) REVERT: B 1111 MET cc_start: 0.9402 (mmm) cc_final: 0.8900 (mmm) REVERT: C 190 ASP cc_start: 0.9113 (t0) cc_final: 0.8695 (t0) REVERT: C 229 TYR cc_start: 0.9263 (m-80) cc_final: 0.8848 (m-10) REVERT: E 22 MET cc_start: 0.9282 (ttp) cc_final: 0.8821 (ttm) REVERT: E 25 ASP cc_start: 0.9117 (m-30) cc_final: 0.8618 (m-30) REVERT: E 58 MET cc_start: 0.8848 (mtp) cc_final: 0.8386 (mtp) REVERT: F 85 MET cc_start: 0.9071 (tmm) cc_final: 0.8712 (tmm) REVERT: F 144 GLU cc_start: 0.8319 (mt-10) cc_final: 0.7978 (mt-10) REVERT: F 151 LEU cc_start: 0.9320 (OUTLIER) cc_final: 0.8904 (mm) REVERT: G 21 ARG cc_start: 0.8595 (ttm110) cc_final: 0.8264 (ttm110) REVERT: G 33 GLU cc_start: 0.8441 (tp30) cc_final: 0.8075 (mm-30) REVERT: G 130 TYR cc_start: 0.6632 (m-80) cc_final: 0.5674 (m-10) REVERT: G 137 ILE cc_start: 0.7043 (mt) cc_final: 0.6686 (pt) REVERT: H 14 GLU cc_start: 0.7070 (tm-30) cc_final: 0.6631 (tm-30) REVERT: H 24 CYS cc_start: 0.9177 (m) cc_final: 0.8876 (m) REVERT: H 27 GLU cc_start: 0.8519 (mp0) cc_final: 0.7392 (mp0) REVERT: H 105 GLU cc_start: 0.8501 (tt0) cc_final: 0.8174 (tm-30) REVERT: H 106 GLU cc_start: 0.8529 (tp30) cc_final: 0.8306 (mm-30) REVERT: H 107 VAL cc_start: 0.9152 (t) cc_final: 0.8446 (t) REVERT: H 130 ARG cc_start: 0.8760 (mmt90) cc_final: 0.8416 (mmt90) REVERT: H 139 ASN cc_start: 0.9025 (m-40) cc_final: 0.8792 (m-40) REVERT: H 146 ARG cc_start: 0.8221 (ttp80) cc_final: 0.7836 (ttp80) REVERT: I 13 MET cc_start: 0.6904 (ppp) cc_final: 0.6045 (ppp) REVERT: I 27 PHE cc_start: 0.8362 (m-80) cc_final: 0.8141 (m-80) REVERT: I 61 ASP cc_start: 0.8278 (t0) cc_final: 0.7997 (t0) REVERT: I 101 PHE cc_start: 0.8661 (m-80) cc_final: 0.8383 (m-80) REVERT: J 12 LYS cc_start: 0.9427 (tttm) cc_final: 0.8901 (ttmm) REVERT: J 26 GLN cc_start: 0.8932 (pp30) cc_final: 0.8697 (pp30) REVERT: J 27 GLU cc_start: 0.8914 (tm-30) cc_final: 0.8431 (pt0) REVERT: J 49 MET cc_start: 0.9362 (mmm) cc_final: 0.8724 (tpp) REVERT: K 36 GLU cc_start: 0.9051 (mm-30) cc_final: 0.8766 (mm-30) REVERT: K 44 ASN cc_start: 0.9294 (t0) cc_final: 0.8984 (t0) REVERT: L 29 TYR cc_start: 0.8968 (m-10) cc_final: 0.8762 (m-10) REVERT: L 67 PHE cc_start: 0.9380 (m-80) cc_final: 0.8943 (m-10) outliers start: 48 outliers final: 29 residues processed: 436 average time/residue: 0.1984 time to fit residues: 145.1601 Evaluate side-chains 396 residues out of total 3426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 364 time to evaluate : 1.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 268 ASP Chi-restraints excluded: chain A residue 449 SER Chi-restraints excluded: chain A residue 472 LEU Chi-restraints excluded: chain A residue 511 ILE Chi-restraints excluded: chain A residue 521 MET Chi-restraints excluded: chain A residue 716 ASP Chi-restraints excluded: chain A residue 755 PHE Chi-restraints excluded: chain A residue 863 VAL Chi-restraints excluded: chain A residue 975 HIS Chi-restraints excluded: chain A residue 997 LEU Chi-restraints excluded: chain A residue 1000 LEU Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1220 PHE Chi-restraints excluded: chain B residue 616 ILE Chi-restraints excluded: chain B residue 782 LEU Chi-restraints excluded: chain B residue 953 LEU Chi-restraints excluded: chain B residue 1021 MET Chi-restraints excluded: chain B residue 1093 GLN Chi-restraints excluded: chain B residue 1095 LEU Chi-restraints excluded: chain B residue 1120 GLU Chi-restraints excluded: chain C residue 240 VAL Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain C residue 258 ILE Chi-restraints excluded: chain D residue 218 GLU Chi-restraints excluded: chain E residue 21 GLU Chi-restraints excluded: chain E residue 115 ASN Chi-restraints excluded: chain E residue 175 LEU Chi-restraints excluded: chain F residue 151 LEU Chi-restraints excluded: chain F residue 153 VAL Chi-restraints excluded: chain G residue 10 ASN Chi-restraints excluded: chain G residue 147 ILE Chi-restraints excluded: chain J residue 50 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 393 random chunks: chunk 88 optimal weight: 3.9990 chunk 368 optimal weight: 4.9990 chunk 358 optimal weight: 7.9990 chunk 226 optimal weight: 4.9990 chunk 80 optimal weight: 1.9990 chunk 149 optimal weight: 30.0000 chunk 72 optimal weight: 9.9990 chunk 195 optimal weight: 8.9990 chunk 19 optimal weight: 6.9990 chunk 156 optimal weight: 10.0000 chunk 8 optimal weight: 1.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 488 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 548 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 862 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 415 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 984 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1093 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 61 GLN E 63 ASN F 100 GLN ** G 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 137 GLN I 90 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.073341 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2775 r_free = 0.2775 target = 0.050731 restraints weight = 125154.616| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.2816 r_free = 0.2816 target = 0.052219 restraints weight = 67060.172| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2842 r_free = 0.2842 target = 0.053197 restraints weight = 44864.896| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2859 r_free = 0.2859 target = 0.053826 restraints weight = 34600.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.2870 r_free = 0.2870 target = 0.054223 restraints weight = 29402.712| |-----------------------------------------------------------------------------| r_work (final): 0.2848 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8598 moved from start: 0.2538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 33706 Z= 0.224 Angle : 0.637 13.160 45901 Z= 0.326 Chirality : 0.044 0.264 5156 Planarity : 0.004 0.047 5608 Dihedral : 17.141 160.046 5260 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 10.85 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.74 % Favored : 95.21 % Rotamer: Outliers : 1.58 % Allowed : 13.78 % Favored : 84.