Starting phenix.real_space_refine on Sun Aug 9 00:20:56 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/30es_57676/08_2026/30es_57676.cif Found real_map, /net/cci-nas-00/data/ceres_data/30es_57676/08_2026/30es_57676.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.54 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/30es_57676/08_2026/30es_57676.cif" } default_model = "/net/cci-nas-00/data/ceres_data/30es_57676/08_2026/30es_57676.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/30es_57676/08_2026/30es_57676.map" default_real_map = "/net/cci-nas-00/data/ceres_data/30es_57676/08_2026/30es_57676.map" } resolution = 2.54 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= -0.001 sd= 0.026 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 105 5.49 5 Mg 2 5.21 5 S 171 5.16 5 C 18924 2.51 5 N 5324 2.21 5 O 5982 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 30516 Number of models: 1 Model: "" Number of chains: 19 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: "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: "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: 297 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 297 Classifications: {'RNA': 14} Modifications used: {'rna3p_pur': 6, 'rna3p_pyr': 7} Link IDs: {'rna3p': 13} 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 18.654 91.980 96.103 1.00 77.13 S ATOM 479 SG CYS A 70 17.798 88.947 98.245 1.00 76.02 S ATOM 532 SG CYS A 77 21.456 90.127 97.789 1.00 64.52 S ATOM 762 SG CYS A 107 33.252 81.477 52.103 1.00 96.04 S ATOM 786 SG CYS A 110 30.208 79.246 52.360 1.00 99.84 S ATOM 1091 SG CYS A 148 33.248 78.171 50.293 1.00 97.45 S ATOM 1105 SG CYS A 167 31.057 81.072 49.078 1.00 99.50 S ATOM 19603 SG CYS B1163 17.400 76.602 87.643 1.00 59.25 S ATOM 19621 SG CYS B1166 20.179 78.666 86.207 1.00 74.92 S ATOM 19746 SG CYS B1182 16.903 80.287 87.456 1.00 77.04 S ATOM 19765 SG CYS B1185 17.038 78.246 84.176 1.00 78.02 S ATOM 20753 SG CYS C 86 49.257 94.815 159.873 1.00 96.81 S ATOM 20770 SG CYS C 88 48.055 97.545 157.593 1.00103.84 S ATOM 20803 SG CYS C 92 50.112 98.438 160.636 1.00 75.45 S ATOM 20826 SG CYS C 95 51.738 96.707 157.627 1.00 78.46 S ATOM 25744 SG CYS I 7 91.728 103.655 42.367 1.00137.33 S ATOM 25769 SG CYS I 10 88.370 105.020 43.401 1.00142.74 S ATOM 25935 SG CYS I 29 88.616 101.496 41.875 1.00139.67 S ATOM 25959 SG CYS I 32 89.138 104.545 39.718 1.00148.76 S ATOM 26286 SG CYS I 75 117.374 86.313 77.153 1.00116.96 S ATOM 26308 SG CYS I 78 119.642 89.268 77.577 1.00121.71 S ATOM 26524 SG CYS I 103 116.049 89.467 78.862 1.00118.33 S ATOM 26544 SG CYS I 106 116.681 89.443 75.133 1.00115.52 S ATOM 26646 SG CYS J 7 78.225 92.368 140.402 1.00 37.88 S ATOM 26669 SG CYS J 10 78.301 90.766 143.925 1.00 49.60 S ATOM 26949 SG CYS J 45 80.832 89.897 141.112 1.00 54.58 S ATOM 26955 SG CYS J 46 81.022 93.194 142.879 1.00 58.61 S ATOM 28078 SG CYS L 31 57.257 128.022 125.966 1.00125.01 S ATOM 28098 SG CYS L 34 57.875 130.488 128.762 1.00123.24 S ATOM 28202 SG CYS L 48 54.556 130.423 126.766 1.00125.96 S ATOM 28225 SG CYS L 51 57.721 131.812 125.230 1.00134.35 S Time building chain proxies: 6.43, per 1000 atoms: 0.21 Number of scatterers: 30516 At special positions: 0 Unit cell: (129.548, 157.508, 178.944, 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 171 16.00 P 105 15.00 Mg 2 11.99 O 5982 8.00 N 5324 7.00 C 18924 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: 2.60 Conformation dependent library (CDL) restraints added in 1.3 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 77 " pdb="ZN ZN A1804 " - pdb=" SG CYS A 70 " pdb=" ZN A1805 " pdb="ZN ZN A1805 " - pdb=" SG CYS A 107 " pdb="ZN ZN A1805 " - pdb=" SG CYS A 148 " pdb="ZN ZN A1805 " - pdb=" SG CYS A 167 " pdb="ZN ZN A1805 " - pdb=" SG CYS A 110 " pdb=" ZN B1301 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1163 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1166 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1182 " 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 92 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 86 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 95 " pdb=" ZN I 201 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 7 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 32 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 10 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 29 " pdb=" ZN I 202 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 75 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 78 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 106 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 103 " pdb=" ZN J 101 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 45 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 7 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 46 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 10 " 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 7048 Ramachandran restraints generated. 3524 Oldfield, 0 Emsley, 3524 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6706 Finding SS restraints... Secondary structure from input PDB file: 128 helices and 44 sheets defined 38.7% alpha, 18.8% beta 39 base pairs and 85 stacking pairs defined. Time for finding SS restraints: 4.11 Creating SS restraints... Processing helix chain 'A' and resid 23 through 31 Processing helix chain 'A' and resid 55 through 59 Processing helix chain 'A' and resid 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 Processing helix chain 'A' and resid 215 through 222 Processing helix chain 'A' and resid 230 through 235 Processing helix chain 'A' and resid 260 through 283 removed outlier: 3.579A 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: 3.727A 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: 3.575A pdb=" N LEU A 528 " --> pdb=" O VAL A 524 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N ARG A 532 " --> pdb=" O LEU A 528 " (cutoff:3.500A) removed outlier: 3.777A 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 661 Processing helix chain 'A' and resid 665 through 670 Processing helix chain 'A' and resid 672 through 699 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 Processing helix chain 'A' and resid 809 through 829 removed outlier: 3.670A pdb=" N GLU A 822 " --> pdb=" O MET A 818 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N GLY A 823 " --> pdb=" O GLY A 819 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LEU A 824 " --> pdb=" O GLY A 820 " (cutoff:3.500A) Processing helix chain 'A' and resid 830 through 845 removed outlier: 3.914A 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: 3.586A 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 996 removed outlier: 3.674A pdb=" N GLN A 994 " --> pdb=" O VAL A 990 