Starting phenix.real_space_refine on Sun Aug 9 09:40:48 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9sbq_54735/08_2026/9sbq_54735.cif Found real_map, /net/cci-nas-00/data/ceres_data/9sbq_54735/08_2026/9sbq_54735.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.88 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9sbq_54735/08_2026/9sbq_54735.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9sbq_54735/08_2026/9sbq_54735.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9sbq_54735/08_2026/9sbq_54735.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9sbq_54735/08_2026/9sbq_54735.map" } resolution = 3.88 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= 0.022 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 8 6.06 5 P 96 5.49 5 Mg 1 5.21 5 S 182 5.16 5 C 20454 2.51 5 N 5733 2.21 5 O 6421 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.03s 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: 32895 Number of models: 1 Model: "" Number of chains: 21 Chain: "A" Number of atoms: 10853 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1378, 10853 Classifications: {'peptide': 1378} Link IDs: {'PCIS': 1, 'PTRANS': 61, 'TRANS': 1315} Chain breaks: 9 Chain: "B" Number of atoms: 9155 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1150, 9155 Classifications: {'peptide': 1150} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 48, 'TRANS': 1100} Chain breaks: 6 Chain: "C" Number of atoms: 2095 Number of conformers: 1 Conformer: "" Number of residues, atoms: 266, 2095 Classifications: {'peptide': 266} Link IDs: {'PTRANS': 11, 'TRANS': 254} Chain: "D" Number of atoms: 1327 Number of conformers: 1 Conformer: "" Number of residues, atoms: 167, 1327 Classifications: {'peptide': 167} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 164} Chain breaks: 2 Chain: "E" Number of atoms: 1744 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1744 Classifications: {'peptide': 213} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 200} Chain: "F" Number of atoms: 670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 670 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 6, 'TRANS': 76} Chain: "G" Number of atoms: 1340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1340 Classifications: {'peptide': 171} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 162} Chain: "H" Number of atoms: 1077 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 1077 Classifications: {'peptide': 134} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 129} Chain breaks: 1 Chain: "I" Number of atoms: 909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 909 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 5, 'TRANS': 106} Chain: "J" Number of atoms: 532 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 532 Classifications: {'peptide': 65} Link IDs: {'PTRANS': 2, 'TRANS': 62} Chain: "K" Number of atoms: 904 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 904 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 5, 'TRANS': 106} Chain: "L" Number of atoms: 359 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 359 Classifications: {'peptide': 45} Modifications used: {'COO': 1} Link IDs: {'TRANS': 44} Chain: "N" Number of atoms: 825 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 825 Classifications: {'DNA': 40} Link IDs: {'rna3p': 39} Chain breaks: 1 Chain: "R" Number of atoms: 197 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 197 Classifications: {'RNA': 9} Modifications used: {'rna3p_pur': 6, 'rna3p_pyr': 2} Link IDs: {'rna3p': 8} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "T" Number of atoms: 886 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 886 Classifications: {'DNA': 44} Link IDs: {'rna3p': 43} Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 14 Unusual residues: {' ZN': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 49 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ATP:plan-1': 1, 'ATP:plan-2': 1} Unresolved non-hydrogen planarities: 13 Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 457 SG CYS A 67 108.193 69.023 95.024 1.00216.95 S ATOM 479 SG CYS A 70 107.711 66.104 92.750 1.00236.40 S ATOM 532 SG CYS A 77 104.934 68.630 93.133 1.00214.46 S ATOM 762 SG CYS A 107 82.802 75.020 135.367 1.00256.88 S ATOM 786 SG CYS A 110 84.184 71.713 136.383 1.00247.90 S ATOM 1091 SG CYS A 148 80.715 72.671 137.585 1.00264.52 S ATOM 1105 SG CYS A 167 83.736 74.697 138.865 1.00265.09 S ATOM 19514 SG CYS B1163 99.845 57.059 104.834 1.00219.15 S ATOM 19532 SG CYS B1166 98.269 60.494 105.207 1.00223.92 S ATOM 19657 SG CYS B1182 102.000 60.134 104.692 1.00225.88 S ATOM 19676 SG CYS B1185 100.363 59.158 108.029 1.00232.08 S ATOM 20664 SG CYS C 86 94.013 74.987 26.780 1.00261.43 S ATOM 20681 SG CYS C 88 96.436 77.094 28.468 1.00276.11 S ATOM 20714 SG CYS C 92 95.432 78.124 25.068 1.00243.40 S ATOM 20737 SG CYS C 95 93.032 78.547 28.104 1.00242.15 S ATOM 28322 SG CYS I 7 38.679 126.638 126.433 1.00403.57 S ATOM 28347 SG CYS I 10 42.461 126.269 126.499 1.00408.01 S ATOM 28513 SG CYS I 29 40.476 123.632 128.312 1.00412.50 S ATOM 28537 SG CYS I 32 40.506 127.147 129.631 1.00425.31 S ATOM 28864 SG CYS I 75 17.656 119.080 87.090 1.00462.25 S ATOM 28886 SG CYS I 78 17.639 122.767 86.290 1.00463.76 S ATOM 29102 SG CYS I 103 20.771 120.691 85.450 1.00451.02 S ATOM 29122 SG CYS I 106 19.919 121.337 89.014 1.00448.42 S ATOM 29224 SG CYS J 7 65.097 90.513 38.136 1.00181.09 S ATOM 29247 SG CYS J 10 64.933 88.278 35.039 1.00188.20 S ATOM 29527 SG CYS J 45 61.726 89.329 36.607 1.00191.73 S ATOM 29533 SG CYS J 46 64.029 91.622 34.537 1.00195.22 S ATOM 30656 SG CYS L 31 98.224 114.052 54.967 1.00344.32 S ATOM 30676 SG CYS L 34 99.488 115.880 51.834 1.00342.56 S ATOM 30780 SG CYS L 48 101.843 114.623 54.570 1.00342.61 S ATOM 30803 SG CYS L 51 99.596 117.643 55.175 1.00336.68 S Time building chain proxies: 6.13, per 1000 atoms: 0.19 Number of scatterers: 32895 At special positions: 0 Unit cell: (154.505, 155.593, 184.971, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 8 29.99 S 182 16.00 P 96 15.00 Mg 1 11.99 O 6421 8.00 N 5733 7.00 C 20454 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.93 Conformation dependent library (CDL) restraints added in 1.1 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1802 " pdb="ZN ZN A1802 " - pdb=" NE2 HIS A 80 " pdb="ZN ZN A1802 " - pdb=" SG CYS A 70 " pdb="ZN ZN A1802 " - pdb=" SG CYS A 67 " pdb="ZN ZN A1802 " - pdb=" SG CYS A 77 " pdb=" ZN A1803 " pdb="ZN ZN A1803 " - pdb=" SG CYS A 107 " pdb="ZN ZN A1803 " - pdb=" SG CYS A 110 " pdb="ZN ZN A1803 " - pdb=" SG CYS A 167 " pdb="ZN ZN A1803 " - pdb=" SG CYS A 148 " pdb=" ZN B1302 " pdb="ZN ZN B1302 " - pdb=" SG CYS B1166 " pdb="ZN ZN B1302 " - pdb=" SG CYS B1182 " pdb="ZN ZN B1302 " - pdb=" SG CYS B1163 " pdb="ZN ZN B1302 " - pdb=" SG CYS B1185 " pdb=" ZN C 401 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 88 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 86 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 92 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 95 " pdb=" ZN I 201 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 32 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 10 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 29 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 7 " pdb=" ZN I 202 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 106 " 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 78 " pdb=" ZN J 101 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 10 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 46 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 45 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 7 " pdb=" ZN L 101 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 48 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 31 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 34 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 51 " Number of angles added : 45 7672 Ramachandran restraints generated. 3836 Oldfield, 0 Emsley, 3836 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7318 Finding SS restraints... Secondary structure from input PDB file: 146 helices and 49 sheets defined 39.6% alpha, 19.5% beta 40 base pairs and 79 stacking pairs defined. Time for finding SS restraints: 3.97 Creating SS restraints... Processing helix chain 'A' and resid 23 through 31 Processing helix chain 'A' and resid 92 through 94 No H-bonds generated for 'chain 'A' and resid 92 through 94' Processing helix chain 'A' and resid 95 through 105 Processing helix chain 'A' and resid 119 through 127 Processing helix chain 'A' and resid 130 through 143 Processing helix chain 'A' and resid 203 through 213 removed outlier: 3.640A pdb=" N HIS A 213 " --> pdb=" O ASN A 209 " (cutoff:3.500A) Processing helix chain 'A' and resid 215 through 222 removed outlier: 3.511A pdb=" N PHE A 219 " --> pdb=" O SER A 215 " (cutoff:3.500A) Processing helix chain 'A' and resid 230 through 235 removed outlier: 3.868A pdb=" N ILE A 235 " --> pdb=" O GLU A 232 " (cutoff:3.500A) Processing helix chain 'A' and resid 243 through 247 Processing helix chain 'A' and resid 260 through 283 removed outlier: 3.554A pdb=" N GLY A 283 " --> pdb=" O LEU A 279 " (cutoff:3.500A) Processing helix chain 'A' and resid 288 through 305 Processing helix chain 'A' and resid 324 through 330 Processing helix chain 'A' and resid 334 through 340 Processing helix chain 'A' and resid 368 through 374 Processing helix chain 'A' and resid 384 through 395 Processing helix chain 'A' and resid 451 through 453 No H-bonds generated for 'chain 'A' and resid 451 through 453' Processing helix chain 'A' and resid 474 through 479 removed outlier: 3.682A pdb=" N TYR A 478 " --> pdb=" O VAL A 474 " (cutoff:3.500A) Processing helix chain 'A' and resid 494 through 505 Processing helix chain 'A' and resid 506 through 510 Processing helix chain 'A' and resid 524 through 536 removed outlier: 3.669A pdb=" N LEU A 528 " --> pdb=" O VAL A 524 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ARG A 532 " --> pdb=" O LEU A 528 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N LYS A 533 " --> pdb=" O CYS A 529 " (cutoff:3.500A) Processing helix chain 'A' and resid 542 through 553 removed outlier: 3.655A pdb=" N VAL A 553 " --> pdb=" O MET A 549 " (cutoff:3.500A) Processing helix chain 'A' and resid 574 through 579 Processing helix chain 'A' and resid 618 through 623 Processing helix chain 'A' and resid 628 through 637 Processing helix chain 'A' and resid 638 through 659 Processing helix chain 'A' and resid 665 through 670 Processing helix chain 'A' and resid 672 through 699 removed outlier: 3.538A pdb=" N ALA A 699 " --> pdb=" O LYS A 695 " (cutoff:3.500A) Processing helix chain 'A' and resid 710 through 737 Processing helix chain 'A' and resid 741 through 750 Processing helix chain 'A' and resid 754 through 763 removed outlier: 3.512A pdb=" N ILE A 758 " --> pdb=" O SER A 754 " (cutoff:3.500A) Processing helix chain 'A' and resid 793 through 798 Processing helix chain 'A' and resid 809 through 845 removed outlier: 3.830A pdb=" N GLY A 823 " --> pdb=" O GLY A 819 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LEU A 824 " --> pdb=" O GLY A 820 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N THR A 831 " --> pdb=" O THR A 827 " (cutoff:3.500A) removed outlier: 4.846A 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 874 through 876 No H-bonds generated for 'chain 'A' and resid 874 through 876' Processing helix chain 'A' and resid 889 through 898 Processing helix chain 'A' and resid 909 through 913 Processing helix chain 'A' and resid 915 through 920 Processing helix chain 'A' and resid 923 through 947 Processing helix chain 'A' and resid 959 through 972 removed outlier: 3.506A pdb=" N ILE A 963 " --> pdb=" O ASN A 959 " (cutoff:3.500A) Processing helix chain 'A' and resid 982 through 994 removed outlier: 3.651A pdb=" N GLN A 994 " --> pdb=" O VAL A 990 " (cutoff:3.500A) Processing helix chain 'A' and resid 1004 through 1015 Processing helix chain 'A' and resid 1015 through 1026 Processing helix chain 'A' and resid 1027 through 1035 Processing helix chain 'A' and resid 1038 through 1056 Processing helix chain 'A' and resid 1063 through 1079 Proline residue: A1075 - end of helix Processing helix chain 'A' and resid 1096 through 1107 Processing helix chain 'A' and resid 1130 through 1139 Processing helix chain 'A' and resid 1142 through 1146 removed outlier: 3.584A pdb=" N VAL A1146 " --> pdb=" O THR A1142 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1142 through 1146' Processing helix chain 'A' and resid 1166 through 1174 removed outlier: 3.929A pdb=" N PHE A1174 " --> pdb=" O ILE A1170 " (cutoff:3.500A) Processing helix chain 'A' and resid 1198 through 1206 Processing helix chain 'A' and resid 1208 through 1221 Processing helix chain 'A' and resid 1257 through 1270 Processing helix chain 'A' and resid 1312 through 1317 removed outlier: 3.697A pdb=" N MET A1317 " --> pdb=" O LEU A1313 " (cutoff:3.500A) Processing helix chain 'A' and resid 1331 through 1340 Processing helix chain 'A' and resid 1340 through 1357 Processing helix chain 'A' and resid 1358 through 1360 No H-bonds generated for 'chain 'A' and resid 1358 through 1360' Processing helix chain 'A' and resid 1364 through 1376 removed outlier: 3.983A pdb=" N MET A1368 " --> pdb=" O ASN A1364 " (cutoff:3.500A) Processing helix chain 'A' and resid 1395 through 1401 Processing helix chain 'A' and resid 1404 through 1416 Processing helix chain 'A' and resid 1423 through 1431 removed outlier: 3.615A pdb=" N ASN A1427 " --> pdb=" O GLY A1423 " (cutoff:3.500A) Processing helix chain 'A' and resid 1447 through 1452 Processing helix chain 'B' and resid 29 through 37 removed outlier: 4.102A pdb=" N VAL B 33 " --> pdb=" O ASP B 29 " (cutoff:3.500A) Processing helix chain 'B' and resid 44 through 66 removed outlier: 3.669A pdb=" N LEU B 48 " --> pdb=" O VAL B 44 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N LEU B 59 " --> pdb=" O VAL B 55 " (cutoff:3.500A) removed outlier: 5.451A pdb=" N GLN B 60 " --> pdb=" O ASP B 56 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N ASP B 66 " --> pdb=" O ILE B 62 " (cutoff:3.500A) Processing helix chain 'B' and resid 113 through 120 Processing helix chain 'B' and resid 160 through 162 No H-bonds generated for 'chain 'B' and resid 160 through 162' Processing helix chain 'B' and resid 185 through 192 Processing helix chain 'B' and resid 282 through 289 Processing helix chain 'B' and resid 293 through 303 removed outlier: 3.857A pdb=" N TYR B 303 " --> pdb=" O GLU B 299 " (cutoff:3.500A) Processing helix chain 'B' and resid 308 through 322 Proline residue: B 316 - end of helix Processing helix chain 'B' and resid 326 through 338 Processing helix chain 'B' and resid 344 through 359 Processing helix chain 'B' and resid 370 through 390 Processing helix chain 'B' and resid 400 through 402 No H-bonds generated for 'chain 'B' and resid 400 through 402' Processing helix chain 'B' and resid 408 through 438 Processing helix chain 'B' and resid 443 through 448 Processing helix chain 'B' and resid 450 through 464 removed outlier: 3.690A pdb=" N THR B 454 " --> pdb=" O ALA B 450 " (cutoff:3.500A) Processing helix chain 'B' and resid 469 through 473 removed outlier: 3.653A pdb=" N ALA B 472 " --> pdb=" O GLN B 469 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N MET B 473 " --> pdb=" O LYS B 470 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 469 through 473' Processing helix chain 'B' and resid 487 through 496 removed outlier: 3.578A pdb=" N ARG B 496 " --> pdb=" O LEU B 492 " (cutoff:3.500A) Processing helix chain 'B' and resid 515 through 519 Processing helix chain 'B' and resid 551 through 561 Processing helix chain 'B' and resid 567 through 569 No H-bonds generated for 'chain 'B' and resid 567 through 569' Processing helix chain 'B' and resid 592 through 607 Processing helix chain 'B' and resid 654 through 667 Processing helix chain 'B' and resid 680 through 687 Processing helix chain 'B' and resid 696 through 701 removed outlier: 3.559A pdb=" N ILE B 701 " --> pdb=" O GLU B 698 " (cutoff:3.500A) Processing helix chain 'B' and resid 706 through 710 Processing helix chain 'B' and resid 744 through 749 Processing helix chain 'B' and resid 752 through 756 Processing helix chain 'B' and resid 758 through 762 Processing helix chain 'B' and resid 763 through 775 removed outlier: 4.053A pdb=" N LYS B 775 " --> pdb=" O SER B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 784 through 788 Processing helix chain 'B' and resid 806 through 811 removed outlier: 3.598A pdb=" N GLU B 810 " --> pdb=" O ARG B 807 " (cutoff:3.500A) Processing helix chain 'B' and resid 843 through 848 Processing helix chain 'B' and resid 995 through 999 Processing helix chain 'B' and resid 1015 through 1021 removed outlier: 4.269A pdb=" N SER B1019 " --> pdb=" O HIS B1015 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ARG B1020 " --> pdb=" O ALA B1016 " (cutoff:3.500A) Processing helix chain 'B' and resid 1022 through 1039 removed outlier: 3.840A pdb=" N LEU B1026 " --> pdb=" O THR B1022 " (cutoff:3.500A) Processing helix chain 'B' and resid 1051 through 1061 removed outlier: 3.694A pdb=" N GLU B1061 " --> pdb=" O LYS B1057 " (cutoff:3.500A) Processing helix chain 'B' and resid 1098 through 1102 Processing helix chain 'B' and resid 1131 through 1142 Processing helix chain 'B' and resid 1143 through 1153 Processing helix chain 'B' and resid 1197 through 1210 Processing helix chain 'C' and resid 26 through 40 Processing helix chain 'C' and resid 59 through 69 removed outlier: 3.806A pdb=" N LEU C 69 " --> pdb=" O HIS C 65 " (cutoff:3.500A) Processing helix chain 'C' and resid 76 through 80 Processing helix chain 'C' and resid 116 through 118 No H-bonds generated for 'chain 'C' and resid 116 through 118' Processing helix chain 'C' and resid 167 through 171 Processing helix chain 'C' and resid 196 through 201 Processing helix chain 'C' and resid 206 through 210 Processing helix chain 'C' and resid 239 through 266 Processing helix chain 'D' and resid 30 through 34 removed outlier: 3.703A pdb=" N GLN D 34 " --> pdb=" O GLN D 31 " (cutoff:3.500A) Processing helix chain 'D' and resid 51 through 73 Processing helix chain 'D' and resid 118 through 132 Processing helix chain 'D' and resid 138 through 151 removed outlier: 3.573A pdb=" N PHE D 151 " --> pdb=" O TYR D 147 " (cutoff:3.500A) Processing helix chain 'D' and resid 156 through 171 removed outlier: 3.807A pdb=" N VAL D 160 " --> pdb=" O ASP D 156 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N THR D 170 " --> pdb=" O LEU D 166 " (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 4 through 26 Processing helix chain 'E' and resid 31 through 36 Processing helix chain 'E' and resid 38 through 46 Processing helix chain 'E' and resid 55 through 59 removed outlier: 3.865A pdb=" N SER E 59 " --> pdb=" O LYS E 56 " (cutoff:3.500A) Processing helix chain 'E' and resid 65 through 72 Processing helix chain 'E' and resid 91 through 104 removed outlier: 3.613A pdb=" N THR E 95 " --> pdb=" O LYS E 91 " (cutoff:3.500A) Processing helix chain 'E' and resid 117 through 124 removed outlier: 3.651A pdb=" N MET E 121 " --> pdb=" O THR E 117 " (cutoff:3.500A) Processing helix chain 'E' and resid 138 through 141 Processing helix chain 'E' and resid 143 through 147 Processing helix chain 'E' and resid 157 through 169 Processing helix chain 'E' and resid 171 through 175 removed outlier: 3.605A pdb=" N LEU E 175 " --> pdb=" O GLU E 172 " (cutoff:3.500A) Processing helix chain 'E' and resid 182 through 189 Processing helix chain 'F' and resid 86 through 103 Processing helix chain 'F' and resid 116 through 127 Processing helix chain 'G' and resid 14 through 18 Processing helix chain 'G' and resid 21 through 35 removed outlier: 3.714A pdb=" N GLU G 32 " --> pdb=" O THR G 28 " (cutoff:3.500A) Processing helix chain 'G' and resid 112 through 115 Processing helix chain 'H' and resid 88 through 93 Processing helix chain 'H' and resid 129 through 133 Processing helix chain 'I' and resid 59 through 65 removed outlier: 4.296A pdb=" N GLY I 63 " --> pdb=" O GLN I 60 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ASP I 65 " --> pdb=" O ILE I 62 " (cutoff:3.500A) Processing helix chain 'J' and resid 14 through 16 No H-bonds generated for 'chain 'J' and resid 14 through 16' Processing helix chain 'J' and resid 17 through 27 Processing helix chain 'J' and resid 31 through 40 Processing helix chain 'J' and resid 43 through 52 removed outlier: 3.754A pdb=" N MET J 49 " --> pdb=" O CYS J 45 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ILE J 50 " --> pdb=" O CYS J 46 " (cutoff:3.500A) Processing helix chain 'J' and resid 56 through 61 removed outlier: 3.539A pdb=" N PHE J 60 " --> pdb=" O LEU J 56 " (cutoff:3.500A) Processing helix chain 'K' and resid 5 through 10 Processing helix chain 'K' and resid 39 through 53 removed outlier: 3.622A pdb=" N ASN K 44 " --> pdb=" O HIS K 40 " (cutoff:3.500A) removed outlier: 4.860A pdb=" N LEU K 45 " --> pdb=" O THR K 41 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLU K 49 " --> pdb=" O LEU K 45 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ASN K 52 " --> pdb=" O ALA K 48 " (cutoff:3.500A) Processing helix chain 'K' and resid 82 through 110 Processing sheet with id=AA1, first strand: chain 'A' and resid 1418 through 1419 Processing sheet with id=AA2, first strand: chain 'A' and resid 82 through 90 removed outlier: 9.974A pdb=" N LEU A 86 " --> pdb=" O PRO A 240 " (cutoff:3.500A) removed outlier: 11.275A pdb=" N LYS A 88 " --> pdb=" O CYS A 238 " (cutoff:3.500A) removed outlier: 7.041A pdb=" N CYS A 238 " --> pdb=" O LYS A 88 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 173 through 177 Processing sheet with id=AA4, first strand: chain 'A' and resid 250 through 252 Processing sheet with id=AA5, first strand: chain 'A' and resid 343 through 345 removed outlier: 3.512A 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: 3.584A pdb=" N SER A 348 " --> pdb=" O ARG B1106 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N THR A 351 " --> pdb=" O MET A 487 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N HIS A 490 " --> pdb=" O LEU A 443 " (cutoff:3.500A) removed outlier: 7.972A pdb=" N PHE A 468 " --> pdb=" O ARG A 350 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N VAL A 352 " --> pdb=" O PHE A 468 " (cutoff:3.500A) removed outlier: 8.187A pdb=" N LEU A 470 " --> pdb=" O VAL A 352 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N SER A 354 " --> pdb=" O LEU A 470 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 375 through 379 removed outlier: 3.605A pdb=" N ARG A 434 " --> pdb=" O TYR A 376 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N TYR A 404 " --> pdb=" O GLU A 433 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N HIS A 435 " --> pdb=" O ALA A 402 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N ALA A 402 " --> pdb=" O HIS A 435 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 512 through 513 removed outlier: 3.516A pdb=" N LYS A 518 " --> pdb=" O SER A 513 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 540 through 541 Processing sheet with id=AB1, first strand: chain 'A' and resid 588 through 590 removed outlier: 6.949A 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: 6.611A pdb=" N THR A 856 " --> pdb=" O ILE A 864 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 878 through 882 Processing sheet with id=AB5, first strand: chain 'A' and resid 1282 through 1292 removed outlier: 3.516A pdb=" N THR A1308 " --> pdb=" O LEU A1116 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N LEU A1116 " --> pdb=" O THR A1308 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 1224 through 1228 removed outlier: 4.033A pdb=" N LEU A1236 " --> pdb=" O LEU A1197 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N ARG A1194 " --> pdb=" O SER A1150 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N SER A1150 " --> pdb=" O ARG A1194 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N GLU A1196 " --> pdb=" O ILE A1148 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N SER A1150 " --> pdb=" O HIS I 46 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N TYR I 44 " --> pdb=" O ILE A1152 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 49 through 50 removed outlier: 4.277A pdb=" N PHE G 2 " --> pdb=" O LEU D 50 " (cutoff:3.500A) removed outlier: 5.395A pdb=" N VAL A1443 " --> pdb=" O ILE G 61 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 49 through 50 removed outlier: 4.277A pdb=" N PHE G 2 " --> pdb=" O LEU D 50 " (cutoff:3.500A) removed outlier: 4.873A pdb=" N ARG G 75 " --> pdb=" O LEU G 49 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N CYS G 47 " --> pdb=" O VAL G 77 " (cutoff:3.500A) removed outlier: 7.074A pdb=" N PHE G 79 " --> pdb=" O ILE G 45 " (cutoff:3.500A) removed outlier: 6.048A pdb=" N ILE G 45 " --> pdb=" O PHE G 79 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 69 through 73 removed outlier: 5.339A pdb=" N ARG B 86 " --> pdb=" O ALA B 139 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N ALA B 139 " --> pdb=" O ARG B 86 " (cutoff:3.500A) removed outlier: 5.253A pdb=" N TYR B 88 " --> pdb=" O TYR B 137 " (cutoff:3.500A) removed outlier: 7.123A pdb=" N TYR B 137 " --> pdb=" O TYR B 88 " (cutoff:3.500A) removed outlier: 5.419A pdb=" N ILE B 90 " --> pdb=" O ARG B 135 " (cutoff:3.500A) removed outlier: 7.175A pdb=" N ARG B 135 " --> pdb=" O ILE B 90 " (cutoff:3.500A) removed outlier: 5.162A pdb=" N PHE B 92 " --> pdb=" O LYS B 133 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N LYS B 133 " --> pdb=" O PHE B 92 " (cutoff:3.500A) removed outlier: 4.784A pdb=" N LYS B 94 " --> pdb=" O ASP B 131 " (cutoff:3.500A) removed outlier: 7.703A pdb=" N VAL B 132 " --> pdb=" O SER B 156 " (cutoff:3.500A) removed outlier: 5.477A pdb=" N SER B 156 " --> pdb=" O VAL B 132 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N LYS B 134 " --> pdb=" O GLU B 154 " (cutoff:3.500A) removed outlier: 5.012A pdb=" N GLU B 154 " --> pdb=" O LYS B 134 " (cutoff:3.500A) removed outlier: 7.553A pdb=" N THR B 136 " --> pdb=" O ILE B 152 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 69 through 73 removed outlier: 5.339A pdb=" N ARG B 86 " --> pdb=" O ALA B 139 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N ALA B 139 " --> pdb=" O ARG B 86 " (cutoff:3.500A) removed outlier: 5.253A pdb=" N TYR B 88 " --> pdb=" O TYR B 137 " (cutoff:3.500A) removed outlier: 7.123A pdb=" N TYR B 137 " --> pdb=" O TYR B 88 " (cutoff:3.500A) removed outlier: 5.419A pdb=" N ILE B 90 " --> pdb=" O ARG B 135 " (cutoff:3.500A) removed outlier: 7.175A pdb=" N ARG B 135 " --> pdb=" O ILE B 90 " (cutoff:3.500A) removed outlier: 5.162A pdb=" N PHE B 92 " --> pdb=" O LYS B 133 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N LYS B 133 " --> pdb=" O PHE B 92 " (cutoff:3.500A) removed outlier: 4.784A pdb=" N LYS B 94 " --> pdb=" O ASP B 131 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N GLY B 168 " --> pdb=" O LEU B 128 " (cutoff:3.500A) removed outlier: 7.168A pdb=" N VAL B 130 " --> pdb=" O PHE B 166 " (cutoff:3.500A) removed outlier: 6.079A pdb=" N PHE B 166 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 7.583A pdb=" N VAL B 132 " --> pdb=" O LYS B 164 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N LYS B 164 " --> pdb=" O VAL B 132 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 101 through 103 Processing sheet with id=AC3, first strand: chain 'B' and resid 203 through 205 Processing sheet with id=AC4, first strand: chain 'B' and resid 404 through 407 removed outlier: 6.125A pdb=" N ALA B 214 " --> pdb=" O ASN B 499 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 224 through 227 removed outlier: 3.930A pdb=" N HIS B 236 " --> pdb=" O LEU B 258 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N GLN B 255 " --> pdb=" O THR B 272 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 544 through 545 Processing sheet with id=AC7, first strand: chain 'B' and resid 564 through 565 removed outlier: 4.980A pdb=" N TRP B 586 " --> pdb=" O VAL B 582 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N VAL B 582 " --> pdb=" O TRP B 586 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N GLY B 588 " --> pdb=" O VAL B 580 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 640 through 641 Processing sheet with id=AC9, first strand: chain 'B' and resid 703 through 704 Processing sheet with id=AD1, first strand: chain 'B' and resid 792 through 796 removed outlier: 3.847A pdb=" N SER B 853 " --> pdb=" O LYS B 972 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N ARG B 969 " --> pdb=" O VAL B 949 " (cutoff:3.500A) removed outlier: 5.643A pdb=" N VAL B 949 " --> pdb=" O ARG B 969 " (cutoff:3.500A) removed outlier: 8.656A pdb=" N THR B 971 " --> pdb=" O GLY B 947 " (cutoff:3.500A) removed outlier: 8.183A pdb=" N GLY B 947 " --> pdb=" O THR B 971 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 792 through 796 removed outlier: 3.847A pdb=" N SER B 853 " --> pdb=" O LYS B 972 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N ARG B 969 " --> pdb=" O VAL B 949 " (cutoff:3.500A) removed outlier: 5.643A pdb=" N VAL B 949 " --> pdb=" O ARG B 969 " (cutoff:3.500A) removed outlier: 8.656A pdb=" N THR B 971 " --> pdb=" O GLY B 947 " (cutoff:3.500A) removed outlier: 8.183A pdb=" N GLY B 947 " --> pdb=" O THR B 971 " (cutoff:3.500A) removed outlier: 5.294A pdb=" N VAL B 952 " --> pdb=" O LYS L 58 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 804 through 805 Processing sheet with id=AD4, first strand: chain 'B' and resid 821 through 827 removed outlier: 8.735A pdb=" N LEU B1010 " --> pdb=" O ASN B 822 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N ILE B 824 " --> pdb=" O LEU B1010 " (cutoff:3.500A) removed outlier: 7.721A pdb=" N ILE B1012 " --> pdb=" O ILE B 824 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N ALA B 826 " --> pdb=" O ILE B1012 " (cutoff:3.500A) removed outlier: 7.175A pdb=" N MET B 839 " --> pdb=" O GLY B 991 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N THR B 993 " --> pdb=" O MET B 839 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N MET B 841 " --> pdb=" O THR B 993 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 910 through 912 Processing sheet with id=AD6, first strand: chain 'B' and resid 1069 through 1070 Processing sheet with id=AD7, first strand: chain 'B' and resid 1158 through 1163 Processing sheet with id=AD8, first strand: chain 'B' and resid 1172 through 1174 Processing sheet with id=AD9, first strand: chain 'C' and resid 7 through 13 removed outlier: 5.596A pdb=" N VAL C 8 " --> pdb=" O SER C 23 " (cutoff:3.500A) removed outlier: 7.110A pdb=" N SER C 23 " --> pdb=" O