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.41 % 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: 3839 helix: 1.62 (0.15), residues: 1320 sheet: -0.20 (0.21), residues: 587 loop : -0.45 (0.15), residues: 1932 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 19 TYR 0.013 0.001 TYR B 994 PHE 0.025 0.001 PHE D 70 TRP 0.008 0.001 TRP C 201 HIS 0.006 0.001 HIS A1173 Details of bonding type rmsd/Z covalent geometry : bond 0.00487 / 0.22 (33674) covalent geometry : angle 0.62474 / 0.32 (45856) hydrogen bonds : bond 0.03663 / 2.45 ( 1414) hydrogen bonds : angle 4.82447 / 3.49 ( 3891) metal coordination : bond 0.00907 / 0.63 ( 32) metal coordination : angle 4.00174 / 2.58 ( 45) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7678 Ramachandran restraints generated. 3839 Oldfield, 0 Emsley, 3839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7678 Ramachandran restraints generated. 3839 Oldfield, 0 Emsley, 3839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 431 residues out of total 3426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 377 time to evaluate : 1.270 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 13 THR cc_start: 0.9348 (OUTLIER) cc_final: 0.8954 (p) REVERT: A 74 MET cc_start: 0.8403 (mtt) cc_final: 0.7837 (tpp) REVERT: A 122 MET cc_start: 0.9159 (mmm) cc_final: 0.8690 (ttt) REVERT: A 265 LYS cc_start: 0.9763 (tppt) cc_final: 0.9442 (tppp) REVERT: A 437 MET cc_start: 0.8197 (mtp) cc_final: 0.7876 (mtm) REVERT: A 455 MET cc_start: 0.8374 (tpp) cc_final: 0.7825 (tpp) REVERT: A 605 MET cc_start: 0.9321 (tpp) cc_final: 0.9029 (tpp) REVERT: A 696 GLU cc_start: 0.8982 (tt0) cc_final: 0.8574 (tp30) REVERT: A 727 ASP cc_start: 0.9106 (m-30) cc_final: 0.8759 (t0) REVERT: A 838 GLN cc_start: 0.9330 (tp40) cc_final: 0.8969 (tm-30) REVERT: A 975 HIS cc_start: 0.8555 (OUTLIER) cc_final: 0.8085 (t-90) REVERT: A 1220 PHE cc_start: 0.8719 (OUTLIER) cc_final: 0.8433 (m-10) REVERT: A 1224 LEU cc_start: 0.9135 (tp) cc_final: 0.8503 (mt) REVERT: A 1280 GLU cc_start: 0.8347 (mm-30) cc_final: 0.8037 (mp0) REVERT: A 1368 MET cc_start: 0.9242 (mtm) cc_final: 0.8790 (mtp) REVERT: A 1373 ASP cc_start: 0.8742 (m-30) cc_final: 0.8395 (m-30) REVERT: A 1378 GLN cc_start: 0.8750 (mm-40) cc_final: 0.8297 (tp40) REVERT: B 86 ARG cc_start: 0.9273 (mmt90) cc_final: 0.8800 (mmm-85) REVERT: B 471 LYS cc_start: 0.7398 (mptt) cc_final: 0.6557 (tttp) REVERT: B 542 MET cc_start: 0.8499 (mtp) cc_final: 0.8043 (mtp) REVERT: B 942 ARG cc_start: 0.7601 (mtt-85) cc_final: 0.7287 (mtp85) REVERT: B 1028 GLU cc_start: 0.9106 (tt0) cc_final: 0.8738 (tt0) REVERT: B 1072 MET cc_start: 0.8827 (mmm) cc_final: 0.8433 (mmm) REVERT: B 1111 MET cc_start: 0.9366 (mmm) cc_final: 0.8840 (mmm) REVERT: B 1206 GLU cc_start: 0.9242 (mt-10) cc_final: 0.8900 (mt-10) REVERT: C 190 ASP cc_start: 0.8986 (t0) cc_final: 0.8601 (t0) REVERT: C 229 TYR cc_start: 0.9275 (m-80) cc_final: 0.8763 (m-10) REVERT: E 25 ASP cc_start: 0.9104 (m-30) cc_final: 0.8642 (m-30) REVERT: E 58 MET cc_start: 0.8685 (mtp) cc_final: 0.8374 (mtp) REVERT: F 130 ILE cc_start: 0.9438 (mt) cc_final: 0.9137 (mm) REVERT: F 144 GLU cc_start: 0.8294 (mt-10) cc_final: 0.8045 (mt-10) REVERT: F 151 LEU cc_start: 0.9356 (OUTLIER) cc_final: 0.8968 (mm) REVERT: G 21 ARG cc_start: 0.8626 (ttm110) cc_final: 0.8358 (ttm110) REVERT: G 32 GLU cc_start: 0.9173 (tm-30) cc_final: 0.8654 (pt0) REVERT: G 137 ILE cc_start: 0.7020 (mt) cc_final: 0.6711 (pt) REVERT: H 14 GLU cc_start: 0.7247 (tm-30) cc_final: 0.6502 (tm-30) REVERT: H 24 CYS cc_start: 0.9123 (m) cc_final: 0.8833 (m) REVERT: H 27 GLU cc_start: 0.8528 (mp0) cc_final: 0.7212 (mp0) REVERT: H 105 GLU cc_start: 0.8496 (tt0) cc_final: 0.8220 (tm-30) REVERT: H 107 VAL cc_start: 0.9136 (t) cc_final: 0.8339 (t) REVERT: H 146 ARG cc_start: 0.8145 (ttp80) cc_final: 0.7755 (ttp80) REVERT: I 13 MET cc_start: 0.6915 (ppp) cc_final: 0.5825 (ppp) REVERT: I 27 PHE cc_start: 0.8451 (m-80) cc_final: 0.8230 (m-80) REVERT: I 61 ASP cc_start: 0.8325 (t0) cc_final: 0.8085 (t0) REVERT: I 101 PHE cc_start: 0.8612 (m-80) cc_final: 0.8318 (m-80) REVERT: J 12 LYS cc_start: 0.9510 (tttm) cc_final: 0.9017 (ttmm) REVERT: J 27 GLU cc_start: 0.8875 (tm-30) cc_final: 0.8456 (pt0) REVERT: K 36 GLU cc_start: 0.9002 (mm-30) cc_final: 0.8760 (mm-30) REVERT: L 67 PHE cc_start: 0.9404 (m-80) cc_final: 0.9026 (m-10) outliers start: 54 outliers final: 35 residues processed: 412 average time/residue: 0.2130 time to fit residues: 146.0196 Evaluate side-chains 392 residues out of total 3426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 353 time to evaluate : 1.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 THR Chi-restraints excluded: chain A residue 103 CYS Chi-restraints excluded: chain A residue 131 SER Chi-restraints excluded: chain A residue 268 ASP Chi-restraints excluded: chain A residue 472 LEU Chi-restraints excluded: chain A residue 716 ASP Chi-restraints excluded: chain A residue 755 PHE Chi-restraints excluded: chain A residue 824 LEU Chi-restraints excluded: chain A residue 863 VAL Chi-restraints excluded: chain A residue 975 HIS Chi-restraints excluded: chain A residue 1000 LEU Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1220 PHE Chi-restraints excluded: chain A residue 1336 MET Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 616 ILE Chi-restraints excluded: chain B residue 782 LEU Chi-restraints excluded: chain B residue 953 LEU Chi-restraints excluded: chain B residue 1021 MET Chi-restraints excluded: chain B residue 1093 GLN Chi-restraints excluded: chain B residue 1095 LEU Chi-restraints excluded: chain B residue 1120 GLU Chi-restraints excluded: chain B residue 1202 LEU Chi-restraints excluded: chain C residue 240 VAL Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain C residue 258 ILE Chi-restraints excluded: chain D residue 218 GLU Chi-restraints excluded: chain E residue 21 GLU Chi-restraints excluded: chain E residue 115 ASN Chi-restraints excluded: chain E residue 175 LEU Chi-restraints excluded: chain F residue 151 LEU Chi-restraints excluded: chain F residue 153 VAL Chi-restraints excluded: chain G residue 4 ILE Chi-restraints excluded: chain G residue 10 ASN Chi-restraints excluded: chain G residue 147 ILE Chi-restraints excluded: chain H residue 59 ILE Chi-restraints excluded: chain J residue 3 VAL Chi-restraints excluded: chain J residue 29 GLU Chi-restraints excluded: chain J residue 50 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 393 random chunks: chunk 375 optimal weight: 7.9990 chunk 67 optimal weight: 0.7980 chunk 28 optimal weight: 3.9990 chunk 318 optimal weight: 6.9990 chunk 305 optimal weight: 6.9990 chunk 283 optimal weight: 20.0000 chunk 365 optimal weight: 1.9990 chunk 140 optimal weight: 5.9990 chunk 280 optimal weight: 8.9990 chunk 342 optimal weight: 10.0000 chunk 341 optimal weight: 4.9990 overall best weight: 3.