Starting phenix.real_space_refine on Mon Aug 10 05:39:08 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8rap_19022/08_2026/8rap_19022.cif Found real_map, /net/cci-nas-00/data/ceres_data/8rap_19022/08_2026/8rap_19022.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8rap_19022/08_2026/8rap_19022.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8rap_19022/08_2026/8rap_19022.map" model { file = "/net/cci-nas-00/data/ceres_data/8rap_19022/08_2026/8rap_19022.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8rap_19022/08_2026/8rap_19022.cif" } resolution = 4.3 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= 0.003 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: 9 Type Number sf(0) Gaussians Zn 9 6.06 5 P 92 5.49 5 Mg 2 5.21 5 S 235 5.16 5 Be 1 3.05 5 C 26772 2.51 5 N 7509 2.21 5 O 8301 1.98 5 F 3 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 205 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: 42924 Number of models: 1 Model: "" Number of chains: 27 Chain: "A" Number of atoms: 11020 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1400, 11020 Classifications: {'peptide': 1400} Link IDs: {'PTRANS': 65, 'TRANS': 1334} Chain breaks: 5 Chain: "B" Number of atoms: 8839 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1113, 8839 Classifications: {'peptide': 1113} Link IDs: {'PTRANS': 50, 'TRANS': 1062} Chain breaks: 6 Chain: "C" Number of atoms: 2078 Number of conformers: 1 Conformer: "" Number of residues, atoms: 264, 2078 Classifications: {'peptide': 264} Link IDs: {'PTRANS': 11, 'TRANS': 252} Chain: "D" Number of atoms: 1270 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1270 Classifications: {'peptide': 159} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 156} Chain breaks: 1 Chain: "E" Number of atoms: 1752 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1752 Classifications: {'peptide': 214} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 201} Chain: "F" Number of atoms: 688 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 688 Classifications: {'peptide': 85} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 78} 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: 1068 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 1068 Classifications: {'peptide': 133} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 128} Chain breaks: 1 Chain: "I" Number of atoms: 964 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 964 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 5, 'TRANS': 112} 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: 920 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 920 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 5, 'TRANS': 109} Unresolved chain link angles: 1 Unresolved chain link dihedrals: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 1 Chain: "L" Number of atoms: 343 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 343 Classifications: {'peptide': 43} Link IDs: {'TRANS': 42} Chain: "M" Number of atoms: 504 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 504 Classifications: {'peptide': 65} Link IDs: {'PTRANS': 1, 'TRANS': 63} Chain: "N" Number of atoms: 547 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 547 Classifications: {'DNA': 27} Link IDs: {'rna3p': 26} Chain breaks: 1 Chain: "O" Number of atoms: 5557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 694, 5557 Classifications: {'peptide': 694} Link IDs: {'PTRANS': 28, 'TRANS': 665} Chain breaks: 2 Chain: "P" Number of atoms: 540 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 540 Classifications: {'RNA': 25} Modifications used: {'rna2p_pur': 7, 'rna2p_pyr': 4, 'rna3p_pur': 8, 'rna3p_pyr': 6} Link IDs: {'rna2p': 11, 'rna3p': 13} Chain breaks: 1 Chain: "T" Number of atoms: 786 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 786 Classifications: {'DNA': 38} Link IDs: {'rna3p': 37} Chain: "Y" Number of atoms: 760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 760 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 6, 'TRANS': 93} Chain: "Z" Number of atoms: 3374 Number of conformers: 1 Conformer: "" Number of residues, atoms: 426, 3374 Classifications: {'peptide': 426} Link IDs: {'PTRANS': 12, 'TRANS': 413} Chain breaks: 6 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: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "M" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "O" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'BEF': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 809 SG CYS A 107 72.081 126.476 148.398 1.00159.88 S ATOM 833 SG CYS A 110 70.241 130.460 149.483 1.00161.51 S ATOM 1276 SG CYS A 167 71.168 128.138 151.640 1.00160.75 S ATOM 504 SG CYS A 67 55.209 127.310 103.572 1.00166.71 S ATOM 579 SG CYS A 77 59.207 125.974 101.921 1.00156.65 S ATOM 19396 SG CYS B1163 66.599 138.198 109.778 1.00153.60 S ATOM 19414 SG CYS B1166 67.647 136.417 112.911 1.00135.24 S ATOM 19539 SG CYS B1182 63.906 136.435 111.733 1.00169.69 S ATOM 19558 SG CYS B1185 65.542 139.534 113.190 1.00161.00 S ATOM 20506 SG CYS C 86 75.142 97.534 44.205 1.00158.82 S ATOM 20523 SG CYS C 88 72.235 97.633 46.596 1.00156.39 S ATOM 20556 SG CYS C 92 72.128 95.072 43.826 1.00143.59 S ATOM 20579 SG CYS C 95 74.558 94.579 46.570 1.00146.86 S ATOM 28101 SG CYS I 7 95.134 64.757 160.123 1.00224.86 S ATOM 28316 SG CYS I 32 92.962 65.105 164.165 1.00222.68 S ATOM 28643 SG CYS I 75 120.506 51.007 127.405 1.00225.25 S ATOM 28665 SG CYS I 78 119.915 47.317 126.874 1.00237.29 S ATOM 28881 SG CYS I 103 117.449 49.787 125.453 1.00226.17 S ATOM 28901 SG CYS I 106 117.640 49.330 129.231 1.00229.10 S ATOM 29073 SG CYS J 7 93.259 77.624 65.170 1.00113.22 S ATOM 29096 SG CYS J 10 94.906 78.251 61.786 1.00121.44 S ATOM 29376 SG CYS J 45 96.876 76.753 64.654 1.00112.37 S ATOM 29382 SG CYS J 46 94.171 74.692 62.870 1.00118.03 S ATOM 30506 SG CYS L 31 52.448 72.540 78.141 1.00140.27 S ATOM 30526 SG CYS L 34 50.761 69.323 76.925 1.00149.36 S ATOM 30630 SG CYS L 48 48.679 72.346 78.063 1.00146.64 S ATOM 30653 SG CYS L 51 50.597 70.214 80.558 1.00148.54 S ATOM 30855 SG CYS M 25 63.714 94.879 159.864 1.00386.99 S ATOM 30880 SG CYS M 28 61.408 97.830 159.412 1.00392.81 S ATOM 31035 SG CYS M 49 65.125 98.431 159.951 1.00374.42 S ATOM 31058 SG CYS M 52 63.080 97.213 162.829 1.00383.35 S Time building chain proxies: 9.28, per 1000 atoms: 0.22 Number of scatterers: 42924 At special positions: 0 Unit cell: (165.9, 200.55, 183.75, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 9 Type Number sf(0) Zn 9 29.99 S 235 16.00 P 92 15.00 Mg 2 11.99 F 3 9.00 O 8301 8.00 N 7509 7.00 C 26772 6.00 Be 1 4.00 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 1.7 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1801 " pdb="ZN ZN A1801 " - pdb=" SG CYS A 167 " pdb="ZN ZN A1801 " - pdb=" SG CYS A 110 " pdb="ZN ZN A1801 " - pdb=" SG CYS A 107 " pdb=" ZN A1802 " pdb="ZN ZN A1802 " - pdb=" SG CYS A 67 " pdb="ZN ZN A1802 " - pdb=" SG CYS A 77 " pdb=" ZN B1301 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1163 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1185 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1166 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1182 " pdb=" ZN C 401 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 88 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 95 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 92 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 86 " pdb=" ZN I 201 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 7 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 32 " pdb=" ZN I 202 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 78 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 75 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 103 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 106 " 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 51 " 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 31 " pdb=" ZN M 201 " pdb="ZN ZN M 201 " - pdb=" SG CYS M 49 " pdb="ZN ZN M 201 " - pdb=" SG CYS M 52 " pdb="ZN ZN M 201 " - pdb=" SG CYS M 28 " pdb="ZN ZN M 201 " - pdb=" SG CYS M 25 " Number of angles added : 36 10180 Ramachandran restraints generated. 5090 Oldfield, 0 Emsley, 5090 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9692 Finding SS restraints... Secondary structure from input PDB file: 190 helices and 62 sheets defined 39.3% alpha, 17.7% beta 35 base pairs and 56 stacking pairs defined. Time for finding SS restraints: 5.25 Creating SS restraints... Processing helix chain 'A' and resid 23 through 31 Processing helix chain 'A' and resid 42 through 46 removed outlier: 4.052A pdb=" N THR A 46 " --> pdb=" O GLU A 43 " (cutoff:3.500A) 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 145 Processing helix chain 'A' and resid 203 through 214 Processing helix chain 'A' and resid 215 through 223 removed outlier: 3.611A pdb=" N PHE A 219 " --> pdb=" O SER A 215 " (cutoff:3.500A) Processing helix chain 'A' and resid 230 through 235 removed outlier: 3.527A pdb=" N MET A 234 " --> pdb=" O ARG A 230 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N ILE A 235 " --> pdb=" O PRO A 231 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 230 through 235' Processing helix chain 'A' and resid 243 through 247 Processing helix chain 'A' and resid 260 through 282 Processing helix chain 'A' and resid 287 through 305 removed outlier: 3.577A pdb=" N GLU A 291 " --> pdb=" O HIS A 287 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 329 Processing helix chain 'A' and resid 334 through 339 Processing helix chain 'A' and resid 368 through 374 Processing helix chain 'A' and resid 384 through 395 Processing helix chain 'A' and resid 420 through 424 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 Processing helix chain 'A' and resid 494 through 504 Processing helix chain 'A' and resid 506 through 510 Processing helix chain 'A' and resid 524 through 536 Processing helix chain 'A' and resid 542 through 553 removed outlier: 3.519A pdb=" N VAL A 553 " --> pdb=" O MET A 549 " (cutoff:3.500A) Processing helix chain 'A' and resid 574 through 580 removed outlier: 3.805A pdb=" N VAL A 580 " --> pdb=" O GLN A 576 " (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 661 Processing helix chain 'A' and resid 665 through 670 removed outlier: 3.895A pdb=" N THR A 669 " --> pdb=" O GLY A 665 " (cutoff:3.500A) Processing helix chain 'A' and resid 672 through 699 Processing helix chain 'A' and resid 709 through 737 Processing helix chain 'A' and resid 741 through 750 Processing helix chain 'A' and resid 754 through 763 Processing helix chain 'A' and resid 793 through 797 Processing helix chain 'A' and resid 809 through 846 removed outlier: 3.731A pdb=" N ALA A 832 " --> pdb=" O ALA A 828 " (cutoff:3.500A) Processing helix chain 'A' and resid 867 through 871 Processing helix chain 'A' and resid 889 through 898 Processing helix chain 'A' and resid 909 through 914 removed outlier: 5.379A pdb=" N GLU A 914 " --> pdb=" O SER A 911 " (cutoff:3.500A) Processing helix chain 'A' and resid 915 through 920 removed outlier: 3.643A pdb=" N ILE A 919 " --> pdb=" O SER A 915 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N LEU A 920 " --> pdb=" O GLY A 916 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 915 through 920' Processing helix chain 'A' and resid 922 through 947 Processing helix chain 'A' and resid 959 through 972 removed outlier: 3.642A pdb=" N ILE A 963 " --> pdb=" O ASN A 959 " (cutoff:3.500A) Processing helix chain 'A' and resid 982 through 997 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 1033 Processing helix chain 'A' and resid 1038 through 1057 Processing helix chain 'A' and resid 1063 through 1079 Proline residue: A1075 - end of helix Processing helix chain 'A' and resid 1097 through 1106 Processing helix chain 'A' and resid 1127 through 1139 Processing helix chain 'A' and resid 1143 through 1146 No H-bonds generated for 'chain 'A' and resid 1143 through 1146' Processing helix chain 'A' and resid 1163 through 1165 No H-bonds generated for 'chain 'A' and resid 1163 through 1165' Processing helix chain 'A' and resid 1166 through 1175 removed outlier: 4.225A pdb=" N ILE A1170 " --> pdb=" O ASP A1166 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N HIS A1173 " --> pdb=" O ILE A1169 " (cutoff:3.500A) Processing helix chain 'A' and resid 1198 through 1206 Processing helix chain 'A' and resid 1208 through 1220 Processing helix chain 'A' and resid 1259 through 1270 Processing helix chain 'A' and resid 1312 through 1317 Processing helix chain 'A' and resid 1331 through 1339 Processing helix chain 'A' and resid 1340 through 1359 removed outlier: 4.459A pdb=" N ASP A1359 " --> pdb=" O VAL A1355 " (cutoff:3.500A) Processing helix chain 'A' and resid 1364 through 1377 removed outlier: 3.722A pdb=" N MET A1368 " --> pdb=" O ASN A1364 " (cutoff:3.500A) Processing helix chain 'A' and resid 1388 through 1392 Processing helix chain 'A' and resid 1395 through 1401 Processing helix chain 'A' and resid 1405 through 1416 removed outlier: 3.638A pdb=" N LEU A1409 " --> pdb=" O THR A1405 " (cutoff:3.500A) Processing helix chain 'A' and resid 1423 through 1431 Processing helix chain 'A' and resid 1436 through 1440 Processing helix chain 'A' and resid 1446 through 1454 removed outlier: 4.009A pdb=" N VAL A1451 " --> pdb=" O GLU A1447 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N LYS A1452 " --> pdb=" O GLU A1448 " (cutoff:3.500A) Processing helix chain 'B' and resid 26 through 41 removed