VAL C 8 " (cutoff:3.500A) removed outlier: 5.693A pdb=" N ILE C 10 " --> pdb=" O ILE C 21 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N ILE C 21 " --> pdb=" O ILE C 10 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 119 through 120 removed outlier: 6.624A pdb=" N GLU C 152 " --> pdb=" O THR C 53 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N THR C 53 " --> pdb=" O GLU C 152 " (cutoff:3.500A) removed outlier: 7.768A pdb=" N LYS C 154 " --> pdb=" O VAL C 51 " (cutoff:3.500A) removed outlier: 4.991A pdb=" N VAL C 51 " --> pdb=" O LYS C 154 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N THR C 156 " --> pdb=" O VAL C 49 " (cutoff:3.500A) removed outlier: 5.160A pdb=" N VAL C 49 " --> pdb=" O THR C 156 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N VAL C 158 " --> pdb=" O ASP C 47 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N VAL L 65 " --> pdb=" O VAL C 51 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 111 through 114 removed outlier: 3.647A 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 47 through 48 removed outlier: 4.799A pdb=" N ARG E 52 " --> pdb=" O ASP E 48 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'E' and resid 60 through 62 removed outlier: 6.319A pdb=" N TRP E 79 " --> pdb=" O ILE E 109 " (cutoff:3.500A) removed outlier: 7.626A pdb=" N VAL E 111 " --> pdb=" O TRP E 79 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N GLU E 81 " --> pdb=" O VAL E 111 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'E' and resid 152 through 155 removed outlier: 3.822A pdb=" N LYS E 152 " --> pdb=" O ILE E 199 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'G' and resid 86 through 87 removed outlier: 3.758A pdb=" N VAL G 145 " --> pdb=" O VAL G 87 " (cutoff:3.500A) removed outlier: 5.259A pdb=" N ILE G 147 " --> pdb=" O SER G 162 " (cutoff:3.500A) removed outlier: 6.068A pdb=" N SER G 162 " --> pdb=" O ILE G 147 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N LYS G 107 " --> pdb=" O ILE G 157 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N ALA G 159 " --> pdb=" O LYS G 107 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N PHE G 99 " --> pdb=" O VAL G 110 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N GLY G 98 " --> pdb=" O CYS G 94 " (cutoff:3.500A) removed outlier: 5.077A pdb=" N CYS G 94 " --> pdb=" O GLY G 98 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N GLU G 100 " --> pdb=" O VAL G 92 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N THR G 90 " --> pdb=" O GLN G 102 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'G' and resid 86 through 87 removed outlier: 3.758A pdb=" N VAL G 145 " --> pdb=" O VAL G 87 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'G' and resid 130 through 131 Processing sheet with id=AF1, first strand: chain 'H' and resid 4 through 16 removed outlier: 5.632A pdb=" N VAL H 12 " --> pdb=" O ALA H 29 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N ALA H 29 " --> pdb=" O VAL H 12 " (cutoff:3.500A) removed outlier: 5.819A pdb=" N LEU H 122 " --> pdb=" O ASP H 41 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N LEU H 121 " --> pdb=" O PHE H 118 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N LYS H 103 " --> pdb=" O TYR H 115 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N SER H 117 " --> pdb=" O ALA H 101 " (cutoff:3.500A) removed outlier: 5.643A pdb=" N ALA H 101 " --> pdb=" O SER H 117 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N LEU H 55 " --> pdb=" O ILE H 9 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N ILE H 9 " --> pdb=" O LEU H 55 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N VAL H 57 " --> pdb=" O ASP H 7 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N ASP H 7 " --> pdb=" O VAL H 57 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N ILE H 59 " --> pdb=" O LEU H 5 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'I' and resid 15 through 19 removed outlier: 3.544A pdb=" N ASP I 19 " --> pdb=" O ARG I 24 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N PHE I 27 " --> pdb=" O GLU I 36 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'I' and resid 70 through 71 removed outlier: 4.199A pdb=" N ASN I 83 " --> pdb=" O SER I 71 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N PHE I 100 " --> pdb=" O PHE I 86 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'K' and resid 19 through 23 1359 hydrogen bonds defined for protein. 3732 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 104 hydrogen bonds 208 hydrogen bond angles 0 basepair planarities 40 basepair parallelities 79 stacking parallelities Total time for adding SS restraints: 10.01 Time building geometry restraints manager: 3.86 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 9929 1.33 - 1.45: 5021 1.45 - 1.57: 18238 1.57 - 1.69: 187 1.69 - 1.81: 292 Bond restraints: 33667 Sorted by residual: bond pdb=" O1A ATP B1301 " pdb=" PA ATP B1301 " ideal model delta sigma weight residual 1.477 1.647 -0.170 1.10e-02 8.26e+03 2.38e+02 bond pdb=" O5' ATP B1301 " pdb=" PA ATP B1301 " ideal model delta sigma weight residual 1.579 1.509 0.070 1.10e-02 8.26e+03 4.01e+01 bond pdb=" C1' DC T 32 " pdb=" N1 DC T 32 " ideal model delta sigma weight residual 1.468 1.556 -0.088 1.40e-02 5.10e+03 3.98e+01 bond pdb=" C1' DC T 22 " pdb=" N1 DC T 22 " ideal model delta sigma weight residual 1.468 1.556 -0.088 1.40e-02 5.10e+03 3.98e+01 bond pdb=" C1' DC T 21 " pdb=" N1 DC T 21 " ideal model delta sigma weight residual 1.468 1.556 -0.088 1.40e-02 5.10e+03 3.97e+01 ... (remaining 33662 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.50: 45685 3.50 - 7.00: 151 7.00 - 10.50: 7 10.50 - 14.00: 0 14.00 - 17.49: 2 Bond angle restraints: 45845 Sorted by residual: angle pdb=" PB ATP B1301 " pdb=" O3B ATP B1301 " pdb=" PG ATP B1301 " ideal model delta sigma weight residual 139.87 122.38 17.49 1.00e+00 1.00e+00 3.06e+02 angle pdb=" PA ATP B1301 " pdb=" O3A ATP B1301 " pdb=" PB ATP B1301 " ideal model delta sigma weight residual 136.83 121.41 15.42 1.00e+00 1.00e+00 2.38e+02 angle pdb=" O4' G R 9 " pdb=" C1' G R 9 " pdb=" N9 G R 9 " ideal model delta sigma weight residual 108.50 104.58 3.92 7.00e-01 2.04e+00 3.14e+01 angle pdb=" O4' DC T 53 " pdb=" C4' DC T 53 " pdb=" C3' DC T 53 " ideal model delta sigma weight residual 106.00 102.82 3.18 6.00e-01 2.78e+00 2.80e+01 angle pdb=" C THR A 709 " pdb=" N LEU A 710 " pdb=" CA LEU A 710 " ideal model delta sigma weight residual 121.54 131.27 -9.73 1.91e+00 2.74e-01 2.59e+01 ... (remaining 45840 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.31: 19794 35.31 - 70.61: 514 70.61 - 105.92: 30 105.92 - 141.22: 3 141.22 - 176.53: 2 Dihedral angle restraints: 20343 sinusoidal: 9045 harmonic: 11298 Sorted by residual: dihedral pdb=" CA THR A 69 " pdb=" C THR A 69 " pdb=" N CYS A 70 " pdb=" CA CYS A 70 " ideal model delta harmonic sigma weight residual 180.00 155.34 24.66 0 5.00e+00 4.00e-02 2.43e+01 dihedral pdb=" CA VAL E 90 " pdb=" C VAL E 90 " pdb=" N LYS E 91 " pdb=" CA LYS E 91 " ideal model delta harmonic sigma weight residual 180.00 157.74 22.26 0 5.00e+00 4.00e-02 1.98e+01 dihedral pdb=" C4' DT N 49 " pdb=" C3' DT N 49 " pdb=" O3' DT N 49 " pdb=" P DT N 50 " ideal model delta sinusoidal sigma weight residual 220.00 43.47 176.53 1 3.50e+01 8.16e-04 1.57e+01 ... (remaining 20340 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 3419 0.034 - 0.068: 1143 0.068 - 0.102: 412 0.102 - 0.136: 174 0.136 - 0.170: 7 Chirality restraints: 5155 Sorted by residual: chirality pdb=" C2' G R 9 " pdb=" C3' G R 9 " pdb=" O2' G R 9 " pdb=" C1' G R 9 " both_signs ideal model delta sigma weight residual False -2.62 -2.79 0.17 2.00e-01 2.50e+01 7.25e-01 chirality pdb=" CB ILE A 867 " pdb=" CA ILE A 867 " pdb=" CG1 ILE A 867 " pdb=" CG2 ILE A 867 " both_signs ideal model delta sigma weight residual False 2.64 2.48 0.16 2.00e-01 2.50e+01 6.80e-01 chirality pdb=" CB VAL A 474 " pdb=" CA VAL A 474 " pdb=" CG1 VAL A 474 " pdb=" CG2 VAL A 474 " both_signs ideal model delta sigma weight residual False -2.63 -2.47 -0.15 2.00e-01 2.50e+01 5.97e-01 ... (remaining 5152 not shown) Planarity restraints: 5606 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU A 710 " -0.017 2.00e-02 2.50e+03 3.37e-02 1.14e+01 pdb=" C LEU A 710 " 0.058 2.00e-02 2.50e+03 pdb=" O LEU A 710 " -0.022 2.00e-02 2.50e+03 pdb=" N ARG A 711 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP B 550 " -0.032 5.00e-02 4.00e+02 4.89e-02 3.82e+00 pdb=" N PRO B 551 " 0.085 5.00e-02 4.00e+02 pdb=" CA PRO B 551 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO B 551 " -0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 797 " -0.014 2.00e-02 2.50e+03 1.30e-02 3.40e+00 pdb=" CG TYR B 797 " 0.032 2.00e-02 2.50e+03 pdb=" CD1 TYR B 797 " -0.008 2.00e-02 2.50e+03 pdb=" CD2 TYR B 797 " -0.007 2.00e-02 2.50e+03 pdb=" CE1 TYR B 797 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR B 797 " -0.002 2.00e-02 2.50e+03 pdb=" CZ TYR B 797 " -0.002 2.00e-02 2.50e+03 pdb=" OH TYR B 797 " -0.001 2.00e-02 2.50e+03 ... (remaining 5603 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 840 2.68 - 3.24: 33035 3.24 - 3.79: 53216 3.79 - 4.35: 69897 4.35 - 4.90: 113098 Nonbonded interactions: 270086 Sorted by model distance: nonbonded pdb=" OD2 ASP B 837 " pdb=" NH2 ARG B1020 " model vdw 2.128 3.120 nonbonded pdb=" OE1 GLU A1256 " pdb=" ND1 HIS A1258 " model vdw 2.169 3.120 nonbonded pdb=" O LYS A1205 " pdb=" NH2 ARG A1274 " model vdw 2.179 3.120 nonbonded pdb=" O VAL A 216 " pdb=" OG1 THR A 220 " model vdw 2.181 3.040 nonbonded pdb=" OH TYR B 797 " pdb=" OG1 THR B 971 " model vdw 2.183 3.040 ... (remaining 270081 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.260 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.540 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 37.240 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.060 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:1.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 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 : 0.005 0.170 33699 Z= 0.297 Angle : 0.638 17.494 45890 Z= 0.414 Chirality : 0.042 0.170 5155 Planarity : 0.003 0.049 5606 Dihedral : 14.611 176.529 13025 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 10.36 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.01 % Favored : 94.92 % Rotamer: Outliers : 0.00 % Allowed : 0.18 % Favored : 99.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.61 (0.14), residues: 3836 helix: 1.77 (0.15), residues: 1314 sheet: -0.16 (0.22), residues: 567 loop : -0.31 (0.15), residues: 1955 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A1366 TYR 0.032 0.001 TYR B 797 PHE 0.013 0.001 PHE A1174 TRP 0.012 0.001 TRP A1044 HIS 0.011 0.001 HIS A 287 Details of bonding type rmsd/Z covalent geometry : bond 0.00460 / 0.30 (33667) covalent geometry : angle 0.62854 / 0.41 (45845) hydrogen bonds : bond 0.18623 / 12.20 ( 1421) hydrogen bonds : angle 6.99877 / 4.99 ( 3940) metal coordination : bond 0.00695 / 0.48 ( 32) metal coordination : angle 3.56458 / 2.62 ( 45) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7672 Ramachandran restraints generated. 3836 Oldfield, 0 Emsley, 3836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7672 Ramachandran restraints generated. 3836 Oldfield, 0 Emsley, 3836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 627 residues out of total 3425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 627 time to evaluate : 1.290 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: A 74 MET cc_start: 0.8985 (mtt) cc_final: 0.8771 (mtp) REVERT: A 122 MET cc_start: 0.9302 (tpp) cc_final: 0.8933 (tpp) REVERT: A 205 GLU cc_start: 0.9333 (tt0) cc_final: 0.8978 (tm-30) REVERT: A 277 GLU cc_start: 0.9429 (tt0) cc_final: 0.9202 (tp30) REVERT: A 360 GLU cc_start: 0.8901 (mm-30) cc_final: 0.8137 (mt-10) REVERT: A 449 SER cc_start: 0.9609 (m) cc_final: 0.9305 (p) REVERT: A 456 MET cc_start: 0.9344 (mtm) cc_final: 0.8833 (mtp) REVERT: A 487 MET cc_start: 0.9272 (mtp) cc_final: 0.8691 (mtt) REVERT: A 496 GLU cc_start: 0.9224 (tt0) cc_final: 0.8840 (tm-30) REVERT: A 521 MET cc_start: 0.9210 (mtt) cc_final: 0.9002 (mtm) REVERT: A 605 MET cc_start: 0.9549 (tpp) cc_final: 0.9335 (tpp) REVERT: A 696 GLU cc_start: 0.9121 (tt0) cc_final: 0.8617 (tm-30) REVERT: A 838 GLN cc_start: 0.9330 (tp40) cc_final: 0.8805 (tp40) REVERT: A 849 MET cc_start: 0.8848 (ttp) cc_final: 0.8611 (ttm) REVERT: A 873 MET cc_start: 0.9357 (mmp) cc_final: 0.8859 (mmp) REVERT: A 1202 MET cc_start: 0.8403 (mtp) cc_final: 0.7929 (mmm) REVERT: A 1207 LEU cc_start: 0.7778 (mt) cc_final: 0.6548 (mp) REVERT: A 1276 VAL cc_start: 0.9012 (t) cc_final: 0.8453 (p) REVERT: A 1278 ASN cc_start: 0.8646 (m-40) cc_final: 0.8319 (t0) REVERT: A 1309 ASP cc_start: 0.8768 (m-30) cc_final: 0.8552 (m-30) REVERT: A 1315 GLU cc_start: 0.9390 (tt0) cc_final: 0.9051 (tm-30) REVERT: A 1336 MET cc_start: 0.9579 (tmm) cc_final: 0.9317 (tmm) REVERT: A 1368 MET cc_start: 0.9318 (mtm) cc_final: 0.8945 (mtm) REVERT: A 1444 MET cc_start: 0.9166 (mmm) cc_final: 0.8836 (mmt) REVERT: B 101 MET cc_start: 0.8805 (mtt) cc_final: 0.8560 (mtp) REVERT: B 216 GLU cc_start: 0.9306 (tt0) cc_final: 0.8792 (tt0) REVERT: B 228 LYS cc_start: 0.9130 (mmmt) cc_final: 0.8886 (mmtp) REVERT: B 302 CYS cc_start: 0.8692 (t) cc_final: 0.8461 (p) REVERT: B 310 MET cc_start: 0.9477 (mtp) cc_final: 0.9070 (mmm) REVERT: B 313 MET cc_start: 0.9089 (tpp) cc_final: 0.8852 (tpt) REVERT: B 393 LYS cc_start: 0.8999 (ttpt) cc_final: 0.8773 (mmtt) REVERT: B 615 MET cc_start: 0.9177 (mtm) cc_final: 0.8426 (mpp) REVERT: B 747 MET cc_start: 0.9410 (mmm) cc_final: 0.8987 (mmt) REVERT: B 778 MET cc_start: 0.9311 (ttm) cc_final: 0.8874 (ttm) REVERT: B 809 MET cc_start: 0.9151 (mtt) cc_final: 0.8712 (mtp) REVERT: B 839 MET cc_start: 0.9100 (ptp) cc_final: 0.8576 (ptp) REVERT: B 874 PHE cc_start: 0.7422 (m-10) cc_final: 0.7075 (m-80) REVERT: B 887 HIS cc_start: 0.7881 (m90) cc_final: 0.7231 (t70) REVERT: B 1072 MET cc_start: 0.9412 (mtp) cc_final: 0.9147 (mtp) REVERT: B 1082 MET cc_start: 0.9208 (tpp) cc_final: 0.8982 (tpp) REVERT: B 1092 TYR cc_start: 0.9270 (m-80) cc_final: 0.8904 (m-80) REVERT: B 1098 MET cc_start: 0.9517 (mtm) cc_final: 0.9146 (mtm) REVERT: B 1111 MET cc_start: 0.8728 (mmm) cc_final: 0.8312 (tpp) REVERT: B 1206 GLU cc_start: 0.9481 (mt-10) cc_final: 0.9195 (mt-10) REVERT: C 37 MET cc_start: 0.9432 (mtm) cc_final: 0.9203 (mtm) REVERT: C 60 ASP cc_start: 0.9437 (t0) cc_final: 0.9227 (t70) REVERT: C 61 GLU cc_start: 0.8862 (pm20) cc_final: 0.8609 (pm20) REVERT: C 75 MET cc_start: 0.9270 (mmm) cc_final: 0.8430 (tpp) REVERT: C 125 MET cc_start: 0.9301 (mtp) cc_final: 0.9030 (mpp) REVERT: C 190 ASP cc_start: 0.9116 (t0) cc_final: 0.8821 (t0) REVERT: D 1 MET cc_start: 0.3044 (ptm) cc_final: 0.2411 (mmt) REVERT: D 138 ASN cc_start: 0.7023 (t0) cc_final: 0.6656 (t0) REVERT: D 151 PHE cc_start: 0.4596 (m-80) cc_final: 0.4369 (m-80) REVERT: D 192 LYS cc_start: 0.4769 (mttt) cc_final: 0.4302 (mtmt) REVERT: D 199 ASN cc_start: 0.5512 (m-40) cc_final: 0.4979 (p0) REVERT: E 48 ASP cc_start: 0.9373 (t0) cc_final: 0.9038 (t70) REVERT: E 112 TYR cc_start: 0.8970 (p90) cc_final: 0.8260 (p90) REVERT: E 182 ASP cc_start: 0.8898 (t0) cc_final: 0.8657 (t0) REVERT: E 214 CYS cc_start: 0.8956 (t) cc_final: 0.8297 (t) REVERT: F 76 LYS cc_start: 0.9562 (tptt) cc_final: 0.9214 (tppt) REVERT: F 77 ASP cc_start: 0.9523 (m-30) cc_final: 0.9187 (p0) REVERT: F 78 GLN cc_start: 0.9396 (mt0) cc_final: 0.9101 (mp10) REVERT: F 89 GLU cc_start: 0.9154 (mt-10) cc_final: 0.8759 (mt-10) REVERT: F 109 VAL cc_start: 0.9088 (t) cc_final: 0.8632 (p) REVERT: F 110 ASP cc_start: 0.8382 (m-30) cc_final: 0.7604 (t0) REVERT: F 116 ASP cc_start: 0.9111 (t0) cc_final: 0.8364 (t0) REVERT: F 144 GLU cc_start: 0.8780 (mt-10) cc_final: 0.8416 (mt-10) REVERT: G 2 PHE cc_start: 0.8232 (m-80) cc_final: 0.7794 (m-10) REVERT: G 33 GLU cc_start: 0.8623 (mm-30) cc_final: 0.8320 (mp0) REVERT: G 60 ARG cc_start: 0.8450 (ttp80) cc_final: 0.8165 (ttp80) REVERT: G 69 GLU cc_start: 0.8878 (tt0) cc_final: 0.8354 (tm-30) REVERT: H 14 GLU cc_start: 0.9218 (tt0) cc_final: 0.8607 (tm-30) REVERT: H 27 GLU cc_start: 0.9268 (mt-10) cc_final: 0.8888 (mp0) REVERT: H 116 TYR cc_start: 0.9143 (m-80) cc_final: 0.8752 (m-80) REVERT: H 123 MET cc_start: 0.8982 (ttt) cc_final: 0.8565 (tmm) REVERT: H 136 LYS cc_start: 0.9199 (mmtp) cc_final: 0.8910 (mtmm) REVERT: H 141 TYR cc_start: 0.9102 (m-80) cc_final: 0.8828 (m-80) REVERT: I 1 MET cc_start: 0.6745 (mtm) cc_final: 0.5950 (tmm) REVERT: I 97 MET cc_start: 0.8439 (mtp) cc_final: 0.8013 (mtm) REVERT: J 1 MET cc_start: 0.9111 (mtm) cc_final: 0.8786 (mtm) REVERT: J 19 GLU cc_start: 0.9421 (mm-30) cc_final: 0.9029 (tm-30) REVERT: K 17 SER cc_start: 0.9294 (m) cc_final: 0.8195 (p) REVERT: K 38 GLU cc_start: 0.9294 (mm-30) cc_final: 0.8937 (mm-30) REVERT: K 39 ASP cc_start: 0.8988 (p0) cc_final: 0.8518 (p0) REVERT: K 41 THR cc_start: 0.9337 (m) cc_final: 0.9020 (p) REVERT: K 64 GLU cc_start: 0.9341 (mt-10) cc_final: 0.9043 (mm-30) REVERT: K 79 GLU cc_start: 0.9385 (tt0) cc_final: 0.9158 (pm20) outliers start: 0 outliers final: 0 residues processed: 627 average time/residue: 0.2407 time to fit residues: 233.1550 Evaluate side-chains 388 residues out of total 3425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 388 time to evaluate : 1.