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 488 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 548 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 862 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 415 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 984 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1093 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 179 GLN F 100 GLN ** G 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 137 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.073340 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2773 r_free = 0.2773 target = 0.050759 restraints weight = 125490.699| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2815 r_free = 0.2815 target = 0.052273 restraints weight = 67189.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.2841 r_free = 0.2841 target = 0.053233 restraints weight = 44783.701| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.2858 r_free = 0.2858 target = 0.053864 restraints weight = 34559.458| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 61)----------------| | r_work = 0.2868 r_free = 0.2868 target = 0.054247 restraints weight = 29333.943| |-----------------------------------------------------------------------------| r_work (final): 0.2844 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8599 moved from start: 0.2660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 33706 Z= 0.215 Angle : 0.647 12.911 45901 Z= 0.330 Chirality : 0.044 0.268 5156 Planarity : 0.004 0.047 5608 Dihedral : 17.171 159.375 5260 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 10.68 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.66 % Favored : 95.29 % Rotamer: Outliers : 1.90 % Allowed : 14.21 % Favored : 83.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.41 % 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: 0.37 (0.14), residues: 3839 helix: 1.56 (0.15), residues: 1323 sheet: -0.26 (0.21), residues: 585 loop : -0.48 (0.15), residues: 1931 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 119 TYR 0.021 0.001 TYR H 141 PHE 0.031 0.001 PHE D 70 TRP 0.009 0.001 TRP B 561 HIS 0.007 0.001 HIS A1173 Details of bonding type rmsd/Z covalent geometry : bond 0.00468 / 0.22 (33674) covalent geometry : angle 0.63639 / 0.33 (45856) hydrogen bonds : bond 0.03685 / 2.46 ( 1414) hydrogen bonds : angle 4.79478 / 3.47 ( 3891) metal coordination : bond 0.00839 / 0.57 ( 32) metal coordination : angle 3.75712 / 2.46 ( 45) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7678 Ramachandran restraints generated. 3839 Oldfield, 0 Emsley, 3839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7678 Ramachandran restraints generated. 3839 Oldfield, 0 Emsley, 3839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 436 residues out of total 3426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 371 time to evaluate : 1.104 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 13 THR cc_start: 0.9363 (OUTLIER) cc_final: 0.8993 (p) REVERT: A 74 MET cc_start: 0.8432 (mtt) cc_final: 0.7837 (tpp) REVERT: A 122 MET cc_start: 0.9167 (mmm) cc_final: 0.8604 (ttm) REVERT: A 265 LYS cc_start: 0.9763 (tppt) cc_final: 0.9442 (tppp) REVERT: A 437 MET cc_start: 0.8242 (mtp) cc_final: 0.7891 (mtm) REVERT: A 455 MET cc_start: 0.8325 (tpp) cc_final: 0.7849 (tpp) REVERT: A 510 GLN cc_start: 0.9066 (mm-40) cc_final: 0.8809 (mp10) REVERT: A 521 MET cc_start: 0.9104 (OUTLIER) cc_final: 0.8498 (mpp) REVERT: A 605 MET cc_start: 0.9264 (tpp) cc_final: 0.8894 (tpp) REVERT: A 696 GLU cc_start: 0.8971 (tt0) cc_final: 0.8552 (tp30) REVERT: A 727 ASP cc_start: 0.9111 (m-30) cc_final: 0.8756 (t0) REVERT: A 838 GLN cc_start: 0.9333 (tp40) cc_final: 0.8974 (tm-30) REVERT: A 846 GLU cc_start: 0.8860 (pt0) cc_final: 0.8511 (mp0) REVERT: A 975 HIS cc_start: 0.8523 (OUTLIER) cc_final: 0.8048 (t-90) REVERT: A 1070 GLN cc_start: 0.9503 (mt0) cc_final: 0.9268 (tt0) REVERT: A 1280 GLU cc_start: 0.8359 (mm-30) cc_final: 0.8035 (mp0) REVERT: A 1368 MET cc_start: 0.9245 (mtm) cc_final: 0.8781 (mtp) REVERT: A 1373 ASP cc_start: 0.8760 (m-30) cc_final: 0.8393 (m-30) REVERT: A 1378 GLN cc_start: 0.8769 (mm-40) cc_final: 0.8370 (tp40) REVERT: A 1444 MET cc_start: 0.8782 (mmt) cc_final: 0.8402 (mmm) REVERT: B 86 ARG cc_start: 0.9268 (mmt90) cc_final: 0.8796 (mmm-85) REVERT: B 471 LYS cc_start: 0.7409 (mptt) cc_final: 0.6550 (tttp) REVERT: B 542 MET cc_start: 0.8494 (mtp) cc_final: 0.8129 (mtp) REVERT: B 942 ARG cc_start: 0.7576 (mtt-85) cc_final: 0.7262 (mtp85) REVERT: B 999 MET cc_start: 0.9407 (mmm) cc_final: 0.9063 (mmm) REVERT: B 1028 GLU cc_start: 0.9112 (tt0) cc_final: 0.8761 (tt0) REVERT: B 1072 MET cc_start: 0.8811 (mmm) cc_final: 0.8417 (mmm) REVERT: B 1111 MET cc_start: 0.9360 (mmm) cc_final: 0.8882 (mmm) REVERT: B 1206 GLU cc_start: 0.9314 (mt-10) cc_final: 0.8983 (mt-10) REVERT: C 190 ASP cc_start: 0.8975 (t0) cc_final: 0.8586 (t0) REVERT: C 229 TYR cc_start: 0.9265 (m-80) cc_final: 0.8754 (m-10) REVERT: E 22 MET cc_start: 0.9321 (ttp) cc_final: 0.8908 (ttm) REVERT: E 25 ASP cc_start: 0.9099 (m-30) cc_final: 0.8615 (m-30) REVERT: E 58 MET cc_start: 0.8719 (mtp) cc_final: 0.8319 (mtp) REVERT: F 85 MET cc_start: 0.9027 (tmm) cc_final: 0.8772 (tmm) REVERT: F 125 LEU cc_start: 0.9302 (tt) cc_final: 0.8945 (tp) REVERT: F 144 GLU cc_start: 0.8291 (mt-10) cc_final: 0.8046 (mt-10) REVERT: F 151 LEU cc_start: 0.9346 (OUTLIER) cc_final: 0.8972 (mm) REVERT: G 21 ARG cc_start: 0.8596 (ttm110) cc_final: 0.8393 (ttm110) REVERT: G 32 GLU cc_start: 0.9288 (tm-30) cc_final: 0.8757 (pt0) REVERT: G 137 ILE cc_start: 0.6914 (mt) cc_final: 0.6589 (pt) REVERT: G 153 GLN cc_start: 0.4260 (OUTLIER) cc_final: 0.3941 (mt0) REVERT: H 14 GLU cc_start: 0.7382 (tm-30) cc_final: 0.6569 (tm-30) REVERT: H 24 CYS cc_start: 0.9143 (m) cc_final: 0.8920 (m) REVERT: H 27 GLU cc_start: 0.8546 (mp0) cc_final: 0.7277 (mp0) REVERT: H 105 GLU cc_start: 0.8512 (tt0) cc_final: 0.8197 (tm-30) REVERT: H 107 VAL cc_start: 0.9130 (t) cc_final: 0.8318 (t) REVERT: H 130 ARG cc_start: 0.8613 (mmt90) cc_final: 0.8349 (mmt90) REVERT: H 137 GLN cc_start: 0.8622 (mm-40) cc_final: 0.8421 (mm-40) REVERT: H 146 ARG cc_start: 0.8163 (ttp80) cc_final: 0.7787 (ttp80) REVERT: I 27 PHE cc_start: 0.8426 (m-80) cc_final: 0.8212 (m-80) REVERT: I 61 ASP cc_start: 0.8332 (t0) cc_final: 0.8108 (t0) REVERT: I 101 PHE cc_start: 0.8599 (m-80) cc_final: 0.8288 (m-80) REVERT: I 108 HIS cc_start: 