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N GLU A 995 " --> pdb=" O LYS A 991 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ASN A 996 " --> pdb=" O ASP A 992 " (cutoff:3.500A) Processing helix chain 'A' and resid 1004 through 1015 Processing helix chain 'A' and resid 1015 through 1026 Processing helix chain 'A' and resid 1027 through 1034 Processing helix chain 'A' and resid 1038 through 1056 Processing helix chain 'A' and resid 1063 through 1083 Proline residue: A1075 - end of helix Processing helix chain 'A' and resid 1084 through 1087 Processing helix chain 'A' and resid 1091 through 1107 removed outlier: 4.208A pdb=" N VAL A1098 " --> pdb=" O VAL A1094 " (cutoff:3.500A) Proline residue: A1099 - end of helix Processing helix chain 'A' and resid 1130 through 1139 Processing helix chain 'A' and resid 1142 through 1145 Processing helix chain 'A' and resid 1166 through 1174 removed outlier: 4.740A pdb=" N PHE A1174 " --> pdb=" O ILE A1170 " (cutoff:3.500A) Processing helix chain 'A' and resid 1198 through 1205 Processing helix chain 'A' and resid 1208 through 1220 removed outlier: 3.544A pdb=" N VAL A1212 " --> pdb=" O THR A1208 " (cutoff:3.500A) removed outlier: 3.569A 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 Processing helix chain 'A' and resid 1331 through 1339 Processing helix chain 'A' and resid 1340 through 1357 Processing helix chain 'A' and resid 1364 through 1376 removed outlier: 3.914A 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: 3.529A pdb=" N ASN A1427 " --> pdb=" O GLY A1423 " (cutoff:3.500A) Processing helix chain 'A' and resid 1436 through 1439 Processing helix chain 'B' and resid 29 through 37 removed outlier: 3.991A pdb=" N VAL B 33 " --> pdb=" O ASP B 29 " (cutoff:3.500A) Processing helix chain 'B' and resid 44 through 66 removed outlier: 4.674A pdb=" N LEU B 59 " --> pdb=" O VAL B 55 " (cutoff:3.500A) removed outlier: 5.530A pdb=" N GLN B 60 " --> pdb=" O ASP B 56 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N ASP B 66 " --> pdb=" O ILE B 62 " (cutoff:3.500A) Processing helix chain 'B' and resid 113 through 120 Processing helix chain 'B' and resid 185 through 192 Processing helix chain 'B' and resid 282 through 290 Processing helix chain 'B' and resid 293 through 303 removed outlier: 3.635A pdb=" N ILE B 297 " --> pdb=" O PRO B 293 " (cutoff:3.500A) removed outlier: 3.761A 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 337 Processing helix chain 'B' and resid 344 through 359 Processing helix chain 'B' and resid 370 through 390 Processing helix chain 'B' and resid 400 through 402 No H-bonds generated for 'chain 'B' and resid 400 through 402' Processing helix chain 'B' and resid 408 through 439 Processing helix chain 'B' and resid 443 through 448 Processing helix chain 'B' and resid 450 through 464 removed outlier: 3.681A pdb=" N THR B 454 " --> pdb=" O ALA B 450 " (cutoff:3.500A) Processing helix chain 'B' and resid 487 through 496 removed outlier: 3.654A pdb=" N ARG B 496 " --> pdb=" O LEU B 492 " (cutoff:3.500A) Processing helix chain 'B' and resid 515 through 519 Processing helix chain 'B' and resid 551 through 561 Processing helix chain 'B' and resid 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: 3.679A pdb=" N ILE B 701 " --> pdb=" O GLU B 698 " (cutoff:3.500A) Processing helix chain 'B' and resid 706 through 710 removed outlier: 3.697A pdb=" N LEU B 710 " --> pdb=" O PRO B 707 " (cutoff:3.500A) Processing helix chain 'B' and resid 744 through 749 removed outlier: 3.526A pdb=" N LEU B 749 " --> pdb=" O SER B 746 " (cutoff:3.500A) Processing helix chain 'B' and resid 752 through 756 Processing helix chain 'B' and resid 758 through 762 removed outlier: 3.547A pdb=" N ASN B 762 " --> pdb=" O PRO B 759 " (cutoff:3.500A) Processing helix chain 'B' and resid 763 through 775 removed outlier: 4.128A pdb=" N LYS B 775 " --> pdb=" O SER B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 784 through 788 Processing helix chain 'B' and resid 808 through 813 removed outlier: 3.506A pdb=" N LEU B 812 " --> pdb=" O ALA B 808 " (cutoff:3.500A) Processing helix chain 'B' and resid 843 through 849 Processing helix chain 'B' and resid 1015 through 1021 removed outlier: 4.284A pdb=" N SER B1019 " --> pdb=" O HIS B1015 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ARG B1020 " --> pdb=" O ALA B1016 " (cutoff:3.500A) Processing helix chain 'B' and resid 1022 through 1039 removed outlier: 3.810A pdb=" N LEU B1026 " --> pdb=" O THR B1022 " (cutoff:3.500A) Processing helix chain 'B' and resid 1051 through 1061 removed outlier: 3.512A pdb=" N GLU B1061 " --> pdb=" O LYS B1057 " (cutoff:3.500A) Processing helix chain 'B' and resid 1098 through 1102 Processing helix chain 'B' and resid 1131 through 1142 Processing helix chain 'B' and resid 1143 through 1153 Processing helix chain 'B' and resid 1197 through 1210 Processing helix chain 'C' and resid 26 through 40 Processing helix chain 'C' and resid 59 through 69 removed outlier: 3.507A pdb=" N LEU C 69 " --> pdb=" O HIS C 65 " (cutoff:3.500A) Processing helix chain 'C' and resid 76 through 80 Processing helix chain 'C' and resid 116 through 118 No H-bonds generated for 'chain 'C' and resid 116 through 118' Processing helix chain 'C' and resid 167 through 171 Processing helix chain 'C' and resid 196 through 201 Processing helix chain 'C' and resid 204 through 210 removed outlier: 4.035A pdb=" N GLU C 208 " --> pdb=" O LYS C 205 " (cutoff:3.500A) Processing helix chain 'C' and resid 239 through 266 Processing helix chain 'E' and resid 4 through 27 removed outlier: 3.533A 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: 3.679A 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: 3.745A pdb=" N THR E 95 " --> pdb=" O LYS E 91 " (cutoff:3.500A) Processing helix chain 'E' and resid 117 through 124 Processing helix chain 'E' and resid 138 through 141 Processing helix chain 'E' and resid 143 through 147 Processing helix chain 'E' and resid 157 through 169 Processing helix chain 'E' and resid 171 through 175 removed outlier: 3.506A pdb=" N LEU E 175 " --> pdb=" O GLU E 172 " (cutoff:3.500A) Processing helix chain 'E' and resid 182 through 189 Processing helix chain 'F' and resid 86 through 103 Processing helix chain 'F' and resid 116 through 127 Processing helix chain 'H' and resid 88 through 93 Processing helix chain 'I' and resid 59 through 65 removed outlier: 3.693A pdb=" N GLY I 63 " --> pdb=" O GLN I 60 " (cutoff:3.500A) Processing helix chain 'J' and resid 17 through 27 Processing helix chain 'J' and resid 31 through 39 Processing helix chain 'J' and resid 43 through 53 removed outlier: 3.534A pdb=" N THR J 52 " --> pdb=" O ARG J 48 " (cutoff:3.500A) removed outlier: 3.718A 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 42 through 53 removed outlier: 3.610A