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 393 random chunks: chunk 197 optimal weight: 0.7980 chunk 388 optimal weight: 5.9990 chunk 215 optimal weight: 7.9990 chunk 20 optimal weight: 0.7980 chunk 132 optimal weight: 0.8980 chunk 261 optimal weight: 2.9990 chunk 248 optimal weight: 3.9990 chunk 207 optimal weight: 2.9990 chunk 155 optimal weight: 6.9990 chunk 244 optimal weight: 3.9990 chunk 183 optimal weight: 5.9990 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 545 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 631 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 994 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1173 HIS B 110 HIS B 761 HIS ** B 986 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 146 GLN E 5 ASN G 24 GLN H 137 GLN J 26 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.079955 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2852 r_free = 0.2852 target = 0.054921 restraints weight = 108078.492| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.2898 r_free = 0.2898 target = 0.056646 restraints weight = 54904.856| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.2926 r_free = 0.2926 target = 0.057752 restraints weight = 35980.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.2944 r_free = 0.2944 target = 0.058442 restraints weight = 27698.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.2954 r_free = 0.2954 target = 0.058863 restraints weight = 23698.033| |-----------------------------------------------------------------------------| r_work (final): 0.2931 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8582 moved from start: 0.1640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 33699 Z= 0.163 Angle : 0.652 12.668 45890 Z= 0.339 Chirality : 0.046 0.224 5155 Planarity : 0.005 0.082 5606 Dihedral : 16.725 178.558 5258 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.04 % Favored : 95.86 % Rotamer: Outliers : 1.26 % Allowed : 6.66 % Favored : 92.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.52 (0.14), residues: 3836 helix: 1.59 (0.14), residues: 1333 sheet: -0.15 (0.21), residues: 599 loop : -0.33 (0.15), residues: 1904 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 320 TYR 0.021 0.002 TYR I 15 PHE 0.025 0.002 PHE D 154 TRP 0.013 0.001 TRP A1228 HIS 0.009 0.001 HIS A 287 Details of bonding type rmsd/Z covalent geometry : bond 0.00351 / 0.16 (33667) covalent geometry : angle 0.63530 / 0.34 (45845) hydrogen bonds : bond 0.05048 / 3.37 ( 1421) hydrogen bonds : angle 5.22774 / 3.72 ( 3940) metal coordination : bond 0.01223 / 0.86 ( 32) metal coordination : angle 4.67225 / 3.44 ( 45) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7672 Ramachandran restraints generated. 3836 Oldfield, 0 Emsley, 3836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7672 Ramachandran restraints generated. 3836 Oldfield, 0 Emsley, 3836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 447 residues out of total 3425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 404 time to evaluate : 1.330 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 455 MET cc_start: 0.9085 (ttp) cc_final: 0.8582 (ttp) REVERT: A 486 GLU cc_start: 0.8312 (tt0) cc_final: 0.8078 (tt0) REVERT: A 620 LYS cc_start: 0.9620 (mtpt) cc_final: 0.9385 (mtmm) REVERT: A 657 LEU cc_start: 0.9748 (tp) cc_final: 0.9506 (tt) REVERT: A 696 GLU cc_start: 0.9114 (tt0) cc_final: 0.8424 (tm-30) REVERT: A 838 GLN cc_start: 0.9291 (tp40) cc_final: 0.8674 (tp40) REVERT: A 1062 GLU cc_start: 0.7403 (mt-10) cc_final: 0.7140 (mt-10) REVERT: A 1207 LEU cc_start: 0.7940 (mt) cc_final: 0.7363 (mp) REVERT: A 1276 VAL cc_start: 0.9496 (t) cc_final: 0.8744 (t) REVERT: A 1309 ASP cc_start: 0.8608 (m-30) cc_final: 0.8039 (m-30) REVERT: A 1336 MET cc_start: 0.9428 (tmm) cc_final: 0.9084 (tmm) REVERT: A 1368 MET cc_start: 0.9075 (mtm) cc_final: 0.8646 (mtm) REVERT: A 1406 VAL cc_start: 0.9418 (OUTLIER) cc_final: 0.9193 (p) REVERT: A 1444 MET cc_start: 0.8900 (mmm) cc_final: 0.8682 (mmt) REVERT: B 296 GLU cc_start: 0.8913 (tt0) cc_final: 0.8501 (tp30) REVERT: B 310 MET cc_start: 0.9132 (mtp) cc_final: 0.8852 (mmm) REVERT: B 313 MET cc_start: 0.9119 (tpp) cc_final: 0.8685 (tpt) REVERT: B 809 MET cc_start: 0.9187 (mtt) cc_final: 0.8952 (mtp) REVERT: B 829 CYS cc_start: 0.7944 (m) cc_final: 0.7464 (m) REVERT: B 1072 MET cc_start: 0.8378 (mtp) cc_final: 0.8105 (mtp) REVERT: B 1098 MET cc_start: 0.8824 (mtm) cc_final: 0.8484 (mtm) REVERT: B 1111 MET cc_start: 0.8816 (mmm) cc_final: 0.8387 (mmt) REVERT: B 1138 MET cc_start: 0.9423 (mmm) cc_final: 0.9122 (tpp) REVERT: B 1206 GLU cc_start: 0.9069 (mt-10) cc_final: 0.8788 (mt-10) REVERT: C 82 TYR cc_start: 0.8509 (m-80) cc_final: 0.8208 (m-80) REVERT: C 190 ASP cc_start: 0.8779 (t0) cc_final: 0.8307 (t0) REVERT: D 1 MET cc_start: 0.1442 (ptm) cc_final: 0.0934 (pmm) REVERT: D 192 LYS cc_start: 0.4656 (mttt) cc_final: 0.4211 (mttt) REVERT: D 199 ASN cc_start: 0.5847 (m-40) cc_final: 0.5301 (p0) REVERT: E 22 MET cc_start: 0.9341 (ttm) cc_final: 0.9046 (ttm) REVERT: E 112 TYR cc_start: 0.9258 (p90) cc_final: 0.8696 (p90) REVERT: E 121 MET cc_start: 0.9426 (mpp) cc_final: 0.9149 (mpp) REVERT: E 214 CYS cc_start: 0.8400 (t) cc_final: 0.7985 (t) REVERT: F 76 LYS cc_start: 0.9370 (tptt) cc_final: 0.9147 (tppt) REVERT: F 110 ASP cc_start: 0.8540 (m-30) cc_final: 0.8246 (t0) REVERT: F 116 ASP cc_start: 0.9024 (t0) cc_final: 0.8675 (t0) REVERT: F 144 GLU cc_start: 0.8850 (mt-10) cc_final: 0.8639 (mt-10) REVERT: G 47 CYS cc_start: 0.9391 (t) cc_final: 0.8871 (t) REVERT: G 60 ARG cc_start: 0.9078 (ttp80) cc_final: 0.8823 (ttp80) REVERT: G 69 GLU cc_start: 0.9005 (tt0) cc_final: 0.8590 (tm-30) REVERT: G 75 ARG cc_start: 0.8503 (ttm170) cc_final: 0.7986 (ttt180) REVERT: G 115 MET cc_start: 0.5632 (mtm) cc_final: 0.4817 (ptm) REVERT: H 116 TYR cc_start: 0.9025 (m-80) cc_final: 0.8635 (m-80) REVERT: H 139 ASN cc_start: 0.9270 (m-40) cc_final: 0.8815 (m-40) REVERT: I 44 TYR cc_start: 0.8785 (t80) cc_final: 0.8467 (t80) REVERT: I 97 MET cc_start: 0.8573 (mtp) cc_final: 0.8152 (mtm) REVERT: K 16 GLU cc_start: 0.6903 (mp0) cc_final: 0.6533 (mp0) REVERT: K 17 SER cc_start: 0.9599 (m) cc_final: 0.9335 (p) REVERT: K 39 ASP cc_start: 0.8984 (p0) cc_final: 0.8579 (p0) REVERT: K 41 THR cc_start: 0.9425 (m) cc_final: 0.9114 (p) outliers start: 43 outliers final: 24 residues processed: 428 average time/residue: 0.2348 time to fit residues: 160.7916 Evaluate side-chains 373 residues out of total 3425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 348 time to evaluate : 1.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 755 PHE Chi-restraints excluded: chain A residue 1174 PHE Chi-restraints excluded: chain A residue 1228 TRP Chi-restraints excluded: chain A residue 1314 SER Chi-restraints excluded: chain A residue 1406 VAL Chi-restraints excluded: chain B residue 298 LEU Chi-restraints excluded: chain B residue 733 HIS Chi-restraints excluded: chain B residue 862 GLN Chi-restraints excluded: chain B residue 910 VAL Chi-restraints excluded: chain C residue 157 CYS Chi-restraints excluded: chain C residue 214 ASN Chi-restraints excluded: chain D residue 72 ARG Chi-restraints excluded: chain E residue 83 CYS Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 122 MET Chi-restraints excluded: chain G residue 1 MET Chi-restraints excluded: chain G residue 45 ILE Chi-restraints excluded: chain G residue 158 HIS Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain H residue 126 GLU Chi-restraints excluded: chain I residue 80 SER Chi-restraints excluded: chain J residue 9 SER Chi-restraints excluded: chain J residue 22 LEU Chi-restraints excluded: chain J residue 61 LEU Chi-restraints excluded: chain L residue 61 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 393 random chunks: chunk 302 optimal weight: 9.9990 chunk 390 optimal weight: 30.0000 chunk 167 optimal weight: 2.9990 chunk 186 optimal weight: 5.9990 chunk 89 optimal weight: 5.9990 chunk 258 optimal weight: 1.9990 chunk 179 optimal weight: 2.9990 chunk 296 optimal weight: 7.9990 chunk 335 optimal weight: 4.9990 chunk 310 optimal weight: 0.1980 chunk 155 optimal weight: 4.9990 overall best weight: 2.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 545 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 631 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 935 GLN A 994 GLN ** A1130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 513 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 734 HIS ** B 986 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 24 GLN H 137 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.079242 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2847 r_free = 0.2847 target = 0.054664 restraints weight = 107605.923| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.2890 r_free = 0.2890 target = 0.056315 restraints weight = 54748.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.2918 r_free = 0.2918 target = 0.057387 restraints weight = 35896.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.2936 r_free = 0.2936 target = 0.058067 restraints weight = 27639.721| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.2946 r_free = 0.2946 target = 0.058478 restraints weight = 23579.578| |-----------------------------------------------------------------------------| r_work (final): 0.2919 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8595 moved from start: 0.1985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 33699 Z= 0.189 Angle : 0.621 11.934 45890 Z= 0.322 Chirality : 0.044 0.216 5155 Planarity : 0.004 0.050 5606 Dihedral : 16.630 178.206 5258 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.33 % Favored : 95.57 % Rotamer: Outliers : 1.43 % Allowed : 8.44 % Favored : 90.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.46 (0.14), residues: 3836 helix: 1.55 (0.14), residues: 1339 sheet: -0.15 (0.21), residues: 599 loop : -0.39 (0.15), residues: 1898 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 320 TYR 0.027 0.001 TYR I 44 PHE 0.023 0.002 PHE A1402 TRP 0.013 0.001 TRP A1228 HIS 0.007 0.001 HIS A 287 Details of bonding type rmsd/Z covalent geometry : bond 0.00413 / 0.19 (33667) covalent geometry : angle 0.60492 / 0.32 (45845) hydrogen bonds : bond 0.04433 / 2.95 ( 1421) hydrogen bonds : angle 4.91983 / 3.51 ( 3940) metal coordination : bond 0.00984 / 0.70 ( 32) metal coordination : angle 4.51308 / 3.27 ( 45) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7672 Ramachandran restraints generated. 3836 Oldfield, 0 Emsley, 3836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7672 Ramachandran restraints generated. 3836 Oldfield, 0 Emsley, 3836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 411 residues out of total 3425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 362 time to evaluate : 1.434 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: A 304 MET cc_start: 0.9281 (mmm) cc_final: 0.8953 (mtp) REVERT: A 455 MET cc_start: 0.9075 (ttp) cc_final: 0.8149 (ttp) REVERT: A 486 GLU cc_start: 0.8270 (tt0) cc_final: 0.7764 (tt0) REVERT: A 620 LYS cc_start: 0.9630 (mtpt) cc_final: 0.9391 (mtmm) REVERT: A 838 GLN cc_start: 0.9301 (tp40) cc_final: 0.8675 (tp40) REVERT: A 1070 GLN cc_start: 0.9217 (mt0) cc_final: 0.8774 (mt0) REVERT: A 1207 LEU cc_start: 0.7317 (mt) cc_final: 0.6942 (mt) REVERT: A 1276 VAL cc_start: 0.9356 (t) cc_final: 0.8997 (p) REVERT: A 1336 MET cc_start: 0.9386 (tmm) cc_final: 0.9030 (tmm) REVERT: A 1368 MET cc_start: 0.9082 (mtm) cc_final: 0.8650 (mtm) REVERT: A 1406 VAL cc_start: 0.9440 (OUTLIER) cc_final: 0.9179 (p) REVERT: B 101 MET cc_start: 0.8692 (mtp) cc_final: 0.8244 (mmm) REVERT: B 173 MET cc_start: 0.8740 (ttp) cc_final: 0.7973 (ttp) REVERT: B 296 GLU cc_start: 0.8852 (tt0) cc_final: 0.8426 (tp30) REVERT: B 310 MET cc_start: 0.9091 (mtp) cc_final: 0.8765 (mmm) REVERT: B 313 MET cc_start: 0.9122 (tpp) cc_final: 0.8709 (tpt) REVERT: B 563 MET cc_start: 0.9095 (tmm) cc_final: 0.8828 (tmm) REVERT: B 615 MET cc_start: 0.8200 (mpp) cc_final: 0.7857 (mpp) REVERT: B 809 MET cc_start: 0.9205 (mtt) cc_final: 0.8956 (mtp) REVERT: B 829 CYS cc_start: 0.7956 (m) cc_final: 0.7723 (m) REVERT: B 860 MET cc_start: 0.8634 (tmm) cc_final: 0.8402 (tmm) REVERT: B 1072 MET cc_start: 0.8262 (mtp) cc_final: 0.7970 (mtp) REVERT: B 1098 MET cc_start: 0.8830 (mtm) cc_final: 0.8354 (mtm) REVERT: B 1111 MET cc_start: 0.8786 (mmm) cc_final: 0.8328 (mmt) REVERT: B 1138 MET cc_start: 0.9420 (mmm) cc_final: 0.9144 (tpp) REVERT: B 1206 GLU cc_start: 0.9066 (mt-10) cc_final: 0.8758 (mt-10) REVERT: C 75 MET cc_start: 0.9012 (mmm) cc_final: 0.8789 (tpp) REVERT: C 82 TYR cc_start: 0.8549 (m-80) cc_final: 0.8257 (m-80) REVERT: C 125 MET cc_start: 0.7813 (mpp) cc_final: 0.7555 (mpp) REVERT: D 1 MET cc_start: 0.1642 (ptm) cc_final: 0.0810 (pmm) REVERT: D 154 PHE cc_start: 0.5405 (m-80) cc_final: 0.4730 (m-80) REVERT: D 192 LYS cc_start: 0.4644 (mttt) cc_final: 0.4402 (mttt) REVERT: E 22 MET cc_start: 0.9338 (ttm) cc_final: 0.8999 (ttm) REVERT: E 112 TYR cc_start: 0.9286 (p90) cc_final: 0.8687 (p90) REVERT: E 121 MET cc_start: 0.9391 (mpp) cc_final: 0.8946 (mpp) REVERT: E 214 CYS cc_start: 0.8384 (t) cc_final: 0.8003 (t) REVERT: F 78 GLN cc_start: 0.9005 (OUTLIER) cc_final: 0.8658 (mp10) REVERT: F 110 ASP cc_start: 0.8586 (m-30) cc_final: 0.8299 (t0) REVERT: F 116 ASP cc_start: 0.9023 (t0) cc_final: 0.8684 (t0) REVERT: F 136 ARG cc_start: 0.9474 (mtt180) cc_final: 0.9234 (mtm-85) REVERT: F 144 GLU cc_start: 0.8868 (mt-10) cc_final: 0.8569 (mt-10) REVERT: G 47 CYS cc_start: 0.9474 (t) cc_final: 0.8894 (t) REVERT: G 60 ARG cc_start: 0.9074 (ttp80) cc_final: 0.8859 (ttp80) REVERT: G 69 GLU cc_start: 0.9059 (tt0) cc_final: 0.8608 (tm-30) REVERT: H 123 MET cc_start: 0.8697 (tmm) cc_final: 0.8038 (tmm) REVERT: H 139 ASN cc_start: 0.9276 (m-40) cc_final: 0.8801 (m-40) REVERT: I 44 TYR cc_start: 0.8845 (t80) cc_final: 0.8459 (t80) REVERT: K 6 ARG cc_start: 0.8846 (mmm-85) cc_final: 0.7998 (mmm-85) REVERT: K 16 GLU cc_start: 0.6856 (mp0) cc_final: 0.6613 (mp0) REVERT: K 17 SER cc_start: 0.9599 (m) cc_final: 0.9298 (p) REVERT: K 38 GLU cc_start: 0.8917 (mm-30) cc_final: 0.8625 (mm-30) REVERT: K 39 ASP cc_start: 0.9016 (p0) cc_final: 0.8521 (p0) REVERT: K 41 THR cc_start: 0.9430 (m) cc_final: 0.9064 (p) outliers start: 49 outliers final: 28 residues processed: 393 average time/residue: 0.2351 time to fit residues: 147.2789 Evaluate side-chains 366 residues out of total 3425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 336 time to evaluate : 1.