0.7405 (t70) cc_final: 0.6957 (m-70) REVERT: J 12 LYS cc_start: 0.9502 (tttm) cc_final: 0.8969 (ttmm) REVERT: J 26 GLN cc_start: 0.8977 (pp30) cc_final: 0.8347 (pp30) REVERT: J 27 GLU cc_start: 0.8826 (tm-30) cc_final: 0.8430 (mt-10) REVERT: J 49 MET cc_start: 0.9464 (mmm) cc_final: 0.8801 (tpp) REVERT: L 66 GLN cc_start: 0.8797 (mm110) cc_final: 0.8574 (mm-40) REVERT: L 67 PHE cc_start: 0.9438 (m-80) cc_final: 0.9090 (m-10) outliers start: 65 outliers final: 44 residues processed: 417 average time/residue: 0.1822 time to fit residues: 126.4927 Evaluate side-chains 407 residues out of total 3426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 358 time to evaluate : 0.884 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 THR Chi-restraints excluded: chain A residue 103 CYS Chi-restraints excluded: chain A residue 268 ASP Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 472 LEU Chi-restraints excluded: chain A residue 511 ILE Chi-restraints excluded: chain A residue 521 MET Chi-restraints excluded: chain A residue 716 ASP Chi-restraints excluded: chain A residue 755 PHE Chi-restraints excluded: chain A residue 824 LEU Chi-restraints excluded: chain A residue 863 VAL Chi-restraints excluded: chain A residue 975 HIS Chi-restraints excluded: chain A residue 1000 LEU Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1209 MET Chi-restraints excluded: chain A residue 1228 TRP Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 394 ASP Chi-restraints excluded: chain B residue 466 TRP Chi-restraints excluded: chain B residue 616 ILE Chi-restraints excluded: chain B residue 782 LEU Chi-restraints excluded: chain B residue 841 MET Chi-restraints excluded: chain B residue 953 LEU Chi-restraints excluded: chain B residue 1021 MET Chi-restraints excluded: chain B residue 1093 GLN Chi-restraints excluded: chain B residue 1095 LEU Chi-restraints excluded: chain B residue 1120 GLU Chi-restraints excluded: chain B residue 1202 LEU Chi-restraints excluded: chain C residue 240 VAL Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain C residue 258 ILE Chi-restraints excluded: chain D residue 144 THR Chi-restraints excluded: chain D residue 218 GLU Chi-restraints excluded: chain E residue 21 GLU Chi-restraints excluded: chain E residue 115 ASN Chi-restraints excluded: chain E residue 175 LEU Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 151 LEU Chi-restraints excluded: chain F residue 153 VAL Chi-restraints excluded: chain G residue 4 ILE Chi-restraints excluded: chain G residue 10 ASN Chi-restraints excluded: chain G residue 39 THR Chi-restraints excluded: chain G residue 109 PHE Chi-restraints excluded: chain G residue 147 ILE Chi-restraints excluded: chain G residue 153 GLN Chi-restraints excluded: chain H residue 15 VAL Chi-restraints excluded: chain H residue 59 ILE Chi-restraints excluded: chain J residue 3 VAL Chi-restraints excluded: chain J residue 50 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 393 random chunks: chunk 204 optimal weight: 0.9990 chunk 70 optimal weight: 9.9990 chunk 95 optimal weight: 1.9990 chunk 168 optimal weight: 9.9990 chunk 14 optimal weight: 10.0000 chunk 276 optimal weight: 6.9990 chunk 271 optimal weight: 2.9990 chunk 39 optimal weight: 2.9990 chunk 35 optimal weight: 4.9990 chunk 155 optimal weight: 0.0670 chunk 233 optimal weight: 4.9990 overall best weight: 1.8126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 488 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 548 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 862 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 415 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 984 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 65 HIS F 100 GLN G 10 ASN G 71 ASN G 131 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.075316 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2793 r_free = 0.2793 target = 0.052241 restraints weight = 125863.779| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.2836 r_free = 0.2836 target = 0.053797 restraints weight = 65327.604| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.2864 r_free = 0.2864 target = 0.054824 restraints weight = 42972.681| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.2882 r_free = 0.2882 target = 0.055482 restraints weight = 32782.545| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.2892 r_free = 0.2892 target = 0.055897 restraints weight = 27683.969| |-----------------------------------------------------------------------------| r_work (final): 0.2868 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8557 moved from start: 0.2746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 33706 Z= 0.142 Angle : 0.621 14.020 45901 Z= 0.315 Chirality : 0.043 0.270 5156 Planarity : 0.004 0.048 5608 Dihedral : 17.137 159.850 5260 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 10.51 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.30 % Favored : 95.65 % Rotamer: Outliers : 1.72 % Allowed : 14.89 % Favored : 83.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.41 % 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 (0.14), residues: 3839 helix: 1.57 (0.15), residues: 1327 sheet: -0.18 (0.22), residues: 577 loop : -0.44 (0.15), residues: 1935 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG B1135 TYR 0.021 0.001 TYR G 167 PHE 0.022 0.001 PHE G 17 TRP 0.009 0.001 TRP C 201 HIS 0.006 0.001 HIS A1173 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.14 (33674) covalent geometry : angle 0.61226 / 0.31 (45856) hydrogen bonds : bond 0.03488 / 2.34 ( 1414) hydrogen bonds : angle 4.68750 / 3.40 ( 3891) metal coordination : bond 0.00577 / 0.40 ( 32) metal coordination : angle 3.34152 / 2.19 ( 45) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7678 Ramachandran restraints generated. 3839 Oldfield, 0 Emsley, 3839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7678 Ramachandran restraints generated. 