Starting phenix.real_space_refine on Sun Aug 9 10:30:52 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9sbw_54741/08_2026/9sbw_54741.cif Found real_map, /net/cci-nas-00/data/ceres_data/9sbw_54741/08_2026/9sbw_54741.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.63 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9sbw_54741/08_2026/9sbw_54741.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9sbw_54741/08_2026/9sbw_54741.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9sbw_54741/08_2026/9sbw_54741.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9sbw_54741/08_2026/9sbw_54741.map" } resolution = 3.63 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= 0.025 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 100 5.49 5 Mg 2 5.21 5 S 182 5.16 5 C 20561 2.51 5 N 5765 2.21 5 O 6465 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.05s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 33083 Number of models: 1 Model: "" Number of chains: 21 Chain: "A" Number of atoms: 10942 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1390, 10942 Classifications: {'peptide': 1390} Link IDs: {'PCIS': 1, 'PTRANS': 61, 'TRANS': 1327} Chain breaks: 6 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: 905 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 905 Classifications: {'DNA': 44} Link IDs: {'rna3p': 43} 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: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 35 Unusual residues: {' MG': 2, ' ZN': 2, 'ATP': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 457 SG CYS A 67 106.634 70.173 94.986 1.00197.01 S ATOM 479 SG CYS A 70 106.145 66.690 93.586 1.00197.82 S ATOM 532 SG CYS A 77 103.435 69.371 93.141 1.00177.46 S ATOM 762 SG CYS A 107 81.472 76.128 135.299 1.00227.62 S ATOM 786 SG CYS A 110 82.897 72.762 135.987 1.00221.85 S ATOM 1091 SG CYS A 148 79.544 73.819 137.579 1.00238.24 S ATOM 1105 SG CYS A 167 82.818 75.389 138.773 1.00233.88 S ATOM 19603 SG CYS B1163 98.539 57.734 105.014 1.00192.05 S ATOM 19621 SG CYS B1166 96.910 61.044 105.452 1.00193.06 S ATOM 19746 SG CYS B1182 100.710 60.679 104.867 1.00199.23 S ATOM 19765 SG CYS B1185 99.137 59.843 108.269 1.00196.56 S ATOM 20753 SG CYS C 86 93.346 74.790 25.937 1.00238.25 S ATOM 20770 SG CYS C 88 95.217 76.993 28.244 1.00246.15 S ATOM 20803 SG CYS C 92 94.376 78.291 24.829 1.00209.79 S ATOM 20826 SG CYS C 95 91.610 77.882 27.455 1.00207.22 S ATOM 28411 SG CYS I 7 40.124 125.640 127.431 1.00343.23 S ATOM 28436 SG CYS I 10 43.855 125.109 127.178 1.00333.76 S ATOM 28602 SG CYS I 29 41.824 122.489 128.976 1.00344.07 S ATOM 28626 SG CYS I 32 42.338 125.830 130.577 1.00342.06 S ATOM 28953 SG CYS I 75 16.995 116.281 89.451 1.00372.28 S ATOM 28975 SG CYS I 78 16.539 119.790 88.107 1.00381.01 S ATOM 29191 SG CYS I 103 19.991 118.198 87.983 1.00364.95 S ATOM 29211 SG CYS I 106 18.494 119.182 91.323 1.00369.32 S ATOM 29313 SG CYS J 7 64.079 90.559 37.845 1.00159.49 S ATOM 29336 SG CYS J 10 63.927 88.394 34.629 1.00169.31 S ATOM 29616 SG CYS J 45 60.761 89.283 36.615 1.00167.67 S ATOM 29622 SG CYS J 46 62.625 91.764 34.446 1.00168.28 S ATOM 30745 SG CYS L 31 97.452 113.915 54.199 1.00280.47 S ATOM 30765 SG CYS L 34 98.549 115.518 50.985 1.00277.32 S ATOM 30869 SG CYS L 48 101.125 114.420 53.625 1.00293.15 S ATOM 30892 SG CYS L 51 98.972 117.466 54.243 1.00291.44 S Time building chain proxies: 6.61, per 1000 atoms: 0.20 Number of scatterers: 33083 At special positions: 0 Unit cell: (152.329, 155.593, 183.883, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 8 29.99 S 182 16.00 P 100 15.00 Mg 2 11.99 O 6465 8.00 N 5765 7.00 C 20561 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 1.4 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1804 " pdb="ZN ZN A1804 " - pdb=" NE2 HIS A 80 " pdb="ZN ZN A1804 " - pdb=" SG CYS A 67 " pdb="ZN ZN A1804 " - pdb=" SG CYS A 70 " pdb="ZN ZN A1804 " - pdb=" SG CYS A 77 " pdb=" ZN A1805 " pdb="ZN ZN A1805 " - pdb=" SG CYS A 107 " pdb="ZN ZN A1805 " - pdb=" SG CYS A 110 " pdb="ZN ZN A1805 " - pdb=" SG CYS A 148 " pdb="ZN ZN A1805 " - pdb=" SG CYS A 167 " pdb=" ZN B1301 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1166 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1182 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1163 " pdb="ZN ZN B1301 " - 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 10 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 32 " 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 78 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 103 " pdb=" ZN J 101 " 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 10 " 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 7708 Ramachandran restraints generated. 3854 Oldfield, 0 Emsley, 3854 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7340 Finding SS restraints... Secondary structure from input PDB file: 146 helices and 50 sheets defined 39.3% alpha, 19.5% beta 41 base pairs and 81 stacking pairs defined. Time for finding SS restraints: 4.20 Creating SS restraints... Processing helix chain 'A' and resid 23 through 31 Processing helix chain 'A' and resid 92 through 94 No H-bonds generated for 'chain 'A' and resid 92 through 94' Processing helix chain 'A' and resid 95 through 106 Processing helix chain 'A' and resid 119 through 127 Processing helix chain 'A' and resid 130 through 143 Processing helix chain 'A' and resid 203 through 213 removed outlier: 3.675A pdb=" N HIS A 213 " --> pdb=" O ASN A 209 " (cutoff:3.500A) Processing helix chain 'A' and resid 215 through 221 Processing helix chain 'A' and resid 230 through 235 Processing helix chain 'A' and resid 243 through 247 Processing helix chain 'A' and resid 260 through 283 removed outlier: 3.697A 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: 3.901A pdb=" N TYR A 478 " --> pdb=" O VAL A 474 " (cutoff:3.500A) Processing helix chain 'A' and resid 494 through 505 Processing helix chain 'A' and resid 507 through 510 Processing helix chain 'A' and resid 524 through 536 removed outlier: 3.738A pdb=" N LEU A 528 " --> pdb=" O VAL A 524 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ARG A 532 " --> pdb=" O LEU A 528 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LYS A 533 " --> pdb=" O CYS A 529 " (cutoff:3.500A) Processing helix chain 'A' and resid 542 through 552 Processing helix chain 'A' and resid 574 through 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 removed outlier: 3.513A pdb=" N HIS A 659 " --> pdb=" O PHE A 655 " (cutoff:3.500A) Processing helix chain 'A' and resid 665 through 670 removed outlier: 3.528A pdb=" N ILE A 670 " --> pdb=" O GLY A 667 " (cutoff:3.500A) Processing helix chain 'A' and resid 672 through 699 removed outlier: 3.617A 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: 3.507A pdb=" N ILE A 758 " --> pdb=" O SER A 754 " (cutoff:3.500A) Processing helix chain 'A' and resid 809 through 829 removed outlier: 4.091A pdb=" N GLU A 822 " --> pdb=" O MET A 818 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N GLY A 823 " --> pdb=" O GLY A 819 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N LEU A 824 " --> pdb=" O GLY A 820 " (cutoff:3.500A) Processing helix chain 'A' and resid 829 through 845 removed outlier: 3.994A pdb=" N GLU A 833 " --> pdb=" O VAL A 829 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N THR A 834 " --> pdb=" O LYS A 830 " (cutoff:3.500A) Processing helix chain 'A' and resid 867 through 871 Processing helix chain 'A' and resid 874 through 876 No H-bonds generated for 'chain 'A' and resid 874 through 876' Processing helix chain 'A' and resid 889 through 898 Processing helix chain 'A' and resid 909 through 913 Processing helix chain 'A' and resid 915 through 920 removed outlier: 3.935A pdb=" N LEU A 920 " --> pdb=" O GLY A 916 " (cutoff:3.500A) Processing helix chain 'A' and resid 923 through 947 Processing helix chain 'A' and resid 959 through 972 Processing helix chain 'A' and resid 982 through 994 removed outlier: 3.727A pdb=" N GLN A 994 " --> pdb=" O VAL A 990 " (cutoff:3.500A) Processing helix chain 'A' and resid 1004 through 1015 removed outlier: 3.558A pdb=" N VAL A1015 " --> pdb=" O GLN A1011 " (cutoff:3.500A) Processing helix chain 'A' and resid 1015 through 1026 Processing helix chain 'A' and resid 1027 through 1034 Processing helix chain 'A' and resid 1038 through 1056 removed outlier: 3.501A pdb=" N VAL A1045 " --> pdb=" O ALA A1041 " (cutoff:3.500A) Processing helix chain 'A' and resid 1063 through 1083 Proline residue: A1075 - end of helix Processing helix chain 'A' and resid 1084 through 1086 No H-bonds generated for 'chain 'A' and resid 1084 through 1086' Processing helix chain 'A' and resid 1091 through 1096 Processing helix chain 'A' and resid 1096 through 1106 Processing helix chain 'A' and resid 1130 through 1139 Processing helix chain 'A' and resid 1143 through 1147 removed outlier: 3.527A pdb=" N THR A1147 " --> pdb=" O LYS A1144 " (cutoff:3.500A) Processing helix chain 'A' and resid 1166 through 1173 Processing helix chain 'A' and resid 1198 through 1205 Processing helix chain 'A' and resid 1208 through 1220 removed outlier: 3.543A pdb=" N VAL A1212 " --> pdb=" O THR A1208 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N PHE A1220 " --> pdb=" O ILE A1216 " (cutoff:3.500A) Processing helix chain 'A' and resid 1257 through 1270 Processing helix chain 'A' and resid 1312 through 1317 removed outlier: 3.598A 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 1364 through 1376 removed outlier: 3.932A 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: 3.547A 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: 4.088A pdb=" N VAL B 33 " --> pdb=" O ASP B 29 " (cutoff:3.500A) Processing helix chain 'B' and resid 44 through 66 removed outlier: 4.698A pdb=" N LEU B 59 " --> pdb=" O VAL B 55 " (cutoff:3.500A) removed outlier: 5.550A pdb=" N GLN B 60 " --> pdb=" O ASP B 56 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N ASP B 66 " --> pdb=" O ILE B 62 " (cutoff:3.500A) Processing helix chain 'B' and resid 79 through 82 Processing helix chain 'B' and resid 113 through 120 Processing helix chain 'B' and resid 185 through 192 Processing helix chain 'B' and resid 282 through 289 Processing helix chain 'B' and resid 293 through 303 removed outlier: 3.612A pdb=" N ILE B 297 " --> pdb=" O PRO B 293 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LEU B 298 " --> pdb=" O ASP B 294 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N GLU B 299 " --> pdb=" O GLY B 295 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N TYR B 303 " --> pdb=" O GLU B 299 " (cutoff:3.500A) Processing helix chain 'B' and resid 308 through 321 Proline residue: B 316 - end of helix Processing helix chain 'B' and resid 326 through 338 Processing helix chain 'B' and resid 344 through 359 removed outlier: 3.563A pdb=" N ARG B 348 " --> pdb=" O LYS B 344 " (cutoff:3.500A) Processing helix chain 'B' and resid 370 through 390 Processing helix chain 'B' and resid 400 through 402 No H-bonds generated for 'chain 'B' and resid 400 through 402' Processing helix chain 'B' and resid 408 through 439 removed outlier: 3.511A pdb=" N LEU B 412 " --> pdb=" O LEU B 408 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLU B 437 " --> pdb=" O GLN B 433 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLU B 438 " --> pdb=" O ARG B 434 " (cutoff:3.500A) Processing helix chain 'B' and resid 443 through 448 Processing helix chain 'B' and resid 450 through 464 removed outlier: 3.749A pdb=" N THR B 454 " --> pdb=" O ALA B 450 " (cutoff:3.500A) Processing helix chain 'B' and resid 487 through 495 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: 3.611A 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 removed outlier: 3.883A pdb=" N ASN B 762 " --> pdb=" O PRO B 759 " (cutoff:3.500A) Processing helix chain 'B' and resid 763 through 774 Processing helix chain 'B' and resid 784 through 788 removed outlier: 3.566A pdb=" N ARG B 788 " --> pdb=" O TYR B 785 " (cutoff:3.500A) Processing helix chain 'B' and resid 806 through 813 removed outlier: 3.919A pdb=" N GLU B 810 " --> pdb=" O ARG B 807 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N TYR B 811 " --> pdb=" O ALA B 808 " (cutoff:3.500A) Processing helix chain 'B' and resid 843 through 848 Processing helix chain 'B' and resid 1015 through 1021 removed outlier: 4.281A pdb=" N SER B1019 " --> pdb=" O HIS B1015 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ARG B1020 " --> pdb=" O ALA B1016 " (cutoff:3.500A) Processing helix chain 'B' and resid 1022 through 1039 removed outlier: 3.762A pdb=" N LEU B1026 " --> pdb=" O THR B1022 " (cutoff:3.500A) Processing helix chain 'B' and resid 1051 through 1061 removed outlier: 3.593A 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 1175 through 1178 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: 3.529A 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 removed outlier: 3.504A pdb=" N TRP C 201 " --> pdb=" O SER C 197 " (cutoff:3.500A) Processing helix chain 'C' and resid 206 through 210 removed outlier: 3.611A pdb=" N GLU C 210 " --> pdb=" O CYS C 207 " (cutoff:3.500A) Processing helix chain 'C' and resid 239 through 266 Processing helix chain 'D' and resid 30 through 34 removed outlier: 3.767A pdb=" N GLN D 34 " --> pdb=" O GLN D 31 " (cutoff:3.500A) Processing helix chain 'D' and resid 51 through 73 Processing helix chain 'D' and resid 118 through 134 Processing helix chain 'D' and resid 138 through 151 removed outlier: 3.500A pdb=" N LYS D 142 " --> pdb=" O ASN D 138 " (cutoff:3.500A) Processing helix chain 'D' and resid 156 through 169 removed outlier: 3.689A pdb=" N VAL D 160 " --> pdb=" O ASP D 156 " (cutoff:3.500A) Processing helix chain 'D' and resid 173 through 183 removed outlier: 3.516A pdb=" N GLY D 181 " --> pdb=" O VAL D 177 " (cutoff:3.500A) Processing helix chain 'D' and resid 187 through 195 Processing helix chain 'D' and resid 196 through 199 Processing helix chain 'D' and resid 203 through 218 Processing helix chain 'E' and resid 4 through 27 removed outlier: 3.835A pdb=" N ASN E 8 " --> pdb=" O GLU E 4 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLY E 27 " --> pdb=" O VAL E 23 " (cutoff:3.500A) Processing helix chain 'E' and resid 31 through 36 Processing helix chain 'E' and resid 38 through 44 Processing helix chain 'E' and resid 55 through 59 removed outlier: 3.670A 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: 3.770A pdb=" N THR E 95 " --> pdb=" O LYS E 91 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LYS E 103 " --> pdb=" O HIS E 99 " (cutoff:3.500A) Processing helix chain 'E' and resid 117 through 124 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 Processing helix chain 'E' and resid 182 through 