outlier: 3.755A pdb=" N SER B 30 " --> pdb=" O THR B 26 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N TRP B 31 " --> pdb=" O ALA B 27 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N ALA B 32 " --> pdb=" O GLU B 28 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N VAL B 33 " --> pdb=" O ASP B 29 " (cutoff:3.500A) Processing helix chain 'B' and resid 44 through 66 removed outlier: 4.816A pdb=" N LEU B 59 " --> pdb=" O VAL B 55 " (cutoff:3.500A) removed outlier: 4.805A pdb=" N GLN B 60 " --> pdb=" O ASP B 56 " (cutoff:3.500A) Processing helix chain 'B' and resid 113 through 121 Processing helix chain 'B' and resid 179 through 184 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 Processing helix chain 'B' and resid 307 through 322 removed outlier: 4.172A pdb=" N LEU B 311 " --> pdb=" O ASP B 307 " (cutoff:3.500A) Proline residue: B 316 - end of helix Processing helix chain 'B' and resid 326 through 337 removed outlier: 4.289A pdb=" N ARG B 337 " --> pdb=" O PHE B 333 " (cutoff:3.500A) Processing helix chain 'B' and resid 348 through 359 Processing helix chain 'B' and resid 371 through 390 removed outlier: 3.739A pdb=" N ALA B 375 " --> pdb=" O GLU B 371 " (cutoff:3.500A) 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 435 removed outlier: 3.583A pdb=" N LEU B 412 " --> pdb=" O LEU B 408 " (cutoff:3.500A) Processing helix chain 'B' and resid 450 through 464 removed outlier: 3.784A pdb=" N GLY B 456 " --> pdb=" O THR B 452 " (cutoff:3.500A) Processing helix chain 'B' and resid 487 through 496 Processing helix chain 'B' and resid 508 through 513 removed outlier: 4.080A pdb=" N ARG B 512 " --> pdb=" O LEU B 508 " (cutoff:3.500A) Processing helix chain 'B' and resid 515 through 519 Processing helix chain 'B' and resid 551 through 562 removed outlier: 3.548A pdb=" N GLY B 562 " --> pdb=" O LEU B 558 " (cutoff:3.500A) Processing helix chain 'B' and resid 567 through 569 No H-bonds generated for 'chain 'B' and resid 567 through 569' Processing helix chain 'B' and resid 570 through 574 Processing helix chain 'B' and resid 592 through 607 Processing helix chain 'B' and resid 654 through 668 Processing helix chain 'B' and resid 680 through 687 Processing helix chain 'B' and resid 696 through 701 removed outlier: 3.656A pdb=" N ILE B 701 " --> pdb=" O GLU B 698 " (cutoff:3.500A) Processing helix chain 'B' and resid 744 through 749 Processing helix chain 'B' and resid 750 through 756 removed outlier: 3.692A pdb=" N ILE B 755 " --> pdb=" O VAL B 751 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ILE B 756 " --> pdb=" O ALA B 752 " (cutoff:3.500A) Processing helix chain 'B' and resid 763 through 775 removed outlier: 4.084A pdb=" N LYS B 775 " --> pdb=" O SER B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 806 through 813 removed outlier: 4.285A pdb=" N GLU B 810 " --> pdb=" O THR B 806 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N TYR B 811 " --> 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: 4.102A pdb=" N SER B1019 " --> pdb=" O HIS B1015 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ARG B1020 " --> pdb=" O ALA B1016 " (cutoff:3.500A) Processing helix chain 'B' and resid 1023 through 1039 removed outlier: 3.550A pdb=" N ILE B1027 " --> pdb=" O VAL B1023 " (cutoff:3.500A) Processing helix chain 'B' and resid 1051 through 1062 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 removed outlier: 3.516A pdb=" N LYS B1201 " --> pdb=" O PRO B1197 " (cutoff:3.500A) Processing helix chain 'C' and resid 26 through 40 Processing helix chain 'C' and resid 59 through 69 Processing helix chain 'C' and resid 114 through 118 Processing helix chain 'C' and resid 167 through 171 Processing helix chain 'C' and resid 196 through 201 Processing helix chain 'C' and resid 204 through 210 removed outlier: 3.573A pdb=" N GLU C 208 " --> pdb=" O LYS C 205 " (cutoff:3.500A) Processing helix chain 'C' and resid 239 through 267 removed outlier: 3.889A pdb=" N GLN C 267 " --> pdb=" O THR C 263 " (cutoff:3.500A) Processing helix chain 'D' and resid 51 through 76 Processing helix chain 'D' and resid 121 through 133 Processing helix chain 'D' and resid 139 through 151 removed outlier: 3.577A pdb=" N ASN D 143 " --> pdb=" O LYS D 139 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N PHE D 151 " --> pdb=" O TYR D 147 " (cutoff:3.500A) Processing helix chain 'D' and resid 156 through 171 removed outlier: 3.541A pdb=" N SER D 169 " --> pdb=" O GLN D 165 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N THR D 170 " --> pdb=" O LEU D 166 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N GLY D 171 " --> pdb=" O LEU D 167 " (cutoff:3.500A) Processing helix chain 'D' and resid 173 through 183 Processing helix chain 'D' and resid 187 through 195 Processing helix chain 'D' and resid 196 through 199 Processing helix chain 'D' and resid 203 through 218 Processing helix chain 'E' and resid 3 through 27 Processing helix chain 'E' and resid 31 through 36 removed outlier: 3.509A pdb=" N VAL E 35 " --> pdb=" O THR E 31 " (cutoff:3.500A) Processing helix chain 'E' and resid 38 through 46 Processing helix chain 'E' and resid 54 through 59 removed outlier: 3.513A pdb=" N SER E 59 " --> pdb=" O ARG E 55 " (cutoff:3.500A) Processing helix chain 'E' and resid 65 through 72 Processing helix chain 'E' and resid 89 through 104 Processing helix chain 'E' and resid 117 through 124 Processing helix chain 'E' and resid 125 through 127 No H-bonds generated for 'chain 'E' and resid 125 through 127' Processing helix chain 'E' and resid 138 through 142 removed outlier: 4.188A pdb=" N VAL E 142 " --> pdb=" O ALA E 139 " (cutoff:3.500A) 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 21 through 32 Processing helix chain 'G' and resid 112 through 115 Processing helix chain 'H' and resid 128 through 134 removed outlier: 4.352A pdb=" N ASN H 133 " --> pdb=" O ARG H 130 " (cutoff:3.500A) Processing helix chain 'I' and resid 61 through 65 Processing helix chain 'J' and resid 16 through 27 removed outlier: 4.383A pdb=" N SER J 20 " --> pdb=" O ASP J 16 " (cutoff:3.500A) Processing helix chain 'J' and resid 31 through 40 Processing helix chain 'J' and resid 43 through 53 removed outlier: 3.551A pdb=" N ARG J 47 " --> pdb=" O ARG J 43 " (cutoff:3.500A) Processing helix chain 'J' and resid 55 through 62 removed outlier: 4.008A pdb=" N LYS J 59 " --> pdb=" O ASP J 55 " (cutoff:3.500A) Processing helix chain 'K' and resid 6 through 10 Processing helix chain 'K' and resid 39 through 52 removed outlier: 3.626A pdb=" N GLY K 43 " --> pdb=" O ASP K 39 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N LEU K 45 " --> pdb=" O THR K 41 " (cutoff:3.500A) Processing helix chain 'K' and resid 82 through 112 Processing helix chain 'M' and resid 65 through 83 Processing helix chain 'O' and resid 1096 through 1110 Processing helix chain 'O' and resid 1113 through 1122 removed outlier: 3.563A pdb=" N GLN O1122 " --> pdb=" O GLU O1118 " (cutoff:3.500A) Processing helix chain 'O' and resid 1136 through 1140 Processing helix chain 'O' and resid 1149 through 1175 Proline residue: O1159 - end of helix Processing helix chain 'O' and resid 1203 through 1210 Processing helix chain 'O' and resid 1232 through 1239 removed outlier: 3.648A pdb=" N PHE O1236 " --> pdb=" O SER O1232 " (cutoff:3.500A) Processing helix chain 'O' and resid 1268 through 1274 Processing helix chain 'O' and resid 1288 through 1301 Processing helix chain 'O' and resid 1302 through 1305 removed outlier: 6.061A pdb=" N ASP O1305 " --> pdb=" O GLU O1302 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 1302 through 1305' Processing helix chain 'O' and resid 1306 through 1313 Processing helix chain 'O' and resid 1322 through 1334 removed outlier: 3.607A pdb=" N ILE O1326 " --> pdb=" O ASP O1322 " (cutoff:3.500A) Processing helix chain 'O' and resid 1336 through 1349 Processing helix chain 'O' and resid 1362 through 1377 Processing helix chain 'O' and resid 1412 through 1425 removed outlier: 3.606A pdb=" N SER O1425 " --> pdb=" O LEU O1421 " (cutoff:3.500A) Processing helix chain 'O' and resid 1452 through 1455 Processing helix chain 'O' and resid 1456 through 1465 Processing helix chain 'O' and resid 1531 through 1562 Processing helix chain 'O' and resid 1570 through 1573 removed outlier: 3.742A pdb=" N ALA O1573 " --> pdb=" O SER O1570 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 1570 through 1573' Processing helix chain 'O' and resid 1574 through 1581 Processing helix chain 'O' and resid 1592 through 1595 removed outlier: 3.566A pdb=" N CYS O1595 " --> pdb=" O ALA O1592 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 1592 through 1595' Processing helix chain 'O' and resid 1596 through 1602 Processing helix chain 'O' and resid 1603 through 1606 removed outlier: 3.845A pdb=" N TYR O1606 " --> pdb=" O PRO O1603 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 1603 through 1606' Processing helix chain 'O' and resid 1626 through 1632 Processing helix chain 'O' and resid 1637 through 1646 Processing helix chain 'O' and resid 1658 through 1669 removed outlier: 4.546A pdb=" N PHE O1664 " --> pdb=" O SER O1660 " (cutoff:3.500A) Proline residue: O1665 - end of helix Processing helix chain 'O' and resid 1679 through 1684 Processing helix chain 'O' and resid 1686 through 1691 removed outlier: 4.044A pdb=" N GLN O1690 " --> pdb=" O ARG O1686 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N LEU O1691 " --> pdb=" O PRO O1687 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 1686 through 1691' Processing helix chain 'O' and resid 1718 through 1736 removed outlier: 3.996A pdb=" N ILE O1722 " --> pdb=" O ASN O1718 " (cutoff:3.500A) Processing helix chain 'O' and resid 1752 through 1767 Processing helix chain 'O' and resid 1770 through 1774 Processing helix chain 'O' and resid 1805 through 1809 removed outlier: 3.890A pdb=" N LEU O1808 " --> pdb=" O VAL O1805 " (cutoff:3.500A) Processing helix chain 'O' and resid 1810 through 1819 removed outlier: 3.594A pdb=" N MET O1814 " --> pdb=" O ASP O1810 " (cutoff:3.500A) Processing helix chain 'O' and resid 1830 through 1836 removed outlier: 3.901A pdb=" N LYS O1836 " --> pdb=" O ARG O1832 " (cutoff:3.500A) Processing helix chain 'O' and resid 1837 through 1850 Processing helix chain 'O' and resid 1865 through 1876 removed outlier: 3.810A pdb=" N GLN O1869 " --> pdb=" O ASN O1865 " (cutoff:3.500A) Processing helix chain 'Y' and resid 14 through 20 Processing helix chain 'Y' and resid 25 through 33 Processing helix chain 'Y' and resid 36 through 38 No H-bonds generated for 'chain 'Y' and resid 36 through 38' Processing helix chain 'Y' and resid 56 through 62 removed outlier: 3.504A pdb=" N LYS Y 60 " --> pdb=" O SER Y 56 " (cutoff:3.500A) Processing helix chain 'Y' and resid 81 through 88 Processing helix chain 'Z' and resid 1 through 6 removed outlier: 4.077A pdb=" N LEU Z 6 " --> pdb=" O ARG Z 3 " (cutoff:3.500A) Processing helix chain 'Z' and resid 23 through 43 Processing helix chain 'Z' and resid 68 through 77 removed outlier: 3.594A pdb=" N ILE Z 72 " --> pdb=" O LYS Z 68 " (cutoff:3.500A) Processing helix chain 'Z' and resid 91 through 93 No H-bonds generated for 'chain 'Z' and resid 91 through 93' Processing helix chain 'Z' and resid 94 through 100 Processing helix chain 'Z' and resid 179 through 188 removed outlier: 3.791A pdb=" N GLN Z 188 " --> pdb=" O LEU Z 184 " (cutoff:3.500A) Processing helix chain 'Z' and resid 218 through 220 No H-bonds generated for 'chain 'Z' and resid 218 through 220' Processing helix chain 'Z' and resid 682 through 684 No H-bonds generated for 'chain 'Z' and resid 682 through 684' Processing helix chain 'Z' and resid 739 through 742 Processing helix chain 'Z' and resid 748 through 750 No H-bonds generated for 'chain 'Z' and resid 748 through 750' Processing helix chain 'Z' and resid 841 through 843 No H-bonds generated for 'chain 'Z' and resid 841 through 843' Processing sheet with id=AA1, first strand: chain 'A' and resid 1418 through 1419 removed outlier: 3.554A pdb=" N ASP A1419 " --> pdb=" O VAL A 17 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N GLY A 20 " --> pdb=" O THR B1213 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 33 through 34 removed outlier: 7.412A pdb=" N ALA A 33 " --> pdb=" O HIS A 83 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 151 through 153 Processing sheet with id=AA4, first strand: chain 'A' and resid 173 through 174 Processing sheet with id=AA5, first strand: chain 'A' and resid 344 through 345 removed outlier: 3.831A pdb=" N LEU B1128 " --> pdb=" O VAL A 345 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 1104 through 1106 removed outlier: 3.707A pdb=" N SER A 348 " --> pdb=" O ARG B1106 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N VAL A 364 " --> pdb=" O LYS A 461 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N ILE A 463 " --> pdb=" O VAL A 364 " (cutoff:3.500A) removed outlier: 5.772A pdb=" N VAL A 366 " --> pdb=" O ILE A 463 " (cutoff:3.500A) removed outlier: 3.591A 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: 4.239A pdb=" N TYR A 404 " --> pdb=" O GLU A 433 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N HIS A 435 " --> pdb=" O ALA A 402 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N ALA A 402 " --> pdb=" O HIS A 435 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N VAL A 405 " --> pdb=" O ILE A 413 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N ILE A 413 " --> pdb=" O VAL A 405 " (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 