3839 Oldfield, 0 Emsley, 3839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 439 residues out of total 3426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 380 time to evaluate : 1.322 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 MET cc_start: 0.8525 (mtt) cc_final: 0.7899 (tpp) REVERT: A 122 MET cc_start: 0.9198 (mmm) cc_final: 0.8671 (ttm) REVERT: A 265 LYS cc_start: 0.9775 (tppt) cc_final: 0.9444 (tppp) REVERT: A 437 MET cc_start: 0.8298 (mtp) cc_final: 0.7935 (mtm) REVERT: A 510 GLN cc_start: 0.9148 (mm-40) cc_final: 0.8710 (mp10) REVERT: A 521 MET cc_start: 0.9120 (OUTLIER) cc_final: 0.8714 (mpp) REVERT: A 605 MET cc_start: 0.9297 (tpp) cc_final: 0.8906 (tpp) REVERT: A 696 GLU cc_start: 0.9047 (tt0) cc_final: 0.8602 (tp30) REVERT: A 727 ASP cc_start: 0.9141 (m-30) cc_final: 0.8770 (t0) REVERT: A 838 GLN cc_start: 0.9329 (tp40) cc_final: 0.9021 (tm-30) REVERT: A 975 HIS cc_start: 0.8565 (OUTLIER) cc_final: 0.8030 (t-90) REVERT: A 1224 LEU cc_start: 0.9153 (tp) cc_final: 0.8455 (mp) REVERT: A 1280 GLU cc_start: 0.8347 (mm-30) cc_final: 0.7901 (mp0) REVERT: A 1368 MET cc_start: 0.9299 (mtm) cc_final: 0.8816 (mtp) REVERT: A 1373 ASP cc_start: 0.8812 (m-30) cc_final: 0.8433 (m-30) REVERT: A 1444 MET cc_start: 0.8824 (mmt) cc_final: 0.8416 (mmm) REVERT: B 86 ARG cc_start: 0.9287 (mmt90) cc_final: 0.8805 (mmm-85) REVERT: B 451 LYS cc_start: 0.9379 (mtmt) cc_final: 0.9162 (pttt) REVERT: B 471 LYS cc_start: 0.7397 (mptt) cc_final: 0.6558 (tttp) REVERT: B 542 MET cc_start: 0.8578 (mtp) cc_final: 0.8040 (mtp) REVERT: B 809 MET cc_start: 0.9269 (ptp) cc_final: 0.8959 (mpp) REVERT: B 942 ARG cc_start: 0.7496 (mtt-85) cc_final: 0.7175 (mtp85) REVERT: B 1028 GLU cc_start: 0.9170 (tt0) cc_final: 0.8768 (tm-30) REVERT: B 1072 MET cc_start: 0.8797 (mmm) cc_final: 0.8359 (mmm) REVERT: B 1111 MET cc_start: 0.9399 (mmm) cc_final: 0.8928 (mmm) REVERT: B 1206 GLU cc_start: 0.9347 (mt-10) cc_final: 0.8980 (mt-10) REVERT: C 190 ASP cc_start: 0.9045 (t0) cc_final: 0.8649 (t0) REVERT: C 229 TYR cc_start: 0.9271 (m-80) cc_final: 0.7996 (m-10) REVERT: D 155 ARG cc_start: 0.6155 (ttp-110) cc_final: 0.5454 (ttp80) REVERT: E 22 MET cc_start: 0.9329 (ttp) cc_final: 0.8896 (ttm) REVERT: E 25 ASP cc_start: 0.9150 (m-30) cc_final: 0.8660 (m-30) REVERT: E 58 MET cc_start: 0.8793 (mtp) cc_final: 0.8317 (mtp) REVERT: F 85 MET cc_start: 0.9038 (tmm) cc_final: 0.8793 (tmm) REVERT: F 144 GLU cc_start: 0.8294 (mt-10) cc_final: 0.7993 (mt-10) REVERT: F 151 LEU cc_start: 0.9302 (OUTLIER) cc_final: 0.8903 (mm) REVERT: G 32 GLU cc_start: 0.9229 (tm-30) cc_final: 0.8792 (pt0) REVERT: G 71 ASN cc_start: 0.8811 (t0) cc_final: 0.8581 (t0) REVERT: G 153 GLN cc_start: 0.4227 (OUTLIER) cc_final: 0.3925 (mt0) REVERT: H 14 GLU cc_start: 0.7311 (tm-30) cc_final: 0.6445 (tm-30) REVERT: H 24 CYS cc_start: 0.9230 (m) cc_final: 0.9028 (m) REVERT: H 27 GLU cc_start: 0.8582 (mp0) cc_final: 0.7257 (mp0) REVERT: H 105 GLU cc_start: 0.8599 (tt0) cc_final: 0.8223 (tm-30) REVERT: H 116 TYR cc_start: 0.8694 (m-80) cc_final: 0.7654 (m-10) REVERT: H 130 ARG cc_start: 0.8715 (mmt90) cc_final: 0.8391 (mmt90) REVERT: H 146 ARG cc_start: 0.8215 (ttp80) cc_final: 0.7849 (ttp80) REVERT: I 13 MET cc_start: 0.6795 (ppp) cc_final: 0.5966 (ppp) REVERT: I 27 PHE cc_start: 0.8355 (m-80) cc_final: 0.8154 (m-80) REVERT: I 61 ASP cc_start: 0.8311 (t0) cc_final: 0.8084 (t0) REVERT: I 101 PHE cc_start: 0.8625 (m-80) cc_final: 0.8326 (m-80) REVERT: I 108 HIS cc_start: 0.7628 (t70) cc_final: 0.7199 (m-70) REVERT: J 12 LYS cc_start: 0.9419 (tttm) cc_final: 0.8859 (ttmm) REVERT: J 27 GLU cc_start: 0.8697 (tm-30) cc_final: 0.8223 (pt0) REVERT: J 49 MET cc_start: 0.9415 (mmm) cc_final: 0.8778 (tpp) REVERT: L 66 GLN cc_start: 0.8797 (mm110) cc_final: 0.8326 (mm-40) REVERT: L 67 PHE cc_start: 0.9451 (m-80) cc_final: 0.9086 (m-10) outliers start: 59 outliers final: 40 residues processed: 417 average time/residue: 0.2147 time to fit residues: 148.3959 Evaluate side-chains 399 residues out of total 3426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 355 time to evaluate : 1.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 CYS Chi-restraints excluded: chain A residue 268 ASP Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 472 LEU Chi-restraints excluded: chain A residue 511 ILE Chi-restraints excluded: chain A residue 521 MET Chi-restraints excluded: chain A residue 716 ASP Chi-restraints excluded: chain A residue 755 PHE Chi-restraints excluded: chain A residue 824 LEU Chi-restraints excluded: chain A residue 863 VAL Chi-restraints excluded: chain A residue 975 HIS Chi-restraints excluded: chain A residue 1000 LEU Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1336 MET Chi-restraints excluded: chain A residue 1436 ILE Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 466 TRP Chi-restraints excluded: chain B residue 616 ILE Chi-restraints excluded: chain B residue 782 LEU Chi-restraints excluded: chain B residue 953 LEU Chi-restraints excluded: chain B residue 1021 MET Chi-restraints excluded: chain B residue 1093 GLN Chi-restraints excluded: chain B residue 1095 LEU Chi-restraints excluded: chain B residue 1120 GLU Chi-restraints excluded: chain B residue 1202 LEU Chi-restraints excluded: chain C residue 240 VAL Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain C residue 258 ILE Chi-restraints excluded: chain D residue 218 GLU Chi-restraints excluded: chain E residue 21 GLU Chi-restraints excluded: chain E residue 115 ASN Chi-restraints excluded: chain E residue 175 LEU Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 151 LEU Chi-restraints excluded: chain F residue 153 VAL Chi-restraints excluded: chain G residue 30 LEU Chi-restraints excluded: chain G residue 39 THR Chi-restraints excluded: chain G residue 106 MET Chi-restraints excluded: chain G residue 147 ILE Chi-restraints excluded: chain G residue 153 GLN Chi-restraints excluded: chain H residue 15 VAL Chi-restraints excluded: chain J residue 3 VAL Chi-restraints excluded: chain J residue 25 LEU Chi-restraints excluded: chain J residue 50 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 393 random chunks: chunk 3 optimal weight: 2.9990 chunk 325 optimal weight: 7.9990 chunk 46 optimal weight: 0.0870 chunk 348 optimal weight: 4.9990 chunk 285 optimal weight: 20.0000 chunk 213 optimal weight: 2.9990 chunk 151 optimal weight: 0.2980 chunk 177 optimal weight: 0.9990 chunk 186 optimal weight: 7.9990 chunk 85 optimal weight: 1.9990 chunk 269 optimal weight: 6.9990 overall best weight: 1.2764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 488 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 548 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 862 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1378 GLN ** B 984 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 100 GLN ** J 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.074832 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2809 r_free = 0.2809 target = 0.051866 restraints weight = 123779.863| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.2851 r_free = 0.2851 target = 0.053422 restraints weight = 64833.416| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2879 r_free = 0.2879 target = 0.054460 restraints weight = 42848.521| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.2896 r_free = 0.2896 target = 0.055106 restraints weight = 32859.