pdb=" N GLU K 49 " --> pdb=" O LEU K 45 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ASN K 52 " --> pdb=" O ALA K 48 " (cutoff:3.500A) Processing helix chain 'K' and resid 82 through 111 removed outlier: 3.598A pdb=" N LEU K 111 " --> pdb=" O THR K 107 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 1418 through 1419 Processing sheet with id=AA2, first strand: chain 'A' and resid 82 through 90 removed outlier: 10.023A pdb=" N LEU A 86 " --> pdb=" O PRO A 240 " (cutoff:3.500A) removed outlier: 11.215A pdb=" N LYS A 88 " --> pdb=" O CYS A 238 " (cutoff:3.500A) removed outlier: 7.378A pdb=" N CYS A 238 " --> pdb=" O LYS A 88 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 175 through 177 removed outlier: 4.761A pdb=" N LEU A 181 " --> pdb=" O LEU A 202 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 250 through 251 Processing sheet with id=AA5, first strand: chain 'A' and resid 343 through 344 Processing sheet with id=AA6, first strand: chain 'B' and resid 1104 through 1106 removed outlier: 3.667A pdb=" N THR A 351 " --> pdb=" O MET A 487 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N MET A 456 " --> pdb=" O PHE A 444 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N VAL A 364 " --> pdb=" O LYS A 461 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N ILE A 463 " --> pdb=" O VAL A 364 " (cutoff:3.500A) removed outlier: 5.541A pdb=" N VAL A 366 " --> pdb=" O ILE A 463 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 375 through 379 removed outlier: 3.651A pdb=" N TYR A 404 " --> pdb=" O GLU A 433 " (cutoff:3.500A) removed outlier: 6.071A pdb=" N HIS A 435 " --> pdb=" O ALA A 402 " (cutoff:3.500A) removed outlier: 6.793A 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: 7.060A 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 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 Processing sheet with id=AB6, first strand: chain 'A' and resid 1224 through 1228 removed outlier: 4.334A pdb=" N LEU A1236 " --> pdb=" O LEU A1197 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N ARG A1194 " --> pdb=" O SER A1150 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N SER A1150 " --> pdb=" O ARG A1194 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N GLU A1196 " --> pdb=" O ILE A1148 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N TYR I 44 " --> pdb=" O ILE A1152 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 1441 through 1445 Processing sheet with id=AB8, first strand: chain 'B' and resid 69 through 73 removed outlier: 5.371A pdb=" N ARG B 86 " --> pdb=" O ALA B 139 " (cutoff:3.500A) removed outlier: 7.212A pdb=" N ALA B 139 " --> pdb=" O ARG B 86 " (cutoff:3.500A) removed outlier: 5.349A pdb=" N TYR B 88 " --> pdb=" O TYR B 137 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N TYR B 137 " --> pdb=" O TYR B 88 " (cutoff:3.500A) removed outlier: 5.069A pdb=" N ILE B 90 " --> pdb=" O ARG B 135 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N ARG B 135 " --> pdb=" O ILE B 90 " (cutoff:3.500A) removed outlier: 5.437A pdb=" N PHE B 92 " --> pdb=" O LYS B 133 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N LYS B 133 " --> pdb=" O PHE B 92 " (cutoff:3.500A) removed outlier: 4.694A pdb=" N LYS B 94 " --> pdb=" O ASP B 131 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N THR B 136 " --> pdb=" O ALA B 153 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N ALA B 153 " --> pdb=" O THR B 136 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N GLU B 138 " --> pdb=" O LEU B 151 " (cutoff:3.500A) removed outlier: 5.414A pdb=" N LEU B 151 " --> pdb=" O GLU B 138 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 69 through 73 removed outlier: 5.371A pdb=" N ARG B 86 " --> pdb=" O ALA B 139 " (cutoff:3.500A) removed outlier: 7.212A pdb=" N ALA B 139 " --> pdb=" O ARG B 86 " (cutoff:3.500A) removed outlier: 5.349A pdb=" N TYR B 88 " --> pdb=" O TYR B 137 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N TYR B 137 " --> pdb=" O TYR B 88 " (cutoff:3.500A) removed outlier: 5.069A pdb=" N ILE B 90 " --> pdb=" O ARG B 135 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N ARG B 135 " --> pdb=" O ILE B 90 " (cutoff:3.500A) removed outlier: 5.437A pdb=" N PHE B 92 " --> pdb=" O LYS B 133 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N LYS B 133 " --> pdb=" O PHE B 92 " (cutoff:3.500A) removed outlier: 4.694A pdb=" N LYS B 94 " --> pdb=" O ASP B 131 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N GLY B 168 " --> pdb=" O LEU B 128 " (cutoff:3.500A) removed outlier: 7.174A pdb=" N VAL B 130 " --> pdb=" O PHE B 166 " (cutoff:3.500A) removed outlier: 5.751A pdb=" N PHE B 166 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 7.188A pdb=" N VAL B 132 " --> pdb=" O LYS B 164 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N LYS B 164 " --> pdb=" O VAL B 132 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 101 through 103 Processing sheet with id=AC2, first strand: chain 'B' and resid 203 through 205 Processing sheet with id=AC3, first strand: chain 'B' and resid 404 through 407 removed outlier: 6.010A pdb=" N ALA B 214 " --> pdb=" O ASN B 499 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 224 through 227 removed outlier: 3.883A pdb=" N HIS B 236 " --> pdb=" O LEU B 258 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N GLN B 255 " --> pdb=" O THR B 272 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 544 through 545 Processing sheet with id=AC6, first strand: chain 'B' and resid 650 through 651 removed outlier: 3.659A pdb=" N GLU B 650 " --> pdb=" O GLU B 641 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 564 through 565 removed outlier: 5.353A pdb=" N TRP B 586 " --> pdb=" O VAL B 582 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N VAL B 582 " --> pdb=" O TRP B 586 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N GLY B 588 " --> pdb=" O VAL B 580 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 792 through 796 removed outlier: 7.024A pdb=" N PHE B 963 " --> pdb=" O VAL B 954 " (cutoff:3.500A) removed outlier: 4.902A pdb=" N VAL B 954 " --> pdb=" O PHE B 963 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N LYS B 965 " --> pdb=" O VAL B 952 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N VAL B 952 " --> pdb=" O LYS B 965 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N ARG B 967 " --> pdb=" O ASP B 950 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N THR B 971 " --> pdb=" O ASN B 946 " (cutoff:3.500A) removed outlier: 8.501A pdb=" N ASN B 946 " --> pdb=" O THR B 971 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 792 through 796 removed outlier: 7.024A pdb=" N PHE B 963 " --> pdb=" O VAL B 954 " (cutoff:3.500A) removed outlier: 4.902A pdb=" N VAL B 954 " --> pdb=" O PHE B 963 