removed outlier: 3.798A pdb=" N TRP A 572 " --> pdb=" O ILE A 541 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 588 through 590 removed outlier: 6.639A 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: 6.810A pdb=" N THR A 856 " --> pdb=" O ILE A 864 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 879 through 882 Processing sheet with id=AB5, first strand: chain 'A' and resid 1282 through 1292 Processing sheet with id=AB6, first strand: chain 'A' and resid 1141 through 1142 removed outlier: 4.013A pdb=" N ARG A1274 " --> pdb=" O THR A1141 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 1147 through 1151 Processing sheet with id=AB8, first strand: chain 'A' and resid 1442 through 1445 removed outlier: 3.868A pdb=" N ASP A1442 " --> pdb=" O ARG F 135 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 91 through 97 removed outlier: 6.143A pdb=" N PHE B 92 " --> pdb=" O LYS B 133 " (cutoff:3.500A) removed outlier: 7.803A pdb=" N LYS B 133 " --> pdb=" O PHE B 92 " (cutoff:3.500A) removed outlier: 5.368A pdb=" N LYS B 94 " --> pdb=" O ASP B 131 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ASP B 131 " --> pdb=" O LYS B 94 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N GLY B 168 " --> pdb=" O LEU B 128 " (cutoff:3.500A) removed outlier: 7.147A pdb=" N VAL B 130 " --> pdb=" O PHE B 166 " (cutoff:3.500A) removed outlier: 5.538A pdb=" N PHE B 166 " --> pdb=" O VAL B 130 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 101 through 102 removed outlier: 3.753A pdb=" N HIS B 110 " --> pdb=" O VAL B 102 " (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: 5.811A pdb=" N ALA B 214 " --> pdb=" O ASN B 499 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 223 through 227 removed outlier: 6.656A pdb=" N LEU B 258 " --> pdb=" O SER B 235 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N VAL B 237 " --> pdb=" O VAL B 256 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N VAL B 256 " --> pdb=" O VAL B 237 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N GLU B 239 " --> pdb=" O LEU B 254 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N LEU B 254 " --> pdb=" O GLU B 239 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N ARG B 241 " --> pdb=" O SER B 252 " (cutoff:3.500A) removed outlier: 5.508A pdb=" N SER B 252 " --> pdb=" O ARG B 241 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N GLN B 255 " --> pdb=" O THR B 272 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N THR B 268 " --> pdb=" O TYR B 259 " (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 650 through 651 removed outlier: 3.731A pdb=" N GLU B 650 " --> pdb=" O GLU B 641 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N CYS B 741 " --> pdb=" O PHE B 638 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 564 through 565 removed outlier: 3.679A pdb=" N VAL B 589 " --> pdb=" O GLU B 564 " (cutoff:3.500A) removed outlier: 5.588A pdb=" N TRP B 586 " --> pdb=" O VAL B 582 " (cutoff:3.500A) removed outlier: 7.383A pdb=" N VAL B 582 " --> pdb=" O TRP B 586 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N GLY B 588 " --> pdb=" O VAL B 580 " (cutoff:3.500A) removed outlier: 6.051A pdb=" N ARG B 579 " --> pdb=" O LEU B 624 " (cutoff:3.500A) removed outlier: 7.519A pdb=" N ILE B 626 " --> pdb=" O ARG B 579 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N PHE B 581 " --> pdb=" O ILE B 626 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 792 through 796 removed outlier: 5.464A pdb=" N ARG B 969 " --> pdb=" O VAL B 949 " (cutoff:3.500A) removed outlier: 4.805A pdb=" N VAL B 949 " --> pdb=" O ARG B 969 " (cutoff:3.500A) removed outlier: 8.186A pdb=" N THR B 971 " --> pdb=" O GLY B 947 " (cutoff:3.500A) removed outlier: 8.409A pdb=" N GLY B 947 " --> pdb=" O THR B 971 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 804 through 805 Processing sheet with id=AD1, first strand: chain 'B' and resid 1069 through 1070 removed outlier: 7.715A pdb=" N MET B 839 " --> pdb=" O GLY B 991 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N THR B 993 " --> pdb=" O MET B 839 " (cutoff:3.500A) removed outlier: 7.136A pdb=" N MET B 841 " --> pdb=" O THR B 993 " (cutoff:3.500A) removed outlier: 8.411A pdb=" N LEU B1010 " --> pdb=" O ASN B 822 " (cutoff:3.500A) removed outlier: 6.037A pdb=" N ILE B 824 " --> pdb=" O LEU B1010 " (cutoff:3.500A) removed outlier: 7.513A pdb=" N ILE B1012 " --> pdb=" O ILE B 824 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N ALA B 826 " --> pdb=" O ILE B1012 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N PHE B1086 " --> pdb=" O ILE B 827 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 910 through 912 removed outlier: 3.907A pdb=" N ILE B 912 " --> pdb=" O THR B 939 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 915 through 917 Processing sheet with id=AD4, first strand: chain 'B' and resid 1001 through 1002 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 12 removed outlier: 5.722A pdb=" N VAL C 8 " --> pdb=" O SER C 23 " (cutoff:3.500A) removed outlier: 7.198A pdb=" N SER C 23 " --> pdb=" O VAL C 8 " (cutoff:3.500A) removed outlier: 5.246A pdb=" N ILE C 10 " --> pdb=" O ILE C 21 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N ILE C 21 " --> pdb=" O ILE C 10 " (cutoff:3.500A) removed outlier: 4.390A 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: 3.509A pdb=" N VAL C 119 " --> pdb=" O THR C 100 " (cutoff:3.500A) removed outlier: 11.405A pdb=" N ARG O1188 " --> pdb=" O VAL C 98 " (cutoff:3.500A) removed outlier: 7.730A pdb=" N THR C 100 " --> pdb=" O ARG O1188 " (cutoff:3.500A) removed outlier: 8.143A pdb=" N ALA O1190 " --> pdb=" O THR C 100 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N GLN C 102 " --> pdb=" O ALA O1190 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'O' and resid 1194 through 1202 current: chain 'C' and resid 42 through 54 removed outlier: 3.984A pdb=" N VAL L 65 " --> pdb=" O VAL C 51 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 119 through 120 removed outlier: 3.509A pdb=" N VAL C 119 " --> pdb=" O THR C 100 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 96 through 104 current: chain 'O' and resid 1242 through 1253 removed outlier: 4.342A pdb=" N ASP O1215 " --> pdb=" O VAL O1247 " (cutoff:3.500A) removed outlier: 7.117A pdb=" N LEU O1216 " --> pdb=" O VAL O1285 " (cutoff:3.500A) removed outlier: 8.878A pdb=" N SER O1182 " --> pdb=" O ALA O1202 " (cutoff:3.500A) removed outlier: 6.015A pdb=" N ALA O1202 " --> pdb=" O SER O1182 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N ILE O1184 " --> pdb=" O SER O1200 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N SER O1200 " --> pdb=" O ILE O1184 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'O' and resid 1194 through 1202 current: chain 'C' and resid 42 through 54 removed outlier: 3.984A pdb=" N VAL L 65 " --> pdb=" O VAL C 51 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 72 through 74 removed outlier: 4.349A pdb=" N GLN C 73 " --> pdb=" O GLY C 130 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 111 through 113 removed outlier: 3.737A pdb=" N CYS C 145 " --> pdb=" O VAL C 113 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'D' and resid 36 through 38 Processing sheet with id=AE4, first strand: chain 'E' and resid 60 through 62 removed outlier: 6.292A pdb=" N TRP E 79 " --> pdb=" O ILE E 109 " (cutoff:3.500A) removed outlier: 7.927A pdb=" N VAL E 111 " --> pdb=" O TRP E 79 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N GLU E 81 " --> pdb=" O VAL E 111 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'E' and resid 152 through 155 Processing sheet with id=AE6, first strand: chain 'G' and resid 3 through 13 removed outlier: 3.677A pdb=" N LYS G 73 " --> pdb=" O ASP G 55 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N ASP G 55 " --> pdb=" O LYS G 73 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'G' and resid 38 through 39 removed outlier: 6.908A pdb=" N VAL G 77 " --> pdb=" O LEU G 46 " (cutoff:3.500A) removed outlier: 5.464A pdb=" N VAL G 48 " --> pdb=" O ARG G 75 " (cutoff:3.500A) removed outlier: 7.970A pdb=" N ARG G 75 " --> pdb=" O VAL G 48 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'G' and resid 169 through 170 removed outlier: 5.563A pdb=" N ILE G 147 " --> pdb=" O SER G 162 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N SER G 162 " --> pdb=" O ILE G 147 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N LYS G 107 " --> pdb=" O ALA G 159 " (cutoff:3.500A) removed outlier: 7.616A pdb=" N GLY G 161 " --> pdb=" O LYS G 107 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N PHE G 109 " --> pdb=" O GLY G 161 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N VAL G 110 " --> pdb=" O PHE G 99 " (cutoff:3.500A) removed outlier: 5.142A pdb=" N PHE G 99 " --> pdb=" O VAL G 110 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N GLY G 98 " --> pdb=" O CYS G 94 " (cutoff:3.500A) removed outlier: 5.039A pdb=" N CYS G 94 " --> pdb=" O GLY G 98 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N GLU G 100 " --> pdb=" O VAL G 92 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'G' and resid 120 through 122 removed outlier: 3.568A pdb=" N TYR G 130 " --> pdb=" O ILE G 137 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ILE G 137 " --> pdb=" O TYR G 130 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'H' and resid 95 through 98 removed outlier: 3.759A pdb=" N PHE H 6 " --> pdb=" O ILE H 59 " (cutoff:3.500A) removed outlier: 7.237A pdb=" N GLU H 27 " --> pdb=" O SER H 13 " (cutoff:3.500A) removed outlier: 4.726A pdb=" N VAL H 15 " --> pdb=" O ARG H 25 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N ARG H 25 " --> pdb=" O VAL H 15 " (cutoff:3.500A) removed outlier: 5.479A pdb=" N LEU H 122 " --> pdb=" O ASP H 41 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N LYS H 103 " --> pdb=" O TYR H 115 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N SER H 117 " --> pdb=" O ALA H 101 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N ALA H 101 " --> pdb=" O SER H 117 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'I' and resid 15 through 19 Processing sheet with id=AF3, first strand: chain 'I' and resid 70 through 71 Processing sheet with id=AF4, first strand: chain 'K' and resid 19 through 24 removed outlier: 4.425A pdb=" N ALA K 30 " --> pdb=" O ASP K 24 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'M' and resid 34 through 39 Processing sheet with id=AF6, first strand: chain 'O' and resid 1439 through 1441 removed outlier: 6.695A pdb=" N VAL O1587 " --> pdb=" O ILE O1612 " (cutoff:3.500A) removed outlier: 7.941A pdb=" N VAL O1614 " --> pdb=" O VAL O1587 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N ILE O1589 " --> pdb=" O VAL O1614 " (cutoff:3.500A) removed outlier: 5.841A pdb=" N GLY O1351 " --> pdb=" O CYS O1611 " (cutoff:3.500A) removed outlier: 7.313A pdb=" N MET O1613 " --> pdb=" O GLY O1351 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N SER O1353 " --> pdb=" O MET O1613 " (cutoff:3.500A) removed outlier: 8.758A pdb=" N TYR O1649 " --> pdb=" O PHE O1352 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N LEU O1354 " --> pdb=" O TYR O1649 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'O' and resid 1427 through 1428 Processing sheet with id=AF8, first strand: chain 'O' and resid 1775 through 1778 removed outlier: 6.760A pdb=" N ILE O1746 " --> pdb=" O ASP O1776 " (cutoff:3.500A) removed outlier: 8.170A pdb=" N ASN O1778 " --> pdb=" O ILE O1746 " (cutoff:3.500A) removed outlier: 6.101A pdb=" N ILE O1748 " --> pdb=" O ASN O1778 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N GLY O1747 " --> pdb=" O LEU O1792 " (cutoff:3.500A) removed outlier: 7.760A pdb=" N SER O1794 " --> pdb=" O GLY O1747 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N ILE O1749 " --> pdb=" O SER O1794 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N GLU O1789 " --> pdb=" O SER O1824 " (cutoff:3.500A) removed outlier: 8.118A pdb=" N TRP O1826 " --> pdb=" O GLU O1789 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N ILE O1791 " --> pdb=" O TRP O1826 " (cutoff:3.500A) removed outlier: 7.701A pdb=" N LEU O1828 " --> pdb=" O ILE O1791 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N ILE O1793 " --> pdb=" O LEU O1828 " (cutoff:3.500A) removed outlier: 7.953A pdb=" N ALA O1854 " --> pdb=" O TYR O1697 " (cutoff:3.500A) removed outlier: 5.898A pdb=" N PHE O1699 " --> pdb=" O ALA O1854 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N ALA O1856 " --> pdb=" O PHE O1699 " (cutoff:3.500A) removed outlier: 5.256A pdb=" N ASP O1701 " --> pdb=" O ALA O1856 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'Y' and resid 11 through 13 Processing sheet with id=AG1, first strand: chain 'Y' and resid 44 through 45 Processing sheet with id=AG2, first strand: chain 'Y' and resid 70 through 72 removed outlier: 3.947A pdb=" N LEU Y 47 " --> pdb=" O GLN Z 54 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N SER Z 51 " --> pdb=" O GLU Z 65 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N GLN Z 86 " --> pdb=" O ARG Z 18 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'Z' and resid 114 through 116 removed outlier: 5.742A pdb=" N VAL Z 129 " --> pdb=" O LYS Z 142 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N LYS Z 142 " --> pdb=" O VAL Z 129 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N GLN Z 131 " --> pdb=" O MET Z 140 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N HIS Z 198 " --> pdb=" O ARG Z 194 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'Z' and resid 621 through 626 removed outlier: 3.639A pdb=" N ARG Z 621 " --> pdb=" O SER Z 616 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N MET Z 606 " --> pdb=" O THR Z 613 " (cutoff:3.500A) removed outlier: 5.822A pdb=" N MET Z 615 " --> pdb=" O VAL Z 604 " (cutoff:3.500A) removed outlier: 5.510A pdb=" N VAL Z 604 " --> pdb=" O MET Z 615 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'Z' and resid 676 through 680 removed outlier: 7.419A pdb=" N ILE Z 666 " --> pdb=" O ALA Z 662 " (cutoff:3.500A) removed outlier: 5.578A pdb=" N ALA Z 662 " --> pdb=" O ILE Z 666 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N LYS Z 668 " --> pdb=" O ILE Z 660 " (cutoff:3.500A) removed outlier: 4.752A pdb=" N ILE Z 648 " --> pdb=" O ILE Z 688 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'Z' and resid 697 through 698 Processing sheet with id=AG7, first strand: chain 'Z' and resid 744 through 747 removed outlier: 7.040A pdb=" N PHE Z 732 " --> pdb=" O LEU Z 724 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'Z' and resid 837 through 840 removed outlier: 3.822A pdb=" N ASP Z 821 " --> pdb=" O THR Z 828 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N GLU Z 830 " --> pdb=" O VAL Z 819 " (cutoff:3.500A) removed outlier: 5.646A pdb=" N VAL Z 819 " --> pdb=" O GLU Z 830 " (cutoff:3.500A) 1709 hydrogen bonds defined for protein. 