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2906 r_free = 0.2906 target = 0.055516 restraints weight = 27848.494| |-----------------------------------------------------------------------------| r_work (final): 0.2884 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8554 moved from start: 0.2847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 33706 Z= 0.125 Angle : 0.628 15.043 45901 Z= 0.316 Chirality : 0.043 0.274 5156 Planarity : 0.004 0.048 5608 Dihedral : 17.092 160.177 5260 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 10.12 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.19 % Favored : 95.75 % Rotamer: Outliers : 1.40 % Allowed : 15.67 % Favored : 82.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.41 % 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: 3839 helix: 1.56 (0.15), residues: 1327 sheet: -0.14 (0.22), residues: 579 loop : -0.44 (0.15), residues: 1933 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B1135 TYR 0.031 0.001 TYR G 167 PHE 0.027 0.001 PHE G 79 TRP 0.009 0.001 TRP A 656 HIS 0.006 0.001 HIS A1173 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.13 (33674) covalent geometry : angle 0.61957 / 0.32 (45856) hydrogen bonds : bond 0.03394 / 2.28 ( 1414) hydrogen bonds : angle 4.62607 / 3.35 ( 3891) metal coordination : bond 0.00505 / 0.34 ( 32) metal coordination : angle 3.32151 / 2.14 ( 45) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7678 Ramachandran restraints generated. 3839 Oldfield, 0 Emsley, 3839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7678 Ramachandran restraints generated. 3839 Oldfield, 0 Emsley, 3839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 430 residues out of total 3426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 382 time to evaluate : 1.247 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 MET cc_start: 0.8519 (mtt) cc_final: 0.7895 (tpp) REVERT: A 122 MET cc_start: 0.9185 (mmm) cc_final: 0.8666 (ttm) REVERT: A 265 LYS cc_start: 0.9781 (tppt) cc_final: 0.9463 (tppp) REVERT: A 437 MET cc_start: 0.8242 (mtp) cc_final: 0.7887 (mtm) REVERT: A 510 GLN cc_start: 0.9144 (mm-40) cc_final: 0.8651 (mp10) REVERT: A 521 MET cc_start: 0.9097 (OUTLIER) cc_final: 0.8669 (mpp) REVERT: A 605 MET cc_start: 0.9315 (tpp) cc_final: 0.9000 (tpp) REVERT: A 696 GLU cc_start: 0.9042 (tt0) cc_final: 0.8679 (tp30) REVERT: A 727 ASP cc_start: 0.9123 (m-30) cc_final: 0.8763 (t0) REVERT: A 748 MET cc_start: 0.9135 (ttm) cc_final: 0.8687 (ppp) REVERT: A 824 LEU cc_start: 0.9269 (OUTLIER) cc_final: 0.9018 (tt) REVERT: A 838 GLN cc_start: 0.9301 (tp40) cc_final: 0.9024 (tm-30) REVERT: A 975 HIS cc_start: 0.8549 (OUTLIER) cc_final: 0.8015 (t-90) REVERT: A 1224 LEU cc_start: 0.9148 (tp) cc_final: 0.8417 (mp) REVERT: A 1280 GLU cc_start: 0.8414 (mm-30) cc_final: 0.8033 (mp0) REVERT: A 1368 MET cc_start: 0.9278 (mtm) cc_final: 0.8767 (mtp) REVERT: A 1373 ASP cc_start: 0.8793 (m-30) cc_final: 0.8370 (m-30) REVERT: A 1444 MET cc_start: 0.8812 (mmt) cc_final: 0.8389 (mmm) REVERT: B 86 ARG cc_start: 0.9254 (mmt90) cc_final: 0.8820 (mmm-85) REVERT: B 239 GLU cc_start: 0.8472 (tm-30) cc_final: 0.8187 (tp30) REVERT: B 451 LYS cc_start: 0.9425 (mtmt) cc_final: 0.9192 (pttt) REVERT: B 471 LYS cc_start: 0.7379 (mptt) cc_final: 0.6544 (tttp) REVERT: B 542 MET cc_start: 0.8526 (mtp) cc_final: 0.7996 (mtp) REVERT: B 942 ARG cc_start: 0.7421 (mtt-85) cc_final: 0.7130 (mtp85) REVERT: B 1028 GLU cc_start: 0.9139 (tt0) cc_final: 0.8752 (tm-30) REVERT: B 1072 MET cc_start: 0.8794 (mmm) cc_final: 0.8357 (mmm) REVERT: B 1111 MET cc_start: 0.9413 (mmm) cc_final: 0.8935 (mmm) REVERT: B 1206 GLU cc_start: 0.9314 (mt-10) cc_final: 0.8972 (mt-10) REVERT: C 190 ASP cc_start: 0.9018 (t0) cc_final: 0.8601 (t0) REVERT: C 229 TYR cc_start: 0.9252 (m-80) cc_final: 0.8125 (m-10) REVERT: D 143 ASN cc_start: 0.7542 (m-40) cc_final: 0.7325 (m110) REVERT: D 155 ARG cc_start: 0.6011 (ttp-110) cc_final: 0.5338 (ttp80) REVERT: E 22 MET cc_start: 0.9321 (ttp) cc_final: 0.8890 (ttm) REVERT: E 25 ASP cc_start: 0.9127 (m-30) cc_final: 0.8645 (m-30) REVERT: E 58 MET cc_start: 0.8760 (mtp) cc_final: 0.8343 (mtp) REVERT: F 85 MET cc_start: 0.9009 (tmm) cc_final: 0.8763 (tmm) REVERT: F 96 THR cc_start: 0.9635 (m) cc_final: 0.9310 (p) REVERT: F 128 LYS cc_start: 0.9530 (mmtp) cc_final: 0.9095 (mmmm) REVERT: F 144 GLU cc_start: 0.8315 (mt-10) cc_final: 0.8050 (mt-10) REVERT: G 32 GLU cc_start: 0.9215 (tm-30) cc_final: 0.8793 (pt0) REVERT: G 57 GLN cc_start: 0.8467 (mt0) cc_final: 0.7419 (mp10) REVERT: G 71 ASN cc_start: 0.8879 (t0) cc_final: 0.8303 (t0) REVERT: G 153 GLN cc_start: 0.4356 (OUTLIER) cc_final: 0.4069 (mt0) REVERT: H 14 GLU cc_start: 0.7281 (tm-30) cc_final: 0.6481 (tm-30) REVERT: H 27 GLU cc_start: 0.8618 (mp0) cc_final: 0.7292 (mp0) REVERT: H 105 GLU cc_start: 0.8636 (tt0) cc_final: 0.8297 (tm-30) REVERT: H 116 TYR cc_start: 0.8632 (m-80) cc_final: 0.7573 (m-10) REVERT: H 126 GLU cc_start: 0.8046 (tp30) cc_final: 0.7654 (tp30) REVERT: H 130 ARG cc_start: 0.8696 (mmt90) cc_final: 0.8345 (mmt90) REVERT: H 146 ARG cc_start: 0.8161 (ttp80) cc_final: 0.7780 (ttp80) REVERT: I 13 MET cc_start: 0.6835 (ppp) cc_final: 0.5922 (ppp) REVERT: I 101 PHE cc_start: 0.8592 (m-80) cc_final: 0.8304 (m-80) REVERT: I 108 HIS cc_start: 0.7735 (t70) cc_final: 0.7347 (m-70) REVERT: J 27 GLU cc_start: 0.8622 (tm-30) cc_final: 0.8392 (pt0) REVERT: J 49 MET cc_start: 0.9434 (mmm) cc_final: 0.8815 (tpp) REVERT: K 44 ASN cc_start: 0.9254 (t0) cc_final: 0.8930 (t0) REVERT: K 49 GLU cc_start: 0.8631 (tm-30) cc_final: 0.8375 (tm-30) REVERT: L 66 GLN cc_start: 0.8910 (mm110) cc_final: 0.8538 (mm-40) REVERT: L 67 PHE cc_start: 0.9443 (m-80) cc_final: 0.9053 (m-10) outliers start: 48 outliers final: 38 residues processed: 414 average time/residue: 0.2095 time to fit residues: 143.9628 Evaluate side-chains 404 residues out of total 3426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 362 time to evaluate : 1.