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 449 SER Chi-restraints excluded: chain A residue 454 SER Chi-restraints excluded: chain A residue 755 PHE Chi-restraints excluded: chain A residue 848 ILE Chi-restraints excluded: chain A residue 1109 LYS Chi-restraints excluded: chain A residue 1174 PHE Chi-restraints excluded: chain A residue 1228 TRP Chi-restraints excluded: chain A residue 1406 VAL Chi-restraints excluded: chain B residue 152 ILE Chi-restraints excluded: chain B residue 298 LEU Chi-restraints excluded: chain B residue 637 LEU Chi-restraints excluded: chain B residue 685 LEU Chi-restraints excluded: chain B residue 733 HIS Chi-restraints excluded: chain B residue 862 GLN Chi-restraints excluded: chain B residue 910 VAL Chi-restraints excluded: chain C residue 157 CYS Chi-restraints excluded: chain C residue 214 ASN Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain E residue 83 CYS Chi-restraints excluded: chain F residue 78 GLN Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain G residue 45 ILE Chi-restraints excluded: chain G residue 158 HIS Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain H residue 105 GLU Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain I residue 80 SER Chi-restraints excluded: chain J residue 22 LEU Chi-restraints excluded: chain J residue 25 LEU Chi-restraints excluded: chain L residue 61 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 393 random chunks: chunk 11 optimal weight: 5.9990 chunk 370 optimal weight: 9.9990 chunk 69 optimal weight: 10.0000 chunk 97 optimal weight: 5.9990 chunk 179 optimal weight: 0.8980 chunk 100 optimal weight: 4.9990 chunk 392 optimal weight: 20.0000 chunk 292 optimal weight: 9.9990 chunk 105 optimal weight: 0.7980 chunk 270 optimal weight: 1.9990 chunk 293 optimal weight: 7.9990 overall best weight: 2.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 631 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1312 ASN B 215 GLN B 513 GLN B 734 HIS ** B 986 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 54 GLN G 24 GLN H 137 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.078938 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2823 r_free = 0.2823 target = 0.053832 restraints weight = 109327.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.2868 r_free = 0.2868 target = 0.055506 restraints weight = 56330.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.2896 r_free = 0.2896 target = 0.056589 restraints weight = 37225.785| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.2913 r_free = 0.2913 target = 0.057270 restraints weight = 28823.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.2923 r_free = 0.2923 target = 0.057655 restraints weight = 24724.982| |-----------------------------------------------------------------------------| r_work (final): 0.2901 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8615 moved from start: 0.2192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 33699 Z= 0.199 Angle : 0.609 12.145 45890 Z= 0.314 Chirality : 0.044 0.219 5155 Planarity : 0.004 0.051 5606 Dihedral : 16.624 178.264 5258 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.33 % Favored : 95.57 % Rotamer: Outliers : 1.55 % Allowed : 9.66 % Favored : 88.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.46 (0.14), residues: 3836 helix: 1.56 (0.14), residues: 1341 sheet: -0.19 (0.21), residues: 601 loop : -0.38 (0.15), residues: 1894 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 617 TYR 0.022 0.001 TYR I 44 PHE 0.025 0.001 PHE B 429 TRP 0.012 0.001 TRP A1228 HIS 0.006 0.001 HIS A 287 Details of bonding type rmsd/Z covalent geometry : bond 0.00436 / 0.20 (33667) covalent geometry : angle 0.59412 / 0.31 (45845) hydrogen bonds : bond 0.04087 / 2.71 ( 1421) hydrogen bonds : angle 4.78666 / 3.42 ( 3940) metal coordination : bond 0.00780 / 0.53 ( 32) metal coordination : angle 4.36466 / 3.18 ( 45) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7672 Ramachandran restraints generated. 3836 Oldfield, 0 Emsley, 3836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7672 Ramachandran restraints generated. 3836 Oldfield, 0 Emsley, 3836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 418 residues out of total 3425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 365 time to evaluate : 1.304 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: A 838 GLN cc_start: 0.9306 (tp40) cc_final: 0.8809 (tm-30) REVERT: A 873 MET cc_start: 0.8709 (mmm) cc_final: 0.7540 (mmp) REVERT: A 919 ILE cc_start: 0.9456 (mm) cc_final: 0.9164 (mm) REVERT: A 1207 LEU cc_start: 0.7448 (mt) cc_final: 0.7248 (mt) REVERT: A 1336 MET cc_start: 0.9381 (tmm) cc_final: 0.9131 (tmm) REVERT: A 1368 MET cc_start: 0.9104 (mtm) cc_final: 0.8665 (mtm) REVERT: A 1406 VAL cc_start: 0.9494 (OUTLIER) cc_final: 0.9266 (p) REVERT: B 101 MET cc_start: 0.8737 (mtp) cc_final: 0.8352 (mmm) REVERT: B 296 GLU cc_start: 0.8909 (tt0) cc_final: 0.8492 (tp30) REVERT: B 310 MET cc_start: 0.9116 (mtp) cc_final: 0.8847 (mmm) REVERT: B 394 ASP cc_start: 0.8245 (t0) cc_final: 0.7759 (t0) REVERT: B 563 MET cc_start: 0.9100 (tmm) cc_final: 0.8840 (tmm) REVERT: B 615 MET cc_start: 0.8320 (mpp) cc_final: 0.7946 (mpp) REVERT: B 809 MET cc_start: 0.9219 (mtt) cc_final: 0.9002 (mtp) REVERT: B 860 MET cc_start: 0.8687 (tmm) cc_final: 0.8287 (tmm) REVERT: B 1072 MET cc_start: 0.8270 (mtp) cc_final: 0.7986 (mtp) REVERT: B 1098 MET cc_start: 0.8846 (mtm) cc_final: 0.8531 (mtm) REVERT: B 1111 MET cc_start: 0.8838 (mmm) cc_final: 0.8347 (mmt) REVERT: B 1206 GLU cc_start: 0.9083 (mt-10) cc_final: 0.8795 (mt-10) REVERT: C 37 MET cc_start: 0.8749 (mtm) cc_final: 0.8437 (mtm) REVERT: C 75 MET cc_start: 0.9038 (mmm) cc_final: 0.8828 (tpp) REVERT: C 82 TYR cc_start: 0.8588 (m-80) cc_final: 0.8264 (m-80) REVERT: C 125 MET cc_start: 0.7898 (mpp) cc_final: 0.7669 (mpp) REVERT: C 265 MET cc_start: 0.8144 (tmm) cc_final: 0.7938 (tmm) REVERT: D 1 MET cc_start: 0.1243 (ptm) cc_final: 0.0516 (pmm) REVERT: D 192 LYS cc_start: 0.4660 (mttt) cc_final: 0.4373 (mttt) REVERT: D 209 ARG cc_start: 0.7495 (ptm160) cc_final: 0.6863 (ptp-170) REVERT: E 112 TYR cc_start: 0.9282 (p90) cc_final: 0.8730 (p90) REVERT: E 121 MET cc_start: 0.9452 (mpp) cc_final: 0.8930 (mpp) REVERT: E 214 CYS cc_start: 0.8376 (t) cc_final: 0.7960 (t) REVERT: F 78 GLN cc_start: 0.8988 (OUTLIER) cc_final: 0.8638 (mp10) REVERT: F 110 ASP cc_start: 0.8666 (m-30) cc_final: 0.8352 (t0) REVERT: F 116 ASP cc_start: 0.9007 (t0) cc_final: 0.8663 (t0) REVERT: F 136 ARG cc_start: 0.9479 (mtt180) cc_final: 0.9028 (ttm170) REVERT: F 144 GLU cc_start: 0.8879 (mt-10) cc_final: 0.8570 (mt-10) REVERT: G 33 GLU cc_start: 0.8501 (mm-30) cc_final: 0.8089 (mp0) REVERT: G 47 CYS cc_start: 0.9475 (t) cc_final: 0.8897 (t) REVERT: G 60 ARG cc_start: 0.9045 (ttp80) cc_final: 0.8778 (ttp80) REVERT: G 69 GLU cc_start: 0.9050 (tt0) cc_final: 0.8572 (tm-30) REVERT: G 75 ARG cc_start: 0.8507 (ttm170) cc_final: 0.8149 (ttt180) REVERT: H 123 MET cc_start: 0.8806 (tmm) cc_final: 0.7984 (tmm) REVERT: H 139 ASN cc_start: 0.9303 (m-40) cc_final: 0.8829 (m-40) REVERT: H 141 TYR cc_start: 0.9308 (m-80) cc_final: 0.8650 (m-10) REVERT: I 44 TYR cc_start: 0.8833 (t80) cc_final: 0.8451 (t80) REVERT: I 45 ARG cc_start: 0.6779 (ttt90) cc_final: 0.6404 (ttt-90) REVERT: I 70 ARG cc_start: 0.7996 (mtt90) cc_final: 0.7184 (mtp180) REVERT: I 91 ARG cc_start: 0.8713 (mmt90) cc_final: 0.8372 (mmm-85) REVERT: K 6 ARG cc_start: 0.8858 (mmm-85) cc_final: 0.8019 (mmm-85) REVERT: K 8 GLU cc_start: 0.9058 (mt-10) cc_final: 0.8414 (mt-10) REVERT: K 16 GLU cc_start: 0.6972 (mp0) cc_final: 0.6646 (mp0) REVERT: K 17 SER cc_start: 0.9602 (m) cc_final: 0.9301 (p) REVERT: K 38 GLU cc_start: 0.8852 (mm-30) cc_final: 0.8578 (mm-30) REVERT: K 39 ASP cc_start: 0.8993 (p0) cc_final: 0.8508 (p0) REVERT: K 41 THR cc_start: 0.9434 (m) cc_final: 0.9066 (p) outliers start: 53 outliers final: 36 residues processed: 399 average time/residue: 0.2474 time to fit residues: 154.9649 Evaluate side-chains 381 residues out of total 3425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 343 time to evaluate : 1.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 449 SER Chi-restraints excluded: chain A residue 755 PHE Chi-restraints excluded: chain A residue 848 ILE Chi-restraints excluded: chain A residue 1109 LYS Chi-restraints excluded: chain A residue 1174 PHE Chi-restraints excluded: chain A residue 1228 TRP Chi-restraints excluded: chain A residue 1406 VAL Chi-restraints excluded: chain A residue 1445 ILE Chi-restraints excluded: chain B residue 152 ILE Chi-restraints excluded: chain B residue 298 LEU Chi-restraints excluded: chain B residue 637 LEU Chi-restraints excluded: chain B residue 685 LEU Chi-restraints excluded: chain B residue 733 HIS Chi-restraints excluded: chain B residue 862 GLN Chi-restraints excluded: chain B residue 910 VAL Chi-restraints excluded: chain B residue 1009 ASP Chi-restraints excluded: chain B residue 1095 LEU Chi-restraints excluded: chain B residue 1202 LEU Chi-restraints excluded: chain C residue 157 CYS Chi-restraints excluded: chain C residue 214 ASN Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain D residue 72 ARG Chi-restraints excluded: chain E residue 83 CYS Chi-restraints excluded: chain F residue 78 GLN Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain G residue 22 MET Chi-restraints excluded: chain G residue 45 ILE Chi-restraints excluded: chain G residue 120 THR Chi-restraints excluded: chain G residue 158 HIS Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain H residue 126 GLU Chi-restraints excluded: chain I residue 80 SER Chi-restraints excluded: chain J residue 3 VAL Chi-restraints excluded: chain J residue 22 LEU Chi-restraints excluded: chain J residue 25 LEU Chi-restraints excluded: chain J residue 52 THR Chi-restraints excluded: chain L residue 61 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 393 random chunks: chunk 370 optimal weight: 9.9990 chunk 11 optimal weight: 3.9990 chunk 63 optimal weight: 6.9990 chunk 22 optimal weight: 3.9990 chunk 275 optimal weight: 5.9990 chunk 98 optimal weight: 3.9990 chunk 269 optimal weight: 5.9990 chunk 245 optimal weight: 4.9990 chunk 85 optimal weight: 5.9990 chunk 376 optimal weight: 5.9990 chunk 76 optimal weight: 3.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 631 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1188 GLN ** A1427 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 366 GLN ** B 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 734 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 770 GLN ** B 986 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 23 ASN ** D 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 143 ASN G 24 GLN H 11 GLN H 131 ASN H 137 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.077803 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2795 r_free = 0.2795 target = 0.052848 restraints weight = 110535.744| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.2840 r_free = 0.2840 target = 0.054483 restraints weight = 57148.254| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.2868 r_free = 0.2868 target = 0.055552 restraints weight = 37927.696| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.2885 r_free = 0.2885 target = 0.056214 restraints weight = 29366.666| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.2895 r_free = 0.2895 target = 0.056620 restraints weight = 25184.475| |-----------------------------------------------------------------------------| r_work (final): 0.2871 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8642 moved from start: 0.2388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 33699 Z= 0.267 Angle : 0.655 13.326 45890 Z= 0.335 Chirality : 0.044 0.221 5155 Planarity : 0.004 0.050 5606 Dihedral : 16.675 178.680 5258 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 10.54 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.77 % Favored : 95.13 % Rotamer: Outliers : 1.69 % Allowed : 10.92 % Favored : 87.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.33 (0.14), residues: 3836 helix: 1.47 (0.14), residues: 1334 sheet: -0.30 (0.21), residues: 604 loop : -0.45 (0.15), residues: 1898 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 119 TYR 0.021 0.002 TYR I 15 PHE 0.031 0.002 PHE D 154 TRP 0.014 0.001 TRP B 561 HIS 0.008 0.001 HIS J 53 Details of bonding type rmsd/Z covalent geometry : bond 0.00583 / 0.27 (33667) covalent geometry : angle 0.63762 / 0.33 (45845) hydrogen bonds : bond 0.04176 / 2.75 ( 1421) hydrogen bonds : angle 4.82002 / 3.44 ( 3940) metal coordination : bond 0.00987 / 0.65 ( 32) metal coordination : angle 4.84598 / 3.47 ( 45) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7672 Ramachandran restraints generated. 3836 Oldfield, 0 Emsley, 3836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7672 Ramachandran restraints generated. 