4740 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 85 hydrogen bonds 170 hydrogen bond angles 0 basepair planarities 35 basepair parallelities 56 stacking parallelities Total time for adding SS restraints: 14.34 Time building geometry restraints manager: 4.52 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: 13809 1.34 - 1.46: 5892 1.46 - 1.57: 23614 1.57 - 1.69: 178 1.69 - 1.81: 371 Bond restraints: 43864 Sorted by residual: bond pdb=" F2 BEF O3003 " pdb="BE BEF O3003 " ideal model delta sigma weight residual 1.476 1.562 -0.086 2.00e-02 2.50e+03 1.84e+01 bond pdb=" F3 BEF O3003 " pdb="BE BEF O3003 " ideal model delta sigma weight residual 1.476 1.547 -0.071 2.00e-02 2.50e+03 1.25e+01 bond pdb=" C3' DC T 34 " pdb=" C2' DC T 34 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 9.45e+00 bond pdb=" C1' DT T 8 " pdb=" N1 DT T 8 " ideal model delta sigma weight residual 1.468 1.511 -0.043 1.40e-02 5.10e+03 9.25e+00 bond pdb=" C1' DC N 44 " pdb=" N1 DC N 44 " ideal model delta sigma weight residual 1.468 1.510 -0.042 1.40e-02 5.10e+03 9.03e+00 ... (remaining 43859 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.52: 59274 2.52 - 5.04: 308 5.04 - 7.56: 5 7.56 - 10.07: 0 10.07 - 12.59: 2 Bond angle restraints: 59589 Sorted by residual: angle pdb=" N3 DT T 13 " pdb=" C4 DT T 13 " pdb=" O4 DT T 13 " ideal model delta sigma weight residual 119.90 122.52 -2.62 6.00e-01 2.78e+00 1.91e+01 angle pdb=" N3 DT T 12 " pdb=" C4 DT T 12 " pdb=" O4 DT T 12 " ideal model delta sigma weight residual 119.90 122.50 -2.60 6.00e-01 2.78e+00 1.87e+01 angle pdb=" F2 BEF O3003 " pdb="BE BEF O3003 " pdb=" F3 BEF O3003 " ideal model delta sigma weight residual 119.96 107.37 12.59 3.00e+00 1.11e-01 1.76e+01 angle pdb=" N3 DT N 39 " pdb=" C4 DT N 39 " pdb=" O4 DT N 39 " ideal model delta sigma weight residual 119.90 122.42 -2.52 6.00e-01 2.78e+00 1.76e+01 angle pdb=" N3 DT T 32 " pdb=" C4 DT T 32 " pdb=" O4 DT T 32 " ideal model delta sigma weight residual 119.90 122.40 -2.50 6.00e-01 2.78e+00 1.74e+01 ... (remaining 59584 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.60: 26252 30.60 - 61.21: 427 61.21 - 91.81: 29 91.81 - 122.42: 2 122.42 - 153.02: 2 Dihedral angle restraints: 26712 sinusoidal: 11734 harmonic: 14978 Sorted by residual: dihedral pdb=" C4' DC T 34 " pdb=" C3' DC T 34 " pdb=" O3' DC T 34 " pdb=" P DA T 35 " ideal model delta sinusoidal sigma weight residual 220.00 66.98 153.02 1 3.50e+01 8.16e-04 1.48e+01 dihedral pdb=" C4' DG T 14 " pdb=" C3' DG T 14 " pdb=" O3' DG T 14 " pdb=" P DA T 15 " ideal model delta sinusoidal sigma weight residual 220.00 70.62 149.38 1 3.50e+01 8.16e-04 1.46e+01 dihedral pdb=" CB ARG G 60 " pdb=" CG ARG G 60 " pdb=" CD ARG G 60 " pdb=" NE ARG G 60 " ideal model delta sinusoidal sigma weight residual 180.00 120.17 59.83 3 1.50e+01 4.44e-03 9.48e+00 ... (remaining 26709 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 4730 0.031 - 0.063: 1173 0.063 - 0.094: 361 0.094 - 0.126: 371 0.126 - 0.157: 73 Chirality restraints: 6708 Sorted by residual: chirality pdb=" C3' DG T 17 " pdb=" C4' DG T 17 " pdb=" O3' DG T 17 " pdb=" C2' DG T 17 " both_signs ideal model delta sigma weight residual False -2.73 -2.57 -0.16 2.00e-01 2.50e+01 6.18e-01 chirality pdb=" C3' DG N 19 " pdb=" C4' DG N 19 " pdb=" O3' DG N 19 " pdb=" C2' DG N 19 " both_signs ideal model delta sigma weight residual False -2.73 -2.58 -0.15 2.00e-01 2.50e+01 5.96e-01 chirality pdb=" C3' DG T 37 " pdb=" C4' DG T 37 " pdb=" O3' DG T 37 " pdb=" C2' DG T 37 " both_signs ideal model delta sigma weight residual False -2.73 -2.58 -0.15 2.00e-01 2.50e+01 5.64e-01 ... (remaining 6705 not shown) Planarity restraints: 7378 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU A1301 " -0.026 5.00e-02 4.00e+02 3.88e-02 2.41e+00 pdb=" N PRO A1302 " 0.067 5.00e-02 4.00e+02 pdb=" CA PRO A1302 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO A1302 " -0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA PHE B 417 " 0.007 2.00e-02 2.50e+03 1.33e-02 1.77e+00 pdb=" C PHE B 417 " -0.023 2.00e-02 2.50e+03 pdb=" O PHE B 417 " 0.009 2.00e-02 2.50e+03 pdb=" N LYS B 418 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL E 124 " -0.019 5.00e-02 4.00e+02 2.92e-02 1.36e+00 pdb=" N PRO E 125 " 0.050 5.00e-02 4.00e+02 pdb=" CA PRO E 125 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO E 125 " -0.016 5.00e-02 4.00e+02 ... (remaining 7375 not shown) Histogram of nonbonded interaction distances: 1.94 - 2.54: 378 2.54 - 3.13: 35403 3.13 - 3.72: 66753 3.72 - 4.31: 94341 4.31 - 4.90: 158005 Nonbonded interactions: 354880 Sorted by model distance: nonbonded pdb=" OD1 ASP A 853 " pdb=" OG1 THR A 855 " model vdw 1.944 3.040 nonbonded pdb=" OH TYR J 21 " pdb=" OE1 GLU J 32 " model vdw 1.999 3.040 nonbonded pdb=" O2B ADP O3001 " pdb="MG MG O3002 " model vdw 2.025 2.170 nonbonded pdb=" OG1 THR B 971 " pdb=" OE1 GLU C 61 " model vdw 2.028 3.040 nonbonded pdb=" OG SER B 906 " pdb=" OE1 GLU Z 830 " model vdw 2.032 3.040 ... (remaining 354875 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: 3.090 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: 0.030 Extract box with map and model: 0.780 Check model and map are aligned: 0.150 Set scattering table: 0.120 Process input model: 52.530 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.490 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 58.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7214 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 : 0.002 0.086 43895 Z= 0.153 Angle : 0.428 12.592 59625 Z= 0.276 Chirality : 0.041 0.157 6708 Planarity : 0.002 0.039 7378 Dihedral : 10.059 153.022 17020 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 0.02 % Allowed : 3.12 % Favored : 96.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.46 % 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: 2.28 (0.13), residues: 5090 helix: 3.31 (0.13), residues: 1780 sheet: 0.79 (0.18), residues: 858 loop : 0.48 (0.13), residues: 2452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG O1820 TYR 0.005 0.000 TYR J 21 PHE 0.008 0.001 PHE A 219 TRP 0.004 0.000 TRP J 18 HIS 0.003 0.000 HIS C 91 Details of bonding type rmsd/Z covalent geometry : bond 0.00212 / 0.15 (43864) covalent geometry : angle 0.42556 / 0.28 (59589) hydrogen bonds : bond 0.13512 / 9.26 ( 1790) hydrogen bonds : angle 5.15281 / 3.73 ( 4910) metal coordination : bond 0.00179 / 0.11 ( 31) metal coordination : angle 1.88109 / 1.07 ( 36) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10180 Ramachandran restraints generated. 5090 Oldfield, 0 Emsley, 5090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10180 Ramachandran restraints generated. 5090 Oldfield, 0 Emsley, 5090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 802 residues out of total 4548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 801 time to evaluate : 1.162 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 340 LEU cc_start: 0.9388 (mt) cc_final: 0.9184 (mt) REVERT: A 353 ILE cc_start: 0.8778 (pt) cc_final: 0.8431 (pt) REVERT: A 572 TRP cc_start: 0.7007 (m-90) cc_final: 0.5689 (m-90) REVERT: A 588 LEU cc_start: 0.8922 (tt) cc_final: 0.8709 (tt) REVERT: A 637 LYS cc_start: 0.8318 (mmmt) cc_final: 0.7974 (mmtm) REVERT: A 644 LYS cc_start: 0.8404 (mmmt) cc_final: 0.8132 (mtmm) REVERT: A 666 ILE cc_start: 0.7453 (mm) cc_final: 0.7128 (tp) REVERT: A 1019 CYS cc_start: 0.9035 (m) cc_final: 0.8734 (m) REVERT: A 1064 VAL cc_start: 0.8589 (t) cc_final: 0.7903 (t) REVERT: A 1273 LEU cc_start: 0.8893 (mp) cc_final: 0.8390 (tt) REVERT: A 1363 VAL cc_start: 0.9009 (t) cc_final: 0.8800 (t) REVERT: A 1403 GLU cc_start: 0.6737 (mt-10) cc_final: 0.6489 (mp0) REVERT: A 1442 ASP cc_start: 0.8538 (m-30) cc_final: 0.8227 (t0) REVERT: A 1444 MET cc_start: 0.7873 (mmt) cc_final: 0.6411 (mmt) REVERT: B 95 ILE cc_start: 0.8239 (tt) cc_final: 0.7810 (tt) REVERT: B 504 ARG cc_start: 0.7355 (mmt90) cc_final: 0.6971 (mtm180) REVERT: B 992 ILE cc_start: 0.6946 (tp) cc_final: 0.6669 (tt) REVERT: B 1092 TYR cc_start: 0.6888 (m-80) cc_final: 0.6626 (m-80) REVERT: C 155 LEU cc_start: 0.9101 (pp) cc_final: 0.8877 (pp) REVERT: C 265 MET cc_start: 0.8280 (ttp) cc_final: 0.7546 (mtt) REVERT: E 179 GLN cc_start: 0.8055 (mm110) cc_final: 0.7797 (mm-40) REVERT: F 84 TYR cc_start: 0.7016 (m-80) cc_final: 0.6723 (m-80) REVERT: G 64 THR cc_start: 0.7745 (t) cc_final: 0.7508 (m) REVERT: G 106 MET cc_start: 0.5097 (mtt) cc_final: 0.4547 (mmt) REVERT: K 7 PHE cc_start: 0.8939 (p90) cc_final: 0.8558 (p90) REVERT: K 8 GLU cc_start: 0.7830 (tp30) cc_final: 0.7327 (tp30) REVERT: K 92 ASN cc_start: 0.9292 (m-40) cc_final: 0.8896 (m-40) REVERT: O 1105 MET cc_start: 0.8815 (tpt) cc_final: 0.8094 (tpp) REVERT: O 1116 LEU cc_start: 0.9403 (tp) cc_final: 0.9091 (tt) REVERT: O 1320 ASN cc_start: 0.8522 (m-40) cc_final: 0.7534 (t0) REVERT: O 1407 LEU cc_start: 0.8765 (tp) cc_final: 0.8490 (tp) outliers start: 1 outliers final: 0 residues processed: 801 average time/residue: 0.2865 time to fit residues: 365.7116 Evaluate side-chains 411 residues out of total 4548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 411 time to evaluate : 1.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 517 random chunks: chunk 394 optimal weight: 0.4980 chunk 430 optimal weight: 7.9990 chunk 41 optimal weight: 9.9990 chunk 265 optimal weight: 0.0970 chunk 497 optimal weight: 50.0000 chunk 414 optimal weight: 7.9990 chunk 310 optimal weight: 6.9990 chunk 488 optimal weight: 0.8980 chunk 366 optimal weight: 0.9980 chunk 223 optimal weight: 10.0000 chunk 516 optimal weight: 9.9990 overall best weight: 1.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 4 GLN A 54 ASN ** A 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 109 HIS ** A 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 209 ASN A 313 GLN ** A 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 358 ASN ** A 447 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 503 GLN A 545 GLN A 736 ASN A 742 ASN ** A 745 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 953 ASN ** A1070 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1432 GLN B 47 GLN B 178 ASN ** B 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1112 GLN ** B1176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1177 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 151 GLN D 28 GLN D 31 GLN G 10 ASN G 24 GLN ** I 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 96 ASN L 66 GLN O1104 HIS O1618 ASN O1654 GLN Z 629 ASN Z 646 HIS Z 722 GLN Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.068727 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.051633 restraints weight = 344577.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.052813 restraints weight = 218746.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.052698 restraints weight = 152272.666| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.053197 restraints weight = 126345.524| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.053253 restraints weight = 110196.993| |-----------------------------------------------------------------------------| r_work (final): 0.3384 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7526 moved from start: 0.2071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 43895 Z= 0.162 Angle : 0.608 12.950 59625 Z= 0.313 Chirality : 0.044 0.256 6708 Planarity : 0.005 0.078 7378 Dihedral : 12.144 163.460 6721 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 0.02 % Allowed : 2.44 % Favored : 97.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.46 % 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: 1.57 (0.12), residues: 5090 helix: 2.40 (0.13), residues: 1789 sheet: 0.59 (0.17), residues: 861 loop : 0.25 (0.13), residues: 2440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG A 47 TYR 0.036 0.002 TYR B1092 PHE 0.036 0.002 PHE B1087 TRP 0.031 0.001 TRP B 586 HIS 0.013 0.001 HIS A 92 Details of bonding type rmsd/Z covalent geometry : bond 0.00357 / 0.16 (43864) covalent geometry : angle 0.60422 / 0.31 (59589) hydrogen bonds : bond 0.03975 / 2.71 ( 1790) hydrogen bonds : angle 4.65939 / 3.38 ( 4910) metal coordination : bond 0.00521 / 0.27 ( 31) metal coordination : angle 2.70558 / 1.57 ( 36) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10180 Ramachandran restraints generated. 