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 CYS Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 472 LEU Chi-restraints excluded: chain A residue 521 MET Chi-restraints excluded: chain A residue 716 ASP Chi-restraints excluded: chain A residue 755 PHE Chi-restraints excluded: chain A residue 824 LEU Chi-restraints excluded: chain A residue 863 VAL Chi-restraints excluded: chain A residue 975 HIS Chi-restraints excluded: chain A residue 997 LEU Chi-restraints excluded: chain A residue 1000 LEU Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1228 TRP Chi-restraints excluded: chain A residue 1336 MET Chi-restraints excluded: chain A residue 1436 ILE Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 466 TRP Chi-restraints excluded: chain B residue 616 ILE Chi-restraints excluded: chain B residue 782 LEU Chi-restraints excluded: chain B residue 841 MET Chi-restraints excluded: chain B residue 903 VAL Chi-restraints excluded: chain B residue 953 LEU Chi-restraints excluded: chain B residue 1021 MET Chi-restraints excluded: chain B residue 1093 GLN Chi-restraints excluded: chain B residue 1095 LEU Chi-restraints excluded: chain C residue 240 VAL Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain C residue 258 ILE Chi-restraints excluded: chain D residue 218 GLU Chi-restraints excluded: chain E residue 21 GLU Chi-restraints excluded: chain E residue 115 ASN Chi-restraints excluded: chain E residue 175 LEU Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 153 VAL Chi-restraints excluded: chain G residue 30 LEU Chi-restraints excluded: chain G residue 106 MET Chi-restraints excluded: chain G residue 147 ILE Chi-restraints excluded: chain G residue 153 GLN Chi-restraints excluded: chain H residue 15 VAL Chi-restraints excluded: chain J residue 3 VAL Chi-restraints excluded: chain J residue 50 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 393 random chunks: chunk 4 optimal weight: 0.7980 chunk 236 optimal weight: 0.9980 chunk 271 optimal weight: 0.5980 chunk 370 optimal weight: 0.3980 chunk 367 optimal weight: 6.9990 chunk 310 optimal weight: 0.9990 chunk 381 optimal weight: 20.0000 chunk 106 optimal weight: 2.9990 chunk 158 optimal weight: 5.9990 chunk 130 optimal weight: 6.9990 chunk 312 optimal weight: 1.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 488 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 515 GLN ** A 548 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 862 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 984 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 100 GLN ** J 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.075479 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2827 r_free = 0.2827 target = 0.052411 restraints weight = 124767.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.2870 r_free = 0.2870 target = 0.053996 restraints weight = 65050.736| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.2898 r_free = 0.2898 target = 0.055046 restraints weight = 42899.795| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.2916 r_free = 0.2916 target = 0.055713 restraints weight = 32883.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.2926 r_free = 0.2926 target = 0.056123 restraints weight = 27846.880| |-----------------------------------------------------------------------------| r_work (final): 0.2903 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8536 moved from start: 0.2968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 33706 Z= 0.114 Angle : 0.637 14.948 45901 Z= 0.318 Chirality : 0.043 0.278 5156 Planarity : 0.004 0.048 5608 Dihedral : 17.035 160.510 5260 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.04 % Favored : 95.91 % Rotamer: Outliers : 1.28 % Allowed : 15.97 % Favored : 82.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.41 % 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 (0.14), residues: 3839 helix: 1.63 (0.15), residues: 1321 sheet: -0.00 (0.21), residues: 604 loop : -0.44 (0.15), residues: 1914 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B1135 TYR 0.028 0.001 TYR G 167 PHE 0.028 0.001 PHE G 79 TRP 0.009 0.001 TRP K 109 HIS 0.005 0.001 HIS A1173 Details of bonding type rmsd/Z covalent geometry : bond 0.00245 / 0.11 (33674) covalent geometry : angle 0.62905 / 0.32 (45856) hydrogen bonds : bond 0.03330 / 2.23 ( 1414) hydrogen bonds : angle 4.58397 / 3.33 ( 3891) metal coordination : bond 0.00446 / 0.30 ( 32) metal coordination : angle 3.25747 / 2.08 ( 45) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7678 Ramachandran restraints generated. 3839 Oldfield, 0 Emsley, 3839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7678 Ramachandran restraints generated. 3839 Oldfield, 0 Emsley, 3839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 425 residues out of total 3426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 381 time to evaluate : 0.975 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 MET cc_start: 0.8525 (mtt) cc_final: 0.7894 (tpp) REVERT: A 122 MET cc_start: 0.9192 (mmm) cc_final: 0.8651 (ttm) REVERT: A 265 LYS cc_start: 0.9779 (tppt) cc_final: 0.9457 (tppp) REVERT: A 437 MET cc_start: 0.8245 (mtp) cc_final: 0.7881 (mtm) REVERT: A 605 MET cc_start: 0.9331 (tpp) cc_final: 0.9017 (tpp) REVERT: A 696 GLU cc_start: 0.9037 (tt0) cc_final: 0.8673 (tp30) REVERT: A 727 ASP cc_start: 0.9113 (m-30) cc_final: 0.8779 (t0) REVERT: A 748 MET cc_start: 0.9154 (ttm) cc_final: 0.8704 (ppp) REVERT: A 838 GLN cc_start: 0.9289 (tp40) cc_final: 0.9037 (tm-30) REVERT: A 975 HIS cc_start: 0.8580 (OUTLIER) cc_final: 0.8040 (t-90) REVERT: A 1005 GLU cc_start: 0.8761 (mm-30) cc_final: 0.8051 (tp30) REVERT: A 1224 LEU cc_start: 0.9106 (tp) cc_final: 0.8334 (mp) REVERT: A 1280 GLU cc_start: 0.8438 (mm-30) cc_final: 0.8050 (mp0) REVERT: A 1368 MET cc_start: 0.9267 (mtm) cc_final: 0.8730 (mtp) REVERT: A 1373 ASP cc_start: 0.8782 (m-30) cc_final: 0.8357 (m-30) REVERT: A 1444 MET cc_start: 0.8745 (mmt) cc_final: 0.8420 (mmm) REVERT: B 86 ARG cc_start: 0.9232 (mmt90) cc_final: 0.8798 (mmm-85) REVERT: B 451 LYS cc_start: 0.9417 (mtmt) cc_final: 0.9207 (pttt) REVERT: B 471 LYS cc_start: 0.7281 (mptt) cc_final: 0.6513 (tttp) REVERT: B 542 MET cc_start: 0.8496 (mtp) cc_final: 0.8000 (mtp) REVERT: B 809 MET cc_start: 0.9263 (ptp) cc_final: 0.9045 (mpp) REVERT: B 1028 GLU cc_start: 0.9127 (tt0) cc_final: 0.8702 (tm-30) REVERT: B 1072 MET cc_start: 0.8800 (mmm) cc_final: 0.8329 (mmm) REVERT: B 1111 MET cc_start: 0.9420 (mmm) cc_final: 0.8887 (mmm) REVERT: B 1206 GLU cc_start: 0.9304 (mt-10) cc_final: 0.8982 (mt-10) REVERT: C 190 ASP cc_start: 0.9037 (t0) cc_final: 0.8613 (t0) REVERT: C 229 