189 Processing helix chain 'F' and resid 86 through 103 Processing helix chain 'F' and resid 116 through 128 Processing helix chain 'G' and resid 14 through 18 Processing helix chain 'G' and resid 21 through 35 Processing helix chain 'H' and resid 45 through 47 No H-bonds generated for 'chain 'H' and resid 45 through 47' Processing helix chain 'H' and resid 88 through 93 Processing helix chain 'H' and resid 131 through 135 removed outlier: 4.389A pdb=" N ASN H 134 " --> pdb=" O ASN H 131 " (cutoff:3.500A) Processing helix chain 'I' and resid 59 through 65 removed outlier: 4.122A pdb=" N GLY I 63 " --> pdb=" O GLN I 60 " (cutoff:3.500A) Processing helix chain 'J' and resid 14 through 16 No H-bonds generated for 'chain 'J' and resid 14 through 16' Processing helix chain 'J' and resid 17 through 27 Processing helix chain 'J' and resid 31 through 40 removed outlier: 3.546A pdb=" N GLY J 40 " --> pdb=" O LEU J 36 " (cutoff:3.500A) Processing helix chain 'J' and resid 43 through 53 removed outlier: 3.813A pdb=" N MET J 49 " --> pdb=" O CYS J 45 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N THR J 52 " --> pdb=" O ARG J 48 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N HIS J 53 " --> pdb=" O MET J 49 " (cutoff:3.500A) Processing helix chain 'J' and resid 56 through 61 Processing helix chain 'K' and resid 5 through 10 Processing helix chain 'K' and resid 39 through 52 removed outlier: 3.504A pdb=" N GLY K 43 " --> pdb=" O ASP K 39 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ASN K 44 " --> pdb=" O HIS K 40 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N LEU K 45 " --> pdb=" O THR K 41 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLU K 49 " --> pdb=" O LEU K 45 " (cutoff:3.500A) removed outlier: 3.751A 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: 7.040A pdb=" N THR A 237 " --> pdb=" O LEU A 86 " (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: 3.704A pdb=" N LYS A 343 " --> pdb=" O PHE B1130 " (cutoff:3.500A) removed outlier: 3.592A 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: 3.862A pdb=" N THR A 351 " --> pdb=" O MET A 487 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N MET A 456 " --> pdb=" O PHE A 444 " (cutoff:3.500A) removed outlier: 7.677A pdb=" N PHE A 468 " --> pdb=" O ARG A 350 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N VAL A 352 " --> pdb=" O PHE A 468 " (cutoff:3.500A) removed outlier: 8.057A pdb=" N LEU A 470 " --> pdb=" O VAL A 352 " (cutoff:3.500A) removed outlier: 6.352A 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: 3.693A pdb=" N ARG A 434 " --> pdb=" O TYR A 376 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N TYR A 404 " --> pdb=" O GLU A 433 " (cutoff:3.500A) removed outlier: 6.021A pdb=" N HIS A 435 " --> pdb=" O ALA A 402 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N ALA A 402 " --> pdb=" O HIS A 435 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 512 through 513 Processing sheet with id=AA9, first strand: chain 'A' and resid 540 through 541 Processing sheet with id=AB1, first strand: chain 'A' and resid 588 through 590 removed outlier: 7.042A 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: 6.806A 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: 3.679A 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: 3.518A pdb=" N ARG A1239 " --> pdb=" O ILE A1227 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N LEU A1236 " --> pdb=" O LEU A1197 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N TYR I 44 " --> pdb=" O ILE A1152 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 48 through 50 removed outlier: 4.741A pdb=" N ILE D 48 " --> pdb=" O ILE G 4 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N PHE G 2 " --> pdb=" O LEU D 50 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ARG G 60 " --> pdb=" O GLU G 69 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLY G 59 " --> pdb=" O ILE A1445 " (cutoff:3.500A) removed outlier: 5.530A pdb=" N VAL A1443 " --> pdb=" O ILE G 61 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 48 through 50 removed outlier: 4.741A pdb=" N ILE D 48 " --> pdb=" O ILE G 4 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N PHE G 2 " --> pdb=" O LEU D 50 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N ARG G 75 " --> pdb=" O LEU G 49 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N CYS G 47 " --> pdb=" O VAL G 77 " (cutoff:3.500A) removed outlier: 7.052A pdb=" N PHE G 79 " --> pdb=" O ILE G 45 " (cutoff:3.500A) removed outlier: 5.947A 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: 5.166A pdb=" N ARG B 86 " --> pdb=" O ALA B 139 " (cutoff:3.500A) removed outlier: 7.204A pdb=" N ALA B 139 " --> pdb=" O ARG B 86 " (cutoff:3.500A) removed outlier: 5.440A pdb=" N TYR B 88 " --> pdb=" O TYR B 137 " (cutoff:3.500A) removed outlier: 7.187A pdb=" N TYR B 137 " --> pdb=" O TYR B 88 " (cutoff:3.500A) removed outlier: 5.238A pdb=" N ILE B 90 " --> pdb=" O ARG B 135 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N ARG B 135 " --> pdb=" O ILE B 90 " (cutoff:3.500A) removed outlier: 5.238A pdb=" N PHE B 92 " --> pdb=" O LYS B 133 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N LYS B 133 " --> pdb=" O PHE B 92 " (cutoff:3.500A) removed outlier: 4.735A pdb=" N LYS B 94 " --> pdb=" O ASP B 131 " (cutoff:3.500A) removed outlier: 7.823A pdb=" N VAL B 132 " --> pdb=" O SER B 156 " (cutoff:3.500A) removed outlier: 5.671A pdb=" N SER B 156 " --> pdb=" O VAL B 132 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N LYS B 134 " --> pdb=" O GLU B 154 " (cutoff:3.500A) removed outlier: 5.236A pdb=" N GLU B 154 " --> pdb=" O LYS B 134 " (cutoff:3.500A) removed outlier: 7.870A pdb=" N THR B 136 " --> pdb=" O ILE B 152 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N ILE B 152 " --> pdb=" O THR B 136 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 69 through 73 removed outlier: 5.166A pdb=" N ARG B 86 " --> pdb=" O ALA B 139 " (cutoff:3.500A) removed outlier: 7.204A pdb=" N ALA B 139 " --> pdb=" O ARG B 86 " (cutoff:3.500A) removed outlier: 5.440A pdb=" N TYR B 88 " --> pdb=" O TYR B 137 " (cutoff:3.500A) removed outlier: 7.187A pdb=" N TYR B 137 " --> pdb=" O TYR B 88 " (cutoff:3.500A) removed outlier: 5.238A pdb=" N ILE B 90 " --> pdb=" O ARG B 135 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N ARG B 135 " --> pdb=" O ILE B 90 " (cutoff:3.500A) removed outlier: 5.238A pdb=" N PHE B 92 " --> pdb=" O LYS B 133 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N LYS B 133 " --> pdb=" O PHE B 92 " (cutoff:3.500A) removed outlier: 4.735A pdb=" N LYS B 94 " --> pdb=" O ASP B 131 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N GLY B 168 " --> pdb=" O LEU B 128 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N VAL B 130 " --> pdb=" O PHE B 166 " (cutoff:3.500A) removed outlier: 5.715A pdb=" N PHE B 166 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 7.450A pdb=" N VAL B 132 " --> pdb=" O LYS B 164 " (cutoff:3.500A) removed outlier: 6.623A 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: 5.996A 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: 4.160A pdb=" N HIS B 236 " --> pdb=" O LEU B 258 " (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: 5.348A pdb=" N TRP B 586 " --> pdb=" O VAL B 582 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N VAL B 582 " --> pdb=" O TRP B 586 " (cutoff:3.500A) removed outlier: 3.995A 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 removed outlier: 3.575A pdb=" N GLU B 650 " --> pdb=" O GLU B 641 " (cutoff:3.500A) 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: 3.858A pdb=" N SER B 853 " --> pdb=" O LYS B 972 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N GLN B 951 " --> pdb=" O ARG B 967 " (cutoff:3.500A) removed outlier: 6.035A pdb=" N ARG B 969 " --> pdb=" O VAL B 949 " (cutoff:3.500A) removed outlier: 5.482A pdb=" N VAL B 949 " --> pdb=" O ARG B 969 " (cutoff:3.500A) removed outlier: 8.483A pdb=" N THR B 971 " --> pdb=" O GLY B 947 " (cutoff:3.500A) removed outlier: 8.092A 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: 3.858A pdb=" N SER B 853 " --> pdb=" O LYS B 972 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N GLN B 951 " --> pdb=" O ARG B 967 " (cutoff:3.500A) removed outlier: 6.035A pdb=" N ARG B 969 " --> pdb=" O VAL B 949 " (cutoff:3.500A) removed outlier: 5.482A pdb=" N VAL B 949 " --> pdb=" O ARG B 969 " (cutoff:3.500A) removed outlier: 8.483A pdb=" N THR B 971 " --> pdb=" O GLY B 947 " (cutoff:3.500A) removed outlier: 8.092A pdb=" N GLY B 947 " --> pdb=" O THR B 971 " (cutoff:3.500A) removed outlier: 5.337A 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 1069 through 1070 removed outlier: 7.118A pdb=" N MET B 839 " --> pdb=" O GLY B 991 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N THR B 993 " --> pdb=" O MET B 839 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N MET B 841 " --> pdb=" O THR B 993 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ILE B1012 " --> pdb=" O ALA B 826 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N PHE B1086 " --> pdb=" O ILE B 827 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 873 through 874 Processing sheet with id=AD6, first strand: chain 'B' and resid 910 through 912 removed outlier: 3.586A pdb=" N ILE B 912 " --> pdb=" O THR B 939 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 1001 through 1002 Processing sheet with id=AD8, first strand: chain 'B' and resid 1158 through 1163 Processing sheet with id=AD9, first strand: chain 'B' and resid 1172 through 1174 Processing sheet with id=AE1, first strand: chain 'C' and resid 7 through 13 removed outlier: 5.550A pdb=" N VAL C 8 " --> pdb=" O SER C 23 " (cutoff:3.500A) removed outlier: 7.078A pdb=" N SER C 23 " --> pdb=" O VAL C 8 " (cutoff:3.500A) removed outlier: 5.651A pdb=" N ILE C 10 " --> pdb=" O ILE C 21 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N ILE C 21 " --> pdb=" O ILE C 10 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 119 through 120 removed outlier: 6.848A pdb=" N GLU C 152 " --> pdb=" O ASN C 54 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N ASN C 54 " --> pdb=" O GLU C 152 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N LYS C 154 " --> pdb=" O GLU C 52 " (cutoff:3.500A) removed outlier: 5.994A pdb=" N LYS C 160 " --> pdb=" O ILE C 46 " (cutoff:3.500A) removed outlier: 5.552A pdb=" N ILE C 46 " --> pdb=" O LYS C 160 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N GLY C 162 " --> pdb=" O LEU C 44 " (cutoff:3.500A) removed outlier: 5.099A pdb=" N LEU C 44 " --> pdb=" O GLY C 162 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N VAL L 65 " --> pdb=" O VAL C 51 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 111 through 114 removed outlier: 6.445A pdb=" N THR C 111 " --> pdb=" O LYS C 146 " (cutoff:3.500A) removed outlier: 4.853A pdb=" N LYS C 146 " --> pdb=" O THR C 111 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N VAL C 113 " --> pdb=" O ILE C 144 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'D' and resid 36 through 38 Processing sheet with id=AE5, first strand: chain 'E' and resid 47 through 48 removed outlier: 4.899A pdb=" N ARG E 52 " --> pdb=" O ASP E 48 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'E' and resid 60 through 62 removed outlier: 6.492A pdb=" N TRP E 79 " --> pdb=" O ILE E 109 " (cutoff:3.500A) removed outlier: 7.591A pdb=" N VAL E 111 " --> pdb=" O TRP E 79 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N GLU E 81 " --> pdb=" O VAL E 111 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'E' and resid 152 through 155 removed outlier: 3.774A pdb=" N LYS E 152 " --> pdb=" O ILE E 199 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'G' and resid 86 through 87 removed outlier: 5.662A pdb=" N ILE G 147 " --> pdb=" O SER G 162 " (cutoff:3.500A) removed outlier: 6.051A pdb=" N SER G 162 " --> pdb=" O ILE G 147 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLY G 149 " --> pdb=" O ILE G 160 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N LYS G 107 " --> pdb=" O ILE G 157 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ALA G 159 " --> pdb=" O LYS G 107 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N THR G 111 " --> pdb=" O GLY G 161 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N GLY G 98 " --> pdb=" O CYS G 94 " (cutoff:3.500A) removed outlier: 5.089A pdb=" N CYS G 94 " --> pdb=" O GLY G 98 " (cutoff:3.500A) removed outlier: 7.126A pdb=" N GLU G 100 " --> pdb=" O VAL G 92 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N VAL G 92 " --> pdb=" O GLU G 100 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N THR G 90 " --> pdb=" O GLN G 102 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'G' and resid 86 through 87 Processing sheet with id=AF1, first strand: chain 'G' and resid 120 through 122 removed outlier: 3.604A pdb=" N SER G 129 " --> pdb=" O ASN G 122 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'H' and resid 4 through 16 removed outlier: 5.654A pdb=" N VAL H 12 " --> pdb=" O ALA H 29 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N ALA H 29 " --> pdb=" O VAL H 12 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLU H 14 " --> pdb=" O GLU H 27 " (cutoff:3.500A) removed outlier: 5.848A pdb=" N LEU H 122 " --> pdb=" O ASP H 41 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N LYS H 103 " --> pdb=" O TYR H 115 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N SER H 117 " --> pdb=" O ALA H 101 " (cutoff:3.500A) removed outlier: 5.814A pdb=" N ALA H 101 " --> pdb=" O SER H 117 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLY H 99 " --> pdb=" O ALA H 140 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N LEU H 55 " --> pdb=" O ILE H 9 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N ILE H 9 " --> pdb=" O LEU H 55 " (cutoff:3.500A) removed outlier: 7.152A pdb=" N VAL H 57 " --> pdb=" O ASP H 7 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N ASP H 7 " --> pdb=" O VAL H 57 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N ILE H 59 " --> pdb=" O LEU H 5 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'I' and resid 15 through 19 Processing sheet with id=AF4, first strand: chain 'I' and resid 70 through 71 removed outlier: 3.639A pdb=" N SER I 71 " --> pdb=" O ASN I 83 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N ASN I 83 " --> pdb=" O SER I 71 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'K' and resid 19 through 23 1349 hydrogen bonds defined for protein. 