5090 Oldfield, 0 Emsley, 5090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10180 Ramachandran restraints generated. 5090 Oldfield, 0 Emsley, 5090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 487 residues out of total 4548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 486 time to evaluate : 1.719 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 588 LEU cc_start: 0.9087 (tt) cc_final: 0.8609 (tt) REVERT: A 637 LYS cc_start: 0.8445 (mmmt) cc_final: 0.8049 (mptt) REVERT: A 644 LYS cc_start: 0.8350 (mmmt) cc_final: 0.7936 (mtmm) REVERT: A 846 GLU cc_start: 0.6989 (pt0) cc_final: 0.6721 (pt0) REVERT: A 849 MET cc_start: 0.8024 (tmm) cc_final: 0.7275 (tmm) REVERT: A 954 TRP cc_start: 0.8213 (m100) cc_final: 0.7866 (m100) REVERT: A 1019 CYS cc_start: 0.9119 (m) cc_final: 0.8811 (m) REVERT: A 1064 VAL cc_start: 0.8490 (t) cc_final: 0.8255 (t) REVERT: A 1102 LYS cc_start: 0.8986 (ttpp) cc_final: 0.8484 (tppt) REVERT: A 1111 MET cc_start: 0.8354 (tpp) cc_final: 0.7445 (tpp) REVERT: A 1209 MET cc_start: 0.8934 (ttm) cc_final: 0.8533 (ttt) REVERT: A 1285 MET cc_start: 0.7330 (mpp) cc_final: 0.6449 (mpp) REVERT: A 1398 MET cc_start: 0.8341 (ttm) cc_final: 0.8079 (tpp) REVERT: A 1409 LEU cc_start: 0.9135 (mm) cc_final: 0.8911 (mm) REVERT: A 1442 ASP cc_start: 0.8673 (m-30) cc_final: 0.8195 (t0) REVERT: A 1444 MET cc_start: 0.8672 (mmt) cc_final: 0.7596 (mmm) REVERT: B 504 ARG cc_start: 0.7606 (mmt90) cc_final: 0.6987 (mtm180) REVERT: B 615 MET cc_start: 0.8364 (mpp) cc_final: 0.8112 (mpp) REVERT: B 992 ILE cc_start: 0.7568 (tp) cc_final: 0.7170 (tt) REVERT: B 1208 MET cc_start: 0.9170 (mmt) cc_final: 0.8911 (mmt) REVERT: B 1210 MET cc_start: 0.8961 (mpp) cc_final: 0.8737 (mpp) REVERT: C 33 LEU cc_start: 0.8878 (tp) cc_final: 0.8542 (tp) REVERT: C 87 PHE cc_start: 0.8451 (t80) cc_final: 0.8214 (t80) REVERT: C 230 MET cc_start: 0.8581 (mpp) cc_final: 0.8290 (mpp) REVERT: C 265 MET cc_start: 0.8118 (ttp) cc_final: 0.7476 (mtt) REVERT: D 31 GLN cc_start: 0.7614 (OUTLIER) cc_final: 0.6523 (mt0) REVERT: D 127 ASP cc_start: 0.8765 (m-30) cc_final: 0.8513 (m-30) REVERT: G 106 MET cc_start: 0.5247 (mtt) cc_final: 0.4592 (mmt) REVERT: G 115 MET cc_start: 0.1806 (mtt) cc_final: 0.0339 (mmt) REVERT: J 1 MET cc_start: 0.6950 (mpp) cc_final: 0.6632 (mpp) REVERT: K 8 GLU cc_start: 0.8522 (tp30) cc_final: 0.7775 (tp30) REVERT: K 92 ASN cc_start: 0.9285 (m-40) cc_final: 0.9005 (m110) REVERT: L 63 ARG cc_start: 0.8297 (ttm110) cc_final: 0.7879 (mmt-90) REVERT: O 1105 MET cc_start: 0.9097 (tpt) cc_final: 0.8472 (tpp) REVERT: O 1153 TYR cc_start: 0.8774 (t80) cc_final: 0.8406 (t80) REVERT: O 1217 ILE cc_start: 0.9705 (pt) cc_final: 0.9480 (mp) REVERT: O 1320 ASN cc_start: 0.8924 (m-40) cc_final: 0.7928 (t0) REVERT: O 1407 LEU cc_start: 0.8987 (tp) cc_final: 0.8745 (tp) REVERT: O 1642 MET cc_start: 0.9309 (tpp) cc_final: 0.9014 (tpt) REVERT: Y 6 MET cc_start: 0.6804 (ptp) cc_final: 0.6198 (ptp) outliers start: 1 outliers final: 0 residues processed: 487 average time/residue: 0.2771 time to fit residues: 220.7005 Evaluate side-chains 347 residues out of total 4548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 346 time to evaluate : 1.693 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 517 random chunks: chunk 246 optimal weight: 9.9990 chunk 25 optimal weight: 9.9990 chunk 406 optimal weight: 20.0000 chunk 239 optimal weight: 2.9990 chunk 92 optimal weight: 9.9990 chunk 362 optimal weight: 6.9990 chunk 18 optimal weight: 8.9990 chunk 348 optimal weight: 5.9990 chunk 279 optimal weight: 5.9990 chunk 344 optimal weight: 4.9990 chunk 229 optimal weight: 4.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 451 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 488 ASN A 517 ASN A 736 ASN ** A 745 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1140 HIS A1270 ASN A1432 GLN ** B 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 300 HIS B 515 HIS B 951 GLN B1117 GLN ** B1176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1177 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 231 ASN D 173 HIS E 61 GLN E 146 HIS E 153 HIS H 21 ASN H 133 ASN I 12 ASN ** I 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 108 HIS O1114 ASN O1267 ASN O1631 ASN ** O1658 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O1709 GLN ** Z 835 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.065115 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.047717 restraints weight = 352642.705| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.048269 restraints weight = 220521.619| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.048452 restraints weight = 168502.443| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.048862 restraints weight = 135543.494| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.048965 restraints weight = 106795.224| |-----------------------------------------------------------------------------| r_work (final): 0.3244 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7711 moved from start: 0.3047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.166 43895 Z= 0.270 Angle : 0.687 13.772 59625 Z= 0.357 Chirality : 0.045 0.236 6708 Planarity : 0.005 0.062 7378 Dihedral : 12.420 161.658 6721 Min Nonbonded Distance : 1.847 Molprobity Statistics. All-atom Clashscore : 11.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 0.09 % Allowed : 2.92 % Favored : 96.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.46 % 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: 1.10 (0.12), residues: 5090 helix: 1.86 (0.12), residues: 1792 sheet: 0.42 (0.17), residues: 859 loop : 0.08 (0.13), residues: 2439 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG J 38 TYR 0.038 0.002 TYR B 190 PHE 0.063 0.002 PHE H 104 TRP 0.032 0.002 TRP B 586 HIS 0.012 0.002 HIS A 92 Details of bonding type rmsd/Z covalent geometry : bond 0.00578 / 0.27 (43864) covalent geometry : angle 0.68263 / 0.36 (59589) hydrogen bonds : bond 0.04295 / 2.86 ( 1790) hydrogen bonds : angle 4.79076 / 3.49 ( 4910) metal coordination : bond 0.01116 / 0.62 ( 31) metal coordination : angle 3.28483 / 1.80 ( 36) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10180 Ramachandran restraints generated. 5090 Oldfield, 0 Emsley, 5090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10180 Ramachandran restraints generated. 5090 Oldfield, 0 Emsley, 5090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 394 residues out of total 4548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 390 time to evaluate : 1.224 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 103 CYS cc_start: 0.9339 (m) cc_final: 0.9073 (m) REVERT: A 108 MET cc_start: 0.7718 (ptp) cc_final: 0.6881 (pmm) REVERT: A 340 LEU cc_start: 0.9582 (mt) cc_final: 0.9329 (mt) REVERT: A 644 LYS cc_start: 0.8614 (mmmt) cc_final: 0.8238 (mtmm) REVERT: A 846 GLU cc_start: 0.7005 (pt0) cc_final: 0.6670 (pt0) REVERT: A 849 MET cc_start: 0.7989 (tmm) cc_final: 0.7280 (tmm) REVERT: A 1019 CYS cc_start: 0.9087 (m) cc_final: 0.8816 (m) REVERT: A 1102 LYS cc_start: 0.9107 (ttpp) cc_final: 0.8610 (tppt) REVERT: A 1111 MET cc_start: 0.8512 (tpp) cc_final: 0.8254 (tpp) REVERT: A 1209 MET cc_start: 0.8970 (ttm) cc_final: 0.8443 (ttm) REVERT: A 1368 MET cc_start: 0.8181 (mtt) cc_final: 0.7973 (mtt) REVERT: A 1398 MET cc_start: 0.8376 (ttm) cc_final: 0.7946 (tpp) REVERT: A 1426 GLU cc_start: 0.8439 (mp0) cc_final: 0.7755 (mp0) REVERT: A 1442 ASP cc_start: 0.8698 (m-30) cc_final: 0.8371 (t0) REVERT: A 1444 MET cc_start: 0.8914 (mmt) cc_final: 0.7896 (mmm) REVERT: B 386 LEU cc_start: 0.9625 (tp) cc_final: 0.9209 (pp) REVERT: B 499 ASN cc_start: 0.8887 (t0) cc_final: 0.8447 (t0) REVERT: B 563 MET cc_start: 0.7023 (tmm) cc_final: 0.6163 (tmm) REVERT: B 789 MET cc_start: 0.8391 (mmm) cc_final: 0.7477 (mmm) REVERT: B 1072 MET cc_start: 0.8511 (mtp) cc_final: 0.7969 (mtp) REVERT: B 1138 MET cc_start: 0.7691 (mmm) cc_final: 0.7358 (tpt) REVERT: B 1152 MET cc_start: 0.7152 (mmm) cc_final: 0.6511 (tpt) REVERT: B 1210 MET cc_start: 0.9136 (mpp) cc_final: 0.8873 (mpp) REVERT: C 230 MET cc_start: 0.8564 (mpp) cc_final: 0.8305 (mpp) REVERT: C 265 MET cc_start: 0.8002 (ttp) cc_final: 0.7527 (mtt) REVERT: D 127 ASP cc_start: 0.8758 (m-30) cc_final: 0.8500 (m-30) REVERT: E 112 TYR cc_start: 0.7829 (p90) cc_final: 0.7625 (p90) REVERT: F 103 MET cc_start: 0.9012 (mmp) cc_final: 0.8674 (mmm) REVERT: G 106 MET cc_start: 0.5377 (mtt) cc_final: 0.4621 (mmt) REVERT: G 115 MET cc_start: 0.1843 (mtt) cc_final: 0.0611 (mmt) REVERT: K 8 GLU cc_start: 0.8737 (tp30) cc_final: 0.7926 (tp30) REVERT: O 1105 MET cc_start: 0.9027 (tpt) cc_final: 0.8493 (tpp) REVERT: O 1153 TYR cc_start: 0.8643 (t80) cc_final: 0.8230 (t80) REVERT: O 1407 LEU cc_start: 0.9081 (tp) cc_final: 0.8705 (tp) REVERT: O 1584 PHE cc_start: 0.8079 (m-80) cc_final: 0.7711 (m-80) REVERT: O 1642 MET cc_start: 0.9310 (tpp) cc_final: 0.9031 (tpt) REVERT: Y 6 MET cc_start: 0.7054 (ptp) cc_final: 0.6356 (ptp) outliers start: 4 outliers final: 3 residues processed: 392 average time/residue: 0.2548 time to fit residues: 165.6576 Evaluate side-chains 300 residues out of total 4548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 297 time to evaluate : 1.605 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 517 random chunks: chunk 19 optimal weight: 5.9990 chunk 352 optimal weight: 0.9980 chunk 270 optimal weight: 6.9990 chunk 309 optimal weight: 0.6980 chunk 381 optimal weight: 0.8980 chunk 73 optimal weight: 3.9990 chunk 89 optimal weight: 8.9990 chunk 481 optimal weight: 6.9990 chunk 162 optimal weight: 9.9990 chunk 457 optimal weight: 9.9990 chunk 169 optimal weight: 3.9990 overall best weight: 2.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 451 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 736 ASN A 745 GLN ** A 757 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 966 ASN A 975 HIS A1432 GLN ** B 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 395 GLN B 573 GLN B1177 HIS C 231 ASN E 179 GLN G 113 HIS ** H 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 96 ASN O1114 ASN O1631 ASN O1658 HIS ** Z 835 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.065373 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.047646 restraints weight = 347038.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.048849 restraints weight = 212361.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.049059 restraints weight = 140909.277| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.049094 restraints weight = 111165.872| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.049251 restraints weight = 98817.970| |-----------------------------------------------------------------------------| r_work (final): 0.3269 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7648 moved from start: 0.3224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 43895 Z= 0.149 Angle : 0.564 10.371 59625 Z= 0.291 Chirality : 0.042 0.208 6708 Planarity : 0.004 0.051 7378 Dihedral : 12.417 159.688 6721 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 10.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 0.02 % Allowed : 2.24 % Favored : 97.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.46 % 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: 1.14 (0.12), residues: 5090 helix: 1.89 (0.12), residues: 1787 sheet: 0.40 (0.18), residues: 850 loop : 0.12 (0.13), residues: 2453 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG A1055 TYR 0.027 0.001 TYR B 486 PHE 0.037 0.001 PHE A 22 TRP 0.025 0.001 TRP B 586 HIS 0.013 0.001 HIS B 300 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.15 (43864) covalent geometry : angle 0.55918 / 0.29 (59589) hydrogen bonds : bond 0.03390 / 2.28 ( 1790) hydrogen bonds : angle 4.59591 / 3.34 ( 4910) metal coordination : bond 0.00785 / 0.41 ( 31) metal coordination : angle 3.10854 / 1.80 ( 36) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10180 Ramachandran restraints generated. 5090 Oldfield, 0 Emsley, 5090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10180 Ramachandran restraints generated. 