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N LYS B 965 " --> pdb=" O VAL B 952 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N VAL B 952 " --> pdb=" O LYS B 965 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N ARG B 967 " --> pdb=" O ASP B 950 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N THR B 971 " --> pdb=" O ASN B 946 " (cutoff:3.500A) removed outlier: 8.501A pdb=" N ASN B 946 " --> pdb=" O THR B 971 " (cutoff:3.500A) removed outlier: 5.235A pdb=" N VAL B 952 " --> pdb=" O LYS L 58 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 804 through 805 Processing sheet with id=AD2, first strand: chain 'B' and resid 1069 through 1070 removed outlier: 7.308A pdb=" N MET B 839 " --> pdb=" O GLY B 991 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N THR B 993 " --> pdb=" O MET B 839 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N MET B 841 " --> pdb=" O THR B 993 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N PHE B1086 " --> pdb=" O ILE B 827 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 873 through 874 Processing sheet with id=AD4, first strand: chain 'B' and resid 910 through 912 Processing sheet with id=AD5, first strand: chain 'B' and resid 1001 through 1002 Processing sheet with id=AD6, first strand: chain 'B' and resid 1158 through 1163 Processing sheet with id=AD7, first strand: chain 'B' and resid 1172 through 1174 Processing sheet with id=AD8, first strand: chain 'C' and resid 7 through 13 removed outlier: 5.362A pdb=" N VAL C 8 " --> pdb=" O SER C 23 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N SER C 23 " --> pdb=" O VAL C 8 " (cutoff:3.500A) removed outlier: 5.528A pdb=" N ILE C 10 " --> pdb=" O ILE C 21 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N ILE C 21 " --> pdb=" O ILE C 10 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N ALA C 175 " --> pdb=" O GLU C 233 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 119 through 120 removed outlier: 6.898A pdb=" N GLU C 152 " --> pdb=" O ASN C 54 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N ASN C 54 " --> pdb=" O GLU C 152 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N LYS C 154 " --> pdb=" O GLU C 52 " (cutoff:3.500A) removed outlier: 5.934A pdb=" N LYS C 160 " --> pdb=" O ILE C 46 " (cutoff:3.500A) removed outlier: 5.491A pdb=" N ILE C 46 " --> pdb=" O LYS C 160 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N GLY C 162 " --> pdb=" O LEU C 44 " (cutoff:3.500A) removed outlier: 5.244A pdb=" N LEU C 44 " --> pdb=" O GLY C 162 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N VAL L 65 " --> pdb=" O VAL C 51 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 111 through 114 Processing sheet with id=AE2, first strand: chain 'E' and resid 47 through 48 removed outlier: 5.021A pdb=" N ARG E 52 " --> pdb=" O ASP E 48 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'E' and resid 60 through 62 removed outlier: 6.424A pdb=" N TRP E 79 " --> pdb=" O ILE E 109 " (cutoff:3.500A) removed outlier: 7.469A pdb=" N VAL E 111 " --> pdb=" O TRP E 79 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N GLU E 81 " --> pdb=" O VAL E 111 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'E' and resid 152 through 156 removed outlier: 3.645A pdb=" N LYS E 152 " --> pdb=" O ILE E 199 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N VAL E 195 " --> pdb=" O LEU E 156 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'H' and resid 4 through 16 removed outlier: 6.688A pdb=" N GLU H 27 " --> pdb=" O SER H 13 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N VAL H 15 " --> pdb=" O ARG H 25 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N ARG H 25 " --> pdb=" O VAL H 15 " (cutoff:3.500A) removed outlier: 5.796A pdb=" N LEU H 122 " --> pdb=" O ASP H 41 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LEU H 121 " --> pdb=" O PHE H 118 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N LYS H 103 " --> pdb=" O TYR H 115 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N SER H 117 " --> pdb=" O ALA H 101 " (cutoff:3.500A) removed outlier: 5.628A pdb=" N ALA H 101 " --> pdb=" O SER H 117 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N LEU H 55 " --> pdb=" O ILE H 9 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N ILE H 9 " --> pdb=" O LEU H 55 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N VAL H 57 " --> pdb=" O ASP H 7 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N ASP H 7 " --> pdb=" O VAL H 57 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N ILE H 59 " --> pdb=" O LEU H 5 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'I' and resid 15 through 19 Processing sheet with id=AE7, first strand: chain 'I' and resid 83 through 86 Processing sheet with id=AE8, first strand: chain 'K' and resid 19 through 24 removed outlier: 4.666A pdb=" N ALA K 30 " --> pdb=" O ASP K 24 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N LYS K 72 " --> pdb=" O TYR K 61 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N TYR K 61 " --> pdb=" O LYS K 72 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N ARG K 74 " --> pdb=" O ALA K 59 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N ALA K 59 " --> pdb=" O ARG K 74 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N GLN K 76 " --> pdb=" O LEU K 57 " (cutoff:3.500A) 1215 hydrogen bonds defined for protein. 3324 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 102 hydrogen bonds 204 hydrogen bond angles 0 basepair planarities 39 basepair parallelities 85 stacking parallelities Total time for adding SS restraints: 9.34 Time building geometry restraints manager: 3.43 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: 4962 1.31 - 1.44: 8370 1.44 - 1.56: 17466 1.56 - 1.69: 206 1.69 - 1.81: 275 Bond restraints: 31279 Sorted by residual: bond pdb=" C4 ATP A1801 " pdb=" N9 ATP A1801 " ideal model delta sigma weight residual 1.374 1.184 0.190 1.00e-02 1.00e+04 3.61e+02 bond pdb=" C8 ATP A1801 " pdb=" N9 ATP A1801 " ideal model delta sigma weight residual 1.370 1.210 0.160 1.20e-02 6.94e+03 1.77e+02 bond pdb=" C6 ATP A1801 " pdb=" N6 ATP A1801 " ideal model delta sigma weight residual 1.337 1.447 -0.110 1.10e-02 8.26e+03 1.01e+02 bond pdb=" C5 ATP A1801 " pdb=" C6 ATP A1801 " ideal model delta sigma weight residual 1.409 1.335 0.074 1.00e-02 1.00e+04 5.43e+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 4.42e+01 ... (remaining 31274 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.30: 42552 3.30 - 6.60: 117 6.60 - 9.91: 8 9.91 - 13.21: 2 13.21 - 16.51: 2 Bond angle restraints: 42681 Sorted by residual: angle pdb=" PB ATP A1801 " pdb=" O3B ATP A1801 " pdb=" PG ATP A1801 " ideal model delta sigma weight residual 139.87 123.36 16.51 1.00e+00 1.00e+00 2.73e+02 angle pdb=" C4 ATP A1801 " pdb=" N9 ATP