3690 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 107 hydrogen bonds 214 hydrogen bond angles 0 basepair planarities 41 basepair parallelities 81 stacking parallelities Total time for adding SS restraints: 10.04 Time building geometry restraints manager: 3.92 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 5402 1.31 - 1.43: 8966 1.43 - 1.56: 19017 1.56 - 1.69: 196 1.69 - 1.81: 292 Bond restraints: 33873 Sorted by residual: bond pdb=" C4 ATP A1801 " pdb=" N9 ATP A1801 " ideal model delta sigma weight residual 1.374 1.180 0.194 1.00e-02 1.00e+04 3.76e+02 bond pdb=" C8 ATP A1801 " pdb=" N9 ATP A1801 " ideal model delta sigma weight residual 1.370 1.213 0.157 1.20e-02 6.94e+03 1.72e+02 bond pdb=" C6 ATP A1801 " pdb=" N6 ATP A1801 " ideal model delta sigma weight residual 1.337 1.446 -0.109 1.10e-02 8.26e+03 9.76e+01 bond pdb=" C5 ATP A1801 " pdb=" C6 ATP A1801 " ideal model delta sigma weight residual 1.409 1.334 0.075 1.00e-02 1.00e+04 5.57e+01 bond pdb=" C5 ATP A1801 " pdb=" N7 ATP A1801 " ideal model delta sigma weight residual 1.387 1.453 -0.066 1.00e-02 1.00e+04 4.38e+01 ... (remaining 33868 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.04: 46021 4.04 - 8.07: 127 8.07 - 12.11: 2 12.11 - 16.14: 2 16.14 - 20.18: 1 Bond angle restraints: 46153 Sorted by residual: angle pdb=" PB ATP A1801 " pdb=" O3B ATP A1801 " pdb=" PG ATP A1801 " ideal model delta sigma weight residual 139.87 119.69 20.18 1.00e+00 1.00e+00 4.07e+02 angle pdb=" C4 ATP A1801 " pdb=" N9 ATP A1801 " pdb=" C8 ATP A1801 " ideal model delta sigma weight residual 105.72 119.66 -13.94 1.00e+00 1.00e+00 1.94e+02 angle pdb=" PA ATP A1801 " pdb=" O3A ATP A1801 " pdb=" PB ATP A1801 " ideal model delta sigma weight residual 136.83 122.95 13.88 1.00e+00 1.00e+00 1.93e+02 angle pdb=" N1 ATP A1801 " pdb=" C2 ATP A1801 " pdb=" N3 ATP A1801 " ideal model delta sigma weight residual 128.69 120.12 8.57 1.00e+00 1.00e+00 7.35e+01 angle pdb=" C GLN A 525 " pdb=" CA GLN A 525 " pdb=" CB GLN A 525 " ideal model delta sigma weight residual 116.63 110.26 6.37 1.16e+00 7.43e-01 3.02e+01 ... (remaining 46148 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.82: 19894 33.82 - 67.64: 533 67.64 - 101.46: 36 101.46 - 135.27: 2 135.27 - 169.09: 2 Dihedral angle restraints: 20467 sinusoidal: 9132 harmonic: 11335 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 180.00 158.36 21.64 0 5.00e+00 4.00e-02 1.87e+01 dihedral pdb=" CA ILE C 38 " pdb=" C ILE C 38 " pdb=" N ALA C 39 " pdb=" CA ALA C 39 " ideal model delta harmonic sigma weight residual 180.00 -159.84 -20.16 0 5.00e+00 4.00e-02 1.63e+01 dihedral pdb=" C4' DC N 38 " pdb=" C3' DC N 38 " pdb=" O3' DC N 38 " pdb=" P DC N 39 " ideal model delta sinusoidal sigma weight residual -140.00 29.09 -169.09 1 3.50e+01 8.16e-04 1.55e+01 ... (remaining 20464 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 3634 0.038 - 0.075: 1051 0.075 - 0.113: 410 0.113 - 0.150: 92 0.150 - 0.188: 3 Chirality restraints: 5190 Sorted by residual: 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 -2.44 -0.19 2.00e-01 2.50e+01 8.83e-01 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 -2.78 0.16 2.00e-01 2.50e+01 6.62e-01 chirality pdb=" CB VAL B 482 " pdb=" CA VAL B 482 " pdb=" CG1 VAL B 482 " pdb=" CG2 VAL B 482 " both_signs ideal model delta sigma weight residual False -2.63 -2.47 -0.16 2.00e-01 2.50e+01 6.53e-01 ... (remaining 5187 not shown) Planarity restraints: 5630 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU A 710 " -0.017 2.00e-02 2.50e+03 3.33e-02 1.11e+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 VAL A1098 " 0.032 5.00e-02 4.00e+02 4.90e-02 3.84e+00 pdb=" N PRO A1099 " -0.085 5.00e-02 4.00e+02 pdb=" CA PRO A1099 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO A1099 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP C 170 " -0.015 2.00e-02 2.50e+03 1.14e-02 3.25e+00 pdb=" CG TRP C 170 " 0.031 2.00e-02 2.50e+03 pdb=" CD1 TRP C 170 " -0.011 2.00e-02 2.50e+03 pdb=" CD2 TRP C 170 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP C 170 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP C 170 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP C 170 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 170 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 170 " -0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP C 170 " -0.002 2.00e-02 2.50e+03 ... (remaining 5627 not shown) Histogram of nonbonded interaction distances: 1.74 - 2.37: 83 2.37 - 3.00: 17782 3.00 - 3.63: 49616 3.63 - 4.27: 76016 4.27 - 4.90: 126657 Nonbonded interactions: 270154 Sorted by model distance: nonbonded pdb=" O2A ATP A1801 " pdb="MG MG A1802 " model vdw 1.735 2.170 nonbonded pdb=" OD2 ASP A 481 " pdb="MG MG A1802 " model vdw 1.787 2.170 nonbonded pdb=" OD2 ASP A 483 " pdb="MG MG A1802 " model vdw 1.835 2.170 nonbonded pdb=" O1G ATP A1801 " pdb="MG MG A1802 " model vdw 1.902 2.170 nonbonded pdb=" O ASN A1354 " pdb=" OG SER A1358 " model vdw 2.179 3.040 ... (remaining 270149 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.190 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.610 Check model and map are aligned: 0.130 Set scattering table: 0.120 Process input model: 40.270 Find NCS groups from input model: 0.180 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:1.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7780 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.194 33905 Z= 0.310 Angle : 0.610 20.178 46198 Z= 0.412 Chirality : 0.042 0.188 5190 Planarity : 0.004 0.052 5630 Dihedral : 14.178 169.092 13127 Min Nonbonded Distance : 1.735 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.43 % Favored : 96.47 % Rotamer: Outliers : 0.00 % Allowed : 0.03 % Favored : 99.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.50 (0.14), residues: 3854 helix: 1.65 (0.15), residues: 1317 sheet: -0.26 (0.21), residues: 615 loop : -0.33 (0.15), residues: 1922 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG A 320 TYR 0.026 0.001 TYR B 797 PHE 0.016 0.001 PHE K 105 TRP 0.031 0.001 TRP C 170 HIS 0.009 0.001 HIS A 287 Details of bonding type rmsd/Z covalent geometry : bond 0.00425 / 0.31 (33873) covalent geometry : angle 0.60526 / 0.41 (46153) hydrogen bonds : bond 0.18532 / 12.35 ( 1413) hydrogen bonds : angle 6.66697 / 4.76 ( 3904) metal coordination : bond 0.00440 / 0.29 ( 32) metal coordination : angle 2.51966 / 1.60 ( 45) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7708 Ramachandran restraints generated. 3854 Oldfield, 0 Emsley, 3854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7708 Ramachandran restraints generated. 3854 Oldfield, 0 Emsley, 3854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 632 residues out of total 3434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 632 time to evaluate : 1.282 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: A 74 MET cc_start: 0.8660 (mtt) cc_final: 0.8087 (mtt) REVERT: A 88 LYS cc_start: 0.8727 (mttt) cc_final: 0.8205 (mtpt) REVERT: A 124 GLN cc_start: 0.9293 (mt0) cc_final: 0.8990 (mt0) REVERT: A 205 GLU cc_start: 0.9139 (tt0) cc_final: 0.8910 (tm-30) REVERT: A 260 ASP cc_start: 0.7777 (t70) cc_final: 0.7492 (t0) REVERT: A 291 GLU cc_start: 0.9004 (tt0) cc_final: 0.8718 (tm-30) REVERT: A 320 ARG cc_start: 0.8839 (mtm110) cc_final: 0.8295 (mtp85) REVERT: A 372 LYS cc_start: 0.8379 (mttp) cc_final: 0.8144 (mttp) REVERT: A 383 TYR cc_start: 0.9312 (m-80) cc_final: 0.9037 (m-80) REVERT: A 453 MET cc_start: 0.9106 (mpp) cc_final: 0.8635 (mmm) REVERT: A 454 SER cc_start: 0.8863 (m) cc_final: 0.8549 (t) REVERT: A 510 GLN cc_start: 0.9246 (mm-40) cc_final: 0.9021 (mm-40) REVERT: A 605 MET cc_start: 0.9368 (tpt) cc_final: 0.9026 (tpp) REVERT: A 696 GLU cc_start: 0.8444 (tt0) cc_final: 0.8064 (tm-30) REVERT: A 698 GLN cc_start: 0.8379 (tt0) cc_final: 0.7883 (tp40) REVERT: A 800 VAL cc_start: 0.9423 (t) cc_final: 0.9133 (p) REVERT: A 1071 SER cc_start: 0.8999 (m) cc_final: 0.8787 (p) REVERT: A 1106 ASN cc_start: 0.8041 (m110) cc_final: 0.7750 (m-40) REVERT: A 1144 LYS cc_start: 0.9355 (ttmm) cc_final: 0.9017 (ttmm) REVERT: A 1225 PHE cc_start: 0.8019 (t80) cc_final: 0.7666 (t80) REVERT: A 1239 ARG cc_start: 0.7301 (mtp-110) cc_final: 0.6976 (mtm180) REVERT: A 1265 ASN cc_start: 0.9056 (t0) cc_final: 0.8636 (t0) REVERT: A 1267 MET cc_start: 0.9135 (mtm) cc_final: 0.8919 (mtp) REVERT: A 1285 MET cc_start: 0.8746 (mmt) cc_final: 0.8382 (mmm) REVERT: A 1307 GLU cc_start: 0.9320 (mm-30) cc_final: 0.9076 (mm-30) REVERT: A 1444 MET cc_start: 0.8703 (mmm) cc_final: 0.8049 (mmm) REVERT: B 100 PRO cc_start: 0.8910 (Cg_exo) cc_final: 0.8593 (Cg_endo) REVERT: B 115 GLN cc_start: 0.8264 (tp40) cc_final: 0.8050 (tp40) REVERT: B 183 GLU cc_start: 0.8978 (mt-10) cc_final: 0.8751 (mm-30) REVERT: B 244 LEU cc_start: 0.7590 (mp) cc_final: 0.6986 (tp) REVERT: B 310 MET cc_start: 0.8735 (mtp) cc_final: 0.8410 (mtm) REVERT: B 314 LEU cc_start: 0.9559 (mt) cc_final: 0.9318 (mt) REVERT: B 470 LYS cc_start: 0.8681 (mppt) cc_final: 0.8190 (mmtt) REVERT: B 572 HIS cc_start: 0.8279 (m90) cc_final: 0.7761 (m90) REVERT: B 615 MET cc_start: 0.8957 (mtm) cc_final: 0.8644 (mtm) REVERT: B 620 ARG cc_start: 0.9112 (ptp-170) cc_final: 0.8893 (ttp-110) REVERT: B 662 MET cc_start: 0.8985 (mtm) cc_final: 0.8451 (mmm) REVERT: B 860 MET cc_start: 0.8706 (ttt) cc_final: 0.8115 (tmm) REVERT: B 872 GLU cc_start: 0.7529 (mt-10) cc_final: 0.7251 (mt-10) REVERT: B 904 ARG cc_start: 0.7534 (ttm-80) cc_final: 0.7256 (ttm110) REVERT: B 1021 MET cc_start: 0.9250 (mtm) cc_final: 0.8877 (mtp) REVERT: B 1032 SER cc_start: 0.9171 (m) cc_final: 0.8935 (t) REVERT: B 1072 MET cc_start: 0.9181 (mtp) cc_final: 0.8938 (mtp) REVERT: C 15 LYS cc_start: 0.8737 (ptpt) cc_final: 0.8380 (ttpp) REVERT: C 78 GLU cc_start: 0.8764 (mt-10) cc_final: 0.8460 (mp0) REVERT: C 160 LYS cc_start: 0.8352 (mttt) cc_final: 0.8012 (mttp) REVERT: C 220 ASP cc_start: 0.8901 (t0) cc_final: 0.8556 (t0) REVERT: C 267 GLN cc_start: 0.8579 (tp40) cc_final: 0.8266 (pm20) REVERT: D 3 VAL cc_start: 0.6268 (t) cc_final: 0.5003 (p) REVERT: D 28 GLN cc_start: 0.3878 (tt0) cc_final: 0.3651 (mm110) REVERT: D 38 ILE cc_start: 0.7517 (mt) cc_final: 0.7237 (mp) REVERT: D 59 ILE cc_start: 0.8185 (mt) cc_final: 0.7919 (tt) REVERT: D 140 ASP cc_start: 0.5749 (m-30) cc_final: 0.5351 (m-30) REVERT: D 145 MET cc_start: 0.8617 (mmm) cc_final: 0.8347 (mmm) REVERT: E 58 MET cc_start: 0.9330 (mtp) cc_final: 0.8892 (mtp) REVERT: E 81 GLU cc_start: 0.7484 (tm-30) cc_final: 0.6674 (tm-30) REVERT: E 106 GLN cc_start: 0.9042 (mm-40) cc_final: 0.8784 (mm-40) REVERT: E 159 ASP cc_start: 0.8806 (m-30) cc_final: 0.8507 (t0) REVERT: E 177 ARG cc_start: 0.8106 (mtt180) cc_final: 0.7792 (mtt-85) REVERT: E 182 ASP cc_start: 0.8338 (t70) cc_final: 0.8120 (t0) REVERT: E 192 ARG cc_start: 0.8954 (ttt180) cc_final: 0.8472 (ttp80) REVERT: E 214 CYS cc_start: 0.9004 (t) cc_final: 0.8537 (t) REVERT: F 76 LYS cc_start: 0.9102 (tptt) cc_final: 0.8596 (tptp) REVERT: F 84 TYR cc_start: 0.8723 (m-80) cc_final: 0.8483 (m-10) REVERT: F 89 GLU cc_start: 0.9082 (mt-10) cc_final: 0.8551 (mt-10) REVERT: F 104 ASN cc_start: 0.9100 (m110) cc_final: 0.8777 (t0) REVERT: F 110 ASP cc_start: 0.8035 (m-30) cc_final: 0.7396 (t0) REVERT: F 112 GLU cc_start: 0.8799 (mp0) cc_final: 0.8064 (mp0) REVERT: F 144 GLU cc_start: 0.8006 (mt-10) cc_final: 0.7529 (mt-10) REVERT: G 6 ASP cc_start: 0.6388 (m-30) cc_final: 0.6094 (m-30) REVERT: G 32 GLU cc_start: 0.8743 (mt-10) cc_final: 0.8528 (tm-30) REVERT: G 50 ASP cc_start: 0.7961 (t0) cc_final: 0.7712 (t0) REVERT: G 69 GLU cc_start: 0.8238 (tt0) cc_final: 0.7510 (tp30) REVERT: G 171 ILE cc_start: 0.6417 (mt) cc_final: 0.5532 (mp) REVERT: H 2 SER cc_start: 0.7772 (p) cc_final: 0.7518 (m) REVERT: H 14 GLU cc_start: 0.8200 (tt0) cc_final: 0.6991 (tt0) REVERT: H 22 LYS cc_start: 0.8218 (mttp) cc_final: 0.7719 (mtpt) REVERT: H 27 GLU cc_start: 0.8699 (mt-10) cc_final: 0.7966 (mp0) REVERT: I 6 PHE cc_start: 0.5117 (m-10) cc_final: 0.4891 (m-10) REVERT: J 26 GLN cc_start: 0.8836 (tt0) cc_final: 0.8521 (tm-30) REVERT: K 29 ASN cc_start: 0.7622 (t0) cc_final: 0.7178 (t0) REVERT: K 49 GLU cc_start: 0.8594 (mm-30) cc_final: 0.8216 (tp30) REVERT: K 54 ARG cc_start: 0.9368 (mtm180) cc_final: 0.8908 (mmm160) REVERT: K 64 GLU cc_start: 0.8945 (mt-10) cc_final: 0.8692 (mt-10) REVERT: K 77 THR cc_start: 0.8913 (p) cc_final: 0.8531 (p) REVERT: K 79 GLU cc_start: 0.9081 (tt0) cc_final: 0.8576 (tp30) REVERT: L 68 GLU cc_start: 0.7802 (mm-30) cc_final: 0.7338 (tp30) outliers start: 0 outliers final: 0 residues processed: 632 average time/residue: 0.2456 time to fit residues: 243.4554 Evaluate side-chains 388 residues out of total 3434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 388 time to evaluate : 1.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 395 random chunks: chunk 197 optimal weight: 6.9990 chunk 388 optimal weight: 50.0000 chunk 215 optimal weight: 5.9990 chunk 20 optimal weight: 0.9990 chunk 132 optimal weight: 5.9990 chunk 261 optimal weight: 0.8980 chunk 248 optimal weight: 0.6980 chunk 207 optimal weight: 0.0570 chunk 155 optimal weight: 8.9990 chunk 244 optimal weight: 5.9990 chunk 183 optimal weight: 0.9980 overall best weight: 0.7300 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 83 HIS A 299 HIS A 339 ASN A 358 ASN A 445 ASN A 975 HIS A1130 GLN B 46 GLN B 538 ASN ** B1093 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 143 ASN D 146 GLN E 3 GLN ** G 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 153 GLN I 12 ASN ** I 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 66 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.109210 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.073666 restraints weight = 69968.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.076205 restraints weight = 32574.332| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.077822 restraints weight = 20748.696| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.078813 restraints weight = 15982.164| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 53)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.079355 restraints weight = 13815.310| |-----------------------------------------------------------------------------| r_work (final): 0.3146 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8528 moved from start: 0.1633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 33905 Z= 0.134 Angle : 0.609 9.792 46198 Z= 0.320 Chirality : 0.045 0.260 5190 Planarity : 0.004 0.076 5630 Dihedral : 16.671 165.536 5346 Min Nonbonded Distance : 1.843 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.45 % Favored : 96.45 % Rotamer: Outliers : 1.05 % Allowed : 6.12 % Favored : 92.84 % 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: 3854 helix: 1.56 (0.15), residues: 1349 sheet: -0.22 (0.21), residues: 602 loop : -0.43 (0.14), residues: 1903 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 498 TYR 0.018 0.001 TYR B 797 PHE 0.028 0.002 PHE B 442 TRP 0.017 0.001 TRP C 170 HIS 0.007 0.001 HIS A 287 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.13 (33873) covalent geometry : angle 0.60366 / 0.32 (46153) hydrogen bonds : bond 0.04500 / 3.01 ( 1413) hydrogen bonds : angle 5.01870 / 3.61 ( 3904) metal coordination : bond 0.00491 / 0.32 ( 32) metal coordination : angle 2.68086 / 1.78 ( 45) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7708 Ramachandran restraints generated. 