5090 Oldfield, 0 Emsley, 5090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 370 residues out of total 4548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 369 time to evaluate : 2.045 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 103 CYS cc_start: 0.9257 (m) cc_final: 0.9009 (m) REVERT: A 340 LEU cc_start: 0.9501 (mt) cc_final: 0.9261 (mt) REVERT: A 644 LYS cc_start: 0.8497 (mmmt) cc_final: 0.8132 (mtmm) REVERT: A 818 MET cc_start: 0.8012 (mtt) cc_final: 0.7739 (mtt) REVERT: A 846 GLU cc_start: 0.6886 (pt0) cc_final: 0.6671 (pt0) REVERT: A 849 MET cc_start: 0.8027 (tmm) cc_final: 0.7377 (tmm) REVERT: A 873 MET cc_start: 0.7731 (mpp) cc_final: 0.7441 (mpp) REVERT: A 1019 CYS cc_start: 0.8980 (m) cc_final: 0.8604 (m) REVERT: A 1064 VAL cc_start: 0.8426 (t) cc_final: 0.8216 (t) REVERT: A 1102 LYS cc_start: 0.9093 (ttpp) cc_final: 0.8633 (tppt) REVERT: A 1259 MET cc_start: 0.9191 (pmm) cc_final: 0.8981 (pmm) REVERT: A 1368 MET cc_start: 0.8042 (mtt) cc_final: 0.7758 (mtt) REVERT: A 1426 GLU cc_start: 0.8389 (mp0) cc_final: 0.6975 (mp0) REVERT: A 1442 ASP cc_start: 0.8564 (m-30) cc_final: 0.8354 (t0) REVERT: A 1444 MET cc_start: 0.8931 (mmt) cc_final: 0.8018 (mmm) REVERT: B 499 ASN cc_start: 0.8706 (t0) cc_final: 0.8489 (t0) REVERT: B 563 MET cc_start: 0.6827 (tmm) cc_final: 0.6036 (tmm) REVERT: B 789 MET cc_start: 0.8451 (mmm) cc_final: 0.7724 (mmm) REVERT: B 1152 MET cc_start: 0.6980 (mmm) cc_final: 0.6195 (tpp) REVERT: B 1210 MET cc_start: 0.9121 (mpp) cc_final: 0.8828 (mpp) REVERT: B 1211 ASN cc_start: 0.8911 (m-40) cc_final: 0.8108 (t0) REVERT: C 148 ARG cc_start: 0.8510 (mmm160) cc_final: 0.8109 (mmm-85) REVERT: C 265 MET cc_start: 0.7869 (ttp) cc_final: 0.7419 (mtt) REVERT: D 127 ASP cc_start: 0.8693 (m-30) cc_final: 0.8430 (m-30) REVERT: E 58 MET cc_start: 0.8987 (mtm) cc_final: 0.8495 (mtp) REVERT: E 112 TYR cc_start: 0.7759 (p90) cc_final: 0.7459 (p90) REVERT: E 215 MET cc_start: 0.5072 (ttp) cc_final: 0.4838 (ttp) REVERT: G 106 MET cc_start: 0.5164 (mtt) cc_final: 0.4400 (mmt) REVERT: G 115 MET cc_start: 0.1363 (mtt) cc_final: 0.0702 (mmt) REVERT: K 8 GLU cc_start: 0.8696 (tp30) cc_final: 0.7866 (tp30) REVERT: L 62 LYS cc_start: 0.8606 (mtpt) cc_final: 0.8326 (mtmm) REVERT: O 1105 MET cc_start: 0.8788 (tpt) cc_final: 0.8222 (tpp) REVERT: O 1114 ASN cc_start: 0.8722 (m-40) cc_final: 0.8488 (m110) REVERT: O 1153 TYR cc_start: 0.8341 (t80) cc_final: 0.7974 (t80) REVERT: O 1407 LEU cc_start: 0.8869 (tp) cc_final: 0.8546 (tp) REVERT: O 1602 ILE cc_start: 0.8944 (mt) cc_final: 0.8552 (mm) REVERT: O 1613 MET cc_start: 0.6374 (pmm) cc_final: 0.5720 (pmm) REVERT: O 1642 MET cc_start: 0.9112 (tpp) cc_final: 0.8809 (tpt) REVERT: O 1759 MET cc_start: 0.8250 (mpp) cc_final: 0.7833 (ptp) REVERT: Y 6 MET cc_start: 0.7162 (ptp) cc_final: 0.6451 (ptp) outliers start: 1 outliers final: 0 residues processed: 370 average time/residue: 0.2594 time to fit residues: 161.0488 Evaluate side-chains 302 residues out of total 4548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 302 time to evaluate : 1.848 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 517 random chunks: chunk 488 optimal weight: 7.9990 chunk 185 optimal weight: 3.9990 chunk 82 optimal weight: 6.9990 chunk 379 optimal weight: 10.0000 chunk 336 optimal weight: 20.0000 chunk 33 optimal weight: 0.7980 chunk 327 optimal weight: 4.9990 chunk 473 optimal weight: 20.0000 chunk 485 optimal weight: 20.0000 chunk 42 optimal weight: 1.9990 chunk 225 optimal weight: 4.9990 overall best weight: 3.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 451 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 736 ASN ** A 757 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 465 ASN ** B1141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 231 ASN D 137 ASN E 179 GLN ** H 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 835 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.064251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.046869 restraints weight = 354796.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.047462 restraints weight = 226750.868| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.047545 restraints weight = 168433.881| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.048001 restraints weight = 134824.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.047977 restraints weight = 121084.326| |-----------------------------------------------------------------------------| r_work (final): 0.3205 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7724 moved from start: 0.3563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 43895 Z= 0.191 Angle : 0.580 8.957 59625 Z= 0.302 Chirality : 0.043 0.217 6708 Planarity : 0.004 0.046 7378 Dihedral : 12.502 159.789 6721 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 10.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 0.02 % Allowed : 2.09 % Favored : 97.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.46 % 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: 1.00 (0.12), residues: 5090 helix: 1.80 (0.13), residues: 1794 sheet: 0.27 (0.18), residues: 839 loop : 0.03 (0.13), residues: 2457 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 350 TYR 0.023 0.001 TYR A 804 PHE 0.038 0.001 PHE A 22 TRP 0.016 0.001 TRP B 586 HIS 0.008 0.001 HIS B 300 Details of bonding type rmsd/Z covalent geometry : bond 0.00408 / 0.19 (43864) covalent geometry : angle 0.57560 / 0.30 (59589) hydrogen bonds : bond 0.03539 / 2.37 ( 1790) hydrogen bonds : angle 4.60281 / 3.35 ( 4910) metal coordination : bond 0.00966 / 0.56 ( 31) metal coordination : angle 3.07712 / 1.85 ( 36) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10180 Ramachandran restraints generated. 5090 Oldfield, 0 Emsley, 5090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10180 Ramachandran restraints generated. 5090 Oldfield, 0 Emsley, 5090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 366 residues out of total 4548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 365 time to evaluate : 1.407 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 103 CYS cc_start: 0.9290 (m) cc_final: 0.9059 (m) REVERT: A 340 LEU cc_start: 0.9462 (mt) cc_final: 0.9206 (mt) REVERT: A 644 LYS cc_start: 0.8631 (mmmt) cc_final: 0.8281 (mtmm) REVERT: A 846 GLU cc_start: 0.6637 (pt0) cc_final: 0.6373 (pt0) REVERT: A 849 MET cc_start: 0.8075 (tmm) cc_final: 0.7723 (tmm) REVERT: A 873 MET cc_start: 0.7849 (mpp) cc_final: 0.7170 (mtm) REVERT: A 1102 LYS cc_start: 0.9113 (ttpp) cc_final: 0.8670 (tppt) REVERT: A 1111 MET cc_start: 0.8407 (tpp) cc_final: 0.8172 (tpt) REVERT: A 1259 MET cc_start: 0.9269 (pmm) cc_final: 0.9059 (pmm) REVERT: A 1442 ASP cc_start: 0.8658 (m-30) cc_final: 0.8365 (t0) REVERT: A 1444 MET cc_start: 0.8963 (mmt) cc_final: 0.8050 (mmm) REVERT: B 386 LEU cc_start: 0.9478 (tp) cc_final: 0.9243 (pp) REVERT: B 499 ASN cc_start: 0.8742 (t0) cc_final: 0.8514 (t0) REVERT: B 563 MET cc_start: 0.7239 (tmm) cc_final: 0.6425 (tmm) REVERT: B 789 MET cc_start: 0.8423 (mmm) cc_final: 0.7677 (mmm) REVERT: B 1072 MET cc_start: 0.8345 (mtp) cc_final: 0.8053 (mtp) REVERT: B 1152 MET cc_start: 0.7284 (mmm) cc_final: 0.6592 (tpt) REVERT: B 1210 MET cc_start: 0.9063 (mpp) cc_final: 0.8768 (mpp) REVERT: B 1211 ASN cc_start: 0.8973 (m-40) cc_final: 0.8197 (t0) REVERT: C 75 MET cc_start: 0.8525 (mmt) cc_final: 0.8324 (mmm) REVERT: C 148 ARG cc_start: 0.8635 (mmm160) cc_final: 0.8328 (mmm-85) REVERT: C 265 MET cc_start: 0.7972 (ttp) cc_final: 0.7529 (mtt) REVERT: D 127 ASP cc_start: 0.8679 (m-30) cc_final: 0.8405 (m-30) REVERT: E 58 MET cc_start: 0.9043 (mtm) cc_final: 0.8517 (mtp) REVERT: E 112 TYR cc_start: 0.7920 (p90) cc_final: 0.7587 (p90) REVERT: E 215 MET cc_start: 0.5315 (ttp) cc_final: 0.5049 (ttp) REVERT: F 103 MET cc_start: 0.8901 (mmp) cc_final: 0.8570 (mmm) REVERT: G 106 MET cc_start: 0.5325 (mtt) cc_final: 0.4470 (mmt) REVERT: G 115 MET cc_start: 0.1024 (mtt) cc_final: -0.0087 (mmt) REVERT: J 49 MET cc_start: 0.7178 (ttp) cc_final: 0.6333 (ttp) REVERT: K 8 GLU cc_start: 0.8788 (tp30) cc_final: 0.7968 (tp30) REVERT: O 1105 MET cc_start: 0.8969 (tpt) cc_final: 0.8430 (tpp) REVERT: O 1114 ASN cc_start: 0.8900 (m-40) cc_final: 0.8700 (m110) REVERT: O 1407 LEU cc_start: 0.9090 (tp) cc_final: 0.8718 (tp) REVERT: O 1584 PHE cc_start: 0.8066 (m-80) cc_final: 0.7822 (m-80) REVERT: O 1602 ILE cc_start: 0.9008 (mt) cc_final: 0.8585 (mm) REVERT: O 1613 MET cc_start: 0.6980 (pmm) cc_final: 0.6390 (pmm) REVERT: O 1642 MET cc_start: 0.9337 (tpp) cc_final: 0.8981 (tpt) REVERT: Y 6 MET cc_start: 0.7536 (ptp) cc_final: 0.6951 (ptp) outliers start: 1 outliers final: 0 residues processed: 366 average time/residue: 0.2629 time to fit residues: 160.4550 Evaluate side-chains 286 residues out of total 4548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 286 time to evaluate : 1.617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 517 random chunks: chunk 16 optimal weight: 3.9990 chunk 503 optimal weight: 0.0470 chunk 37 optimal weight: 9.9990 chunk 30 optimal weight: 2.9990 chunk 11 optimal weight: 9.9990 chunk 228 optimal weight: 4.9990 chunk 13 optimal weight: 9.9990 chunk 375 optimal weight: 20.0000 chunk 387 optimal weight: 5.9990 chunk 123 optimal weight: 9.9990 chunk 487 optimal weight: 9.9990 overall best weight: 3.6086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 451 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 736 ASN A 757 ASN B 224 GLN ** B 761 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1161 HIS ** B1195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 231 ASN E 179 GLN G 10 ASN G 71 ASN ** H 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 96 ASN Z 102 ASN ** Z 835 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.063635 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.045873 restraints weight = 351183.237| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.046761 restraints weight = 217554.057| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.047053 restraints weight = 155465.848| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.047457 restraints weight = 118704.177| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.047435 restraints weight = 96136.781| |-----------------------------------------------------------------------------| r_work (final): 0.3205 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7727 moved from start: 0.3843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.097 43895 Z= 0.196 Angle : 0.589 11.078 59625 Z= 0.305 Chirality : 0.043 0.228 6708 Planarity : 0.004 0.103 7378 Dihedral : 12.560 159.860 6721 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 11.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 0.02 % Allowed : 1.61 % Favored : 98.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.46 % 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: 0.89 (0.12), residues: 5090 helix: 1.73 (0.12), residues: 1802 sheet: 0.15 (0.18), residues: 835 loop : -0.02 (0.13), residues: 2453 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG K 54 TYR 0.026 0.001 TYR B 486 PHE 0.037 0.001 PHE A 22 TRP 0.013 0.001 TRP B 466 HIS 0.012 0.001 HIS B 515 Details of bonding type rmsd/Z covalent geometry : bond 0.00422 / 0.20 (43864) covalent geometry : angle 0.58412 / 0.30 (59589) hydrogen bonds : bond 0.03470 / 2.31 ( 1790) hydrogen bonds : angle 4.62721 / 3.36 ( 4910) metal coordination : bond 0.00931 / 0.53 ( 31) metal coordination : angle 3.03292 / 1.81 ( 36) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10180 Ramachandran restraints generated. 5090 Oldfield, 0 Emsley, 5090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10180 Ramachandran restraints generated. 5090 Oldfield, 0 Emsley, 5090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 361 residues out of total 4548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 360 time to evaluate : 1.735 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 103 CYS cc_start: 0.9232 (m) cc_final: 0.9020 (m) REVERT: A 340 LEU cc_start: 0.9434 (mt) cc_final: 0.9132 (mt) REVERT: A 544 ASP cc_start: 0.9020 (m-30) cc_final: 0.8710 (m-30) REVERT: A 644 LYS cc_start: 0.8652 (mmmt) cc_final: 0.8303 (mtmm) REVERT: A 818 MET cc_start: 0.8788 (mmm) cc_final: 0.8348 (mmt) REVERT: A 849 MET cc_start: 0.8104 (tmm) cc_final: 0.7575 (tmm) REVERT: A 1102 LYS cc_start: 0.9108 (ttpp) cc_final: 0.8741 (tppt) REVERT: A 1111 MET cc_start: 0.8415 (tpp) cc_final: 0.8187 (tpt) REVERT: A 1209 MET cc_start: 0.8887 (ttm) cc_final: 0.8338 (ttm) REVERT: A 1444 MET cc_start: 0.8955 (mmt) cc_final: 0.8258 (mmt) REVERT: B 563 MET cc_start: 0.7102 (tmm) cc_final: 0.6225 (tmm) REVERT: B 789 MET cc_start: 0.8510 (mmm) cc_final: 0.7862 (mmm) REVERT: B 1072 MET cc_start: 0.8321 (mtp) cc_final: 0.7906 (mtp) REVERT: B 1152 MET cc_start: 0.7511 (mmm) cc_final: 0.7114 (tpp) REVERT: B 1211 ASN cc_start: 0.8896 (m-40) cc_final: 0.8157 (t0) REVERT: C 148 ARG cc_start: 0.8687 (mmm160) cc_final: 0.8435 (mmm-85) REVERT: C 265 MET cc_start: 0.7837 (ttp) cc_final: 0.7488 (mtt) REVERT: D 127 ASP cc_start: 0.8623 (m-30) cc_final: 0.8357 (m-30) REVERT: E 58 MET cc_start: 0.9010 (mtm) cc_final: 0.8496 (mtp) REVERT: E 112 TYR cc_start: 0.7887 (p90) cc_final: 0.7579 (p90) REVERT: E 215 MET cc_start: 0.5416 (ttp) cc_final: 0.5136 (ttp) REVERT: G 106 MET cc_start: 0.5224 (mtt) cc_final: 0.4390 (mmt) REVERT: G 115 MET cc_start: 0.1064 (mtt) cc_final: -0.0019 (mmt) REVERT: J 25 LEU cc_start: 0.9220 (mt) cc_final: 0.9017 (mt) REVERT: J 49 MET cc_start: 0.7576 (ttp) cc_final: 0.7166 (ttp) REVERT: K 8 GLU cc_start: 0.8778 (tp30) cc_final: 0.7910 (tp30) REVERT: K 52 ASN cc_start: 0.8412 (m-40) cc_final: 0.8025 (m-40) REVERT: O 1105 MET cc_start: 0.8865 (tpt) cc_final: 0.8325 (tpp) REVERT: O 1114 ASN cc_start: 0.8937 (m-40) cc_final: 0.8681 (m110) REVERT: O 1187 ASN cc_start: 0.8247 (p0) cc_final: 0.7930 (t0) REVERT: O 1407 LEU cc_start: 0.9006 (tp) cc_final: 0.8619 (tp) REVERT: O 1602 ILE cc_start: 0.8971 (mt) cc_final: 0.8553 (mm) REVERT: O 1613 MET cc_start: 0.6878 (pmm) cc_final: 0.6289 (pmm) REVERT: O 1642 MET cc_start: 0.9247 (tpp) cc_final: 0.8913 (tpt) REVERT: O 1814 MET cc_start: 0.9315 (ptp) cc_final: 0.9104 (ptp) REVERT: Y 6 MET cc_start: 0.7369 (ptp) cc_final: 0.6671 (ptp) outliers start: 1 outliers final: 0 residues processed: 361 average time/residue: 0.2417 time to fit residues: 147.0431 Evaluate side-chains 287 residues out of total 4548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 287 time to evaluate : 1.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 517 random chunks: chunk 358 optimal weight: 20.0000 chunk 266 optimal weight: 10.0000 chunk 501 optimal weight: 20.0000 chunk 450 optimal weight: 20.0000 chunk 437 optimal weight: 10.0000 chunk 207 optimal weight: 3.9990 chunk 325 optimal weight: 0.9980 chunk 305 optimal weight: 5.9990 chunk 130 optimal weight: 0.3980 chunk 192 optimal weight: 5.9990 chunk 248 optimal weight: 5.9990 overall best weight: 3.