A1801 " pdb=" C8 ATP A1801 " ideal model delta sigma weight residual 105.72 119.39 -13.67 1.00e+00 1.00e+00 1.87e+02 angle pdb=" PA ATP A1801 " pdb=" O3A ATP A1801 " pdb=" PB ATP A1801 " ideal model delta sigma weight residual 136.83 123.68 13.15 1.00e+00 1.00e+00 1.73e+02 angle pdb=" N1 ATP A1801 " pdb=" C2 ATP A1801 " pdb=" N3 ATP A1801 " ideal model delta sigma weight residual 128.69 119.87 8.82 1.00e+00 1.00e+00 7.78e+01 angle pdb=" N3 ATP A1801 " pdb=" C4 ATP A1801 " pdb=" N9 ATP A1801 " ideal model delta sigma weight residual 127.04 133.25 -6.21 1.15e+00 7.59e-01 2.93e+01 ... (remaining 42676 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.73: 18300 35.73 - 71.47: 562 71.47 - 107.20: 24 107.20 - 142.94: 1 142.94 - 178.67: 1 Dihedral angle restraints: 18888 sinusoidal: 8529 harmonic: 10359 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 180.00 157.24 22.76 0 5.00e+00 4.00e-02 2.07e+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 38.67 -178.67 1 3.50e+01 8.16e-04 1.57e+01 dihedral pdb=" CA VAL E 90 " pdb=" C VAL E 90 " pdb=" N LYS E 91 " pdb=" CA LYS E 91 " ideal model delta harmonic sigma weight residual 180.00 160.22 19.78 0 5.00e+00 4.00e-02 1.57e+01 ... (remaining 18885 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 3578 0.043 - 0.086: 855 0.086 - 0.129: 336 0.129 - 0.172: 23 0.172 - 0.215: 2 Chirality restraints: 4794 Sorted by residual: chirality pdb=" CB ILE A 336 " pdb=" CA ILE A 336 " pdb=" CG1 ILE A 336 " pdb=" CG2 ILE A 336 " both_signs ideal model delta sigma weight residual False 2.64 2.43 0.22 2.00e-01 2.50e+01 1.16e+00 chirality pdb=" CG LEU A 472 " pdb=" CB LEU A 472 " pdb=" CD1 LEU A 472 " pdb=" CD2 LEU A 472 " both_signs ideal model delta sigma weight residual False -2.59 -2.40 -0.19 2.00e-01 2.50e+01 8.86e-01 chirality pdb=" C2' G R 19 " pdb=" C3' G R 19 " pdb=" O2' G R 19 " pdb=" C1' G R 19 " both_signs ideal model delta sigma weight residual False -2.62 -2.78 0.16 2.00e-01 2.50e+01 6.31e-01 ... (remaining 4791 not shown) Planarity restraints: 5163 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU A 710 " 0.017 2.00e-02 2.50e+03 3.47e-02 1.20e+01 pdb=" C LEU A 710 " -0.060 2.00e-02 2.50e+03 pdb=" O LEU A 710 " 0.023 2.00e-02 2.50e+03 pdb=" N ARG A 711 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA A 480 " -0.013 2.00e-02 2.50e+03 2.74e-02 7.49e+00 pdb=" C ALA A 480 " 0.047 2.00e-02 2.50e+03 pdb=" O ALA A 480 " -0.018 2.00e-02 2.50e+03 pdb=" N ASP A 481 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' U R 7 " -0.029 2.00e-02 2.50e+03 1.39e-02 4.36e+00 pdb=" N1 U R 7 " 0.024 2.00e-02 2.50e+03 pdb=" C2 U R 7 " 0.006 2.00e-02 2.50e+03 pdb=" O2 U R 7 " 0.004 2.00e-02 2.50e+03 pdb=" N3 U R 7 " -0.002 2.00e-02 2.50e+03 pdb=" C4 U R 7 " -0.005 2.00e-02 2.50e+03 pdb=" O4 U R 7 " -0.009 2.00e-02 2.50e+03 pdb=" C5 U R 7 " -0.001 2.00e-02 2.50e+03 pdb=" C6 U R 7 " 0.012 2.00e-02 2.50e+03 ... (remaining 5160 not shown) Histogram of nonbonded interaction distances: 1.91 - 2.51: 158 2.51 - 3.11: 22116 3.11 - 3.70: 47977 3.70 - 4.30: 69757 4.30 - 4.90: 114168 Nonbonded interactions: 254176 Sorted by model distance: nonbonded pdb=" OD2 ASP A 481 " pdb="MG MG A1802 " model vdw 1.911 2.170 nonbonded pdb=" O1A ATP A1801 " pdb="MG MG A1802 " model vdw 1.917 2.170 nonbonded pdb=" O1G ATP A1801 " pdb="MG MG A1802 " model vdw 1.928 2.170 nonbonded pdb=" OD1 ASP A 481 " pdb="MG MG A1803 " model vdw 2.010 2.170 nonbonded pdb=" OG1 THR A 675 " pdb=" ND2 ASN A 736 " model vdw 2.162 3.120 ... (remaining 254171 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.840 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: 0.010 Extract box with map and model: 0.500 Check model and map are aligned: 0.100 Set scattering table: 0.070 Process input model: 37.350 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.050 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: 0.000 Load rotamer database and sin/cos tables:6.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8773 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 0.190 31311 Z= 0.282 Angle : 0.586 16.510 42726 Z= 0.396 Chirality : 0.043 0.215 4794 Planarity : 0.003 0.046 5163 Dihedral : 15.024 178.669 12182 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.23 % Allowed : 2.95 % Favored : 96.82 % Rotamer: Outliers : 0.16 % Allowed : 0.29 % Favored : 99.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.57 (0.14), residues: 3524 helix: 1.40 (0.15), residues: 1213 sheet: 0.36 (0.22), residues: 566 loop : -0.29 (0.15), residues: 1745 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A1366 TYR 0.028 0.001 TYR B 797 PHE 0.018 0.001 PHE B 376 TRP 0.012 0.001 TRP A 552 HIS 0.009 0.001 HIS A 706 Details of bonding type rmsd/Z covalent geometry : bond 0.00370 / 0.28 (31279) covalent geometry : angle 0.58263 / 0.40 (42681) hydrogen bonds : bond 0.17868 / 11.69 ( 1293) hydrogen bonds : angle 6.61659 / 4.75 ( 3528) metal coordination : bond 0.00360 / 0.23 ( 32) metal coordination : angle 2.07021 / 1.26 ( 45) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7048 Ramachandran restraints generated. 3524 Oldfield, 0 Emsley, 3524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7048 Ramachandran restraints generated. 3524 Oldfield, 0 Emsley, 3524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 752 residues out of total 3133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 747 time to evaluate : 1.336 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 75 ASN cc_start: 0.8719 (t0) cc_final: 0.8450 (t0) REVERT: A 277 GLU cc_start: 0.8278 (tt0) cc_final: 0.8062 (tm-30) REVERT: A 601 LYS cc_start: 0.8785 (mtmt) cc_final: 0.8512 (mmtm) REVERT: A 873 MET cc_start: 0.9061 (mmp) cc_final: 0.8845 (mmt) REVERT: A 895 LYS cc_start: 0.8619 (ttmm) cc_final: 0.8143 (tptp) REVERT: A 909 ASP cc_start: 0.8875 (t0) cc_final: 0.8629 (t0) REVERT: A 934 LYS cc_start: 0.8341 (tttm) cc_final: 0.7772 (mmmt) REVERT: A 977 LYS cc_start: 0.9011 (tttp) cc_final: 0.8588 (mmpt) REVERT: A 1003 LYS cc_start: 0.8498 (mtmm) cc_final: 0.8213 (mppt) REVERT: A 1209 MET cc_start: 0.7950 (mmp) cc_final: 0.7623 (tmm) REVERT: A 1259 MET cc_start: 0.8139 (mmp) cc_final: 0.7301 (mpt) REVERT: A 1287 TYR cc_start: 0.8599 (m-10) cc_final: 0.7754 (m-80) REVERT: B 61 ASP cc_start: 0.8446 (m-30) cc_final: 0.8186 (m-30) REVERT: B 328 GLU cc_start: 0.8556 (mm-30) cc_final: 0.8297 (mm-30) REVERT: B 429 PHE cc_start: 0.8722 (t80) cc_final: 0.8516 (t80) REVERT: B 887 HIS cc_start: 0.7704 (m90) cc_final: 0.7464 (m170) REVERT: C 19 ASP cc_start: 0.8741 (t0) cc_final: 0.8527 (t0) REVERT: C 75 MET cc_start: 0.9170 (mmm) cc_final: 0.8930 (mmm) REVERT: E 8 ASN cc_start: 0.8544 (m110) cc_final: 0.7870 (m110) REVERT: F 119 ARG cc_start: 0.8250 (tpp80) cc_final: 0.7986 (mtm110) REVERT: F 122 MET cc_start: 0.8978 (mtp) cc_final: 0.8770 (mtm) REVERT: F 127 GLU cc_start: 0.8647 (mt-10) cc_final: 0.8382 (mt-10) REVERT: H 129 TYR cc_start: 0.8303 (p90) cc_final: 0.7893 (p90) REVERT: I 45 ARG cc_start: 0.8500 (ttt90) cc_final: 0.7993 (ttt90) REVERT: I 58 VAL cc_start: 0.8566 (OUTLIER) cc_final: 0.8241 (t) REVERT: J 26 GLN cc_start: 0.8673 (tt0) cc_final: 0.8347 (mt0) REVERT: L 28 LYS cc_start: 0.8728 (mmtt) cc_final: 0.8262 (mptt) outliers start: 5 outliers final: 0 residues processed: 751 average time/residue: 0.8334 time to fit residues: 716.4505 Evaluate side-chains 391 residues out of total 3133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 390 time to evaluate : 1.