3854 Oldfield, 0 Emsley, 3854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7708 Ramachandran restraints generated. 3854 Oldfield, 0 Emsley, 3854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 464 residues out of total 3434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 428 time to evaluate : 1.245 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 MET cc_start: 0.8267 (mtt) cc_final: 0.7822 (mtt) REVERT: A 88 LYS cc_start: 0.8891 (mttt) cc_final: 0.8537 (mtpt) REVERT: A 498 ARG cc_start: 0.8520 (OUTLIER) cc_final: 0.7985 (mtm-85) REVERT: A 698 GLN cc_start: 0.8311 (tt0) cc_final: 0.7758 (tp40) REVERT: A 873 MET cc_start: 0.9315 (tpp) cc_final: 0.8520 (mpp) REVERT: A 1071 SER cc_start: 0.9418 (m) cc_final: 0.9160 (p) REVERT: A 1104 ILE cc_start: 0.9283 (mt) cc_final: 0.9018 (mm) REVERT: A 1106 ASN cc_start: 0.8640 (m110) cc_final: 0.8287 (m-40) REVERT: A 1130 GLN cc_start: 0.8360 (OUTLIER) cc_final: 0.8131 (pm20) REVERT: A 1154 TYR cc_start: 0.4774 (t80) cc_final: 0.4476 (t80) REVERT: A 1267 MET cc_start: 0.9057 (mtm) cc_final: 0.8782 (mtp) REVERT: A 1444 MET cc_start: 0.8208 (mmm) cc_final: 0.7406 (mmm) REVERT: B 101 MET cc_start: 0.8644 (mtp) cc_final: 0.8363 (mtt) REVERT: B 115 GLN cc_start: 0.8378 (tp40) cc_final: 0.8170 (tp40) REVERT: B 244 LEU cc_start: 0.7935 (mp) cc_final: 0.7397 (tp) REVERT: B 310 MET cc_start: 0.8925 (mtp) cc_final: 0.8705 (mtm) REVERT: B 314 LEU cc_start: 0.9675 (mt) cc_final: 0.9440 (mt) REVERT: B 470 LYS cc_start: 0.8265 (mppt) cc_final: 0.7812 (mmtt) REVERT: B 572 HIS cc_start: 0.7804 (m90) cc_final: 0.7384 (m90) REVERT: B 872 GLU cc_start: 0.7871 (mt-10) cc_final: 0.7638 (mt-10) REVERT: B 1152 MET cc_start: 0.8589 (mmm) cc_final: 0.7864 (mmm) REVERT: C 220 ASP cc_start: 0.8404 (t0) cc_final: 0.8059 (t0) REVERT: D 65 GLU cc_start: 0.8890 (mm-30) cc_final: 0.8667 (mm-30) REVERT: D 68 ARG cc_start: 0.7504 (tpp-160) cc_final: 0.7041 (tpt90) REVERT: D 145 MET cc_start: 0.8891 (mmm) cc_final: 0.8665 (mmm) REVERT: E 48 ASP cc_start: 0.8846 (t0) cc_final: 0.8545 (m-30) REVERT: E 54 GLN cc_start: 0.7961 (mt0) cc_final: 0.6386 (mt0) REVERT: E 58 MET cc_start: 0.8703 (mtp) cc_final: 0.8317 (mtp) REVERT: E 81 GLU cc_start: 0.7265 (tm-30) cc_final: 0.7063 (tm-30) REVERT: E 101 GLN cc_start: 0.8340 (mm110) cc_final: 0.7974 (mm110) REVERT: E 214 CYS cc_start: 0.8900 (t) cc_final: 0.8596 (t) REVERT: F 76 LYS cc_start: 0.9029 (tptt) cc_final: 0.8816 (tptp) REVERT: F 81 THR cc_start: 0.9465 (m) cc_final: 0.9119 (p) REVERT: F 104 ASN cc_start: 0.8795 (m110) cc_final: 0.8592 (t0) REVERT: F 112 GLU cc_start: 0.8397 (mp0) cc_final: 0.8070 (mp0) REVERT: G 14 HIS cc_start: 0.8485 (t-90) cc_final: 0.8222 (t-90) REVERT: G 49 LEU cc_start: 0.9473 (mt) cc_final: 0.9025 (pp) REVERT: G 50 ASP cc_start: 0.8839 (t0) cc_final: 0.8329 (t0) REVERT: G 51 TYR cc_start: 0.8338 (t80) cc_final: 0.7885 (t80) REVERT: G 69 GLU cc_start: 0.8131 (tt0) cc_final: 0.7688 (tp30) REVERT: G 137 ILE cc_start: 0.6613 (mt) cc_final: 0.6404 (mm) REVERT: H 14 GLU cc_start: 0.7828 (tt0) cc_final: 0.6977 (tt0) REVERT: H 22 LYS cc_start: 0.9105 (mttp) cc_final: 0.8654 (mtpt) REVERT: H 130 ARG cc_start: 0.8077 (mtm-85) cc_final: 0.7868 (mtm-85) REVERT: I 13 MET cc_start: 0.6348 (ppp) cc_final: 0.5378 (ppp) REVERT: K 29 ASN cc_start: 0.8199 (t0) cc_final: 0.7808 (t0) REVERT: K 77 THR cc_start: 0.9291 (p) cc_final: 0.8863 (p) outliers start: 36 outliers final: 16 residues processed: 452 average time/residue: 0.2259 time to fit residues: 166.5694 Evaluate side-chains 375 residues out of total 3434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 357 time to evaluate : 1.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 287 HIS Chi-restraints excluded: chain A residue 498 ARG Chi-restraints excluded: chain A residue 1130 GLN Chi-restraints excluded: chain A residue 1228 TRP Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 771 SER Chi-restraints excluded: chain B residue 792 MET Chi-restraints excluded: chain B residue 939 THR Chi-restraints excluded: chain B residue 1082 MET Chi-restraints excluded: chain C residue 38 ILE Chi-restraints excluded: chain C residue 83 SER Chi-restraints excluded: chain D residue 31 GLN Chi-restraints excluded: chain E residue 3 GLN Chi-restraints excluded: chain E residue 22 MET Chi-restraints excluded: chain E residue 83 CYS Chi-restraints excluded: chain H residue 61 SER Chi-restraints excluded: chain J residue 22 LEU Chi-restraints excluded: chain K residue 94 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 395 random chunks: chunk 242 optimal weight: 6.9990 chunk 191 optimal weight: 4.9990 chunk 5 optimal weight: 0.0970 chunk 373 optimal weight: 3.9990 chunk 22 optimal weight: 7.9990 chunk 333 optimal weight: 10.0000 chunk 304 optimal weight: 10.0000 chunk 239 optimal weight: 7.9990 chunk 7 optimal weight: 3.9990 chunk 249 optimal weight: 8.9990 chunk 222 optimal weight: 8.9990 overall best weight: 4.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1124 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1265 ASN D 9 GLN ** D 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 143 ASN D 146 GLN D 199 ASN E 3 GLN ** G 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 89 GLN J 26 GLN ** K 2 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.105320 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.2946 r_free = 0.2946 target = 0.068918 restraints weight = 71352.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.071360 restraints weight = 34756.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 59)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.072898 restraints weight = 22677.066| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 51)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.073818 restraints weight = 17720.006| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 49)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.074368 restraints weight = 15452.572| |-----------------------------------------------------------------------------| r_work (final): 0.3060 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8623 moved from start: 0.2044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.063 33905 Z= 0.300 Angle : 0.671 12.057 46198 Z= 0.348 Chirality : 0.046 0.255 5190 Planarity : 0.005 0.063 5630 Dihedral : 16.665 166.747 5346 Min Nonbonded Distance : 1.806 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.57 % Favored : 95.33 % Rotamer: Outliers : 1.78 % Allowed : 8.10 % 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: 0.16 (0.14), residues: 3854 helix: 1.40 (0.14), residues: 1333 sheet: -0.46 (0.20), residues: 622 loop : -0.58 (0.14), residues: 1899 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 320 TYR 0.017 0.002 TYR A 836 PHE 0.021 0.002 PHE G 109 TRP 0.037 0.002 TRP B 308 HIS 0.011 0.001 HIS A1124 Details of bonding type rmsd/Z covalent geometry : bond 0.00685 / 0.30 (33873) covalent geometry : angle 0.66350 / 0.35 (46153) hydrogen bonds : bond 0.04455 / 2.96 ( 1413) hydrogen bonds : angle 4.95289 / 3.57 ( 3904) metal coordination : bond 0.01112 / 0.71 ( 32) metal coordination : angle 3.37558 / 2.15 ( 45) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7708 Ramachandran restraints generated. 3854 Oldfield, 0 Emsley, 3854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7708 Ramachandran restraints generated. 3854 Oldfield, 0 Emsley, 3854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 410 residues out of total 3434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 349 time to evaluate : 1.263 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: A 74 MET cc_start: 0.8305 (mtt) cc_final: 0.7878 (mtt) REVERT: A 88 LYS cc_start: 0.8911 (mttt) cc_final: 0.8504 (mtpt) REVERT: A 122 MET cc_start: 0.8603 (tpp) cc_final: 0.8332 (ttm) REVERT: A 234 MET cc_start: 0.9214 (ttm) cc_final: 0.8665 (mtp) REVERT: A 498 ARG cc_start: 0.8601 (OUTLIER) cc_final: 0.7996 (mtm-85) REVERT: A 698 GLN cc_start: 0.8469 (tt0) cc_final: 0.7833 (tp40) REVERT: A 712 GLU cc_start: 0.8251 (tt0) cc_final: 0.8011 (tt0) REVERT: A 1071 SER cc_start: 0.9455 (m) cc_final: 0.9207 (p) REVERT: A 1239 ARG cc_start: 0.7150 (mtp-110) cc_final: 0.6927 (mtm180) REVERT: A 1285 MET cc_start: 0.8295 (mmm) cc_final: 0.7949 (mmm) REVERT: A 1373 ASP cc_start: 0.8670 (OUTLIER) cc_final: 0.8054 (t0) REVERT: A 1444 MET cc_start: 0.8551 (mmm) cc_final: 0.7487 (mmm) REVERT: B 115 GLN cc_start: 0.8535 (tp40) cc_final: 0.8229 (tp40) REVERT: B 244 LEU cc_start: 0.7990 (mp) cc_final: 0.7458 (tp) REVERT: B 314 LEU cc_start: 0.9697 (mt) cc_final: 0.9483 (mt) REVERT: B 470 LYS cc_start: 0.8296 (mppt) cc_final: 0.7829 (mmtt) REVERT: B 572 HIS cc_start: 0.7845 (m90) cc_final: 0.7372 (m90) REVERT: B 865 LYS cc_start: 0.2413 (tmtt) cc_final: 0.2165 (tptt) REVERT: B 872 GLU cc_start: 0.7944 (mt-10) cc_final: 0.7376 (mt-10) REVERT: C 220 ASP cc_start: 0.8382 (t0) cc_final: 0.8152 (t0) REVERT: D 65 GLU cc_start: 0.8911 (mm-30) cc_final: 0.8693 (mm-30) REVERT: D 68 ARG cc_start: 0.7496 (tpp-160) cc_final: 0.7048 (tpt90) REVERT: D 145 MET cc_start: 0.8847 (mmm) cc_final: 0.8646 (mmm) REVERT: E 57 MET cc_start: 0.8701 (mtp) cc_final: 0.8388 (mtm) REVERT: E 58 MET cc_start: 0.8751 (mtp) cc_final: 0.8448 (mtp) REVERT: E 81 GLU cc_start: 0.7284 (tm-30) cc_final: 0.7021 (tm-30) REVERT: F 104 ASN cc_start: 0.8830 (m110) cc_final: 0.8621 (t0) REVERT: F 110 ASP cc_start: 0.7749 (t0) cc_final: 0.7251 (t0) REVERT: F 112 GLU cc_start: 0.8449 (mp0) cc_final: 0.8206 (mp0) REVERT: G 1 MET cc_start: 0.7235 (OUTLIER) cc_final: 0.6687 (ttt) REVERT: G 3 PHE cc_start: 0.8276 (m-80) cc_final: 0.7520 (m-80) REVERT: G 49 LEU cc_start: 0.9474 (mt) cc_final: 0.9013 (pp) REVERT: G 50 ASP cc_start: 0.8831 (t0) cc_final: 0.8304 (t0) REVERT: G 51 TYR cc_start: 0.8337 (t80) cc_final: 0.8101 (t80) REVERT: G 53 ASN cc_start: 0.8009 (t0) cc_final: 0.7160 (t0) REVERT: G 69 GLU cc_start: 0.8173 (tt0) cc_final: 0.7821 (tp30) REVERT: G 153 GLN cc_start: 0.6271 (tm130) cc_final: 0.5670 (tm130) REVERT: H 14 GLU cc_start: 0.7612 (tt0) cc_final: 0.6819 (tt0) REVERT: H 22 LYS cc_start: 0.9119 (mttp) cc_final: 0.8815 (mtpt) REVERT: H 27 GLU cc_start: 0.7430 (mp0) cc_final: 0.6507 (mp0) REVERT: H 130 ARG cc_start: 0.8102 (mtm-85) cc_final: 0.7897 (mtm-85) REVERT: I 12 ASN cc_start: 0.6815 (m-40) cc_final: 0.6537 (m110) REVERT: I 13 MET cc_start: 0.5845 (ppp) cc_final: 0.5437 (tmm) REVERT: K 29 ASN cc_start: 0.8450 (t0) cc_final: 0.8061 (t0) REVERT: L 33 GLU cc_start: 0.8780 (mt-10) cc_final: 0.8470 (mt-10) outliers start: 61 outliers final: 41 residues processed: 386 average time/residue: 0.2244 time to fit residues: 141.5340 Evaluate side-chains 377 residues out of total 3434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 333 time to evaluate : 1.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 287 HIS Chi-restraints excluded: chain A residue 437 MET Chi-restraints excluded: chain A residue 487 MET Chi-restraints excluded: chain A residue 498 ARG Chi-restraints excluded: chain A residue 550 LEU Chi-restraints excluded: chain A residue 683 ILE Chi-restraints excluded: chain A residue 878 ILE Chi-restraints excluded: chain A residue 886 ILE Chi-restraints excluded: chain A residue 1020 CYS Chi-restraints excluded: chain A residue 1228 TRP Chi-restraints excluded: chain A residue 1358 SER Chi-restraints excluded: chain A residue 1373 ASP Chi-restraints excluded: chain A residue 1374 VAL Chi-restraints excluded: chain B residue 70 ILE Chi-restraints excluded: chain B residue 305 VAL Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 350 GLN Chi-restraints excluded: chain B residue 771 SER Chi-restraints excluded: chain B residue 837 ASP Chi-restraints excluded: chain C residue 38 ILE Chi-restraints excluded: chain C residue 61 GLU Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain C residue 222 LYS Chi-restraints excluded: chain C residue 240 VAL Chi-restraints excluded: chain D residue 3 VAL Chi-restraints excluded: chain D residue 120 GLU Chi-restraints excluded: chain D residue 159 THR Chi-restraints excluded: chain D residue 165 GLN Chi-restraints excluded: chain E residue 22 MET Chi-restraints excluded: chain E residue 83 CYS Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain F residue 93 ILE Chi-restraints excluded: chain G residue 1 MET Chi-restraints excluded: chain G residue 6 ASP Chi-restraints excluded: chain G residue 39 THR Chi-restraints excluded: chain G residue 47 CYS Chi-restraints excluded: chain H residue 2 SER Chi-restraints excluded: chain H residue 61 SER Chi-restraints excluded: chain J residue 22 LEU Chi-restraints excluded: chain J residue 26 GLN Chi-restraints excluded: chain K residue 9 LEU Chi-restraints excluded: chain K residue 16 GLU Chi-restraints excluded: chain L residue 61 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 395 random chunks: chunk 0 optimal weight: 8.9990 chunk 345 optimal weight: 4.9990 chunk 138 optimal weight: 3.9990 chunk 183 optimal weight: 0.8980 chunk 169 optimal weight: 10.0000 chunk 216 optimal weight: 0.8980 chunk 286 optimal weight: 20.0000 chunk 108 optimal weight: 8.9990 chunk 251 optimal weight: 0.7980 chunk 308 optimal weight: 3.9990 chunk 352 optimal weight: 1.9990 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1093 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 3 GLN G 57 GLN ** G 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 2 ASN ** 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 = 0.3652 r_free = 0.3652 target = 0.107029 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.070905 restraints weight = 70462.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.073403 restraints weight = 33629.243| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.074989 restraints weight = 21677.016| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.075966 restraints weight = 16807.965| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.076528 restraints weight = 14560.649| |-----------------------------------------------------------------------------| r_work (final): 0.3103 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8576 moved from start: 0.2184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 33905 Z= 0.158 Angle : 0.572 9.589 46198 Z= 0.300 Chirality : 0.044 0.258 5190 Planarity : 0.004 0.059 5630 Dihedral : 16.658 166.421 5346 Min Nonbonded Distance : 1.880 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.50 % Favored : 96.39 % Rotamer: Outliers : 1.54 % Allowed : 9.96 % Favored : 88.