3836 Oldfield, 0 Emsley, 3836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 393 residues out of total 3425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 335 time to evaluate : 1.264 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: A 486 GLU cc_start: 0.8460 (tt0) cc_final: 0.8078 (tt0) REVERT: A 838 GLN cc_start: 0.9335 (tp40) cc_final: 0.8689 (tp40) REVERT: A 1062 GLU cc_start: 0.7732 (mt-10) cc_final: 0.7459 (mt-10) REVERT: A 1276 VAL cc_start: 0.9322 (t) cc_final: 0.9053 (p) REVERT: A 1336 MET cc_start: 0.9373 (tmm) cc_final: 0.9119 (tmm) REVERT: A 1368 MET cc_start: 0.9113 (mtm) cc_final: 0.8713 (mtm) REVERT: A 1406 VAL cc_start: 0.9513 (OUTLIER) cc_final: 0.9282 (p) REVERT: B 101 MET cc_start: 0.8732 (mtp) cc_final: 0.8344 (mmm) REVERT: B 296 GLU cc_start: 0.8755 (tt0) cc_final: 0.8350 (tp30) REVERT: B 310 MET cc_start: 0.9072 (mtp) cc_final: 0.8863 (mmm) REVERT: B 615 MET cc_start: 0.8419 (mpp) cc_final: 0.8043 (mpp) REVERT: B 778 MET cc_start: 0.8696 (ttp) cc_final: 0.8428 (ttm) REVERT: B 809 MET cc_start: 0.9247 (mtt) cc_final: 0.9020 (mtp) REVERT: B 860 MET cc_start: 0.8756 (tmm) cc_final: 0.8336 (tmm) REVERT: B 887 HIS cc_start: 0.7279 (t70) cc_final: 0.7059 (t70) REVERT: B 1072 MET cc_start: 0.8308 (mtp) cc_final: 0.7991 (mtp) REVERT: B 1098 MET cc_start: 0.8849 (mtm) cc_final: 0.8446 (mtm) REVERT: B 1111 MET cc_start: 0.8818 (mmm) cc_final: 0.8272 (mmt) REVERT: C 82 TYR cc_start: 0.8632 (m-80) cc_final: 0.8353 (m-80) REVERT: C 125 MET cc_start: 0.7965 (mpp) cc_final: 0.7657 (mpp) REVERT: C 265 MET cc_start: 0.8118 (tmm) cc_final: 0.7884 (tmm) REVERT: D 1 MET cc_start: 0.1195 (ptm) cc_final: 0.0873 (mmt) REVERT: D 192 LYS cc_start: 0.4850 (mttt) cc_final: 0.4472 (mtmt) REVERT: E 112 TYR cc_start: 0.9315 (p90) cc_final: 0.8718 (p90) REVERT: E 214 CYS cc_start: 0.8402 (t) cc_final: 0.8031 (t) REVERT: F 78 GLN cc_start: 0.9008 (OUTLIER) cc_final: 0.8643 (mp10) REVERT: F 81 THR cc_start: 0.9525 (OUTLIER) cc_final: 0.9229 (p) REVERT: F 116 ASP cc_start: 0.9025 (t0) cc_final: 0.8661 (t0) REVERT: F 144 GLU cc_start: 0.8851 (mt-10) cc_final: 0.8552 (mt-10) REVERT: G 47 CYS cc_start: 0.9491 (t) cc_final: 0.8901 (t) REVERT: G 57 GLN cc_start: 0.8582 (mm-40) cc_final: 0.8210 (mm110) REVERT: G 60 ARG cc_start: 0.9070 (ttp80) cc_final: 0.8822 (ttp80) REVERT: G 69 GLU cc_start: 0.9017 (tt0) cc_final: 0.8548 (tm-30) REVERT: G 75 ARG cc_start: 0.8403 (ttm170) cc_final: 0.8108 (ttt180) REVERT: H 22 LYS cc_start: 0.9119 (mmmt) cc_final: 0.8827 (mtpt) REVERT: H 123 MET cc_start: 0.8988 (tmm) cc_final: 0.8516 (tmm) REVERT: H 139 ASN cc_start: 0.9321 (m-40) cc_final: 0.9072 (m-40) REVERT: H 141 TYR cc_start: 0.9336 (m-80) cc_final: 0.8661 (m-10) REVERT: I 44 TYR cc_start: 0.8809 (t80) cc_final: 0.8440 (t80) REVERT: J 49 MET cc_start: 0.9177 (tpp) cc_final: 0.8893 (tpp) REVERT: K 16 GLU cc_start: 0.6965 (mp0) cc_final: 0.6599 (mp0) REVERT: K 17 SER cc_start: 0.9593 (m) cc_final: 0.9218 (p) REVERT: K 38 GLU cc_start: 0.8839 (mm-30) cc_final: 0.8591 (mm-30) REVERT: K 39 ASP cc_start: 0.9021 (p0) cc_final: 0.8562 (p0) REVERT: K 41 THR cc_start: 0.9437 (m) cc_final: 0.9070 (p) REVERT: L 37 LYS cc_start: 0.9184 (mmtm) cc_final: 0.8447 (mmtt) outliers start: 58 outliers final: 39 residues processed: 374 average time/residue: 0.2340 time to fit residues: 139.8952 Evaluate side-chains 366 residues out of total 3425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 324 time to evaluate : 1.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 454 SER Chi-restraints excluded: chain A residue 755 PHE Chi-restraints excluded: chain A residue 790 ASP Chi-restraints excluded: chain A residue 848 ILE Chi-restraints excluded: chain A residue 1109 LYS Chi-restraints excluded: chain A residue 1174 PHE Chi-restraints excluded: chain A residue 1228 TRP Chi-restraints excluded: chain A residue 1406 VAL Chi-restraints excluded: chain A residue 1445 ILE Chi-restraints excluded: chain B residue 152 ILE Chi-restraints excluded: chain B residue 298 LEU Chi-restraints excluded: chain B residue 391 ASP Chi-restraints excluded: chain B residue 637 LEU Chi-restraints excluded: chain B residue 685 LEU Chi-restraints excluded: chain B residue 733 HIS Chi-restraints excluded: chain B residue 862 GLN Chi-restraints excluded: chain B residue 910 VAL Chi-restraints excluded: chain B residue 1009 ASP Chi-restraints excluded: chain B residue 1095 LEU Chi-restraints excluded: chain B residue 1196 ILE Chi-restraints excluded: chain C residue 157 CYS Chi-restraints excluded: chain C residue 214 ASN Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain D residue 72 ARG Chi-restraints excluded: chain E residue 83 CYS Chi-restraints excluded: chain E residue 199 ILE Chi-restraints excluded: chain F residue 78 GLN Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain G residue 120 THR Chi-restraints excluded: chain G residue 158 HIS Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain H residue 126 GLU Chi-restraints excluded: chain I residue 43 VAL Chi-restraints excluded: chain I residue 80 SER Chi-restraints excluded: chain J residue 3 VAL Chi-restraints excluded: chain J residue 22 LEU Chi-restraints excluded: chain J residue 25 LEU Chi-restraints excluded: chain J residue 42 LYS Chi-restraints excluded: chain K residue 25 THR Chi-restraints excluded: chain L residue 61 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 393 random chunks: chunk 320 optimal weight: 0.8980 chunk 260 optimal weight: 0.9990 chunk 327 optimal weight: 20.0000 chunk 19 optimal weight: 0.8980 chunk 9 optimal weight: 1.9990 chunk 166 optimal weight: 3.9990 chunk 80 optimal weight: 0.4980 chunk 294 optimal weight: 9.9990 chunk 373 optimal weight: 3.9990 chunk 202 optimal weight: 6.9990 chunk 151 optimal weight: 3.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 631 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1203 ASN B 734 HIS ** B 986 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1117 GLN ** D 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 24 GLN H 137 GLN J 53 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.079736 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2860 r_free = 0.2860 target = 0.055106 restraints weight = 107010.522| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.2905 r_free = 0.2905 target = 0.056793 restraints weight = 54358.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.2933 r_free = 0.2933 target = 0.057892 restraints weight = 35586.863| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.2950 r_free = 0.2950 target = 0.058573 restraints weight = 27344.852| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.058991 restraints weight = 23292.668| |-----------------------------------------------------------------------------| r_work (final): 0.2932 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8581 moved from start: 0.2537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 33699 Z= 0.119 Angle : 0.576 11.162 45890 Z= 0.296 Chirality : 0.043 0.228 5155 Planarity : 0.004 0.048 5606 Dihedral : 16.544 178.288 5258 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.91 % Favored : 95.99 % Rotamer: Outliers : 1.43 % Allowed : 11.82 % Favored : 86.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.53 (0.14), residues: 3836 helix: 1.63 (0.15), residues: 1333 sheet: -0.07 (0.21), residues: 591 loop : -0.37 (0.15), residues: 1912 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 617 TYR 0.019 0.001 TYR D 147 PHE 0.025 0.001 PHE D 154 TRP 0.014 0.001 TRP A1228 HIS 0.008 0.001 HIS A 287 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.12 (33667) covalent geometry : angle 0.56079 / 0.30 (45845) hydrogen bonds : bond 0.03692 / 2.47 ( 1421) hydrogen bonds : angle 4.51329 / 3.23 ( 3940) metal coordination : bond 0.00671 / 0.44 ( 32) metal coordination : angle 4.27225 / 3.26 ( 45) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7672 Ramachandran restraints generated. 3836 Oldfield, 0 Emsley, 3836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7672 Ramachandran restraints generated. 3836 Oldfield, 0 Emsley, 3836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 426 residues out of total 3425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 377 time to evaluate : 1.302 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: A 122 MET cc_start: 0.9053 (tpp) cc_final: 0.8647 (tpp) REVERT: A 261 ASP cc_start: 0.8761 (m-30) cc_final: 0.8248 (m-30) REVERT: A 487 MET cc_start: 0.8769 (mtp) cc_final: 0.8244 (mmm) REVERT: A 838 GLN cc_start: 0.9263 (tp40) cc_final: 0.8650 (tp40) REVERT: A 919 ILE cc_start: 0.9468 (mm) cc_final: 0.9151 (mm) REVERT: A 1062 GLU cc_start: 0.7609 (mt-10) cc_final: 0.7318 (mt-10) REVERT: A 1336 MET cc_start: 0.9371 (tmm) cc_final: 0.9149 (tmm) REVERT: A 1368 MET cc_start: 0.9030 (mtm) cc_final: 0.8597 (mtm) REVERT: A 1406 VAL cc_start: 0.9464 (OUTLIER) cc_final: 0.9193 (p) REVERT: B 101 MET cc_start: 0.8688 (mtp) cc_final: 0.8290 (mmm) REVERT: B 296 GLU cc_start: 0.8827 (tt0) cc_final: 0.8414 (tp30) REVERT: B 615 MET cc_start: 0.8356 (mpp) cc_final: 0.8005 (mpp) REVERT: B 809 MET cc_start: 0.9189 (mtt) cc_final: 0.8972 (mtp) REVERT: B 860 MET cc_start: 0.8716 (tmm) cc_final: 0.8255 (tmm) REVERT: B 887 HIS cc_start: 0.7225 (t70) cc_final: 0.7020 (t70) REVERT: B 1020 ARG cc_start: 0.7725 (mtt180) cc_final: 0.7195 (mtt90) REVERT: B 1098 MET cc_start: 0.8817 (mtm) cc_final: 0.8478 (mtm) REVERT: B 1111 MET cc_start: 0.8847 (mmm) cc_final: 0.8395 (mmt) REVERT: C 82 TYR cc_start: 0.8607 (m-80) cc_final: 0.8323 (m-80) REVERT: C 125 MET cc_start: 0.8001 (mpp) cc_final: 0.7696 (mpp) REVERT: D 1 MET cc_start: 0.1308 (ptm) cc_final: 0.0507 (pmm) REVERT: D 192 LYS cc_start: 0.4640 (mttt) cc_final: 0.4270 (mtmt) REVERT: D 209 ARG cc_start: 0.7611 (ptm160) cc_final: 0.7014 (ptp-170) REVERT: E 112 TYR cc_start: 0.9250 (p90) cc_final: 0.8710 (p90) REVERT: E 214 CYS cc_start: 0.8377 (t) cc_final: 0.7989 (t) REVERT: F 78 GLN cc_start: 0.8994 (OUTLIER) cc_final: 0.8658 (mp10) REVERT: F 89 GLU cc_start: 0.9118 (mt-10) cc_final: 0.8664 (mt-10) REVERT: F 114 GLU cc_start: 0.8320 (tp30) cc_final: 0.8100 (tm-30) REVERT: F 116 ASP cc_start: 0.9003 (t0) cc_final: 0.8514 (t0) REVERT: F 144 GLU cc_start: 0.8847 (mt-10) cc_final: 0.8524 (mt-10) REVERT: G 31 LEU cc_start: 0.9026 (mt) cc_final: 0.8750 (pp) REVERT: G 35 GLU cc_start: 0.8267 (mm-30) cc_final: 0.7986 (mm-30) REVERT: G 47 CYS cc_start: 0.9517 (t) cc_final: 0.8779 (t) REVERT: G 60 ARG cc_start: 0.9052 (ttp80) cc_final: 0.8799 (ttp80) REVERT: G 69 GLU cc_start: 0.9006 (tt0) cc_final: 0.8527 (tm-30) REVERT: G 75 ARG cc_start: 0.8416 (ttm170) cc_final: 0.8092 (ttt180) REVERT: H 22 LYS cc_start: 0.9064 (mmmt) cc_final: 0.8812 (mtpt) REVERT: H 139 ASN cc_start: 0.9290 (m-40) cc_final: 0.8796 (m-40) REVERT: H 141 TYR cc_start: 0.9273 (m-80) cc_final: 0.8652 (m-10) REVERT: I 44 TYR cc_start: 0.8834 (t80) cc_final: 0.8552 (t80) REVERT: K 6 ARG cc_start: 0.8747 (mmm-85) cc_final: 0.7892 (mmm-85) REVERT: K 8 GLU cc_start: 0.9005 (mt-10) cc_final: 0.8596 (mt-10) REVERT: K 16 GLU cc_start: 0.6982 (mp0) cc_final: 0.6585 (mp0) REVERT: K 17 SER cc_start: 0.9592 (m) cc_final: 0.9235 (p) REVERT: K 38 GLU cc_start: 0.8824 (mm-30) cc_final: 0.8551 (mm-30) REVERT: K 39 ASP cc_start: 0.8896 (p0) cc_final: 0.8379 (p0) REVERT: K 41 THR cc_start: 0.9420 (m) cc_final: 0.9042 (p) outliers start: 49 outliers final: 29 residues processed: 407 average time/residue: 0.2312 time to fit residues: 151.5659 Evaluate side-chains 364 residues out of total 3425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 333 time to evaluate : 1.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 436 ILE Chi-restraints excluded: chain A residue 449 SER Chi-restraints excluded: chain A residue 755 PHE Chi-restraints excluded: chain A residue 848 ILE Chi-restraints excluded: chain A residue 1109 LYS Chi-restraints excluded: chain A residue 1174 PHE Chi-restraints excluded: chain A residue 1228 TRP Chi-restraints excluded: chain A residue 1406 VAL Chi-restraints excluded: chain A residue 1445 ILE Chi-restraints excluded: chain B residue 152 ILE Chi-restraints excluded: chain B residue 298 LEU Chi-restraints excluded: chain B residue 305 VAL Chi-restraints excluded: chain B residue 637 LEU Chi-restraints excluded: chain B residue 733 HIS Chi-restraints excluded: chain B residue 862 GLN Chi-restraints excluded: chain B residue 1009 ASP Chi-restraints excluded: chain B residue 1095 LEU Chi-restraints excluded: chain C residue 157 CYS Chi-restraints excluded: chain C residue 214 ASN Chi-restraints excluded: chain D residue 72 ARG Chi-restraints excluded: chain F residue 78 GLN Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain G residue 22 MET Chi-restraints excluded: chain G residue 144 ARG Chi-restraints excluded: chain G residue 158 HIS Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain H residue 97 MET Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain I residue 43 VAL Chi-restraints excluded: chain I residue 80 SER Chi-restraints excluded: chain J residue 22 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 393 random chunks: chunk 294 optimal weight: 8.9990 chunk 19 optimal weight: 3.9990 chunk 12 optimal weight: 7.9990 chunk 98 optimal weight: 7.9990 chunk 305 optimal weight: 0.9980 chunk 261 optimal weight: 1.9990 chunk 218 optimal weight: 10.0000 chunk 196 optimal weight: 8.9990 chunk 17 optimal weight: 3.9990 chunk 129 optimal weight: 5.9990 chunk 83 optimal weight: 8.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 545 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 631 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1427 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 734 HIS ** B 986 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.078389 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2816 r_free = 0.2816 target = 0.053599 restraints weight = 109755.393| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.2860 r_free = 0.2860 target = 0.055230 restraints weight = 56711.971| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.2889 r_free = 0.2889 target = 0.056322 restraints weight = 37650.029| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 50)----------------| | r_work = 0.2906 r_free = 0.2906 target = 0.056999 restraints weight = 28987.193| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.2917 r_free = 0.2917 target = 0.057386 restraints weight = 24766.728| |-----------------------------------------------------------------------------| r_work (final): 0.2889 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8627 moved from start: 0.2613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 33699 Z= 0.225 Angle : 0.635 11.863 45890 Z= 0.324 Chirality : 0.044 0.225 5155 Planarity : 0.004 0.047 5606 Dihedral : 16.512 178.553 5258 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.56 % Favored : 95.36 % Rotamer: Outliers : 1.43 % Allowed : 13.20 % Favored : 85.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.43 (0.14), residues: 3836 helix: 1.57 (0.15), residues: 1331 sheet: -0.19 (0.21), residues: 591 loop : -0.43 (0.15), residues: 1914 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG D 56 TYR 0.023 0.001 TYR A 852 PHE 0.020 0.001 PHE D 151 TRP 0.015 0.001 TRP B 308 HIS 0.007 0.001 HIS A 287 Details of bonding type rmsd/Z covalent geometry : bond 0.00495 / 0.22 (33667) covalent geometry : angle 0.62029 / 0.32 (45845) hydrogen bonds : bond 0.03847 / 2.54 ( 1421) hydrogen bonds : angle 4.59373 / 3.27 ( 3940) metal coordination : bond 0.00782 / 0.52 ( 32) metal coordination : angle 4.40844 / 3.23 ( 45) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7672 Ramachandran restraints generated. 3836 Oldfield, 0 Emsley, 3836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7672 Ramachandran restraints generated. 