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 313 GLN ** A 451 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 736 ASN A1011 GLN A1432 GLN B 515 HIS ** B 761 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1195 HIS C 231 ASN E 179 GLN G 10 ASN G 71 ASN ** H 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O1555 GLN ** Z 835 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.062974 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.045208 restraints weight = 352070.222| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.046246 restraints weight = 222963.882| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.046174 restraints weight = 151045.186| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.046535 restraints weight = 131968.591| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.046584 restraints weight = 116862.036| |-----------------------------------------------------------------------------| r_work (final): 0.3170 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7783 moved from start: 0.4152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 43895 Z= 0.190 Angle : 0.587 9.648 59625 Z= 0.306 Chirality : 0.043 0.211 6708 Planarity : 0.004 0.065 7378 Dihedral : 12.618 159.580 6721 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 11.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.46 % 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: 0.80 (0.12), residues: 5090 helix: 1.63 (0.13), residues: 1799 sheet: 0.08 (0.18), residues: 830 loop : -0.04 (0.13), residues: 2461 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG B1106 TYR 0.024 0.001 TYR A 868 PHE 0.046 0.002 PHE A 22 TRP 0.012 0.001 TRP H 79 HIS 0.012 0.001 HIS A 399 Details of bonding type rmsd/Z covalent geometry : bond 0.00405 / 0.19 (43864) covalent geometry : angle 0.58281 / 0.31 (59589) hydrogen bonds : bond 0.03518 / 2.33 ( 1790) hydrogen bonds : angle 4.65390 / 3.38 ( 4910) metal coordination : bond 0.00896 / 0.51 ( 31) metal coordination : angle 3.06625 / 1.80 ( 36) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10180 Ramachandran restraints generated. 5090 Oldfield, 0 Emsley, 5090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10180 Ramachandran restraints generated. 5090 Oldfield, 0 Emsley, 5090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 351 residues out of total 4548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 351 time to evaluate : 1.580 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 103 CYS cc_start: 0.9320 (m) cc_final: 0.9101 (m) REVERT: A 340 LEU cc_start: 0.9422 (mt) cc_final: 0.9128 (mt) REVERT: A 544 ASP cc_start: 0.9049 (m-30) cc_final: 0.8793 (m-30) REVERT: A 644 LYS cc_start: 0.8552 (mmmt) cc_final: 0.8195 (mttp) REVERT: A 1102 LYS cc_start: 0.9151 (ttpp) cc_final: 0.8814 (tptt) REVERT: A 1111 MET cc_start: 0.8433 (tpp) cc_final: 0.8189 (tpt) REVERT: A 1209 MET cc_start: 0.8984 (ttm) cc_final: 0.8384 (ttm) REVERT: A 1259 MET cc_start: 0.9309 (pmm) cc_final: 0.9105 (pmm) REVERT: A 1444 MET cc_start: 0.8640 (mmt) cc_final: 0.8430 (mmt) REVERT: A 1454 MET cc_start: 0.7597 (ptm) cc_final: 0.7214 (ptt) REVERT: B 313 MET cc_start: 0.8818 (ptp) cc_final: 0.8580 (ptp) REVERT: B 499 ASN cc_start: 0.8733 (t0) cc_final: 0.8472 (t0) REVERT: B 563 MET cc_start: 0.7402 (tmm) cc_final: 0.6557 (tmm) REVERT: B 789 MET cc_start: 0.8478 (mmm) cc_final: 0.7822 (mmm) REVERT: B 1021 MET cc_start: 0.8108 (mmt) cc_final: 0.7437 (mmm) REVERT: B 1072 MET cc_start: 0.8517 (mtp) cc_final: 0.8102 (mtp) REVERT: B 1138 MET cc_start: 0.7724 (mmm) cc_final: 0.7510 (tpt) REVERT: B 1152 MET cc_start: 0.7601 (mmm) cc_final: 0.7159 (tpp) REVERT: B 1210 MET cc_start: 0.9110 (mpp) cc_final: 0.8744 (mpp) REVERT: B 1211 ASN cc_start: 0.8996 (m-40) cc_final: 0.8258 (t0) REVERT: C 33 LEU cc_start: 0.8979 (tp) cc_final: 0.8777 (tp) REVERT: C 37 MET cc_start: 0.8800 (ptm) cc_final: 0.8379 (ptt) REVERT: C 75 MET cc_start: 0.8589 (mmt) cc_final: 0.8303 (mmm) REVERT: C 190 ASP cc_start: 0.8517 (t70) cc_final: 0.8253 (p0) REVERT: C 265 MET cc_start: 0.8075 (ttm) cc_final: 0.7704 (mtt) REVERT: E 58 MET cc_start: 0.9110 (mtm) cc_final: 0.8875 (mpp) REVERT: E 112 TYR cc_start: 0.8167 (p90) cc_final: 0.7646 (p90) REVERT: G 106 MET cc_start: 0.5284 (mtt) cc_final: 0.4401 (mmt) REVERT: G 115 MET cc_start: 0.1273 (mtt) cc_final: 0.0187 (mmt) REVERT: K 8 GLU cc_start: 0.8887 (tp30) cc_final: 0.8001 (tp30) REVERT: K 52 ASN cc_start: 0.8471 (m-40) cc_final: 0.8092 (m-40) REVERT: M 59 ARG cc_start: 0.8842 (tmm160) cc_final: 0.8533 (tmm160) REVERT: O 1105 MET cc_start: 0.9007 (tpt) cc_final: 0.8526 (tpp) REVERT: O 1187 ASN cc_start: 0.8415 (p0) cc_final: 0.8119 (t0) REVERT: O 1219 MET cc_start: 0.8920 (pmm) cc_final: 0.8704 (pmm) REVERT: O 1407 LEU cc_start: 0.9145 (tp) cc_final: 0.8768 (tp) REVERT: O 1584 PHE cc_start: 0.8295 (m-80) cc_final: 0.7971 (m-80) REVERT: O 1602 ILE cc_start: 0.9040 (mt) cc_final: 0.8620 (mm) REVERT: O 1613 MET cc_start: 0.7252 (pmm) cc_final: 0.6611 (pmm) REVERT: O 1642 MET cc_start: 0.9368 (tpp) cc_final: 0.9092 (tpt) REVERT: O 1814 MET cc_start: 0.9401 (ptp) cc_final: 0.9169 (ptp) REVERT: Y 6 MET cc_start: 0.7433 (ptp) cc_final: 0.6777 (ptp) outliers start: 0 outliers final: 0 residues processed: 351 average time/residue: 0.2428 time to fit residues: 144.0453 Evaluate side-chains 283 residues out of total 4548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 283 time to evaluate : 1.596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 517 random chunks: chunk 6 optimal weight: 20.0000 chunk 9 optimal weight: 5.9990 chunk 343 optimal weight: 9.9990 chunk 301 optimal weight: 10.0000 chunk 440 optimal weight: 2.9990 chunk 404 optimal weight: 3.9990 chunk 150 optimal weight: 6.9990 chunk 446 optimal weight: 20.0000 chunk 491 optimal weight: 50.0000 chunk 27 optimal weight: 3.9990 chunk 429 optimal weight: 9.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 390 GLN A 736 ASN B 515 HIS ** B 761 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1093 GLN C 188 HIS C 231 ASN E 179 GLN ** H 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O1555 GLN ** Z 835 ASN ** 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 = 0.3768 r_free = 0.3768 target = 0.062037 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.044755 restraints weight = 355009.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.045300 restraints weight = 234383.508| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.045478 restraints weight = 158276.674| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.045707 restraints weight = 140151.136| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.045746 restraints weight = 124644.922| |-----------------------------------------------------------------------------| r_work (final): 0.3127 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7832 moved from start: 0.4490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 43895 Z= 0.249 Angle : 0.646 12.256 59625 Z= 0.336 Chirality : 0.043 0.222 6708 Planarity : 0.005 0.063 7378 Dihedral : 12.741 160.526 6721 Min Nonbonded Distance : 1.890 Molprobity Statistics. All-atom Clashscore : 13.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.46 % 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: 0.60 (0.12), residues: 5090 helix: 1.39 (0.12), residues: 1805 sheet: -0.03 (0.18), residues: 814 loop : -0.11 (0.13), residues: 2471 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG A1055 TYR 0.050 0.002 TYR O1153 PHE 0.040 0.002 PHE A 22 TRP 0.015 0.002 TRP B 561 HIS 0.012 0.002 HIS A 299 Details of bonding type rmsd/Z covalent geometry : bond 0.00530 / 0.25 (43864) covalent geometry : angle 0.63965 / 0.34 (59589) hydrogen bonds : bond 0.03918 / 2.61 ( 1790) hydrogen bonds : angle 4.83596 / 3.50 ( 4910) metal coordination : bond 0.01184 / 0.67 ( 31) metal coordination : angle 3.60769 / 2.07 ( 36) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10180 Ramachandran restraints generated. 5090 Oldfield, 0 Emsley, 5090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10180 Ramachandran restraints generated. 5090 Oldfield, 0 Emsley, 5090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 335 residues out of total 4548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 335 time to evaluate : 1.741 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: A 103 CYS cc_start: 0.9315 (m) cc_final: 0.9090 (m) REVERT: A 340 LEU cc_start: 0.9412 (mt) cc_final: 0.9056 (mt) REVERT: A 487 MET cc_start: 0.8637 (ttm) cc_final: 0.7984 (ttm) REVERT: A 544 ASP cc_start: 0.9040 (m-30) cc_final: 0.8802 (m-30) REVERT: A 644 LYS cc_start: 0.8641 (mmmt) cc_final: 0.8306 (mttp) REVERT: A 666 ILE cc_start: 0.7922 (mm) cc_final: 0.7696 (mm) REVERT: A 846 GLU cc_start: 0.7478 (pt0) cc_final: 0.7240 (pt0) REVERT: A 1102 LYS cc_start: 0.9163 (ttpp) cc_final: 0.8910 (tptt) REVERT: A 1111 MET cc_start: 0.8460 (tpp) cc_final: 0.8251 (tpp) REVERT: A 1285 MET cc_start: 0.7113 (mpp) cc_final: 0.6809 (mpp) REVERT: A 1444 MET cc_start: 0.8585 (mmt) cc_final: 0.8326 (mmm) REVERT: A 1454 MET cc_start: 0.7626 (ptm) cc_final: 0.7264 (ptt) REVERT: B 173 MET cc_start: 0.7950 (ttm) cc_final: 0.7704 (ttp) REVERT: B 386 LEU cc_start: 0.9625 (tt) cc_final: 0.9364 (pp) REVERT: B 499 ASN cc_start: 0.8825 (t0) cc_final: 0.8565 (t0) REVERT: B 552 MET cc_start: 0.9377 (mmp) cc_final: 0.9112 (mmm) REVERT: B 789 MET cc_start: 0.8471 (mmm) cc_final: 0.7771 (mmm) REVERT: B 1021 MET cc_start: 0.8053 (mmt) cc_final: 0.7475 (mmm) REVERT: B 1072 MET cc_start: 0.8751 (mtp) cc_final: 0.8130 (mtp) REVERT: B 1111 MET cc_start: 0.8446 (mmp) cc_final: 0.7923 (mmp) REVERT: B 1152 MET cc_start: 0.7710 (mmm) cc_final: 0.6993 (mmm) REVERT: B 1210 MET cc_start: 0.9218 (mpp) cc_final: 0.8876 (mpp) REVERT: B 1211 ASN cc_start: 0.9036 (m-40) cc_final: 0.8243 (t0) REVERT: C 33 LEU cc_start: 0.9039 (tp) cc_final: 0.8757 (tp) REVERT: C 37 MET cc_start: 0.8859 (ptm) cc_final: 0.8404 (ptt) REVERT: C 75 MET cc_start: 0.8812 (mmt) cc_final: 0.8457 (mmm) REVERT: C 190 ASP cc_start: 0.8708 (t70) cc_final: 0.8370 (p0) REVERT: C 265 MET cc_start: 0.8079 (ttm) cc_final: 0.7718 (mtt) REVERT: D 189 ASP cc_start: 0.9580 (t0) cc_final: 0.9207 (p0) REVERT: E 22 MET cc_start: 0.9114 (ppp) cc_final: 0.8888 (ppp) REVERT: E 82 PHE cc_start: 0.8457 (m-80) cc_final: 0.8234 (m-80) REVERT: E 112 TYR cc_start: 0.8439 (p90) cc_final: 0.7657 (p90) REVERT: F 103 MET cc_start: 0.8963 (mmp) cc_final: 0.8755 (mmm) REVERT: F 154 ASP cc_start: 0.7984 (p0) cc_final: 0.7439 (m-30) REVERT: G 106 MET cc_start: 0.5455 (mtt) cc_final: 0.4535 (mmt) REVERT: G 115 MET cc_start: 0.1220 (mtt) cc_final: 0.0461 (mmt) REVERT: K 8 GLU cc_start: 0.8958 (tp30) cc_final: 0.8046 (tp30) REVERT: K 52 ASN cc_start: 0.8541 (m-40) cc_final: 0.8114 (m-40) REVERT: O 1105 MET cc_start: 0.9003 (tpt) cc_final: 0.8523 (tpp) REVERT: O 1187 ASN cc_start: 0.8524 (p0) cc_final: 0.8208 (t0) REVERT: O 1219 MET cc_start: 0.8989 (pmm) cc_final: 0.8769 (pmm) REVERT: O 1407 LEU cc_start: 0.9177 (tp) cc_final: 0.8847 (tp) REVERT: O 1584 PHE cc_start: 0.8500 (m-80) cc_final: 0.8153 (m-80) REVERT: O 1602 ILE cc_start: 0.9083 (mt) cc_final: 0.8653 (mm) REVERT: O 1613 MET cc_start: 0.7188 (pmm) cc_final: 0.6719 (pmm) REVERT: O 1719 MET cc_start: 0.9610 (ppp) cc_final: 0.9392 (ppp) REVERT: O 1814 MET cc_start: 0.9471 (ptp) cc_final: 0.9249 (ptp) REVERT: Y 6 MET cc_start: 0.7564 (ptp) cc_final: 0.6957 (ptp) outliers start: 0 outliers final: 0 residues processed: 335 average time/residue: 0.2696 time to fit residues: 152.5656 Evaluate side-chains 274 residues out of total 4548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 274 time to evaluate : 1.702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 517 random chunks: chunk 402 optimal weight: 9.9990 chunk 329 optimal weight: 20.0000 chunk 252 optimal weight: 10.0000 chunk 424 optimal weight: 5.9990 chunk 82 optimal weight: 0.9990 chunk 455 optimal weight: 20.0000 chunk 248 optimal weight: 2.9990 chunk 244 optimal weight: 5.9990 chunk 173 optimal weight: 3.9990 chunk 275 optimal weight: 3.9990 chunk 237 optimal weight: 0.6980 overall best weight: 2.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 80 HIS A 358 ASN A 736 ASN ** B 761 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1093 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 188 HIS C 231 ASN E 179 GLN F 100 GLN ** H 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 87 GLN O1555 GLN ** Z 835 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.062513 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.044922 restraints weight = 351968.575| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.045957 restraints weight = 219245.934| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.045911 restraints weight = 148390.624| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.046155 restraints weight = 127100.172| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.046221 restraints weight = 126205.857| |-----------------------------------------------------------------------------| r_work (final): 0.3143 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7825 moved from start: 0.4565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 43895 Z= 0.164 Angle : 0.590 8.090 59625 Z= 0.306 Chirality : 0.043 0.256 6708 Planarity : 0.004 0.063 7378 Dihedral : 12.749 159.335 6721 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 12.