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.24 (0.14), residues: 3854 helix: 1.52 (0.15), residues: 1332 sheet: -0.51 (0.20), residues: 611 loop : -0.55 (0.14), residues: 1911 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 320 TYR 0.015 0.001 TYR C 82 PHE 0.021 0.001 PHE A 444 TRP 0.030 0.001 TRP B 308 HIS 0.007 0.001 HIS A1173 Details of bonding type rmsd/Z covalent geometry : bond 0.00358 / 0.16 (33873) covalent geometry : angle 0.56436 / 0.30 (46153) hydrogen bonds : bond 0.03787 / 2.54 ( 1413) hydrogen bonds : angle 4.66054 / 3.36 ( 3904) metal coordination : bond 0.00669 / 0.44 ( 32) metal coordination : angle 2.94144 / 1.85 ( 45) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7708 Ramachandran restraints generated. 3854 Oldfield, 0 Emsley, 3854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7708 Ramachandran restraints generated. 3854 Oldfield, 0 Emsley, 3854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 412 residues out of total 3434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 359 time to evaluate : 1.353 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 MET cc_start: 0.8277 (mtt) cc_final: 0.7872 (mtt) REVERT: A 88 LYS cc_start: 0.8958 (mttt) cc_final: 0.8532 (mtpt) REVERT: A 122 MET cc_start: 0.8649 (tpp) cc_final: 0.8416 (tpp) REVERT: A 234 MET cc_start: 0.9209 (ttm) cc_final: 0.8765 (mtp) REVERT: A 498 ARG cc_start: 0.8537 (OUTLIER) cc_final: 0.7972 (mtm-85) REVERT: A 698 GLN cc_start: 0.8486 (tt0) cc_final: 0.7633 (tp40) REVERT: A 880 LYS cc_start: 0.9140 (tttt) cc_final: 0.8902 (ttmt) REVERT: A 1071 SER cc_start: 0.9407 (m) cc_final: 0.9183 (p) REVERT: A 1224 LEU cc_start: 0.8199 (mm) cc_final: 0.7710 (mm) REVERT: A 1285 MET cc_start: 0.8324 (mmm) cc_final: 0.8019 (mmm) REVERT: A 1373 ASP cc_start: 0.8558 (OUTLIER) cc_final: 0.7935 (t0) REVERT: A 1444 MET cc_start: 0.8541 (mmm) cc_final: 0.7583 (mmm) REVERT: A 1454 MET cc_start: 0.7686 (tmm) cc_final: 0.7373 (tmm) REVERT: B 101 MET cc_start: 0.8689 (mtp) cc_final: 0.8468 (mtt) REVERT: B 115 GLN cc_start: 0.8435 (tp40) cc_final: 0.8207 (tp40) REVERT: B 244 LEU cc_start: 0.7983 (mp) cc_final: 0.7475 (tp) REVERT: B 314 LEU cc_start: 0.9687 (mt) cc_final: 0.9433 (mt) REVERT: B 470 LYS cc_start: 0.8278 (mppt) cc_final: 0.7812 (mmtt) REVERT: B 572 HIS cc_start: 0.7837 (m90) cc_final: 0.7364 (m90) REVERT: B 872 GLU cc_start: 0.7779 (mt-10) cc_final: 0.7204 (mt-10) REVERT: C 220 ASP cc_start: 0.8380 (t0) cc_final: 0.8168 (t0) REVERT: D 65 GLU cc_start: 0.8906 (mm-30) cc_final: 0.8685 (mm-30) REVERT: D 68 ARG cc_start: 0.7667 (tpp-160) cc_final: 0.7282 (tpt90) REVERT: D 131 GLU cc_start: 0.7140 (mt-10) cc_final: 0.6866 (tm-30) REVERT: D 145 MET cc_start: 0.8812 (mmm) cc_final: 0.8611 (mmm) REVERT: E 54 GLN cc_start: 0.8018 (mt0) cc_final: 0.7634 (mt0) REVERT: E 58 MET cc_start: 0.8694 (mtp) cc_final: 0.8317 (mtp) REVERT: E 101 GLN cc_start: 0.8288 (mm110) cc_final: 0.7979 (mm110) REVERT: F 104 ASN cc_start: 0.8814 (m110) cc_final: 0.8598 (t0) REVERT: F 110 ASP cc_start: 0.7731 (t0) cc_final: 0.7169 (t0) REVERT: F 112 GLU cc_start: 0.8408 (mp0) cc_final: 0.8114 (mp0) REVERT: G 1 MET cc_start: 0.7111 (OUTLIER) cc_final: 0.6317 (ttt) REVERT: G 3 PHE cc_start: 0.8132 (m-80) cc_final: 0.7316 (m-80) REVERT: G 49 LEU cc_start: 0.9479 (mt) cc_final: 0.9034 (pp) REVERT: G 50 ASP cc_start: 0.8861 (t0) cc_final: 0.8441 (t0) REVERT: G 51 TYR cc_start: 0.8342 (t80) cc_final: 0.8123 (t80) REVERT: G 69 GLU cc_start: 0.8170 (tt0) cc_final: 0.7760 (tp30) REVERT: G 153 GLN cc_start: 0.6522 (tm130) cc_final: 0.6014 (tm-30) REVERT: H 14 GLU cc_start: 0.7632 (tt0) cc_final: 0.7022 (tt0) REVERT: H 22 LYS cc_start: 0.9111 (mttp) cc_final: 0.8778 (mtpt) REVERT: H 27 GLU cc_start: 0.7476 (mp0) cc_final: 0.6428 (mp0) REVERT: H 41 ASP cc_start: 0.8666 (m-30) cc_final: 0.8419 (m-30) REVERT: I 12 ASN cc_start: 0.6786 (m-40) cc_final: 0.6568 (m110) REVERT: I 13 MET cc_start: 0.6229 (ppp) cc_final: 0.5877 (tmm) REVERT: J 26 GLN cc_start: 0.8473 (OUTLIER) cc_final: 0.7943 (pp30) REVERT: J 27 GLU cc_start: 0.8645 (tp30) cc_final: 0.8427 (tp30) REVERT: K 29 ASN cc_start: 0.8412 (t0) cc_final: 0.7937 (t0) REVERT: K 77 THR cc_start: 0.9371 (p) cc_final: 0.8970 (p) REVERT: L 33 GLU cc_start: 0.8732 (mt-10) cc_final: 0.8323 (mt-10) outliers start: 53 outliers final: 30 residues processed: 390 average time/residue: 0.2261 time to fit residues: 144.2071 Evaluate side-chains 372 residues out of total 3434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 338 time to evaluate : 1.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 287 HIS Chi-restraints excluded: chain A residue 437 MET Chi-restraints excluded: chain A residue 487 MET Chi-restraints excluded: chain A residue 498 ARG Chi-restraints excluded: chain A residue 550 LEU Chi-restraints excluded: chain A residue 886 ILE Chi-restraints excluded: chain A residue 1228 TRP Chi-restraints excluded: chain A residue 1265 ASN Chi-restraints excluded: chain A residue 1373 ASP Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 305 VAL Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 837 ASP Chi-restraints excluded: chain B residue 863 GLU Chi-restraints excluded: chain B residue 1082 MET Chi-restraints excluded: chain C residue 38 ILE Chi-restraints excluded: chain C residue 61 GLU Chi-restraints excluded: chain C residue 240 VAL Chi-restraints excluded: chain D residue 3 VAL Chi-restraints excluded: chain D residue 120 GLU Chi-restraints excluded: chain D residue 159 THR Chi-restraints excluded: chain D residue 165 GLN Chi-restraints excluded: chain E residue 22 MET Chi-restraints excluded: chain E residue 83 CYS Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain F residue 93 ILE Chi-restraints excluded: chain G residue 1 MET Chi-restraints excluded: chain G residue 6 ASP Chi-restraints excluded: chain G residue 39 THR Chi-restraints excluded: chain G residue 101 VAL Chi-restraints excluded: chain G residue 121 PHE Chi-restraints excluded: chain H residue 61 SER Chi-restraints excluded: chain J residue 26 GLN Chi-restraints excluded: chain K residue 9 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 395 random chunks: chunk 46 optimal weight: 3.9990 chunk 140 optimal weight: 5.9990 chunk 136 optimal weight: 1.9990 chunk 106 optimal weight: 0.7980 chunk 95 optimal weight: 0.3980 chunk 105 optimal weight: 3.9990 chunk 111 optimal weight: 0.0010 chunk 182 optimal weight: 0.0060 chunk 71 optimal weight: 1.9990 chunk 138 optimal weight: 4.9990 chunk 103 optimal weight: 2.9990 overall best weight: 0.6404 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 451 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 603 ASN ** B1093 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 9 GLN D 34 GLN ** D 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 199 ASN E 3 GLN ** E 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 26 GLN K 2 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.108462 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.072578 restraints weight = 70188.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 57)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.075121 restraints weight = 32988.326| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.076754 restraints weight = 21063.892| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 56)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.077734 restraints weight = 16240.312| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 49)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.078293 restraints weight = 14068.944| |-----------------------------------------------------------------------------| r_work (final): 0.3139 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8544 moved from start: 0.2354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 33905 Z= 0.109 Angle : 0.539 8.994 46198 Z= 0.282 Chirality : 0.042 0.258 5190 Planarity : 0.004 0.063 5630 Dihedral : 16.602 165.850 5346 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.37 % Favored : 96.52 % Rotamer: Outliers : 1.54 % Allowed : 10.66 % Favored : 87.80 % 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: 0.35 (0.14), residues: 3854 helix: 1.59 (0.15), residues: 1342 sheet: -0.42 (0.20), residues: 645 loop : -0.48 (0.15), residues: 1867 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 320 TYR 0.013 0.001 TYR H 129 PHE 0.031 0.001 PHE G 18 TRP 0.037 0.001 TRP B 308 HIS 0.008 0.001 HIS G 14 Details of bonding type rmsd/Z covalent geometry : bond 0.00234 / 0.11 (33873) covalent geometry : angle 0.53343 / 0.28 (46153) hydrogen bonds : bond 0.03405 / 2.29 ( 1413) hydrogen bonds : angle 4.42862 / 3.19 ( 3904) metal coordination : bond 0.00465 / 0.31 ( 32) metal coordination : angle 2.55223 / 1.59 ( 45) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7708 Ramachandran restraints generated. 3854 Oldfield, 0 Emsley, 3854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7708 Ramachandran restraints generated. 3854 Oldfield, 0 Emsley, 3854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 433 residues out of total 3434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 380 time to evaluate : 1.308 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 MET cc_start: 0.8264 (mtt) cc_final: 0.7868 (mtt) REVERT: A 88 LYS cc_start: 0.8961 (mttt) cc_final: 0.8544 (mtpt) REVERT: A 122 MET cc_start: 0.8665 (tpp) cc_final: 0.8357 (tpp) REVERT: A 234 MET cc_start: 0.9288 (ttm) cc_final: 0.8777 (mtp) REVERT: A 470 LEU cc_start: 0.9226 (OUTLIER) cc_final: 0.8715 (pp) REVERT: A 698 GLN cc_start: 0.8492 (tt0) cc_final: 0.7757 (tp40) REVERT: A 708 MET cc_start: 0.7279 (mmm) cc_final: 0.6990 (mmt) REVERT: A 880 LYS cc_start: 0.9125 (tttt) cc_final: 0.8884 (ttmt) REVERT: A 930 ASP cc_start: 0.8134 (m-30) cc_final: 0.7588 (m-30) REVERT: A 1071 SER cc_start: 0.9386 (m) cc_final: 0.9163 (p) REVERT: A 1420 ASP cc_start: 0.7965 (p0) cc_final: 0.7717 (p0) REVERT: A 1444 MET cc_start: 0.8526 (mmm) cc_final: 0.7563 (mmm) REVERT: B 101 MET cc_start: 0.8653 (mtp) cc_final: 0.8396 (mtt) REVERT: B 115 GLN cc_start: 0.8372 (tp40) cc_final: 0.8169 (tp40) REVERT: B 244 LEU cc_start: 0.7928 (mp) cc_final: 0.7439 (tp) REVERT: B 310 MET cc_start: 0.8493 (mtm) cc_final: 0.8110 (mtp) REVERT: B 314 LEU cc_start: 0.9686 (mt) cc_final: 0.9461 (mt) REVERT: B 470 LYS cc_start: 0.8231 (mppt) cc_final: 0.7770 (mmtt) REVERT: B 572 HIS cc_start: 0.7820 (m90) cc_final: 0.7453 (m90) REVERT: B 872 GLU cc_start: 0.7781 (mt-10) cc_final: 0.7395 (mt-10) REVERT: B 935 ARG cc_start: 0.2938 (tpp-160) cc_final: 0.2659 (tpp-160) REVERT: C 47 ASP cc_start: 0.8698 (t70) cc_final: 0.8224 (t0) REVERT: C 220 ASP cc_start: 0.8457 (t0) cc_final: 0.8230 (t0) REVERT: D 65 GLU cc_start: 0.8911 (mm-30) cc_final: 0.8690 (mm-30) REVERT: D 68 ARG cc_start: 0.7661 (tpp-160) cc_final: 0.7278 (tpt90) REVERT: D 131 GLU cc_start: 0.7122 (mt-10) cc_final: 0.6890 (tm-30) REVERT: D 145 MET cc_start: 0.8812 (mmm) cc_final: 0.8580 (mmm) REVERT: D 153 ARG cc_start: 0.6419 (mtm-85) cc_final: 0.6145 (ptp90) REVERT: E 58 MET cc_start: 0.8658 (mtp) cc_final: 0.8238 (mtp) REVERT: F 81 THR cc_start: 0.9461 (m) cc_final: 0.9161 (p) REVERT: F 89 GLU cc_start: 0.8660 (mt-10) cc_final: 0.8309 (mt-10) REVERT: F 104 ASN cc_start: 0.8867 (m110) cc_final: 0.8634 (t0) REVERT: F 110 ASP cc_start: 0.7814 (t0) cc_final: 0.7210 (t0) REVERT: F 112 GLU cc_start: 0.8367 (mp0) cc_final: 0.8080 (mp0) REVERT: G 1 MET cc_start: 0.6968 (OUTLIER) cc_final: 0.6104 (ttt) REVERT: G 3 PHE cc_start: 0.8109 (m-80) cc_final: 0.7323 (m-80) REVERT: G 14 HIS cc_start: 0.8601 (t-90) cc_final: 0.8218 (t-90) REVERT: G 49 LEU cc_start: 0.9493 (mt) cc_final: 0.9059 (pp) REVERT: G 50 ASP cc_start: 0.8866 (t0) cc_final: 0.8310 (t0) REVERT: G 51 TYR cc_start: 0.8321 (t80) cc_final: 0.8106 (t80) REVERT: G 53 ASN cc_start: 0.8047 (t0) cc_final: 0.7294 (t0) REVERT: G 69 GLU cc_start: 0.8091 (tt0) cc_final: 0.7653 (tp30) REVERT: H 14 GLU cc_start: 0.7652 (tt0) cc_final: 0.6806 (tt0) REVERT: H 22 LYS cc_start: 0.9124 (mttp) cc_final: 0.8855 (mtpt) REVERT: H 27 GLU cc_start: 0.7466 (mp0) cc_final: 0.6504 (mt-10) REVERT: H 41 ASP cc_start: 0.8642 (m-30) cc_final: 0.8391 (m-30) REVERT: I 13 MET cc_start: 0.6187 (ppp) cc_final: 0.5887 (tmm) REVERT: J 26 GLN cc_start: 0.8507 (OUTLIER) cc_final: 0.8228 (pp30) REVERT: K 6 ARG cc_start: 0.9228 (mmm-85) cc_final: 0.7630 (mmm-85) REVERT: K 29 ASN cc_start: 0.8355 (t0) cc_final: 0.7910 (t0) REVERT: K 77 THR cc_start: 0.9362 (p) cc_final: 0.8991 (p) REVERT: L 33 GLU cc_start: 0.8777 (mt-10) cc_final: 0.8332 (mt-10) outliers start: 53 outliers final: 33 residues processed: 413 average time/residue: 0.2112 time to fit residues: 144.4404 Evaluate side-chains 390 residues out of total 3434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 354 time to evaluate : 1.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 287 HIS Chi-restraints excluded: chain A residue 437 MET Chi-restraints excluded: chain A residue 470 LEU Chi-restraints excluded: chain A residue 550 LEU Chi-restraints excluded: chain A residue 886 ILE Chi-restraints excluded: chain A residue 1228 TRP Chi-restraints excluded: chain A residue 1240 CYS Chi-restraints excluded: chain B residue 305 VAL Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 508 LEU Chi-restraints excluded: chain B residue 837 ASP Chi-restraints excluded: chain B residue 863 GLU Chi-restraints excluded: chain B residue 1082 MET Chi-restraints excluded: chain C residue 38 ILE Chi-restraints excluded: chain C residue 61 GLU Chi-restraints excluded: chain D residue 3 VAL Chi-restraints excluded: chain D residue 35 LEU Chi-restraints excluded: chain D residue 120 GLU Chi-restraints excluded: chain D residue 159 THR Chi-restraints excluded: chain D residue 165 GLN Chi-restraints excluded: chain E residue 3 GLN Chi-restraints excluded: chain E residue 22 MET Chi-restraints excluded: chain E residue 83 CYS Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain F residue 93 ILE Chi-restraints excluded: chain G residue 1 MET Chi-restraints excluded: chain G residue 6 ASP Chi-restraints excluded: chain G residue 39 THR Chi-restraints excluded: chain G residue 47 CYS Chi-restraints excluded: chain G residue 101 VAL Chi-restraints excluded: chain G residue 121 PHE Chi-restraints excluded: chain H residue 61 SER Chi-restraints excluded: chain J residue 26 GLN Chi-restraints excluded: chain K residue 9 LEU Chi-restraints excluded: chain K residue 94 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 395 random chunks: chunk 317 optimal weight: 0.0050 chunk 101 optimal weight: 7.9990 chunk 159 optimal weight: 7.9990 chunk 89 optimal weight: 6.9990 chunk 65 optimal weight: 7.9990 chunk 143 optimal weight: 0.9980 chunk 114 optimal weight: 9.9990 chunk 150 optimal weight: 3.9990 chunk 144 optimal weight: 3.9990 chunk 31 optimal weight: 6.9990 chunk 293 optimal weight: 20.0000 overall best weight: 3.2000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 363 GLN A1265 ASN D 9 GLN ** D 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 143 ASN E 54 GLN ** G 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 83 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.106034 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.070247 restraints weight = 71195.498| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.072692 restraints weight = 34197.189| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 58)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.074251 restraints weight = 22136.