TYR cc_start: 0.9215 (m-80) cc_final: 0.8140 (m-10) REVERT: D 155 ARG cc_start: 0.5981 (ttp-110) cc_final: 0.5339 (ttp80) REVERT: E 25 ASP cc_start: 0.9110 (m-30) cc_final: 0.8634 (m-30) REVERT: E 58 MET cc_start: 0.8723 (mtp) cc_final: 0.8252 (mtp) REVERT: F 85 MET cc_start: 0.9006 (tmm) cc_final: 0.8722 (tmm) REVERT: F 93 ILE cc_start: 0.9719 (pt) cc_final: 0.9381 (mt) REVERT: F 128 LYS cc_start: 0.9547 (mmtp) cc_final: 0.9098 (mmmm) REVERT: F 144 GLU cc_start: 0.8273 (mt-10) cc_final: 0.8042 (mt-10) REVERT: G 1 MET cc_start: 0.8150 (tpt) cc_final: 0.7780 (tpt) REVERT: G 32 GLU cc_start: 0.9198 (tm-30) cc_final: 0.8773 (pt0) REVERT: G 153 GLN cc_start: 0.4617 (OUTLIER) cc_final: 0.4400 (mt0) REVERT: H 14 GLU cc_start: 0.7288 (tm-30) cc_final: 0.6496 (tm-30) REVERT: H 27 GLU cc_start: 0.8647 (mp0) cc_final: 0.7362 (mp0) REVERT: H 93 TYR cc_start: 0.9201 (m-80) cc_final: 0.8966 (m-10) REVERT: H 105 GLU cc_start: 0.8582 (tt0) cc_final: 0.8231 (tm-30) REVERT: H 116 TYR cc_start: 0.8604 (m-80) cc_final: 0.7568 (m-10) REVERT: H 126 GLU cc_start: 0.8034 (tp30) cc_final: 0.7625 (tp30) REVERT: H 130 ARG cc_start: 0.8703 (mmt90) cc_final: 0.8337 (mmt90) REVERT: H 146 ARG cc_start: 0.8176 (ttp80) cc_final: 0.7803 (ttp80) REVERT: I 13 MET cc_start: 0.6835 (ppp) cc_final: 0.5964 (ppp) REVERT: I 101 PHE cc_start: 0.8576 (m-80) cc_final: 0.8305 (m-80) REVERT: I 108 HIS cc_start: 0.7781 (t70) cc_final: 0.7383 (m-70) REVERT: J 49 MET cc_start: 0.9425 (mmm) cc_final: 0.8856 (tpp) REVERT: K 44 ASN cc_start: 0.9239 (t0) cc_final: 0.8901 (t0) REVERT: K 49 GLU cc_start: 0.8626 (tm-30) cc_final: 0.8381 (tm-30) REVERT: L 29 TYR cc_start: 0.8990 (m-10) cc_final: 0.8645 (m-10) REVERT: L 66 GLN cc_start: 0.8908 (mm110) cc_final: 0.8540 (mm-40) REVERT: L 67 PHE cc_start: 0.9426 (m-80) cc_final: 0.9007 (m-10) outliers start: 44 outliers final: 36 residues processed: 407 average time/residue: 0.1955 time to fit residues: 131.5681 Evaluate side-chains 403 residues out of total 3426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 365 time to evaluate : 1.077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 CYS Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 470 LEU Chi-restraints excluded: chain A residue 472 LEU Chi-restraints excluded: chain A residue 716 ASP Chi-restraints excluded: chain A residue 755 PHE Chi-restraints excluded: chain A residue 863 VAL Chi-restraints excluded: chain A residue 975 HIS Chi-restraints excluded: chain A residue 997 LEU Chi-restraints excluded: chain A residue 1000 LEU Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1209 MET Chi-restraints excluded: chain A residue 1336 MET Chi-restraints excluded: chain A residue 1436 ILE Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 616 ILE Chi-restraints excluded: chain B residue 782 LEU Chi-restraints excluded: chain B residue 841 MET Chi-restraints excluded: chain B residue 903 VAL Chi-restraints excluded: chain B residue 953 LEU Chi-restraints excluded: chain B residue 1021 MET Chi-restraints excluded: chain B residue 1095 LEU Chi-restraints excluded: chain C residue 240 VAL Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain C residue 258 ILE Chi-restraints excluded: chain D residue 218 GLU Chi-restraints excluded: chain E residue 21 GLU Chi-restraints excluded: chain E residue 115 ASN Chi-restraints excluded: chain E residue 175 LEU Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 153 VAL Chi-restraints excluded: chain G residue 30 LEU Chi-restraints excluded: chain G residue 147 ILE Chi-restraints excluded: chain G residue 153 GLN Chi-restraints excluded: chain H residue 15 VAL Chi-restraints excluded: chain J residue 3 VAL Chi-restraints excluded: chain J residue 50 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 393 random chunks: chunk 38 optimal weight: 7.9990 chunk 169 optimal weight: 4.9990 chunk 8 optimal weight: 0.8980 chunk 228 optimal weight: 5.9990 chunk 226 optimal weight: 2.9990 chunk 198 optimal weight: 0.8980 chunk 213 optimal weight: 3.9990 chunk 385 optimal weight: 50.0000 chunk 208 optimal weight: 0.5980 chunk 230 optimal weight: 0.9990 chunk 134 optimal weight: 9.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 488 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 862 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 984 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 100 GLN H 11 GLN ** J 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.075389 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2826 r_free = 0.2826 target = 0.052420 restraints weight = 124535.971| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2870 r_free = 0.2870 target = 0.054003 restraints weight = 65296.993| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.2898 r_free = 0.2898 target = 0.055044 restraints weight = 42978.523| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.2915 r_free = 0.2915 target = 0.055715 restraints weight = 32919.822| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.2926 r_free = 0.2926 target = 0.056139 restraints weight = 27858.903| |-----------------------------------------------------------------------------| r_work (final): 0.2900 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8543 moved from start: 0.3031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 33706 Z= 0.122 Angle : 0.631 14.630 45901 Z= 0.315 Chirality : 0.043 0.283 5156 Planarity : 0.004 0.062 5608 Dihedral : 16.994 160.269 5260 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 9.91 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.06 % Favored : 95.88 % Rotamer: Outliers : 1.28 % Allowed : 16.20 % Favored : 82.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.41 % 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: 0.52 (0.14), residues: 3839 helix: 1.64 (0.15), residues: 1324 sheet: 0.01 (0.21), residues: 594 loop : -0.43 (0.15), residues: 1921 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG I 5 TYR 0.034 0.001 TYR H 98 PHE 0.026 0.001 PHE G 79 TRP 0.011 0.001 TRP K 109 HIS 0.005 0.001 HIS A1173 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.12 (33674) covalent geometry : angle 0.62445 / 0.31 (45856) hydrogen bonds : bond 0.03296 / 2.19 ( 1414) hydrogen bonds : angle 4.56696 / 3.32 ( 3891) metal coordination : bond 0.00472 / 0.32 ( 32) metal coordination : angle 3.01584 / 1.94 ( 45) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5670.57 seconds wall clock time: 99 minutes 1.35 seconds (5941.35 seconds total)