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 58 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 197 optimal weight: 0.8980 chunk 215 optimal weight: 3.9990 chunk 20 optimal weight: 0.0470 chunk 132 optimal weight: 0.6980 chunk 261 optimal weight: 4.9990 chunk 248 optimal weight: 0.6980 chunk 207 optimal weight: 4.9990 chunk 155 optimal weight: 0.0980 chunk 244 optimal weight: 5.9990 chunk 183 optimal weight: 4.9990 chunk 298 optimal weight: 2.9990 overall best weight: 0.4878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 256 GLN A 510 GLN A 736 ASN A 742 ASN A 975 HIS B 46 GLN B 740 HIS ** B 762 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 878 GLN B 951 GLN ** B1093 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 179 GLN I 46 HIS I 87 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.121426 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.081613 restraints weight = 42336.111| |-----------------------------------------------------------------------------| r_work (start): 0.3084 rms_B_bonded: 2.13 r_work: 0.2978 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2864 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.2864 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8467 moved from start: 0.1902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 31311 Z= 0.127 Angle : 0.574 10.935 42726 Z= 0.306 Chirality : 0.043 0.315 4794 Planarity : 0.005 0.053 5163 Dihedral : 16.967 169.520 5068 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.84 % Favored : 97.08 % Rotamer: Outliers : 2.81 % Allowed : 9.96 % Favored : 87.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % 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: 0.48 (0.14), residues: 3524 helix: 1.33 (0.15), residues: 1257 sheet: 0.23 (0.22), residues: 533 loop : -0.34 (0.15), residues: 1734 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 63 TYR 0.018 0.001 TYR B 797 PHE 0.024 0.002 PHE A 219 TRP 0.014 0.001 TRP A 185 HIS 0.024 0.001 HIS A1258 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.13 (31279) covalent geometry : angle 0.56764 / 0.31 (42681) hydrogen bonds : bond 0.04568 / 3.06 ( 1293) hydrogen bonds : angle 5.02233 / 3.59 ( 3528) metal coordination : bond 0.00403 / 0.24 ( 32) metal coordination : angle 2.64430 / 1.73 ( 45) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7048 Ramachandran restraints generated. 3524 Oldfield, 0 Emsley, 3524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7048 Ramachandran restraints generated. 3524 Oldfield, 0 Emsley, 3524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 491 residues out of total 3133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 403 time to evaluate : 1.156 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 75 ASN cc_start: 0.8819 (t0) cc_final: 0.8433 (t0) REVERT: A 277 GLU cc_start: 0.8020 (tt0) cc_final: 0.7725 (tm-30) REVERT: A 286 HIS cc_start: 0.7207 (OUTLIER) cc_final: 0.6906 (t-90) REVERT: A 601 LYS cc_start: 0.8746 (mtmt) cc_final: 0.8267 (mmtm) REVERT: A 895 LYS cc_start: 0.8403 (ttmm) cc_final: 0.7875 (tptp) REVERT: A 909 ASP cc_start: 0.8570 (t0) cc_final: 0.8307 (t0) REVERT: A 934 LYS cc_start: 0.7861 (tttm) cc_final: 0.7228 (mmmt) REVERT: A 977 LYS cc_start: 0.9059 (tttp) cc_final: 0.8511 (mmpt) REVERT: A 1003 LYS cc_start: 0.8654 (mtmm) cc_final: 0.8150 (mppt) REVERT: A 1148 ILE cc_start: 0.8526 (mm) cc_final: 0.8259 (mm) REVERT: A 1209 MET cc_start: 0.7788 (mmp) cc_final: 0.7510 (tmm) REVERT: A 1239 ARG cc_start: 0.7192 (mtp-110) cc_final: 0.6975 (mtp-110) REVERT: A 1241 ARG cc_start: 0.6578 (mtt180) cc_final: 0.6298 (ttm-80) REVERT: A 1259 MET cc_start: 0.8230 (mmp) cc_final: 0.7883 (mpt) REVERT: A 1285 MET cc_start: 0.8712 (mmm) cc_final: 0.8427 (mmm) REVERT: A 1287 TYR cc_start: 0.8156 (m-10) cc_final: 0.7792 (m-80) REVERT: A 1297 GLU cc_start: 0.8421 (pm20) cc_final: 0.8097 (pm20) REVERT: A 1315 GLU cc_start: 0.8097 (OUTLIER) cc_final: 0.7791 (mt-10) REVERT: A 1334 ASP cc_start: 0.8831 (m-30) cc_final: 0.8342 (m-30) REVERT: A 1393 ASN cc_start: 0.8346 (p0) cc_final: 0.8003 (m-40) REVERT: B 61 ASP cc_start: 0.8363 (m-30) cc_final: 0.8046 (m-30) REVERT: B 133 LYS cc_start: 0.8256 (OUTLIER) cc_final: 0.7820 (tptm) REVERT: B 328 GLU cc_start: 0.8709 (mm-30) cc_final: 0.8338 (mm-30) REVERT: B 394 ASP cc_start: 0.8932 (OUTLIER) cc_final: 0.8729 (m-30) REVERT: B 652 LYS cc_start: 0.8263 (mttt) cc_final: 0.8022 (mtpp) REVERT: B 887 HIS cc_start: 0.7709 (m90) cc_final: 0.7416 (m170) REVERT: B 1072 MET cc_start: 0.9552 (mtp) cc_final: 0.9319 (mtm) REVERT: C 19 ASP cc_start: 0.8767 (t0) cc_final: 0.8527 (t0) REVERT: C 249 ASP cc_start: 0.8565 (t0) cc_final: 0.8045 (m-30) REVERT: E 48 ASP cc_start: 0.6497 (OUTLIER) cc_final: 0.6248 (p0) REVERT: E 54 GLN cc_start: 0.7855 (mm-40) cc_final: 0.7432 (mt0) REVERT: E 67 GLU cc_start: 0.7617 (tp30) cc_final: 0.7370 (tp30) REVERT: F 119 ARG cc_start: 0.8040 (tpp80) cc_final: 0.7472 (mtm110) REVERT: F 122 MET cc_start: 0.8538 (mtp) cc_final: 0.8314 (mtp) REVERT: F 127 GLU cc_start: 0.8501 (mt-10) cc_final: 0.8282 (mt-10) REVERT: H 77 ARG cc_start: 0.7149 (pmt170) cc_final: 0.6888 (pmt170) REVERT: I 1 MET cc_start: 0.5834 (tmt) cc_final: 0.4981 (tpp) REVERT: J 26 GLN cc_start: 0.8547 (tt0) cc_final: 0.8062 (mt0) REVERT: K 102 LYS cc_start: 0.8683 (OUTLIER) cc_final: 0.8064 (tttt) REVERT: L 28 LYS cc_start: 0.8505 (mmtt) cc_final: 0.7856 (mptt) REVERT: L 36 SER cc_start: 0.7963 (m) cc_final: 0.7733 (p) outliers start: 88 outliers final: 28 residues processed: 455 average time/residue: 0.8215 time to fit residues: 431.5078 Evaluate side-chains 402 residues out of total 3133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 368 time to evaluate : 1.