3836 Oldfield, 0 Emsley, 3836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 382 residues out of total 3425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 333 time to evaluate : 1.302 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 261 ASP cc_start: 0.8816 (m-30) cc_final: 0.8297 (m-30) REVERT: A 838 GLN cc_start: 0.9304 (tp40) cc_final: 0.8816 (tm-30) REVERT: A 919 ILE cc_start: 0.9473 (mm) cc_final: 0.9155 (mm) REVERT: A 1062 GLU cc_start: 0.7659 (mt-10) cc_final: 0.7349 (mt-10) REVERT: A 1070 GLN cc_start: 0.9298 (OUTLIER) cc_final: 0.9017 (tm-30) REVERT: A 1315 GLU cc_start: 0.8549 (tm-30) cc_final: 0.8348 (tm-30) REVERT: A 1368 MET cc_start: 0.9021 (mtm) cc_final: 0.8613 (mtm) REVERT: A 1406 VAL cc_start: 0.9517 (OUTLIER) cc_final: 0.9280 (p) REVERT: B 101 MET cc_start: 0.8746 (mtp) cc_final: 0.8329 (mmm) REVERT: B 296 GLU cc_start: 0.8749 (tt0) cc_final: 0.8343 (tp30) REVERT: B 615 MET cc_start: 0.8414 (mpp) cc_final: 0.8033 (mpp) REVERT: B 778 MET cc_start: 0.8674 (ttp) cc_final: 0.8462 (ttm) REVERT: B 809 MET cc_start: 0.9237 (mtt) cc_final: 0.9008 (mtp) REVERT: B 860 MET cc_start: 0.8741 (tmm) cc_final: 0.8285 (tmm) REVERT: B 887 HIS cc_start: 0.7268 (t70) cc_final: 0.7053 (t70) REVERT: B 1098 MET cc_start: 0.8825 (mtm) cc_final: 0.8529 (mtm) REVERT: B 1111 MET cc_start: 0.8834 (mmm) cc_final: 0.8313 (mmt) REVERT: C 82 TYR cc_start: 0.8642 (m-80) cc_final: 0.8368 (m-80) REVERT: C 125 MET cc_start: 0.8004 (mpp) cc_final: 0.7697 (mpp) REVERT: D 192 LYS cc_start: 0.4786 (mttt) cc_final: 0.4409 (mtmt) REVERT: D 209 ARG cc_start: 0.7565 (ptm160) cc_final: 0.6965 (ptp-170) REVERT: E 112 TYR cc_start: 0.9316 (p90) cc_final: 0.8766 (p90) REVERT: E 214 CYS cc_start: 0.8426 (t) cc_final: 0.8066 (t) REVERT: F 78 GLN cc_start: 0.9032 (OUTLIER) cc_final: 0.8679 (mp10) REVERT: F 114 GLU cc_start: 0.8385 (tp30) cc_final: 0.8138 (tm-30) REVERT: F 116 ASP cc_start: 0.9027 (t0) cc_final: 0.8530 (t0) REVERT: F 144 GLU cc_start: 0.8903 (mt-10) cc_final: 0.8537 (mt-10) REVERT: G 33 GLU cc_start: 0.7870 (mp0) cc_final: 0.7518 (mp0) REVERT: G 35 GLU cc_start: 0.8285 (mm-30) cc_final: 0.8015 (mm-30) REVERT: G 47 CYS cc_start: 0.9510 (t) cc_final: 0.8717 (t) REVERT: G 57 GLN cc_start: 0.8534 (mm-40) cc_final: 0.8181 (mm110) REVERT: G 60 ARG cc_start: 0.9062 (ttp80) cc_final: 0.8840 (ttp80) REVERT: G 69 GLU cc_start: 0.9038 (tt0) cc_final: 0.8563 (tm-30) REVERT: G 75 ARG cc_start: 0.8389 (ttm170) cc_final: 0.8067 (ttt180) REVERT: H 14 GLU cc_start: 0.8130 (tm-30) cc_final: 0.7740 (tm-30) REVERT: H 123 MET cc_start: 0.8907 (tmm) cc_final: 0.8393 (tmm) REVERT: H 139 ASN cc_start: 0.9353 (m-40) cc_final: 0.9103 (m-40) REVERT: H 141 TYR cc_start: 0.9345 (m-80) cc_final: 0.8670 (m-10) REVERT: I 44 TYR cc_start: 0.8852 (t80) cc_final: 0.8540 (t80) REVERT: J 49 MET cc_start: 0.9102 (tpp) cc_final: 0.8809 (tpp) REVERT: K 17 SER cc_start: 0.9594 (m) cc_final: 0.9225 (p) REVERT: K 38 GLU cc_start: 0.8797 (mm-30) cc_final: 0.8515 (mm-30) REVERT: K 39 ASP cc_start: 0.8973 (p0) cc_final: 0.8438 (p0) REVERT: K 41 THR cc_start: 0.9417 (m) cc_final: 0.9063 (p) REVERT: L 37 LYS cc_start: 0.9177 (mmtm) cc_final: 0.8427 (mmtt) outliers start: 49 outliers final: 39 residues processed: 369 average time/residue: 0.2373 time to fit residues: 140.3067 Evaluate side-chains 367 residues out of total 3425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 325 time to evaluate : 1.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 454 SER Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain A residue 755 PHE Chi-restraints excluded: chain A residue 848 ILE Chi-restraints excluded: chain A residue 1070 GLN Chi-restraints excluded: chain A residue 1109 LYS Chi-restraints excluded: chain A residue 1174 PHE Chi-restraints excluded: chain A residue 1228 TRP Chi-restraints excluded: chain A residue 1406 VAL Chi-restraints excluded: chain A residue 1445 ILE Chi-restraints excluded: chain B residue 152 ILE Chi-restraints excluded: chain B residue 298 LEU Chi-restraints excluded: chain B residue 305 VAL Chi-restraints excluded: chain B residue 391 ASP Chi-restraints excluded: chain B residue 637 LEU Chi-restraints excluded: chain B residue 733 HIS Chi-restraints excluded: chain B residue 862 GLN Chi-restraints excluded: chain B residue 1009 ASP Chi-restraints excluded: chain B residue 1095 LEU Chi-restraints excluded: chain C residue 157 CYS Chi-restraints excluded: chain C residue 214 ASN Chi-restraints excluded: chain C residue 240 VAL Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain D residue 72 ARG Chi-restraints excluded: chain E residue 48 ASP Chi-restraints excluded: chain E residue 83 CYS Chi-restraints excluded: chain E residue 199 ILE Chi-restraints excluded: chain F residue 78 GLN Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain G residue 22 MET Chi-restraints excluded: chain G residue 39 THR Chi-restraints excluded: chain G residue 158 HIS Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain I residue 18 GLU Chi-restraints excluded: chain I residue 43 VAL Chi-restraints excluded: chain I residue 80 SER Chi-restraints excluded: chain J residue 3 VAL Chi-restraints excluded: chain J residue 22 LEU Chi-restraints excluded: chain J residue 25 LEU Chi-restraints excluded: chain K residue 56 VAL Chi-restraints excluded: chain L residue 61 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 393 random chunks: chunk 343 optimal weight: 2.9990 chunk 7 optimal weight: 0.9990 chunk 171 optimal weight: 0.7980 chunk 319 optimal weight: 5.9990 chunk 299 optimal weight: 5.9990 chunk 345 optimal weight: 8.9990 chunk 389 optimal weight: 50.0000 chunk 301 optimal weight: 0.6980 chunk 127 optimal weight: 3.9990 chunk 251 optimal weight: 1.9990 chunk 233 optimal weight: 7.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 545 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 631 HIS ** A1130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 433 GLN B 734 HIS ** B 986 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.080097 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2868 r_free = 0.2868 target = 0.055816 restraints weight = 107628.434| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.2912 r_free = 0.2912 target = 0.057473 restraints weight = 54321.021| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.2940 r_free = 0.2940 target = 0.058557 restraints weight = 35395.588| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.059235 restraints weight = 27129.694| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.059652 restraints weight = 23092.529| |-----------------------------------------------------------------------------| r_work (final): 0.2931 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8585 moved from start: 0.2739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 33699 Z= 0.130 Angle : 0.592 11.053 45890 Z= 0.302 Chirality : 0.043 0.229 5155 Planarity : 0.003 0.048 5606 Dihedral : 16.424 178.359 5258 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.94 % Favored : 95.99 % Rotamer: Outliers : 1.52 % Allowed : 13.26 % Favored : 85.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.49 (0.14), residues: 3836 helix: 1.59 (0.15), residues: 1333 sheet: -0.10 (0.21), residues: 596 loop : -0.39 (0.15), residues: 1907 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG L 60 TYR 0.020 0.001 TYR D 147 PHE 0.019 0.001 PHE D 154 TRP 0.019 0.001 TRP B 308 HIS 0.008 0.001 HIS A 287 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.13 (33667) covalent geometry : angle 0.57960 / 0.30 (45845) hydrogen bonds : bond 0.03575 / 2.37 ( 1421) hydrogen bonds : angle 4.45341 / 3.17 ( 3940) metal coordination : bond 0.00613 / 0.42 ( 32) metal coordination : angle 3.87002 / 2.85 ( 45) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7672 Ramachandran restraints generated. 3836 Oldfield, 0 Emsley, 3836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7672 Ramachandran restraints generated. 3836 Oldfield, 0 Emsley, 3836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 401 residues out of total 3425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 349 time to evaluate : 1.289 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: A 122 MET cc_start: 0.9014 (tpp) cc_final: 0.8661 (tpp) REVERT: A 261 ASP cc_start: 0.8767 (m-30) cc_final: 0.8225 (m-30) REVERT: A 455 MET cc_start: 0.9048 (OUTLIER) cc_final: 0.8429 (ttp) REVERT: A 487 MET cc_start: 0.8809 (mtp) cc_final: 0.8530 (mmm) REVERT: A 831 THR cc_start: 0.9121 (p) cc_final: 0.8896 (p) REVERT: A 838 GLN cc_start: 0.9271 (tp40) cc_final: 0.8820 (tm-30) REVERT: A 919 ILE cc_start: 0.9445 (mm) cc_final: 0.9127 (mm) REVERT: A 1062 GLU cc_start: 0.7782 (mt-10) cc_final: 0.7432 (mt-10) REVERT: A 1315 GLU cc_start: 0.8570 (tm-30) cc_final: 0.8353 (tm-30) REVERT: A 1368 MET cc_start: 0.9006 (mtm) cc_final: 0.8607 (mtm) REVERT: A 1406 VAL cc_start: 0.9504 (OUTLIER) cc_final: 0.9246 (p) REVERT: B 101 MET cc_start: 0.8693 (mtp) cc_final: 0.8294 (mmm) REVERT: B 199 MET cc_start: 0.8007 (mmm) cc_final: 0.7795 (mmp) REVERT: B 296 GLU cc_start: 0.8763 (tt0) cc_final: 0.8409 (tp30) REVERT: B 310 MET cc_start: 0.9401 (mmp) cc_final: 0.9025 (mmp) REVERT: B 386 LEU cc_start: 0.9752 (mp) cc_final: 0.9481 (mt) REVERT: B 563 MET cc_start: 0.9156 (tmm) cc_final: 0.8909 (tmm) REVERT: B 615 MET cc_start: 0.8414 (mpp) cc_final: 0.8074 (mpp) REVERT: B 809 MET cc_start: 0.9196 (mtt) cc_final: 0.8975 (mtp) REVERT: B 860 MET cc_start: 0.8743 (tmm) cc_final: 0.8266 (tmm) REVERT: B 1098 MET cc_start: 0.8806 (mtm) cc_final: 0.8470 (mtm) REVERT: B 1111 MET cc_start: 0.8846 (mmm) cc_final: 0.8393 (mmt) REVERT: B 1133 MET cc_start: 0.8068 (mtm) cc_final: 0.6968 (mtm) REVERT: B 1138 MET cc_start: 0.9303 (mmm) cc_final: 0.8943 (tpp) REVERT: C 82 TYR cc_start: 0.8618 (m-80) cc_final: 0.8391 (m-80) REVERT: C 125 MET cc_start: 0.7993 (mpp) cc_final: 0.7646 (mpp) REVERT: D 138 ASN cc_start: 0.7726 (t0) cc_final: 0.7285 (t0) REVERT: D 192 LYS cc_start: 0.4655 (mttt) cc_final: 0.4283 (mtmt) REVERT: D 209 ARG cc_start: 0.7585 (ptm160) cc_final: 0.6973 (ptp-170) REVERT: E 112 TYR cc_start: 0.9270 (p90) cc_final: 0.8740 (p90) REVERT: E 121 MET cc_start: 0.9451 (mpp) cc_final: 0.9140 (mpp) REVERT: E 214 CYS cc_start: 0.8409 (t) cc_final: 0.8064 (t) REVERT: F 78 GLN cc_start: 0.9013 (OUTLIER) cc_final: 0.8687 (mp10) REVERT: F 116 ASP cc_start: 0.9004 (t0) cc_final: 0.8492 (t0) REVERT: F 144 GLU cc_start: 0.8898 (mt-10) cc_final: 0.8530 (mt-10) REVERT: G 33 GLU cc_start: 0.8183 (mp0) cc_final: 0.7582 (mp0) REVERT: G 60 ARG cc_start: 0.9047 (ttp80) cc_final: 0.8828 (ttp80) REVERT: G 69 GLU cc_start: 0.9036 (tt0) cc_final: 0.8586 (tm-30) REVERT: G 75 ARG cc_start: 0.8369 (ttm170) cc_final: 0.8079 (ttt180) REVERT: H 22 LYS cc_start: 0.9200 (mmtm) cc_final: 0.8822 (mmtp) REVERT: H 139 ASN cc_start: 0.9310 (m-40) cc_final: 0.8827 (m-40) REVERT: H 141 TYR cc_start: 0.9284 (m-80) cc_final: 0.8566 (m-10) REVERT: I 44 TYR cc_start: 0.8912 (t80) cc_final: 0.8639 (t80) REVERT: K 17 SER cc_start: 0.9581 (m) cc_final: 0.9214 (p) REVERT: K 38 GLU cc_start: 0.8834 (mm-30) cc_final: 0.8577 (mm-30) REVERT: K 39 ASP cc_start: 0.8909 (p0) cc_final: 0.8485 (p0) REVERT: K 41 THR cc_start: 0.9417 (m) cc_final: 0.9068 (p) REVERT: L 37 LYS cc_start: 0.9141 (mmtm) cc_final: 0.8391 (mmtt) REVERT: L 47 ARG cc_start: 0.7802 (ptm160) cc_final: 0.7591 (ttp80) outliers start: 52 outliers final: 33 residues processed: 384 average time/residue: 0.2345 time to fit residues: 144.3903 Evaluate side-chains 368 residues out of total 3425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 332 time to evaluate : 1.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 436 ILE Chi-restraints excluded: chain A residue 449 SER Chi-restraints excluded: chain A residue 454 SER Chi-restraints excluded: chain A residue 455 MET Chi-restraints excluded: chain A residue 755 PHE Chi-restraints excluded: chain A residue 848 ILE Chi-restraints excluded: chain A residue 1109 LYS Chi-restraints excluded: chain A residue 1174 PHE Chi-restraints excluded: chain A residue 1228 TRP Chi-restraints excluded: chain A residue 1406 VAL Chi-restraints excluded: chain A residue 1445 ILE Chi-restraints excluded: chain B residue 152 ILE Chi-restraints excluded: chain B residue 298 LEU Chi-restraints excluded: chain B residue 305 VAL Chi-restraints excluded: chain B residue 391 ASP Chi-restraints excluded: chain B residue 637 LEU Chi-restraints excluded: chain B residue 733 HIS Chi-restraints excluded: chain B residue 862 GLN Chi-restraints excluded: chain B residue 1009 ASP Chi-restraints excluded: chain B residue 1095 LEU Chi-restraints excluded: chain C residue 214 ASN Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain E residue 48 ASP Chi-restraints excluded: chain E residue 83 CYS Chi-restraints excluded: chain F residue 78 GLN Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain G residue 22 MET Chi-restraints excluded: chain G residue 158 HIS Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain I residue 18 GLU Chi-restraints excluded: chain I residue 43 VAL Chi-restraints excluded: chain J residue 22 LEU Chi-restraints excluded: chain J residue 25 LEU Chi-restraints excluded: chain K residue 56 VAL Chi-restraints excluded: chain L residue 61 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 393 random chunks: chunk 116 optimal weight: 9.9990 chunk 294 optimal weight: 7.9990 chunk 315 optimal weight: 0.9990 chunk 40 optimal weight: 3.9990 chunk 112 optimal weight: 6.9990 chunk 358 optimal weight: 20.0000 chunk 115 optimal weight: 0.0070 chunk 31 optimal weight: 6.9990 chunk 28 optimal weight: 6.9990 chunk 122 optimal weight: 6.9990 chunk 185 optimal weight: 8.9990 overall best weight: 3.8006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 545 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1427 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 433 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 734 HIS ** B 986 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 5 ASN ** G 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.078286 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2811 r_free = 0.2811 target = 0.053410 restraints weight = 109945.704| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.2855 r_free = 0.2855 target = 0.055048 restraints weight = 56931.115| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.2883 r_free = 0.2883 target = 0.056127 restraints weight = 37729.840| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.2900 r_free = 0.2900 target = 0.056798 restraints weight = 29259.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.2911 r_free = 0.2911 target = 0.057188 restraints weight = 25069.901| |-----------------------------------------------------------------------------| r_work (final): 0.2885 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8637 moved from start: 0.2761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 33699 Z= 0.243 Angle : 0.649 10.873 45890 Z= 0.330 Chirality : 0.044 0.227 5155 Planarity : 0.004 0.056 5606 Dihedral : 16.421 178.766 5258 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 10.49 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.56 % Favored : 95.36 % Rotamer: Outliers : 1.31 % Allowed : 13.49 % Favored : 85.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.39 (0.14), residues: 3836 helix: 1.49 (0.15), residues: 1334 sheet: -0.15 (0.21), residues: 588 loop : -0.44 (0.15), residues: 1914 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG L 60 TYR 0.019 0.001 TYR D 147 PHE 0.019 0.001 PHE D 154 TRP 0.019 0.001 TRP B 308 HIS 0.007 0.001 HIS A 287 Details of bonding type rmsd/Z covalent geometry : bond 0.00534 / 0.24 (33667) covalent geometry : angle 0.63516 / 0.33 (45845) hydrogen bonds : bond 0.03790 / 2.49 ( 1421) hydrogen bonds : angle 4.57178 / 3.26 ( 3940) metal coordination : bond 0.00872 / 0.58 ( 32) metal coordination : angle 4.27267 / 3.06 ( 45) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7672 Ramachandran restraints generated. 3836 Oldfield, 0 Emsley, 3836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7672 Ramachandran restraints generated. 