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.075198 restraints weight = 17204.867| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.075743 restraints weight = 14941.137| |-----------------------------------------------------------------------------| r_work (final): 0.3081 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8613 moved from start: 0.2443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.061 33905 Z= 0.244 Angle : 0.601 8.781 46198 Z= 0.312 Chirality : 0.044 0.256 5190 Planarity : 0.004 0.067 5630 Dihedral : 16.650 167.079 5346 Min Nonbonded Distance : 1.864 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.49 % Favored : 95.43 % Rotamer: Outliers : 1.69 % Allowed : 11.21 % Favored : 87.10 % 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: 0.27 (0.14), residues: 3854 helix: 1.54 (0.15), residues: 1339 sheet: -0.52 (0.20), residues: 642 loop : -0.51 (0.15), residues: 1873 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG A 320 TYR 0.013 0.001 TYR H 98 PHE 0.025 0.002 PHE G 109 TRP 0.035 0.002 TRP B 308 HIS 0.007 0.001 HIS A1173 Details of bonding type rmsd/Z covalent geometry : bond 0.00562 / 0.24 (33873) covalent geometry : angle 0.59466 / 0.31 (46153) hydrogen bonds : bond 0.03697 / 2.45 ( 1413) hydrogen bonds : angle 4.49883 / 3.24 ( 3904) metal coordination : bond 0.00886 / 0.57 ( 32) metal coordination : angle 2.89080 / 1.83 ( 45) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7708 Ramachandran restraints generated. 3854 Oldfield, 0 Emsley, 3854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7708 Ramachandran restraints generated. 3854 Oldfield, 0 Emsley, 3854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 411 residues out of total 3434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 353 time to evaluate : 1.244 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: A 74 MET cc_start: 0.8293 (mtt) cc_final: 0.7903 (mtt) REVERT: A 88 LYS cc_start: 0.8931 (mttt) cc_final: 0.8521 (mtpt) REVERT: A 122 MET cc_start: 0.8639 (tpp) cc_final: 0.8315 (tpp) REVERT: A 234 MET cc_start: 0.9279 (OUTLIER) cc_final: 0.8732 (mtp) REVERT: A 470 LEU cc_start: 0.9219 (OUTLIER) cc_final: 0.8719 (pp) REVERT: A 698 GLN cc_start: 0.8545 (tt0) cc_final: 0.7716 (tp40) REVERT: A 708 MET cc_start: 0.7273 (mmm) cc_final: 0.6963 (mmt) REVERT: A 930 ASP cc_start: 0.8155 (m-30) cc_final: 0.7646 (m-30) REVERT: A 1071 SER cc_start: 0.9421 (m) cc_final: 0.9207 (p) REVERT: A 1373 ASP cc_start: 0.8499 (OUTLIER) cc_final: 0.7890 (t0) REVERT: A 1420 ASP cc_start: 0.8075 (p0) cc_final: 0.7845 (p0) REVERT: A 1444 MET cc_start: 0.8639 (mmm) cc_final: 0.7644 (mmm) REVERT: B 115 GLN cc_start: 0.8503 (tp40) cc_final: 0.8223 (tp40) REVERT: B 244 LEU cc_start: 0.8024 (mp) cc_final: 0.7525 (tp) REVERT: B 314 LEU cc_start: 0.9712 (mt) cc_final: 0.9465 (mt) REVERT: B 470 LYS cc_start: 0.8297 (mppt) cc_final: 0.7848 (mmtt) REVERT: B 552 MET cc_start: 0.8603 (mmm) cc_final: 0.8311 (tpp) REVERT: B 572 HIS cc_start: 0.7885 (m90) cc_final: 0.7443 (m90) REVERT: B 872 GLU cc_start: 0.7866 (mt-10) cc_final: 0.7477 (mt-10) REVERT: B 935 ARG cc_start: 0.2927 (tpp-160) cc_final: 0.2714 (tpp-160) REVERT: D 65 GLU cc_start: 0.8897 (mm-30) cc_final: 0.8670 (mm-30) REVERT: D 68 ARG cc_start: 0.7712 (tpp-160) cc_final: 0.7349 (tpt90) REVERT: D 131 GLU cc_start: 0.7125 (mt-10) cc_final: 0.6880 (tm-30) REVERT: D 145 MET cc_start: 0.8849 (mmm) cc_final: 0.8580 (mmm) REVERT: D 153 ARG cc_start: 0.6447 (mtm-85) cc_final: 0.6152 (ptp90) REVERT: D 175 PHE cc_start: 0.7596 (t80) cc_final: 0.7351 (t80) REVERT: E 58 MET cc_start: 0.8708 (mtp) cc_final: 0.8418 (mtp) REVERT: E 137 GLU cc_start: 0.8697 (OUTLIER) cc_final: 0.8425 (tt0) REVERT: F 104 ASN cc_start: 0.8862 (m110) cc_final: 0.8646 (t0) REVERT: F 110 ASP cc_start: 0.7938 (t0) cc_final: 0.7197 (t0) REVERT: F 112 GLU cc_start: 0.8331 (mp0) cc_final: 0.8124 (mp0) REVERT: G 1 MET cc_start: 0.7254 (OUTLIER) cc_final: 0.6493 (ttt) REVERT: G 3 PHE cc_start: 0.8221 (m-80) cc_final: 0.7568 (m-80) REVERT: G 14 HIS cc_start: 0.8532 (t-90) cc_final: 0.8242 (t-90) REVERT: G 49 LEU cc_start: 0.9496 (mt) cc_final: 0.9059 (pp) REVERT: G 50 ASP cc_start: 0.8886 (t0) cc_final: 0.8322 (t0) REVERT: G 53 ASN cc_start: 0.8027 (t0) cc_final: 0.7238 (t0) REVERT: G 69 GLU cc_start: 0.8133 (tt0) cc_final: 0.7785 (tp30) REVERT: G 109 PHE cc_start: 0.7592 (t80) cc_final: 0.6633 (m-80) REVERT: G 115 MET cc_start: 0.3985 (mtt) cc_final: 0.2930 (ppp) REVERT: H 14 GLU cc_start: 0.7684 (tt0) cc_final: 0.7008 (tt0) REVERT: H 27 GLU cc_start: 0.7608 (mp0) cc_final: 0.6437 (mp0) REVERT: H 41 ASP cc_start: 0.8610 (m-30) cc_final: 0.8389 (m-30) REVERT: H 86 ASP cc_start: 0.8159 (m-30) cc_final: 0.7860 (m-30) REVERT: I 13 MET cc_start: 0.6210 (ppp) cc_final: 0.5889 (tmm) REVERT: K 29 ASN cc_start: 0.8457 (t0) cc_final: 0.7925 (t0) REVERT: L 33 GLU cc_start: 0.8737 (mt-10) cc_final: 0.8259 (mt-10) outliers start: 58 outliers final: 39 residues processed: 384 average time/residue: 0.2047 time to fit residues: 130.4219 Evaluate side-chains 385 residues out of total 3434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 341 time to evaluate : 1.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 234 MET Chi-restraints excluded: chain A residue 287 HIS Chi-restraints excluded: chain A residue 437 MET Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 470 LEU Chi-restraints excluded: chain A residue 550 LEU Chi-restraints excluded: chain A residue 886 ILE Chi-restraints excluded: chain A residue 1228 TRP Chi-restraints excluded: chain A residue 1240 CYS Chi-restraints excluded: chain A residue 1265 ASN Chi-restraints excluded: chain A residue 1368 MET Chi-restraints excluded: chain A residue 1373 ASP Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 305 VAL Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 771 SER Chi-restraints excluded: chain B residue 837 ASP Chi-restraints excluded: chain B residue 863 GLU Chi-restraints excluded: chain B residue 1082 MET Chi-restraints excluded: chain C residue 38 ILE Chi-restraints excluded: chain C residue 61 GLU Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain D residue 3 VAL Chi-restraints excluded: chain D residue 35 LEU Chi-restraints excluded: chain D residue 120 GLU Chi-restraints excluded: chain D residue 159 THR Chi-restraints excluded: chain D residue 165 GLN Chi-restraints excluded: chain E residue 22 MET Chi-restraints excluded: chain E residue 83 CYS Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain E residue 137 GLU Chi-restraints excluded: chain F residue 93 ILE Chi-restraints excluded: chain G residue 1 MET Chi-restraints excluded: chain G residue 6 ASP Chi-restraints excluded: chain G residue 47 CYS Chi-restraints excluded: chain G residue 101 VAL Chi-restraints excluded: chain G residue 121 PHE Chi-restraints excluded: chain H residue 45 GLU Chi-restraints excluded: chain H residue 61 SER Chi-restraints excluded: chain J residue 22 LEU Chi-restraints excluded: chain J residue 25 LEU Chi-restraints excluded: chain K residue 9 LEU Chi-restraints excluded: chain K residue 94 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 395 random chunks: chunk 382 optimal weight: 3.9990 chunk 3 optimal weight: 5.9990 chunk 200 optimal weight: 3.9990 chunk 306 optimal weight: 6.9990 chunk 78 optimal weight: 4.9990 chunk 354 optimal weight: 0.9980 chunk 270 optimal weight: 0.9980 chunk 70 optimal weight: 7.9990 chunk 357 optimal weight: 20.0000 chunk 254 optimal weight: 3.9990 chunk 351 optimal weight: 3.9990 overall best weight: 2.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 395 GLN D 9 GLN ** D 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 199 ASN E 3 GLN ** G 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 83 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.106226 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.070468 restraints weight = 71407.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.072933 restraints weight = 34200.219| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.074489 restraints weight = 22069.530| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.075441 restraints weight = 17135.010| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.075980 restraints weight = 14889.618| |-----------------------------------------------------------------------------| r_work (final): 0.3082 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8612 moved from start: 0.2524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 33905 Z= 0.216 Angle : 0.588 10.042 46198 Z= 0.305 Chirality : 0.044 0.256 5190 Planarity : 0.004 0.066 5630 Dihedral : 16.670 167.544 5346 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.33 % Favored : 95.56 % Rotamer: Outliers : 1.86 % Allowed : 11.71 % Favored : 86.43 % 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: 0.23 (0.14), residues: 3854 helix: 1.54 (0.15), residues: 1335 sheet: -0.60 (0.20), residues: 628 loop : -0.54 (0.14), residues: 1891 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG A 320 TYR 0.016 0.001 TYR G 167 PHE 0.022 0.001 PHE A 444 TRP 0.044 0.001 TRP B 308 HIS 0.009 0.001 HIS B 587 Details of bonding type rmsd/Z covalent geometry : bond 0.00497 / 0.22 (33873) covalent geometry : angle 0.58098 / 0.31 (46153) hydrogen bonds : bond 0.03650 / 2.42 ( 1413) hydrogen bonds : angle 4.47102 / 3.21 ( 3904) metal coordination : bond 0.00829 / 0.54 ( 32) metal coordination : angle 3.03908 / 1.90 ( 45) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7708 Ramachandran restraints generated. 3854 Oldfield, 0 Emsley, 3854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7708 Ramachandran restraints generated. 3854 Oldfield, 0 Emsley, 3854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 409 residues out of total 3434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 345 time to evaluate : 1.360 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 MET cc_start: 0.8305 (mtt) cc_final: 0.7922 (mtt) REVERT: A 88 LYS cc_start: 0.8949 (mttt) cc_final: 0.8530 (mtpt) REVERT: A 122 MET cc_start: 0.8668 (tpp) cc_final: 0.8331 (tpp) REVERT: A 234 MET cc_start: 0.9273 (OUTLIER) cc_final: 0.8743 (mtp) REVERT: A 470 LEU cc_start: 0.9211 (OUTLIER) cc_final: 0.8729 (pp) REVERT: A 698 GLN cc_start: 0.8534 (tt0) cc_final: 0.7594 (tp40) REVERT: A 708 MET cc_start: 0.7284 (mmm) cc_final: 0.6996 (mmt) REVERT: A 930 ASP cc_start: 0.8158 (m-30) cc_final: 0.7641 (m-30) REVERT: A 1071 SER cc_start: 0.9418 (m) cc_final: 0.9209 (p) REVERT: A 1287 TYR cc_start: 0.8103 (m-10) cc_final: 0.7850 (m-10) REVERT: A 1307 GLU cc_start: 0.8987 (mm-30) cc_final: 0.8763 (mt-10) REVERT: A 1373 ASP cc_start: 0.8489 (OUTLIER) cc_final: 0.7867 (t0) REVERT: A 1420 ASP cc_start: 0.8089 (p0) cc_final: 0.7827 (p0) REVERT: A 1444 MET cc_start: 0.8596 (mmm) cc_final: 0.7566 (mmm) REVERT: B 101 MET cc_start: 0.8788 (mtp) cc_final: 0.8579 (mtp) REVERT: B 115 GLN cc_start: 0.8504 (tp40) cc_final: 0.8249 (tp40) REVERT: B 244 LEU cc_start: 0.8019 (mp) cc_final: 0.7513 (tp) REVERT: B 314 LEU cc_start: 0.9718 (mt) cc_final: 0.9470 (mt) REVERT: B 470 LYS cc_start: 0.8306 (mppt) cc_final: 0.7865 (mmtt) REVERT: B 572 HIS cc_start: 0.7835 (m90) cc_final: 0.7420 (m90) REVERT: B 872 GLU cc_start: 0.7870 (mt-10) cc_final: 0.7478 (mt-10) REVERT: C 47 ASP cc_start: 0.8718 (t70) cc_final: 0.8241 (t0) REVERT: D 68 ARG cc_start: 0.7777 (tpp-160) cc_final: 0.7431 (tpt90) REVERT: D 131 GLU cc_start: 0.7187 (mt-10) cc_final: 0.6878 (tm-30) REVERT: D 145 MET cc_start: 0.8847 (mmm) cc_final: 0.8580 (mmm) REVERT: D 153 ARG cc_start: 0.6369 (mtm-85) cc_final: 0.6060 (ptp90) REVERT: D 175 PHE cc_start: 0.7627 (t80) cc_final: 0.7402 (t80) REVERT: E 32 GLN cc_start: 0.8622 (mm-40) cc_final: 0.8383 (mm-40) REVERT: E 137 GLU cc_start: 0.8679 (OUTLIER) cc_final: 0.8399 (tt0) REVERT: F 110 ASP cc_start: 0.7942 (t0) cc_final: 0.7215 (t0) REVERT: F 112 GLU cc_start: 0.8332 (mp0) cc_final: 0.8075 (mp0) REVERT: F 119 ARG cc_start: 0.9136 (tpp80) cc_final: 0.8868 (tpp80) REVERT: G 1 MET cc_start: 0.7203 (OUTLIER) cc_final: 0.6451 (ttt) REVERT: G 3 PHE cc_start: 0.8219 (m-80) cc_final: 0.7508 (m-80) REVERT: G 14 HIS cc_start: 0.8571 (t-90) cc_final: 0.8330 (t-90) REVERT: G 49 LEU cc_start: 0.9502 (mt) cc_final: 0.9069 (pp) REVERT: G 50 ASP cc_start: 0.8908 (t0) cc_final: 0.8351 (t0) REVERT: G 51 TYR cc_start: 0.8357 (t80) cc_final: 0.8144 (t80) REVERT: G 53 ASN cc_start: 0.8047 (t0) cc_final: 0.7256 (t0) REVERT: G 69 GLU cc_start: 0.8171 (tt0) cc_final: 0.7767 (tp30) REVERT: G 109 PHE cc_start: 0.7559 (t80) cc_final: 0.6711 (m-80) REVERT: H 14 GLU cc_start: 0.7662 (tt0) cc_final: 0.6974 (tt0) REVERT: H 27 GLU cc_start: 0.7689 (mp0) cc_final: 0.6545 (mp0) REVERT: H 41 ASP cc_start: 0.8589 (m-30) cc_final: 0.8370 (m-30) REVERT: I 13 MET cc_start: 0.6240 (ppp) cc_final: 0.5898 (tmm) REVERT: I 97 MET cc_start: 0.6988 (tpp) cc_final: 0.6193 (tpt) REVERT: K 29 ASN cc_start: 0.8476 (t0) cc_final: 0.7979 (t0) REVERT: K 77 THR cc_start: 0.9374 (p) cc_final: 0.8962 (p) REVERT: L 33 GLU cc_start: 0.8709 (mt-10) cc_final: 0.8225 (mt-10) outliers start: 64 outliers final: 43 residues processed: 381 average time/residue: 0.2016 time to fit residues: 126.6291 Evaluate side-chains 383 residues out of total 3434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 335 time to evaluate : 1.096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 234 MET Chi-restraints excluded: chain A residue 287 HIS Chi-restraints excluded: chain A residue 437 MET Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 470 LEU Chi-restraints excluded: chain A residue 550 LEU Chi-restraints excluded: chain A residue 625 SER Chi-restraints excluded: chain A residue 878 ILE Chi-restraints excluded: chain A residue 886 ILE Chi-restraints excluded: chain A residue 1020 