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 PHE Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 286 HIS Chi-restraints excluded: chain A residue 336 ILE Chi-restraints excluded: chain A residue 393 ARG Chi-restraints excluded: chain A residue 416 ARG Chi-restraints excluded: chain A residue 494 SER Chi-restraints excluded: chain A residue 883 LEU Chi-restraints excluded: chain A residue 1067 LEU Chi-restraints excluded: chain A residue 1263 ILE Chi-restraints excluded: chain A residue 1314 SER Chi-restraints excluded: chain A residue 1315 GLU Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 133 LYS Chi-restraints excluded: chain B residue 272 THR Chi-restraints excluded: chain B residue 323 VAL Chi-restraints excluded: chain B residue 394 ASP Chi-restraints excluded: chain B residue 415 GLN Chi-restraints excluded: chain B residue 598 GLU Chi-restraints excluded: chain B residue 943 SER Chi-restraints excluded: chain B residue 1210 MET Chi-restraints excluded: chain C residue 211 ASP Chi-restraints excluded: chain E residue 31 THR Chi-restraints excluded: chain E residue 48 ASP Chi-restraints excluded: chain H residue 11 GLN Chi-restraints excluded: chain H residue 78 SER Chi-restraints excluded: chain H residue 100 THR Chi-restraints excluded: chain H residue 110 ASP Chi-restraints excluded: chain I residue 52 ILE Chi-restraints excluded: chain I residue 77 LYS Chi-restraints excluded: chain J residue 52 THR Chi-restraints excluded: chain K residue 17 SER Chi-restraints excluded: chain K residue 102 LYS Chi-restraints excluded: chain L residue 46 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 25 optimal weight: 6.9990 chunk 3 optimal weight: 6.9990 chunk 226 optimal weight: 5.9990 chunk 116 optimal weight: 10.0000 chunk 31 optimal weight: 4.9990 chunk 335 optimal weight: 5.9990 chunk 362 optimal weight: 10.0000 chunk 112 optimal weight: 7.9990 chunk 118 optimal weight: 9.9990 chunk 300 optimal weight: 6.9990 chunk 60 optimal weight: 1.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 54 ASN A 171 GLN A 256 GLN A 358 ASN A 363 GLN ** A 451 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 742 ASN A 786 HIS A1033 GLN ** A1258 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1432 GLN B 395 GLN B 494 HIS B 862 GLN B 878 GLN ** B1074 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 17 ASN I 46 HIS I 87 GLN ** L 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.110884 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2883 r_free = 0.2883 target = 0.070082 restraints weight = 42475.891| |-----------------------------------------------------------------------------| r_work (start): 0.2886 rms_B_bonded: 2.17 r_work: 0.2764 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2647 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.2647 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8625 moved from start: 0.2898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.170 31311 Z= 0.454 Angle : 0.805 10.399 42726 Z= 0.418 Chirality : 0.056 0.266 4794 Planarity : 0.007 0.074 5163 Dihedral : 17.255 159.634 5067 Min Nonbonded Distance : 1.884 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.52 % Favored : 96.37 % Rotamer: Outliers : 3.96 % Allowed : 10.50 % Favored : 85.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % 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: -0.03 (0.14), residues: 3524 helix: 0.79 (0.15), residues: 1251 sheet: 0.13 (0.21), residues: 561 loop : -0.63 (0.14), residues: 1712 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG E 212 TYR 0.046 0.003 TYR J 63 PHE 0.043 0.003 PHE A 219 TRP 0.017 0.003 TRP B 31 HIS 0.017 0.003 HIS A 816 Details of bonding type rmsd/Z covalent geometry : bond 0.01109 / 0.45 (31279) covalent geometry : angle 0.79151 / 0.42 (42681) hydrogen bonds : bond 0.06045 / 4.02 ( 1293) hydrogen bonds : angle 5.09226 / 3.63 ( 3528) metal coordination : bond 0.01252 / 0.81 ( 32) metal coordination : angle 4.52741 / 2.93 ( 45) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7048 Ramachandran restraints generated. 3524 Oldfield, 0 Emsley, 3524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7048 Ramachandran restraints generated. 3524 Oldfield, 0 Emsley, 3524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 500 residues out of total 3133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 376 time to evaluate : 1.021 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 75 ASN cc_start: 0.8899 (t0) cc_final: 0.8520 (t0) REVERT: A 601 LYS cc_start: 0.8924 (mtmt) cc_final: 0.8422 (mmtm) REVERT: A 618 GLU cc_start: 0.8103 (pm20) cc_final: 0.7900 (pm20) REVERT: A 761 MET cc_start: 0.9430 (mtm) cc_final: 0.9174 (mtp) REVERT: A 895 LYS cc_start: 0.8493 (ttmm) cc_final: 0.8013 (tptp) REVERT: A 909 ASP cc_start: 0.8580 (t0) cc_final: 0.8322 (t0) REVERT: A 934 LYS cc_start: 0.7929 (tttm) cc_final: 0.7315 (mmmt) REVERT: A 977 LYS cc_start: 0.9124 (tttp) cc_final: 0.8554 (mmpt) REVERT: A 1062 GLU cc_start: 0.8961 (OUTLIER) cc_final: 0.8660 (tp30) REVERT: A 1196 GLU cc_start: 0.8269 (pt0) cc_final: 0.7866 (tm-30) REVERT: A 1199 ARG cc_start: 0.7020 (mtp-110) cc_final: 0.6700 (mtp85) REVERT: A 1209 MET cc_start: 0.7995 (mmp) cc_final: 0.7588 (tmm) REVERT: A 1239 ARG cc_start: 0.7377 (mtp-110) cc_final: 0.6996 (mtp-110) REVERT: A 1241 ARG cc_start: 0.6404 (mtt180) cc_final: 0.5844 (mtt-85) REVERT: A 1259 MET cc_start: 0.8247 (mmp) cc_final: 0.7868 (mpt) REVERT: A 1287 TYR cc_start: 0.8339 (m-10) cc_final: 0.8118 (m-80) REVERT: A 1307 GLU cc_start: 0.9004 (OUTLIER) cc_final: 0.8743 (mt-10) REVERT: A 1393 ASN cc_start: 0.8487 (OUTLIER) cc_final: 0.8154 (m-40) REVERT: B 133 LYS cc_start: 0.8267 (OUTLIER) cc_final: 0.7395 (mmmm) REVERT: B 328 GLU cc_start: 0.8642 (mm-30) cc_final: 0.8240 (mm-30) REVERT: B 336 ARG cc_start: 0.8676 (OUTLIER) cc_final: 0.7879 (mtt-85) REVERT: B 426 LYS cc_start: 0.8233 (mtpt) cc_final: 0.7957 (mttt) REVERT: B 444 MET cc_start: 0.8651 (tpt) cc_final: 0.8247 (tpp) REVERT: B 448 ILE cc_start: 0.8831 (OUTLIER) cc_final: 0.8483 (pp) REVERT: B 451 LYS cc_start: 0.8659 (OUTLIER) cc_final: 0.8093 (mtmp) REVERT: B 637 LEU cc_start: 0.8807 (OUTLIER) cc_final: 0.8579 (pp) REVERT: B 641 GLU cc_start: 0.8246 (OUTLIER) cc_final: 0.7985 (pt0) REVERT: B 652 LYS cc_start: 0.8708 (mttt) cc_final: 0.8351 (mtpp) REVERT: B 862 GLN cc_start: 0.8399 (OUTLIER) cc_final: 0.8085 (tt0) REVERT: B 864 LYS cc_start: 0.7815 (mtmt) cc_final: 0.6654 (pptt) REVERT: B 875 GLU cc_start: 0.8557 (OUTLIER) cc_final: 0.7488 (pp20) REVERT: B 1071 VAL cc_start: 0.9262 (OUTLIER) cc_final: 0.9031 (t) REVERT: C 195 GLN cc_start: 0.8761 (OUTLIER) cc_final: 0.8307 (mp10) REVERT: E 48 ASP cc_start: 0.6569 (OUTLIER) cc_final: 0.5909 (p0) REVERT: E 54 GLN cc_start: 0.7932 (mm-40) cc_final: 0.7414 (mt0) REVERT: E 67 GLU cc_start: 0.7822 (tp30) cc_final: 0.7575 (tp30) REVERT: E 106 GLN cc_start: 0.8373 (tp-100) cc_final: 0.7918 (tp-100) REVERT: F 127 GLU cc_start: 0.8550 (mt-10) cc_final: 0.8316 (mt-10) REVERT: H 130 ARG cc_start: 0.8710 (mtt90) cc_final: 0.8487 (mtt90) REVERT: I 1 MET cc_start: 0.5766 (OUTLIER) cc_final: 0.5321 (tpp) REVERT: I 47 GLU cc_start: 0.7605 (OUTLIER) cc_final: 0.6500 (mm-30) REVERT: J 19 GLU cc_start: 0.8741 (OUTLIER) cc_final: 0.8419 (mt-10) REVERT: J 26 GLN cc_start: 0.8659 (tt0) cc_final: 0.8108 (mt0) REVERT: K 54 ARG cc_start: 0.8715 (mmm160) cc_final: 0.8155 (tpt90) REVERT: L 28 LYS cc_start: 0.8511 (mmtt) cc_final: 0.7760 (mptt) outliers start: 124 outliers final: 47 residues processed: 453 average time/residue: 0.8057 time to fit residues: 419.7102 Evaluate side-chains 411 residues out of total 3133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 347 time to evaluate : 1.