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 0.00 % Allowed : 0.77 % Favored : 99.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.46 % 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: 0.64 (0.12), residues: 5090 helix: 1.45 (0.12), residues: 1805 sheet: -0.14 (0.17), residues: 834 loop : -0.04 (0.13), residues: 2451 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG A 57 TYR 0.048 0.001 TYR O1153 PHE 0.040 0.001 PHE A 22 TRP 0.016 0.001 TRP B 681 HIS 0.011 0.001 HIS A 299 Details of bonding type rmsd/Z covalent geometry : bond 0.00356 / 0.16 (43864) covalent geometry : angle 0.58427 / 0.31 (59589) hydrogen bonds : bond 0.03476 / 2.32 ( 1790) hydrogen bonds : angle 4.74215 / 3.42 ( 4910) metal coordination : bond 0.00797 / 0.46 ( 31) metal coordination : angle 3.33468 / 1.97 ( 36) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10180 Ramachandran restraints generated. 5090 Oldfield, 0 Emsley, 5090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10180 Ramachandran restraints generated. 5090 Oldfield, 0 Emsley, 5090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 340 residues out of total 4548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 340 time to evaluate : 1.760 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: A 103 CYS cc_start: 0.9331 (m) cc_final: 0.9083 (m) REVERT: A 340 LEU cc_start: 0.9460 (mt) cc_final: 0.9127 (mt) REVERT: A 437 MET cc_start: 0.7403 (mmm) cc_final: 0.7133 (mmm) REVERT: A 544 ASP cc_start: 0.9080 (m-30) cc_final: 0.8860 (m-30) REVERT: A 644 LYS cc_start: 0.8612 (mmmt) cc_final: 0.8267 (mttp) REVERT: A 1102 LYS cc_start: 0.9135 (ttpp) cc_final: 0.8852 (tptt) REVERT: A 1111 MET cc_start: 0.8450 (tpp) cc_final: 0.8185 (tpt) REVERT: A 1209 MET cc_start: 0.9024 (ttm) cc_final: 0.8473 (ttm) REVERT: A 1398 MET cc_start: 0.8276 (mmt) cc_final: 0.7868 (mmt) REVERT: A 1409 LEU cc_start: 0.9238 (mm) cc_final: 0.8862 (mm) REVERT: A 1426 GLU cc_start: 0.8732 (mp0) cc_final: 0.8062 (mp0) REVERT: A 1454 MET cc_start: 0.7670 (ptm) cc_final: 0.7380 (ptt) REVERT: B 173 MET cc_start: 0.7931 (ttm) cc_final: 0.7723 (ttp) REVERT: B 386 LEU cc_start: 0.9624 (tt) cc_final: 0.9347 (pp) REVERT: B 499 ASN cc_start: 0.8836 (t0) cc_final: 0.8540 (t0) REVERT: B 552 MET cc_start: 0.9332 (mmp) cc_final: 0.9080 (mmm) REVERT: B 789 MET cc_start: 0.8476 (mmm) cc_final: 0.7796 (mmm) REVERT: B 841 MET cc_start: 0.8905 (ttt) cc_final: 0.8640 (ttt) REVERT: B 1021 MET cc_start: 0.8100 (mmt) cc_final: 0.7467 (mmm) REVERT: B 1072 MET cc_start: 0.8644 (mtp) cc_final: 0.8099 (mtp) REVERT: B 1152 MET cc_start: 0.7559 (mmm) cc_final: 0.6830 (mmm) REVERT: B 1211 ASN cc_start: 0.9066 (m-40) cc_final: 0.8286 (t0) REVERT: C 33 LEU cc_start: 0.9101 (tp) cc_final: 0.8848 (tp) REVERT: C 37 MET cc_start: 0.8848 (ptm) cc_final: 0.8439 (ptt) REVERT: C 75 MET cc_start: 0.8803 (mmt) cc_final: 0.8429 (mmm) REVERT: C 190 ASP cc_start: 0.8576 (t70) cc_final: 0.8273 (p0) REVERT: C 265 MET cc_start: 0.8095 (ttm) cc_final: 0.7704 (mtt) REVERT: D 189 ASP cc_start: 0.9620 (t0) cc_final: 0.9275 (p0) REVERT: E 22 MET cc_start: 0.9146 (ppp) cc_final: 0.8942 (ppp) REVERT: E 82 PHE cc_start: 0.8640 (m-80) cc_final: 0.8308 (m-80) REVERT: E 112 TYR cc_start: 0.8485 (p90) cc_final: 0.7667 (p90) REVERT: F 103 MET cc_start: 0.9040 (mmp) cc_final: 0.8744 (mmm) REVERT: F 154 ASP cc_start: 0.7968 (p0) cc_final: 0.7392 (m-30) REVERT: G 106 MET cc_start: 0.5407 (mtt) cc_final: 0.4534 (mmt) REVERT: G 115 MET cc_start: 0.1768 (mtt) cc_final: 0.0792 (mmt) REVERT: K 8 GLU cc_start: 0.9008 (tp30) cc_final: 0.8125 (tp30) REVERT: K 52 ASN cc_start: 0.8499 (m-40) cc_final: 0.8079 (m-40) REVERT: O 1105 MET cc_start: 0.9049 (tpt) cc_final: 0.8560 (tpp) REVERT: O 1187 ASN cc_start: 0.8507 (p0) cc_final: 0.8234 (t0) REVERT: O 1219 MET cc_start: 0.9034 (pmm) cc_final: 0.8807 (pmm) REVERT: O 1407 LEU cc_start: 0.9234 (tp) cc_final: 0.8908 (tp) REVERT: O 1584 PHE cc_start: 0.8531 (m-80) cc_final: 0.8172 (m-80) REVERT: O 1602 ILE cc_start: 0.9060 (mt) cc_final: 0.8616 (mm) REVERT: O 1719 MET cc_start: 0.9652 (ppp) cc_final: 0.9431 (ppp) REVERT: O 1814 MET cc_start: 0.9499 (ptp) cc_final: 0.9256 (ptp) REVERT: Y 6 MET cc_start: 0.7428 (ptp) cc_final: 0.6777 (ptp) outliers start: 0 outliers final: 0 residues processed: 340 average time/residue: 0.2666 time to fit residues: 152.8267 Evaluate side-chains 284 residues out of total 4548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 284 time to evaluate : 1.775 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 517 random chunks: chunk 514 optimal weight: 0.7980 chunk 361 optimal weight: 0.9990 chunk 121 optimal weight: 0.2980 chunk 444 optimal weight: 10.0000 chunk 14 optimal weight: 0.6980 chunk 194 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 chunk 201 optimal weight: 5.9990 chunk 209 optimal weight: 7.9990 chunk 348 optimal weight: 7.9990 chunk 378 optimal weight: 9.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 736 ASN ** A 757 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 231 ASN E 179 GLN ** H 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O1267 ASN ** Z 835 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.063418 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.044221 restraints weight = 348286.255| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.045358 restraints weight = 204202.480| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.046072 restraints weight = 143170.209| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.046520 restraints weight = 113735.069| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.046649 restraints weight = 99147.243| |-----------------------------------------------------------------------------| r_work (final): 0.3218 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7783 moved from start: 0.4556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 43895 Z= 0.119 Angle : 0.577 10.661 59625 Z= 0.298 Chirality : 0.043 0.180 6708 Planarity : 0.004 0.116 7378 Dihedral : 12.716 157.546 6721 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 10.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 0.00 % Allowed : 0.20 % Favored : 99.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.46 % 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: 0.71 (0.12), residues: 5090 helix: 1.54 (0.13), residues: 1793 sheet: -0.18 (0.17), residues: 865 loop : 0.01 (0.13), residues: 2432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG J 38 TYR 0.032 0.001 TYR O1153 PHE 0.048 0.001 PHE L 67 TRP 0.020 0.001 TRP B 681 HIS 0.011 0.001 HIS A 299 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.12 (43864) covalent geometry : angle 0.57228 / 0.30 (59589) hydrogen bonds : bond 0.03240 / 2.18 ( 1790) hydrogen bonds : angle 4.66275 / 3.36 ( 4910) metal coordination : bond 0.00471 / 0.28 ( 31) metal coordination : angle 2.89447 / 1.74 ( 36) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10180 Ramachandran restraints generated. 5090 Oldfield, 0 Emsley, 5090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10180 Ramachandran restraints generated. 5090 Oldfield, 0 Emsley, 5090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 354 residues out of total 4548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 354 time to evaluate : 1.563 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: A 103 CYS cc_start: 0.9280 (m) cc_final: 0.9059 (m) REVERT: A 437 MET cc_start: 0.7230 (mmm) cc_final: 0.6999 (mmm) REVERT: A 544 ASP cc_start: 0.9071 (m-30) cc_final: 0.8840 (m-30) REVERT: A 605 MET cc_start: 0.8835 (tpp) cc_final: 0.8297 (tmm) REVERT: A 644 LYS cc_start: 0.8723 (mmmt) cc_final: 0.8365 (mttp) REVERT: A 666 ILE cc_start: 0.7830 (mm) cc_final: 0.7579 (mm) REVERT: A 1019 CYS cc_start: 0.9023 (m) cc_final: 0.8759 (m) REVERT: A 1102 LYS cc_start: 0.9091 (ttpp) cc_final: 0.8683 (tppt) REVERT: A 1111 MET cc_start: 0.8475 (tpp) cc_final: 0.8218 (tpt) REVERT: A 1209 MET cc_start: 0.8987 (ttm) cc_final: 0.8444 (ttt) REVERT: A 1285 MET cc_start: 0.7072 (mpp) cc_final: 0.6835 (mpp) REVERT: A 1409 LEU cc_start: 0.9190 (mm) cc_final: 0.8761 (mm) REVERT: A 1426 GLU cc_start: 0.8752 (mp0) cc_final: 0.8045 (mp0) REVERT: A 1427 ASN cc_start: 0.9244 (m-40) cc_final: 0.8926 (m110) REVERT: B 386 LEU cc_start: 0.9530 (tt) cc_final: 0.9235 (pp) REVERT: B 421 PHE cc_start: 0.9004 (t80) cc_final: 0.8753 (t80) REVERT: B 499 ASN cc_start: 0.8794 (t0) cc_final: 0.8500 (t0) REVERT: B 552 MET cc_start: 0.9291 (mmp) cc_final: 0.9038 (mmm) REVERT: B 789 MET cc_start: 0.8409 (mmm) cc_final: 0.7791 (mmm) REVERT: B 841 MET cc_start: 0.8804 (ttt) cc_final: 0.8467 (ttt) REVERT: B 989 THR cc_start: 0.8914 (m) cc_final: 0.8353 (t) REVERT: B 1072 MET cc_start: 0.8465 (mtp) cc_final: 0.7964 (mtp) REVERT: B 1152 MET cc_start: 0.7476 (mmm) cc_final: 0.6757 (mmm) REVERT: B 1210 MET cc_start: 0.9019 (mpp) cc_final: 0.8751 (mpp) REVERT: B 1211 ASN cc_start: 0.9049 (m-40) cc_final: 0.8362 (t0) REVERT: C 33 LEU cc_start: 0.9023 (tp) cc_final: 0.8779 (tp) REVERT: C 37 MET cc_start: 0.8830 (ptm) cc_final: 0.8407 (ptt) REVERT: C 75 MET cc_start: 0.8730 (mmt) cc_final: 0.8369 (mmm) REVERT: C 190 ASP cc_start: 0.8555 (t70) cc_final: 0.8198 (p0) REVERT: C 265 MET cc_start: 0.7969 (ttm) cc_final: 0.7704 (mtt) REVERT: D 189 ASP cc_start: 0.9565 (t0) cc_final: 0.9183 (p0) REVERT: E 22 MET cc_start: 0.9115 (ppp) cc_final: 0.8876 (ppp) REVERT: E 82 PHE cc_start: 0.8552 (m-80) cc_final: 0.8255 (m-80) REVERT: E 112 TYR cc_start: 0.8322 (p90) cc_final: 0.7800 (p90) REVERT: F 154 ASP cc_start: 0.7906 (p0) cc_final: 0.7379 (m-30) REVERT: G 106 MET cc_start: 0.5190 (mtt) cc_final: 0.4339 (mmt) REVERT: G 115 MET cc_start: 0.1488 (mtt) cc_final: 0.0674 (mmt) REVERT: J 2 ILE cc_start: 0.8584 (mm) cc_final: 0.8323 (mm) REVERT: J 62 ARG cc_start: 0.8958 (mtp-110) cc_final: 0.8725 (mtp-110) REVERT: K 8 GLU cc_start: 0.9001 (tp30) cc_final: 0.8108 (tp30) REVERT: K 52 ASN cc_start: 0.8356 (m-40) cc_final: 0.7949 (m-40) REVERT: O 1105 MET cc_start: 0.8981 (tpt) cc_final: 0.8486 (tpp) REVERT: O 1187 ASN cc_start: 0.8397 (p0) cc_final: 0.8184 (t0) REVERT: O 1407 LEU cc_start: 0.9097 (tp) cc_final: 0.8779 (tp) REVERT: O 1580 MET cc_start: 0.8294 (pmm) cc_final: 0.8063 (pmm) REVERT: O 1584 PHE cc_start: 0.8231 (m-80) cc_final: 0.8023 (m-80) REVERT: O 1613 MET cc_start: 0.6484 (pmm) cc_final: 0.6142 (pmm) REVERT: O 1719 MET cc_start: 0.9502 (ppp) cc_final: 0.9301 (ppp) REVERT: O 1814 MET cc_start: 0.9362 (ptp) cc_final: 0.9088 (ptp) REVERT: Y 6 MET cc_start: 0.6576 (ptp) cc_final: 0.5881 (ptp) outliers start: 0 outliers final: 0 residues processed: 354 average time/residue: 0.2606 time to fit residues: 156.1754 Evaluate side-chains 296 residues out of total 4548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 296 time to evaluate : 1.664 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 517 random chunks: chunk 467 optimal weight: 30.0000 chunk 53 optimal weight: 0.6980 chunk 382 optimal weight: 6.9990 chunk 435 optimal weight: 10.0000 chunk 324 optimal weight: 20.0000 chunk 134 optimal weight: 0.8980 chunk 176 optimal weight: 1.9990 chunk 370 optimal weight: 3.9990 chunk 138 optimal weight: 0.6980 chunk 500 optimal weight: 7.9990 chunk 16 optimal weight: 7.9990 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 736 ASN ** A 757 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 761 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1093 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 188 HIS C 231 ASN E 179 GLN F 100 GLN ** H 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 76 GLN ** Z 835 ASN ** 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 = 0.3799 r_free = 0.3799 target = 0.063163 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.044069 restraints weight = 351828.325| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.045077 restraints weight = 207426.424| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.045793 restraints weight = 146601.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.046257 restraints weight = 116612.767| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.046401 restraints weight = 102042.735| |-----------------------------------------------------------------------------| r_work (final): 0.3209 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7796 moved from start: 0.4610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 43895 Z= 0.130 Angle : 0.567 9.249 59625 Z= 0.294 Chirality : 0.042 0.185 6708 Planarity : 0.004 0.101 7378 Dihedral : 12.688 157.517 6721 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 10.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 0.00 % Allowed : 0.20 % Favored : 99.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.46 % 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: 0.71 (0.12), residues: 5090 helix: 1.53 (0.12), residues: 1794 sheet: -0.15 (0.17), residues: 864 loop : 0.01 (0.13), residues: 2432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG L 63 TYR 0.023 0.001 TYR B 866 PHE 0.038 0.001 PHE A 22 TRP 0.018 0.001 TRP B 681 HIS 0.011 0.001 HIS A 299 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.13 (43864) covalent geometry : angle 0.56355 / 0.29 (59589) hydrogen bonds : bond 0.03245 / 2.18 ( 1790) hydrogen bonds : angle 4.62818 / 3.34 ( 4910) metal coordination : bond 0.00551 / 0.32 ( 31) metal coordination : angle 2.72890 / 1.64 ( 36) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7868.95 seconds wall clock time: 137 minutes 12.38 seconds (8232.38 seconds total)