CYS Chi-restraints excluded: chain A residue 1228 TRP Chi-restraints excluded: chain A residue 1240 CYS Chi-restraints excluded: chain A residue 1368 MET Chi-restraints excluded: chain A residue 1373 ASP Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 305 VAL Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 508 LEU Chi-restraints excluded: chain B residue 837 ASP Chi-restraints excluded: chain B residue 863 GLU Chi-restraints excluded: chain B residue 1082 MET Chi-restraints excluded: chain B residue 1156 ASP Chi-restraints excluded: chain C residue 38 ILE Chi-restraints excluded: chain C residue 61 GLU Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain D residue 3 VAL Chi-restraints excluded: chain D residue 120 GLU Chi-restraints excluded: chain D residue 159 THR Chi-restraints excluded: chain D residue 165 GLN Chi-restraints excluded: chain E residue 22 MET Chi-restraints excluded: chain E residue 83 CYS Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain E residue 137 GLU Chi-restraints excluded: chain F residue 93 ILE Chi-restraints excluded: chain G residue 1 MET Chi-restraints excluded: chain G residue 6 ASP Chi-restraints excluded: chain G residue 47 CYS Chi-restraints excluded: chain G residue 101 VAL Chi-restraints excluded: chain G residue 121 PHE Chi-restraints excluded: chain H residue 2 SER Chi-restraints excluded: chain H residue 61 SER Chi-restraints excluded: chain H residue 122 LEU Chi-restraints excluded: chain I residue 48 LEU Chi-restraints excluded: chain J residue 25 LEU Chi-restraints excluded: chain K residue 9 LEU Chi-restraints excluded: chain K residue 94 ILE Chi-restraints excluded: chain L residue 61 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 395 random chunks: chunk 20 optimal weight: 0.0770 chunk 80 optimal weight: 0.8980 chunk 121 optimal weight: 1.9990 chunk 363 optimal weight: 20.0000 chunk 243 optimal weight: 3.9990 chunk 331 optimal weight: 7.9990 chunk 139 optimal weight: 6.9990 chunk 56 optimal weight: 4.9990 chunk 12 optimal weight: 7.9990 chunk 126 optimal weight: 2.9990 chunk 275 optimal weight: 0.7980 overall best weight: 1.3542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 395 GLN D 9 GLN ** D 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 3 GLN ** G 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 83 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.107322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.071410 restraints weight = 70801.848| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.073919 restraints weight = 33594.447| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.075502 restraints weight = 21566.012| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.076469 restraints weight = 16721.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 58)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.077032 restraints weight = 14479.976| |-----------------------------------------------------------------------------| r_work (final): 0.3110 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8573 moved from start: 0.2600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 33905 Z= 0.134 Angle : 0.554 12.128 46198 Z= 0.288 Chirality : 0.042 0.259 5190 Planarity : 0.004 0.074 5630 Dihedral : 16.635 167.266 5346 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.87 % Favored : 96.06 % Rotamer: Outliers : 1.54 % Allowed : 12.41 % Favored : 86.05 % 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: 0.29 (0.14), residues: 3854 helix: 1.59 (0.15), residues: 1338 sheet: -0.58 (0.20), residues: 648 loop : -0.50 (0.15), residues: 1868 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.000 ARG A 320 TYR 0.012 0.001 TYR G 167 PHE 0.022 0.001 PHE G 109 TRP 0.051 0.001 TRP B 308 HIS 0.008 0.001 HIS B 587 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.13 (33873) covalent geometry : angle 0.54733 / 0.29 (46153) hydrogen bonds : bond 0.03408 / 2.26 ( 1413) hydrogen bonds : angle 4.33284 / 3.12 ( 3904) metal coordination : bond 0.00562 / 0.37 ( 32) metal coordination : angle 2.77598 / 1.72 ( 45) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7708 Ramachandran restraints generated. 3854 Oldfield, 0 Emsley, 3854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7708 Ramachandran restraints generated. 3854 Oldfield, 0 Emsley, 3854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 408 residues out of total 3434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 355 time to evaluate : 1.859 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 MET cc_start: 0.8323 (mtt) cc_final: 0.7917 (mtt) REVERT: A 88 LYS cc_start: 0.8993 (mttt) cc_final: 0.8554 (mtpt) REVERT: A 122 MET cc_start: 0.8698 (tpp) cc_final: 0.8353 (tpp) REVERT: A 234 MET cc_start: 0.9289 (OUTLIER) cc_final: 0.8750 (mtp) REVERT: A 470 LEU cc_start: 0.9183 (OUTLIER) cc_final: 0.8661 (pp) REVERT: A 698 GLN cc_start: 0.8549 (tt0) cc_final: 0.7582 (tp40) REVERT: A 708 MET cc_start: 0.7243 (mmm) cc_final: 0.6951 (mmt) REVERT: A 880 LYS cc_start: 0.9181 (tttt) cc_final: 0.8960 (ttmt) REVERT: A 930 ASP cc_start: 0.8184 (m-30) cc_final: 0.7626 (m-30) REVERT: A 1071 SER cc_start: 0.9407 (m) cc_final: 0.9197 (p) REVERT: A 1287 TYR cc_start: 0.8137 (m-10) cc_final: 0.7823 (m-10) REVERT: A 1307 GLU cc_start: 0.8996 (mm-30) cc_final: 0.8785 (mt-10) REVERT: A 1420 ASP cc_start: 0.8080 (p0) cc_final: 0.7812 (p0) REVERT: A 1444 MET cc_start: 0.8628 (OUTLIER) cc_final: 0.7632 (mmm) REVERT: B 101 MET cc_start: 0.8743 (mtp) cc_final: 0.8449 (mtt) REVERT: B 115 GLN cc_start: 0.8427 (tp40) cc_final: 0.8209 (tp40) REVERT: B 244 LEU cc_start: 0.7983 (mp) cc_final: 0.7484 (tp) REVERT: B 310 MET cc_start: 0.8663 (mtm) cc_final: 0.8193 (mtp) REVERT: B 314 LEU cc_start: 0.9721 (mt) cc_final: 0.9462 (mt) REVERT: B 470 LYS cc_start: 0.8314 (mppt) cc_final: 0.7865 (mmtt) REVERT: B 572 HIS cc_start: 0.7867 (m90) cc_final: 0.7439 (m90) REVERT: B 620 ARG cc_start: 0.9148 (ptp-110) cc_final: 0.8835 (ttp-110) REVERT: B 863 GLU cc_start: 0.7357 (OUTLIER) cc_final: 0.6655 (pt0) REVERT: B 999 MET cc_start: 0.9401 (mmm) cc_final: 0.9188 (mmm) REVERT: C 47 ASP cc_start: 0.8686 (t70) cc_final: 0.8226 (t0) REVERT: D 35 LEU cc_start: 0.7708 (mt) cc_final: 0.7479 (pt) REVERT: D 131 GLU cc_start: 0.7210 (mt-10) cc_final: 0.6925 (tm-30) REVERT: D 145 MET cc_start: 0.8844 (mmm) cc_final: 0.8578 (mmm) REVERT: D 153 ARG cc_start: 0.6374 (mtm-85) cc_final: 0.6068 (ptp90) REVERT: E 32 GLN cc_start: 0.8607 (mm-40) cc_final: 0.8373 (mm-40) REVERT: E 137 GLU cc_start: 0.8646 (OUTLIER) cc_final: 0.8345 (tt0) REVERT: F 110 ASP cc_start: 0.7991 (t0) cc_final: 0.7407 (t0) REVERT: F 112 GLU cc_start: 0.8321 (mp0) cc_final: 0.8030 (mp0) REVERT: F 119 ARG cc_start: 0.9111 (tpp80) cc_final: 0.8863 (tpp80) REVERT: G 1 MET cc_start: 0.6974 (OUTLIER) cc_final: 0.6540 (ttt) REVERT: G 14 HIS cc_start: 0.8484 (t-90) cc_final: 0.8209 (t-90) REVERT: G 33 GLU cc_start: 0.9198 (tp30) cc_final: 0.8964 (tp30) REVERT: G 49 LEU cc_start: 0.9505 (mt) cc_final: 0.9083 (pp) REVERT: G 50 ASP cc_start: 0.8884 (t0) cc_final: 0.8322 (t0) REVERT: G 51 TYR cc_start: 0.8330 (t80) cc_final: 0.8117 (t80) REVERT: G 53 ASN cc_start: 0.8163 (t0) cc_final: 0.7439 (t0) REVERT: G 69 GLU cc_start: 0.8121 (tt0) cc_final: 0.7689 (tp30) REVERT: G 109 PHE cc_start: 0.7596 (t80) cc_final: 0.6811 (m-80) REVERT: H 14 GLU cc_start: 0.7669 (tt0) cc_final: 0.6951 (tt0) REVERT: H 27 GLU cc_start: 0.7679 (mp0) cc_final: 0.6490 (mp0) REVERT: H 41 ASP cc_start: 0.8582 (m-30) cc_final: 0.8254 (m-30) REVERT: I 13 MET cc_start: 0.6117 (ppp) cc_final: 0.5897 (tmm) REVERT: I 97 MET cc_start: 0.6885 (tpp) cc_final: 0.6133 (tpt) REVERT: K 6 ARG cc_start: 0.9216 (mmm-85) cc_final: 0.7647 (mmm-85) REVERT: K 29 ASN cc_start: 0.8429 (t0) cc_final: 0.7953 (t0) REVERT: K 77 THR cc_start: 0.9367 (p) cc_final: 0.8976 (p) REVERT: L 33 GLU cc_start: 0.8720 (mt-10) cc_final: 0.8234 (mt-10) outliers start: 53 outliers final: 35 residues processed: 384 average time/residue: 0.2057 time to fit residues: 129.4938 Evaluate side-chains 379 residues out of total 3434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 338 time to evaluate : 0.871 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 234 MET Chi-restraints excluded: chain A residue 287 HIS Chi-restraints excluded: chain A residue 437 MET Chi-restraints excluded: chain A residue 470 LEU Chi-restraints excluded: chain A residue 550 LEU Chi-restraints excluded: chain A residue 625 SER Chi-restraints excluded: chain A residue 878 ILE Chi-restraints excluded: chain A residue 886 ILE Chi-restraints excluded: chain A residue 1228 TRP Chi-restraints excluded: chain A residue 1240 CYS Chi-restraints excluded: chain A residue 1368 MET Chi-restraints excluded: chain A residue 1444 MET Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 173 MET Chi-restraints excluded: chain B residue 305 VAL Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 508 LEU Chi-restraints excluded: chain B residue 837 ASP Chi-restraints excluded: chain B residue 863 GLU Chi-restraints excluded: chain B residue 1082 MET Chi-restraints excluded: chain C residue 38 ILE Chi-restraints excluded: chain C residue 61 GLU Chi-restraints excluded: chain D residue 3 VAL Chi-restraints excluded: chain D residue 120 GLU Chi-restraints excluded: chain D residue 159 THR Chi-restraints excluded: chain D residue 165 GLN Chi-restraints excluded: chain E residue 3 GLN Chi-restraints excluded: chain E residue 22 MET Chi-restraints excluded: chain E residue 83 CYS Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain E residue 137 GLU Chi-restraints excluded: chain F residue 93 ILE Chi-restraints excluded: chain G residue 1 MET Chi-restraints excluded: chain G residue 6 ASP Chi-restraints excluded: chain G residue 47 CYS Chi-restraints excluded: chain G residue 101 VAL Chi-restraints excluded: chain G residue 121 PHE Chi-restraints excluded: chain H residue 61 SER Chi-restraints excluded: chain K residue 9 LEU Chi-restraints excluded: chain K residue 94 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 395 random chunks: chunk 58 optimal weight: 3.9990 chunk 377 optimal weight: 5.9990 chunk 167 optimal weight: 9.9990 chunk 196 optimal weight: 8.9990 chunk 62 optimal weight: 3.9990 chunk 6 optimal weight: 7.9990 chunk 99 optimal weight: 5.9990 chunk 331 optimal weight: 7.9990 chunk 134 optimal weight: 1.9990 chunk 247 optimal weight: 0.7980 chunk 163 optimal weight: 8.9990 overall best weight: 3.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 395 GLN ** D 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 122 ASN ** 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 = 0.3626 r_free = 0.3626 target = 0.105688 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.069956 restraints weight = 71340.756| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.072386 restraints weight = 34262.514| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.073938 restraints weight = 22151.707| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.074872 restraints weight = 17201.220| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.075397 restraints weight = 14943.849| |-----------------------------------------------------------------------------| r_work (final): 0.3069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8616 moved from start: 0.2663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.061 33905 Z= 0.254 Angle : 0.623 12.753 46198 Z= 0.320 Chirality : 0.044 0.255 5190 Planarity : 0.004 0.076 5630 Dihedral : 16.667 168.209 5346 Min Nonbonded Distance : 1.835 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.77 % Favored : 95.12 % Rotamer: Outliers : 1.54 % Allowed : 12.61 % Favored : 85.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.14 (0.14), residues: 3854 helix: 1.45 (0.14), residues: 1343 sheet: -0.68 (0.20), residues: 631 loop : -0.57 (0.14), residues: 1880 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.000 ARG A 320 TYR 0.020 0.001 TYR G 167 PHE 0.019 0.002 PHE A 219 TRP 0.056 0.002 TRP B 308 HIS 0.008 0.001 HIS B 587 Details of bonding type rmsd/Z covalent geometry : bond 0.00587 / 0.25 (33873) covalent geometry : angle 0.61545 / 0.32 (46153) hydrogen bonds : bond 0.03691 / 2.44 ( 1413) hydrogen bonds : angle 4.47154 / 3.21 ( 3904) metal coordination : bond 0.00937 / 0.60 ( 32) metal coordination : angle 3.17309 / 2.00 ( 45) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7708 Ramachandran restraints generated. 3854 Oldfield, 0 Emsley, 3854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7708 Ramachandran restraints generated. 3854 Oldfield, 0 Emsley, 3854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 388 residues out of total 3434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 335 time to evaluate : 1.177 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: A 74 MET cc_start: 0.8346 (mtt) cc_final: 0.7941 (mtt) REVERT: A 88 LYS cc_start: 0.8962 (mttt) cc_final: 0.8525 (mtpt) REVERT: A 122 MET cc_start: 0.8706 (tpp) cc_final: 0.8340 (tpp) REVERT: A 234 MET cc_start: 0.9281 (OUTLIER) cc_final: 0.8894 (mtp) REVERT: A 470 LEU cc_start: 0.9219 (OUTLIER) cc_final: 0.8684 (pp) REVERT: A 605 MET cc_start: 0.9169 (tpp) cc_final: 0.8854 (tpp) REVERT: A 698 GLN cc_start: 0.8578 (tt0) cc_final: 0.7679 (tp40) REVERT: A 708 MET cc_start: 0.7270 (mmm) cc_final: 0.6959 (mmt) REVERT: A 930 ASP cc_start: 0.8191 (m-30) cc_final: 0.7672 (m-30) REVERT: A 1071 SER cc_start: 0.9433 (m) cc_final: 0.9222 (p) REVERT: A 1225 PHE cc_start: 0.7294 (t80) cc_final: 0.6715 (t80) REVERT: A 1239 ARG cc_start: 0.7138 (ttm170) cc_final: 0.6109 (ttp80) REVERT: A 1287 TYR cc_start: 0.8174 (m-10) cc_final: 0.7869 (m-10) REVERT: A 1307 GLU cc_start: 0.9002 (mm-30) cc_final: 0.8764 (mt-10) REVERT: A 1373 ASP cc_start: 0.8563 (OUTLIER) cc_final: 0.7971 (t0) REVERT: A 1398 MET cc_start: 0.8949 (ttp) cc_final: 0.8714 (ptm) REVERT: A 1420 ASP cc_start: 0.8125 (p0) cc_final: 0.7855 (p0) REVERT: A 1444 MET cc_start: 0.8654 (OUTLIER) cc_final: 0.7638 (mmm) REVERT: B 101 MET cc_start: 0.8812 (mtp) cc_final: 0.8541 (mtt) REVERT: B 115 GLN cc_start: 0.8539 (tp40) cc_final: 0.8242 (tp40) REVERT: B 244 LEU cc_start: 0.7996 (mp) cc_final: 0.7470 (tp) REVERT: B 314 LEU cc_start: 0.9725 (mt) cc_final: 0.9486 (mt) REVERT: B 470 LYS cc_start: 0.8356 (mppt) cc_final: 0.7919 (mmtt) REVERT: B 572 HIS cc_start: 0.7938 (m90) cc_final: 0.7491 (m90) REVERT: B 863 GLU cc_start: 0.7456 (OUTLIER) cc_final: 0.6928 (pt0) REVERT: C 47 ASP cc_start: 0.8723 (t70) cc_final: 0.8234 (t0) REVERT: D 35 LEU cc_start: 0.7716 (mt) cc_final: 0.7483 (pt) REVERT: D 131 GLU cc_start: 0.7182 (mt-10) cc_final: 0.6889 (tm-30) REVERT: D 145 MET cc_start: 0.8828 (mmm) cc_final: 0.8538 (mmm) REVERT: D 153 ARG cc_start: 0.6346 (mtm-85) cc_final: 0.6004 (ptp90) REVERT: E 32 GLN cc_start: 0.8659 (mm-40) cc_final: 0.8351 (mm-40) REVERT: F 110 ASP cc_start: 0.8001 (t0) cc_final: 0.7432 (t0) REVERT: F 112 GLU cc_start: 0.8376 (mp0) cc_final: 0.8056 (mp0) REVERT: F 119 ARG cc_start: 0.9138 (tpp80) cc_final: 0.8918 (tpp80) REVERT: G 1 MET cc_start: 0.7208 (OUTLIER) cc_final: 0.6757 (ttt) REVERT: G 14 HIS cc_start: 0.8579 (t-90) cc_final: 0.8266 (t-90) REVERT: G 33 GLU cc_start: 0.9210 (tp30) cc_final: 0.8985 (tp30) REVERT: G 49 LEU cc_start: 0.9508 (mt) cc_final: 0.9071 (pp) REVERT: G 50 ASP cc_start: 0.8890 (t0) cc_final: 0.8336 (t0) REVERT: G 51 TYR cc_start: 0.8293 (t80) cc_final: 0.8074 (t80) REVERT: G 53 ASN cc_start: 0.8051 (t0) cc_final: 0.7271 (t0) REVERT: G 69 GLU cc_start: 0.8194 (tt0) cc_final: 0.7759 (tp30) REVERT: G 109 PHE cc_start: 0.7487 (t80) cc_final: 0.6729 (m-80) REVERT: H 14 GLU cc_start: 0.7705 (tt0) cc_final: 0.6921 (tt0) REVERT: H 27 GLU cc_start: 0.7752 (mp0) cc_final: 0.6572 (mp0) REVERT: H 41 ASP cc_start: 0.8612 (m-30) cc_final: 0.8380 (m-30) REVERT: I 13 MET cc_start: 0.5867 (ppp) cc_final: 0.5541 (tmm) REVERT: I 48 LEU cc_start: 0.6483 (OUTLIER) cc_final: 0.6255 (pp) REVERT: K 29 ASN cc_start: 0.8513 (t0) cc_final: 0.8125 (t0) REVERT: K 77 THR cc_start: 0.9394 (p) cc_final: 0.9084 (p) REVERT: L 33 GLU cc_start: 0.8701 (mt-10) cc_final: 0.8217 (mt-10) outliers start: 53 outliers final: 42 residues processed: 363 average time/residue: 0.2186 time to fit residues: 130.0117 Evaluate side-chains 378 residues out of total 3434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 329 time to evaluate : 1.