3836 Oldfield, 0 Emsley, 3836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 373 residues out of total 3425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 328 time to evaluate : 1.395 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 122 MET cc_start: 0.9027 (tpp) cc_final: 0.8684 (tpp) REVERT: A 261 ASP cc_start: 0.8737 (m-30) cc_final: 0.8322 (m-30) REVERT: A 455 MET cc_start: 0.9036 (OUTLIER) cc_final: 0.8399 (ttp) REVERT: A 838 GLN cc_start: 0.9289 (tp40) cc_final: 0.8831 (tm-30) REVERT: A 919 ILE cc_start: 0.9466 (mm) cc_final: 0.9142 (mm) REVERT: A 1062 GLU cc_start: 0.7807 (mt-10) cc_final: 0.7443 (mt-10) REVERT: A 1315 GLU cc_start: 0.8617 (tm-30) cc_final: 0.8416 (tm-30) REVERT: A 1368 MET cc_start: 0.9058 (mtm) cc_final: 0.8675 (mtm) REVERT: A 1406 VAL cc_start: 0.9509 (OUTLIER) cc_final: 0.9256 (p) REVERT: B 101 MET cc_start: 0.8758 (mtp) cc_final: 0.8329 (mmm) REVERT: B 296 GLU cc_start: 0.8780 (tt0) cc_final: 0.8389 (tp30) REVERT: B 310 MET cc_start: 0.9484 (mmp) cc_final: 0.9049 (mmp) REVERT: B 386 LEU cc_start: 0.9753 (mp) cc_final: 0.9428 (mt) REVERT: B 563 MET cc_start: 0.9133 (tmm) cc_final: 0.8873 (tmm) REVERT: B 615 MET cc_start: 0.8456 (mpp) cc_final: 0.8064 (mpp) REVERT: B 809 MET cc_start: 0.9242 (mtt) cc_final: 0.9012 (mtp) REVERT: B 860 MET cc_start: 0.8772 (tmm) cc_final: 0.8306 (tmm) REVERT: B 1021 MET cc_start: 0.8979 (mtm) cc_final: 0.8369 (mpp) REVERT: B 1098 MET cc_start: 0.8783 (mtm) cc_final: 0.8394 (mtm) REVERT: B 1111 MET cc_start: 0.8822 (mmm) cc_final: 0.8265 (mmt) REVERT: B 1138 MET cc_start: 0.9315 (mmm) cc_final: 0.8964 (tpp) REVERT: C 82 TYR cc_start: 0.8657 (m-80) cc_final: 0.8406 (m-80) REVERT: C 125 MET cc_start: 0.8017 (mpp) cc_final: 0.7669 (mpp) REVERT: D 192 LYS cc_start: 0.4860 (mttt) cc_final: 0.4464 (mtmt) REVERT: D 209 ARG cc_start: 0.7543 (ptm160) cc_final: 0.6942 (ptp-170) REVERT: E 112 TYR cc_start: 0.9306 (p90) cc_final: 0.8817 (p90) REVERT: E 121 MET cc_start: 0.9464 (mpp) cc_final: 0.9037 (mpp) REVERT: E 214 CYS cc_start: 0.8429 (t) cc_final: 0.8042 (t) REVERT: F 78 GLN cc_start: 0.9019 (OUTLIER) cc_final: 0.8674 (mp10) REVERT: F 114 GLU cc_start: 0.7582 (tm-30) cc_final: 0.7356 (tm-30) REVERT: F 116 ASP cc_start: 0.8824 (t0) cc_final: 0.8576 (t0) REVERT: F 144 GLU cc_start: 0.8920 (mt-10) cc_final: 0.8552 (mt-10) REVERT: G 33 GLU cc_start: 0.8150 (mp0) cc_final: 0.7490 (mp0) REVERT: G 57 GLN cc_start: 0.8505 (mm-40) cc_final: 0.8146 (mm110) REVERT: G 60 ARG cc_start: 0.9068 (ttp80) cc_final: 0.8852 (ttp80) REVERT: G 69 GLU cc_start: 0.9019 (tt0) cc_final: 0.8588 (tm-30) REVERT: G 75 ARG cc_start: 0.8372 (ttm170) cc_final: 0.8079 (ttt180) REVERT: H 14 GLU cc_start: 0.8175 (tm-30) cc_final: 0.7946 (tm-30) REVERT: H 22 LYS cc_start: 0.9207 (mmtm) cc_final: 0.8818 (mmtp) REVERT: H 123 MET cc_start: 0.8908 (tmm) cc_final: 0.8350 (tmm) REVERT: H 139 ASN cc_start: 0.9345 (m-40) cc_final: 0.9094 (m-40) REVERT: H 141 TYR cc_start: 0.9340 (m-80) cc_final: 0.8651 (m-10) REVERT: I 44 TYR cc_start: 0.8780 (t80) cc_final: 0.8471 (t80) REVERT: K 17 SER cc_start: 0.9591 (m) cc_final: 0.9194 (p) REVERT: K 38 GLU cc_start: 0.8817 (mm-30) cc_final: 0.8554 (mm-30) REVERT: K 39 ASP cc_start: 0.8964 (p0) cc_final: 0.8554 (p0) REVERT: K 41 THR cc_start: 0.9422 (m) cc_final: 0.9085 (p) outliers start: 45 outliers final: 38 residues processed: 359 average time/residue: 0.2345 time to fit residues: 134.4538 Evaluate side-chains 365 residues out of total 3425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 324 time to evaluate : 1.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 436 ILE Chi-restraints excluded: chain A residue 449 SER Chi-restraints excluded: chain A residue 454 SER Chi-restraints excluded: chain A residue 455 MET Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain A residue 755 PHE Chi-restraints excluded: chain A residue 848 ILE Chi-restraints excluded: chain A residue 1109 LYS Chi-restraints excluded: chain A residue 1174 PHE Chi-restraints excluded: chain A residue 1228 TRP Chi-restraints excluded: chain A residue 1406 VAL Chi-restraints excluded: chain A residue 1445 ILE Chi-restraints excluded: chain B residue 152 ILE Chi-restraints excluded: chain B residue 298 LEU Chi-restraints excluded: chain B residue 305 VAL Chi-restraints excluded: chain B residue 391 ASP Chi-restraints excluded: chain B residue 637 LEU Chi-restraints excluded: chain B residue 733 HIS Chi-restraints excluded: chain B residue 862 GLN Chi-restraints excluded: chain B residue 1009 ASP Chi-restraints excluded: chain B residue 1095 LEU Chi-restraints excluded: chain C residue 214 ASN Chi-restraints excluded: chain C residue 240 VAL Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain E residue 48 ASP Chi-restraints excluded: chain E residue 83 CYS Chi-restraints excluded: chain E residue 199 ILE Chi-restraints excluded: chain F residue 78 GLN Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain G residue 22 MET Chi-restraints excluded: chain G residue 115 MET Chi-restraints excluded: chain G residue 158 HIS Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain I residue 18 GLU Chi-restraints excluded: chain I residue 43 VAL Chi-restraints excluded: chain J residue 3 VAL Chi-restraints excluded: chain J residue 22 LEU Chi-restraints excluded: chain J residue 25 LEU Chi-restraints excluded: chain K residue 56 VAL Chi-restraints excluded: chain L residue 61 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 393 random chunks: chunk 156 optimal weight: 6.9990 chunk 136 optimal weight: 0.9980 chunk 370 optimal weight: 10.0000 chunk 316 optimal weight: 0.5980 chunk 258 optimal weight: 0.9980 chunk 302 optimal weight: 0.8980 chunk 18 optimal weight: 0.8980 chunk 31 optimal weight: 3.9990 chunk 35 optimal weight: 7.9990 chunk 72 optimal weight: 9.9990 chunk 338 optimal weight: 0.0370 overall best weight: 0.6858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 545 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1427 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 433 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 734 HIS B 794 ASN ** B 986 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1025 HIS ** G 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.080839 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2901 r_free = 0.2901 target = 0.056438 restraints weight = 107298.659| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.2946 r_free = 0.2946 target = 0.058168 restraints weight = 54240.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.059267 restraints weight = 35230.804| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 52)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.059977 restraints weight = 26941.526| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.060406 restraints weight = 22855.499| |-----------------------------------------------------------------------------| r_work (final): 0.2973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8572 moved from start: 0.2902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 33699 Z= 0.116 Angle : 0.606 11.173 45890 Z= 0.308 Chirality : 0.043 0.233 5155 Planarity : 0.004 0.048 5606 Dihedral : 16.327 178.348 5258 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.65 % Favored : 96.27 % Rotamer: Outliers : 1.14 % Allowed : 13.87 % Favored : 84.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.46 (0.14), residues: 3836 helix: 1.56 (0.15), residues: 1339 sheet: -0.20 (0.20), residues: 607 loop : -0.39 (0.15), residues: 1890 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG L 60 TYR 0.021 0.001 TYR D 147 PHE 0.030 0.001 PHE J 8 TRP 0.017 0.001 TRP B 308 HIS 0.008 0.001 HIS A 287 Details of bonding type rmsd/Z covalent geometry : bond 0.00253 / 0.12 (33667) covalent geometry : angle 0.59684 / 0.31 (45845) hydrogen bonds : bond 0.03485 / 2.31 ( 1421) hydrogen bonds : angle 4.36434 / 3.12 ( 3940) metal coordination : bond 0.00654 / 0.44 ( 32) metal coordination : angle 3.32897 / 2.35 ( 45) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7672 Ramachandran restraints generated. 3836 Oldfield, 0 Emsley, 3836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7672 Ramachandran restraints generated. 3836 Oldfield, 0 Emsley, 3836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 397 residues out of total 3425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 358 time to evaluate : 1.322 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 122 MET cc_start: 0.9006 (tpp) cc_final: 0.8649 (tpp) REVERT: A 261 ASP cc_start: 0.8744 (m-30) cc_final: 0.8213 (m-30) REVERT: A 455 MET cc_start: 0.8895 (OUTLIER) cc_final: 0.8302 (ttp) REVERT: A 831 THR cc_start: 0.9122 (p) cc_final: 0.8910 (p) REVERT: A 838 GLN cc_start: 0.9232 (tp40) cc_final: 0.8591 (tp40) REVERT: A 919 ILE cc_start: 0.9432 (mm) cc_final: 0.9101 (mm) REVERT: A 1315 GLU cc_start: 0.8562 (tm-30) cc_final: 0.8340 (tm-30) REVERT: A 1368 MET cc_start: 0.8971 (mtm) cc_final: 0.8554 (mtm) REVERT: A 1371 LEU cc_start: 0.9715 (tt) cc_final: 0.9486 (tp) REVERT: A 1406 VAL cc_start: 0.9486 (OUTLIER) cc_final: 0.9221 (p) REVERT: B 101 MET cc_start: 0.8689 (mtp) cc_final: 0.8285 (mmm) REVERT: B 296 GLU cc_start: 0.8674 (tt0) cc_final: 0.8352 (tp30) REVERT: B 310 MET cc_start: 0.9408 (mmp) cc_final: 0.8968 (mmp) REVERT: B 386 LEU cc_start: 0.9752 (mp) cc_final: 0.9437 (mt) REVERT: B 563 MET cc_start: 0.9187 (tmm) cc_final: 0.8981 (tmm) REVERT: B 615 MET cc_start: 0.8370 (mpp) cc_final: 0.8022 (mpp) REVERT: B 809 MET cc_start: 0.9163 (mtt) cc_final: 0.8951 (mtp) REVERT: B 860 MET cc_start: 0.8747 (tmm) cc_final: 0.8247 (tmm) REVERT: B 1021 MET cc_start: 0.8820 (mtm) cc_final: 0.8299 (mpp) REVERT: B 1085 ILE cc_start: 0.9611 (mm) cc_final: 0.9387 (mm) REVERT: B 1098 MET cc_start: 0.8754 (mtm) cc_final: 0.8547 (mtm) REVERT: B 1111 MET cc_start: 0.8823 (mmm) cc_final: 0.8408 (mmt) REVERT: B 1138 MET cc_start: 0.9182 (mmm) cc_final: 0.8807 (tpp) REVERT: C 82 TYR cc_start: 0.8622 (m-80) cc_final: 0.8371 (m-80) REVERT: C 125 MET cc_start: 0.8040 (mpp) cc_final: 0.7651 (mpp) REVERT: D 192 LYS cc_start: 0.4655 (mttt) cc_final: 0.4282 (mtmt) REVERT: D 209 ARG cc_start: 0.7587 (ptm160) cc_final: 0.6935 (ptp-170) REVERT: E 112 TYR cc_start: 0.9238 (p90) cc_final: 0.8728 (p90) REVERT: E 121 MET cc_start: 0.9428 (mpp) cc_final: 0.9096 (mpp) REVERT: E 214 CYS cc_start: 0.8357 (t) cc_final: 0.7976 (t) REVERT: F 78 GLN cc_start: 0.8977 (OUTLIER) cc_final: 0.8650 (mp10) REVERT: F 116 ASP cc_start: 0.8820 (t0) cc_final: 0.8525 (t0) REVERT: F 144 GLU cc_start: 0.8874 (mt-10) cc_final: 0.8511 (mt-10) REVERT: G 4 ILE cc_start: 0.8551 (OUTLIER) cc_final: 0.8267 (tp) REVERT: G 33 GLU cc_start: 0.8196 (mp0) cc_final: 0.7555 (mp0) REVERT: G 60 ARG cc_start: 0.9046 (ttp80) cc_final: 0.8831 (ttp80) REVERT: G 69 GLU cc_start: 0.8990 (tt0) cc_final: 0.8585 (tm-30) REVERT: H 22 LYS cc_start: 0.9150 (mmtm) cc_final: 0.8775 (mmtp) REVERT: H 123 MET cc_start: 0.8955 (tmm) cc_final: 0.8426 (tmm) REVERT: H 139 ASN cc_start: 0.9308 (m-40) cc_final: 0.8815 (m-40) REVERT: H 141 TYR cc_start: 0.9264 (m-80) cc_final: 0.8563 (m-10) REVERT: I 44 TYR cc_start: 0.8865 (t80) cc_final: 0.8594 (t80) REVERT: K 17 SER cc_start: 0.9582 (m) cc_final: 0.9214 (p) REVERT: K 38 GLU cc_start: 0.8799 (mm-30) cc_final: 0.8451 (mm-30) REVERT: K 39 ASP cc_start: 0.8884 (p0) cc_final: 0.8450 (p0) REVERT: K 41 THR cc_start: 0.9475 (m) cc_final: 0.9222 (p) outliers start: 39 outliers final: 32 residues processed: 385 average time/residue: 0.2352 time to fit residues: 144.0687 Evaluate side-chains 372 residues out of total 3425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 336 time to evaluate : 1.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 436 ILE Chi-restraints excluded: chain A residue 449 SER Chi-restraints excluded: chain A residue 454 SER Chi-restraints excluded: chain A residue 455 MET Chi-restraints excluded: chain A residue 755 PHE Chi-restraints excluded: chain A residue 848 ILE Chi-restraints excluded: chain A residue 1109 LYS Chi-restraints excluded: chain A residue 1174 PHE Chi-restraints excluded: chain A residue 1228 TRP Chi-restraints excluded: chain A residue 1406 VAL Chi-restraints excluded: chain A residue 1445 ILE Chi-restraints excluded: chain B residue 152 ILE Chi-restraints excluded: chain B residue 298 LEU Chi-restraints excluded: chain B residue 305 VAL Chi-restraints excluded: chain B residue 391 ASP Chi-restraints excluded: chain B residue 637 LEU Chi-restraints excluded: chain B residue 733 HIS Chi-restraints excluded: chain B residue 862 GLN Chi-restraints excluded: chain B residue 1009 ASP Chi-restraints excluded: chain B residue 1095 LEU Chi-restraints excluded: chain C residue 214 ASN Chi-restraints excluded: chain C residue 240 VAL Chi-restraints excluded: chain E residue 48 ASP Chi-restraints excluded: chain E residue 83 CYS Chi-restraints excluded: chain E residue 199 ILE Chi-restraints excluded: chain F residue 78 GLN Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain G residue 4 ILE Chi-restraints excluded: chain G residue 115 MET Chi-restraints excluded: chain G residue 158 HIS Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain I residue 18 GLU Chi-restraints excluded: chain I residue 43 VAL Chi-restraints excluded: chain J residue 22 LEU Chi-restraints excluded: chain J residue 25 LEU Chi-restraints excluded: chain K residue 56 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 393 random chunks: chunk 293 optimal weight: 0.8980 chunk 59 optimal weight: 0.9990 chunk 128 optimal weight: 10.0000 chunk 46 optimal weight: 0.0980 chunk 370 optimal weight: 1.9990 chunk 14 optimal weight: 2.9990 chunk 146 optimal weight: 0.9990 chunk 249 optimal weight: 1.9990 chunk 54 optimal weight: 3.9990 chunk 381 optimal weight: 30.0000 chunk 83 optimal weight: 3.9990 overall best weight: 0.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 545 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 734 HIS B 986 GLN ** G 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.080841 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2899 r_free = 0.2899 target = 0.056321 restraints weight = 106980.698| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 58)----------------| | r_work = 0.2944 r_free = 0.2944 target = 0.058034 restraints weight = 54656.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.059146 restraints weight = 35699.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.059852 restraints weight = 27361.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.060279 restraints weight = 23295.129| |-----------------------------------------------------------------------------| r_work (final): 0.2970 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8580 moved from start: 0.2979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 33699 Z= 0.121 Angle : 0.603 10.557 45890 Z= 0.308 Chirality : 0.042 0.232 5155 Planarity : 0.004 0.048 5606 Dihedral : 16.256 178.462 5258 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.04 % Favored : 95.88 % Rotamer: Outliers : 1.05 % Allowed : 14.45 % Favored : 84.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.51 (0.14), residues: 3836 helix: 1.59 (0.15), residues: 1337 sheet: -0.05 (0.21), residues: 596 loop : -0.39 (0.15), residues: 1903 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG L 60 TYR 0.020 0.001 TYR D 147 PHE 0.035 0.001 PHE D 154 TRP 0.018 0.001 TRP B 308 HIS 0.008 0.001 HIS A 287 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.12 (33667) covalent geometry : angle 0.59473 / 0.31 (45845) hydrogen bonds : bond 0.03454 / 2.28 ( 1421) hydrogen bonds : angle 4.35870 / 3.12 ( 3940) metal coordination : bond 0.00586 / 0.40 ( 32) metal coordination : angle 3.20392 / 2.20 ( 45) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6069.93 seconds wall clock time: 106 minutes 0.09 seconds (6360.09 seconds total)