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 234 MET Chi-restraints excluded: chain A residue 287 HIS Chi-restraints excluded: chain A residue 437 MET Chi-restraints excluded: chain A residue 470 LEU Chi-restraints excluded: chain A residue 550 LEU Chi-restraints excluded: chain A residue 625 SER Chi-restraints excluded: chain A residue 746 MET Chi-restraints excluded: chain A residue 878 ILE Chi-restraints excluded: chain A residue 886 ILE Chi-restraints excluded: chain A residue 1020 CYS Chi-restraints excluded: chain A residue 1228 TRP Chi-restraints excluded: chain A residue 1240 CYS Chi-restraints excluded: chain A residue 1322 ILE Chi-restraints excluded: chain A residue 1368 MET Chi-restraints excluded: chain A residue 1373 ASP Chi-restraints excluded: chain A residue 1444 MET Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 173 MET Chi-restraints excluded: chain B residue 305 VAL Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 771 SER Chi-restraints excluded: chain B residue 837 ASP Chi-restraints excluded: chain B residue 863 GLU Chi-restraints excluded: chain B residue 1082 MET Chi-restraints excluded: chain B residue 1156 ASP Chi-restraints excluded: chain C residue 38 ILE Chi-restraints excluded: chain C residue 61 GLU Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain D residue 3 VAL Chi-restraints excluded: chain D residue 38 ILE Chi-restraints excluded: chain D residue 159 THR Chi-restraints excluded: chain D residue 165 GLN Chi-restraints excluded: chain E residue 22 MET Chi-restraints excluded: chain E residue 83 CYS Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain E residue 137 GLU Chi-restraints excluded: chain F residue 93 ILE Chi-restraints excluded: chain G residue 1 MET Chi-restraints excluded: chain G residue 6 ASP Chi-restraints excluded: chain G residue 47 CYS Chi-restraints excluded: chain G residue 101 VAL Chi-restraints excluded: chain G residue 121 PHE Chi-restraints excluded: chain H residue 15 VAL Chi-restraints excluded: chain H residue 61 SER Chi-restraints excluded: chain I residue 48 LEU Chi-restraints excluded: chain J residue 50 ILE Chi-restraints excluded: chain K residue 9 LEU Chi-restraints excluded: chain K residue 94 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 395 random chunks: chunk 308 optimal weight: 0.0870 chunk 268 optimal weight: 2.9990 chunk 200 optimal weight: 4.9990 chunk 176 optimal weight: 10.0000 chunk 232 optimal weight: 0.0870 chunk 49 optimal weight: 0.8980 chunk 314 optimal weight: 0.0570 chunk 73 optimal weight: 4.9990 chunk 164 optimal weight: 0.9990 chunk 321 optimal weight: 3.9990 chunk 241 optimal weight: 3.9990 overall best weight: 0.4256 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 363 GLN B 395 GLN ** D 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 3 GLN ** G 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 83 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.108615 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.073027 restraints weight = 71045.887| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.075578 restraints weight = 33204.873| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.077200 restraints weight = 21167.019| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 60)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.078186 restraints weight = 16282.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 50)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.078751 restraints weight = 14091.613| |-----------------------------------------------------------------------------| r_work (final): 0.3140 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8553 moved from start: 0.2737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 33905 Z= 0.109 Angle : 0.556 12.871 46198 Z= 0.289 Chirality : 0.042 0.257 5190 Planarity : 0.004 0.074 5630 Dihedral : 16.607 167.217 5346 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.43 % Favored : 96.47 % Rotamer: Outliers : 1.19 % Allowed : 13.13 % Favored : 85.67 % 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: 0.31 (0.14), residues: 3854 helix: 1.59 (0.15), residues: 1342 sheet: -0.59 (0.20), residues: 640 loop : -0.47 (0.15), residues: 1872 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.000 ARG A 320 TYR 0.018 0.001 TYR G 167 PHE 0.021 0.001 PHE G 109 TRP 0.059 0.001 TRP B 308 HIS 0.005 0.001 HIS B 587 Details of bonding type rmsd/Z covalent geometry : bond 0.00236 / 0.11 (33873) covalent geometry : angle 0.55063 / 0.29 (46153) hydrogen bonds : bond 0.03294 / 2.18 ( 1413) hydrogen bonds : angle 4.27140 / 3.08 ( 3904) metal coordination : bond 0.00511 / 0.34 ( 32) metal coordination : angle 2.61945 / 1.63 ( 45) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7708 Ramachandran restraints generated. 3854 Oldfield, 0 Emsley, 3854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7708 Ramachandran restraints generated. 3854 Oldfield, 0 Emsley, 3854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 407 residues out of total 3434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 366 time to evaluate : 1.285 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 MET cc_start: 0.8320 (mtt) cc_final: 0.7927 (mtt) REVERT: A 88 LYS cc_start: 0.8989 (mttt) cc_final: 0.8561 (mtpt) REVERT: A 122 MET cc_start: 0.8686 (tpp) cc_final: 0.8335 (tpp) REVERT: A 234 MET cc_start: 0.9299 (OUTLIER) cc_final: 0.8768 (mtp) REVERT: A 470 LEU cc_start: 0.9132 (OUTLIER) cc_final: 0.8607 (pp) REVERT: A 486 GLU cc_start: 0.7769 (mt-10) cc_final: 0.7528 (mt-10) REVERT: A 605 MET cc_start: 0.9189 (tpp) cc_final: 0.8929 (tpp) REVERT: A 698 GLN cc_start: 0.8559 (tt0) cc_final: 0.7573 (tp40) REVERT: A 708 MET cc_start: 0.7311 (mmm) cc_final: 0.7052 (mmt) REVERT: A 930 ASP cc_start: 0.8227 (m-30) cc_final: 0.7671 (m-30) REVERT: A 1225 PHE cc_start: 0.7379 (t80) cc_final: 0.7017 (t80) REVERT: A 1287 TYR cc_start: 0.8141 (m-10) cc_final: 0.7779 (m-10) REVERT: A 1307 GLU cc_start: 0.9006 (mm-30) cc_final: 0.8796 (mt-10) REVERT: A 1398 MET cc_start: 0.8875 (ttp) cc_final: 0.8555 (ptm) REVERT: A 1420 ASP cc_start: 0.8086 (p0) cc_final: 0.7802 (p0) REVERT: A 1444 MET cc_start: 0.8616 (mmm) cc_final: 0.7672 (mmm) REVERT: B 101 MET cc_start: 0.8732 (mtp) cc_final: 0.8471 (mtt) REVERT: B 244 LEU cc_start: 0.7963 (mp) cc_final: 0.7476 (tp) REVERT: B 310 MET cc_start: 0.8610 (mtm) cc_final: 0.8332 (mtp) REVERT: B 314 LEU cc_start: 0.9712 (mt) cc_final: 0.9483 (mt) REVERT: B 470 LYS cc_start: 0.8269 (mppt) cc_final: 0.7824 (mmtt) REVERT: B 572 HIS cc_start: 0.7945 (m90) cc_final: 0.7520 (m90) REVERT: B 620 ARG cc_start: 0.9192 (ptp-110) cc_final: 0.8886 (ttp-110) REVERT: C 47 ASP cc_start: 0.8719 (t70) cc_final: 0.8276 (t0) REVERT: D 1 MET cc_start: 0.3286 (ttp) cc_final: 0.3003 (tmm) REVERT: D 35 LEU cc_start: 0.7673 (mt) cc_final: 0.7473 (pt) REVERT: D 68 ARG cc_start: 0.7750 (tpp-160) cc_final: 0.7416 (tpt90) REVERT: D 131 GLU cc_start: 0.7117 (mt-10) cc_final: 0.6885 (tm-30) REVERT: D 145 MET cc_start: 0.8820 (mmm) cc_final: 0.8534 (mmm) REVERT: D 153 ARG cc_start: 0.6356 (mtm-85) cc_final: 0.6035 (ptp90) REVERT: E 3 GLN cc_start: 0.8071 (OUTLIER) cc_final: 0.7863 (pm20) REVERT: E 32 GLN cc_start: 0.8592 (mm-40) cc_final: 0.8318 (mm-40) REVERT: E 101 GLN cc_start: 0.8333 (mm110) cc_final: 0.8050 (mm110) REVERT: F 110 ASP cc_start: 0.7994 (t0) cc_final: 0.7420 (t0) REVERT: F 112 GLU cc_start: 0.8294 (mp0) cc_final: 0.8007 (mp0) REVERT: F 119 ARG cc_start: 0.9089 (tpp80) cc_final: 0.8861 (tpp80) REVERT: G 1 MET cc_start: 0.6925 (OUTLIER) cc_final: 0.6627 (ttt) REVERT: G 14 HIS cc_start: 0.8526 (t-90) cc_final: 0.8221 (t-90) REVERT: G 49 LEU cc_start: 0.9506 (mt) cc_final: 0.9092 (pp) REVERT: G 50 ASP cc_start: 0.8869 (t0) cc_final: 0.8306 (t0) REVERT: G 53 ASN cc_start: 0.8194 (t0) cc_final: 0.7530 (t0) REVERT: G 69 GLU cc_start: 0.8144 (tt0) cc_final: 0.7657 (tp30) REVERT: G 99 PHE cc_start: 0.5404 (p90) cc_final: 0.5147 (p90) REVERT: G 109 PHE cc_start: 0.7566 (t80) cc_final: 0.6792 (m-80) REVERT: H 14 GLU cc_start: 0.7665 (tt0) cc_final: 0.6920 (tt0) REVERT: H 22 LYS cc_start: 0.9043 (mmtm) cc_final: 0.8787 (mmtm) REVERT: H 24 CYS cc_start: 0.8706 (m) cc_final: 0.8236 (m) REVERT: H 27 GLU cc_start: 0.7685 (mp0) cc_final: 0.6499 (mp0) REVERT: H 41 ASP cc_start: 0.8610 (m-30) cc_final: 0.8326 (m-30) REVERT: I 13 MET cc_start: 0.6060 (ppp) cc_final: 0.5842 (tmm) REVERT: I 97 MET cc_start: 0.6854 (tpp) cc_final: 0.6102 (tpt) REVERT: K 6 ARG cc_start: 0.9189 (mmm-85) cc_final: 0.7639 (mmm-85) REVERT: K 29 ASN cc_start: 0.8409 (t0) cc_final: 0.7946 (t0) REVERT: K 77 THR cc_start: 0.9351 (p) cc_final: 0.8951 (p) REVERT: L 33 GLU cc_start: 0.8758 (mt-10) cc_final: 0.8276 (mt-10) outliers start: 41 outliers final: 29 residues processed: 388 average time/residue: 0.2103 time to fit residues: 133.6791 Evaluate side-chains 380 residues out of total 3434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 347 time to evaluate : 1.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 234 MET Chi-restraints excluded: chain A residue 287 HIS Chi-restraints excluded: chain A residue 437 MET Chi-restraints excluded: chain A residue 470 LEU Chi-restraints excluded: chain A residue 550 LEU Chi-restraints excluded: chain A residue 625 SER Chi-restraints excluded: chain A residue 878 ILE Chi-restraints excluded: chain A residue 886 ILE Chi-restraints excluded: chain A residue 1058 VAL Chi-restraints excluded: chain A residue 1228 TRP Chi-restraints excluded: chain A residue 1240 CYS Chi-restraints excluded: chain B residue 173 MET Chi-restraints excluded: chain B residue 305 VAL Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 437 GLU Chi-restraints excluded: chain B residue 837 ASP Chi-restraints excluded: chain B residue 1082 MET Chi-restraints excluded: chain B residue 1156 ASP Chi-restraints excluded: chain C residue 38 ILE Chi-restraints excluded: chain C residue 61 GLU Chi-restraints excluded: chain D residue 3 VAL Chi-restraints excluded: chain D residue 159 THR Chi-restraints excluded: chain D residue 165 GLN Chi-restraints excluded: chain E residue 3 GLN Chi-restraints excluded: chain E residue 22 MET Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain F residue 93 ILE Chi-restraints excluded: chain G residue 1 MET Chi-restraints excluded: chain G residue 6 ASP Chi-restraints excluded: chain G residue 101 VAL Chi-restraints excluded: chain G residue 121 PHE Chi-restraints excluded: chain H residue 61 SER Chi-restraints excluded: chain K residue 94 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 395 random chunks: chunk 352 optimal weight: 4.9990 chunk 284 optimal weight: 9.9990 chunk 354 optimal weight: 1.9990 chunk 214 optimal weight: 5.9990 chunk 374 optimal weight: 0.0470 chunk 155 optimal weight: 2.9990 chunk 56 optimal weight: 4.9990 chunk 343 optimal weight: 8.9990 chunk 296 optimal weight: 0.4980 chunk 250 optimal weight: 4.9990 chunk 10 optimal weight: 7.9990 overall best weight: 2.1084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 363 GLN ** A 451 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1367 HIS ** B 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 395 GLN ** D 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 83 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.108426 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.073135 restraints weight = 70763.680| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.075682 restraints weight = 33328.003| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.077295 restraints weight = 21189.710| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.078263 restraints weight = 16319.537| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.078820 restraints weight = 14126.666| |-----------------------------------------------------------------------------| r_work (final): 0.3138 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8557 moved from start: 0.2752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.212 33905 Z= 0.177 Angle : 0.666 59.180 46198 Z= 0.369 Chirality : 0.042 0.260 5190 Planarity : 0.004 0.068 5630 Dihedral : 16.603 167.182 5346 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.45 % Favored : 96.45 % Rotamer: Outliers : 1.08 % Allowed : 13.54 % Favored : 85.38 % Cbeta Deviations : 0.03 % 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: 0.30 (0.14), residues: 3854 helix: 1.56 (0.15), residues: 1342 sheet: -0.58 (0.20), residues: 640 loop : -0.47 (0.15), residues: 1872 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG A 320 TYR 0.016 0.001 TYR G 167 PHE 0.019 0.001 PHE A 219 TRP 0.050 0.001 TRP B 308 HIS 0.005 0.001 HIS A1173 Details of bonding type rmsd/Z covalent geometry : bond 0.00391 / 0.18 (33873) covalent geometry : angle 0.66143 / 0.37 (46153) hydrogen bonds : bond 0.03312 / 2.19 ( 1413) hydrogen bonds : angle 4.27136 / 3.08 ( 3904) metal coordination : bond 0.00617 / 0.40 ( 32) metal coordination : angle 2.63641 / 1.65 ( 45) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6339.33 seconds wall clock time: 110 minutes 12.85 seconds (6612.85 seconds total)