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 PHE Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 177 ASP Chi-restraints excluded: chain A residue 257 ARG Chi-restraints excluded: chain A residue 316 GLN Chi-restraints excluded: chain A residue 416 ARG Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 494 SER Chi-restraints excluded: chain A residue 883 LEU Chi-restraints excluded: chain A residue 965 GLN Chi-restraints excluded: chain A residue 975 HIS Chi-restraints excluded: chain A residue 991 LYS Chi-restraints excluded: chain A residue 992 ASP Chi-restraints excluded: chain A residue 1062 GLU Chi-restraints excluded: chain A residue 1067 LEU Chi-restraints excluded: chain A residue 1124 HIS Chi-restraints excluded: chain A residue 1130 GLN Chi-restraints excluded: chain A residue 1207 LEU Chi-restraints excluded: chain A residue 1240 CYS Chi-restraints excluded: chain A residue 1263 ILE Chi-restraints excluded: chain A residue 1307 GLU Chi-restraints excluded: chain A residue 1314 SER Chi-restraints excluded: chain A residue 1393 ASN Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 133 LYS Chi-restraints excluded: chain B residue 306 ASN Chi-restraints excluded: chain B residue 323 VAL Chi-restraints excluded: chain B residue 336 ARG Chi-restraints excluded: chain B residue 367 LEU Chi-restraints excluded: chain B residue 448 ILE Chi-restraints excluded: chain B residue 451 LYS Chi-restraints excluded: chain B residue 455 SER Chi-restraints excluded: chain B residue 598 GLU Chi-restraints excluded: chain B residue 637 LEU Chi-restraints excluded: chain B residue 641 GLU Chi-restraints excluded: chain B residue 648 HIS Chi-restraints excluded: chain B residue 862 GLN Chi-restraints excluded: chain B residue 875 GLU Chi-restraints excluded: chain B residue 903 VAL Chi-restraints excluded: chain B residue 943 SER Chi-restraints excluded: chain B residue 1071 VAL Chi-restraints excluded: chain B residue 1162 ILE Chi-restraints excluded: chain B residue 1175 LEU Chi-restraints excluded: chain C residue 12 GLU Chi-restraints excluded: chain C residue 83 SER Chi-restraints excluded: chain C residue 195 GLN Chi-restraints excluded: chain C residue 249 ASP Chi-restraints excluded: chain C residue 253 LYS Chi-restraints excluded: chain E residue 31 THR Chi-restraints excluded: chain E residue 48 ASP Chi-restraints excluded: chain E residue 91 LYS Chi-restraints excluded: chain E residue 116 ILE Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain H residue 78 SER Chi-restraints excluded: chain H residue 100 THR Chi-restraints excluded: chain H residue 110 ASP Chi-restraints excluded: chain I residue 1 MET Chi-restraints excluded: chain I residue 47 GLU Chi-restraints excluded: chain I residue 90 GLN Chi-restraints excluded: chain J residue 19 GLU Chi-restraints excluded: chain J residue 52 THR Chi-restraints excluded: chain K residue 17 SER Chi-restraints excluded: chain L residue 46 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 69 optimal weight: 1.9990 chunk 264 optimal weight: 0.1980 chunk 270 optimal weight: 0.9990 chunk 39 optimal weight: 0.9990 chunk 227 optimal weight: 2.9990 chunk 323 optimal weight: 0.8980 chunk 287 optimal weight: 3.9990 chunk 314 optimal weight: 1.9990 chunk 156 optimal weight: 0.8980 chunk 97 optimal weight: 0.8980 chunk 134 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 451 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 862 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 46 HIS I 87 GLN ** L 53 HIS ** 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 = 0.3576 r_free = 0.3576 target = 0.115616 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.074968 restraints weight = 41925.261| |-----------------------------------------------------------------------------| r_work (start): 0.2953 rms_B_bonded: 2.09 r_work: 0.2840 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2724 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.2724 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8574 moved from start: 0.2851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 31311 Z= 0.138 Angle : 0.571 7.976 42726 Z= 0.304 Chirality : 0.044 0.264 4794 Planarity : 0.004 0.055 5163 Dihedral : 17.020 157.402 5067 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.70 % Favored : 97.22 % Rotamer: Outliers : 2.68 % Allowed : 13.31 % Favored : 84.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % 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: 3524 helix: 1.07 (0.15), residues: 1256 sheet: 0.16 (0.22), residues: 543 loop : -0.58 (0.14), residues: 1725 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 677 TYR 0.018 0.001 TYR J 63 PHE 0.022 0.001 PHE A 219 TRP 0.014 0.001 TRP C 201 HIS 0.011 0.001 HIS A1258 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.14 (31279) covalent geometry : angle 0.56078 / 0.30 (42681) hydrogen bonds : bond 0.04187 / 2.81 ( 1293) hydrogen bonds : angle 4.70926 / 3.33 ( 3528) metal coordination : bond 0.00529 / 0.31 ( 32) metal coordination : angle 3.29358 / 2.15 ( 45) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7048 Ramachandran restraints generated. 3524 Oldfield, 0 Emsley, 3524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7048 Ramachandran restraints generated. 3524 Oldfield, 0 Emsley, 3524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 453 residues out of total 3133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 369 time to evaluate : 1.423 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 75 ASN cc_start: 0.8832 (t0) cc_final: 0.8452 (t0) REVERT: A 393 ARG cc_start: 0.8993 (mpt180) cc_final: 0.8734 (mmt180) REVERT: A 601 LYS cc_start: 0.8883 (mtmt) cc_final: 0.8300 (mmtp) REVERT: A 895 LYS cc_start: 0.8466 (ttmm) cc_final: 0.7962 (tptp) REVERT: A 909 ASP cc_start: 0.8575 (t0) cc_final: 0.8355 (t0) REVERT: A 912 LEU cc_start: 0.8214 (OUTLIER) cc_final: 0.7964 (pp) REVERT: A 934 LYS cc_start: 0.7947 (tttm) cc_final: 0.7365 (mmmt) REVERT: A 969 GLN cc_start: 0.7963 (mm-40) cc_final: 0.7309 (tm-30) REVERT: A 977 LYS cc_start: 0.9069 (tttp) cc_final: 0.8481 (mmpt) REVERT: A 1196 GLU cc_start: 0.8265 (pt0) cc_final: 0.8037 (pp20) REVERT: A 1199 ARG cc_start: 0.6994 (mtp-110) cc_final: 0.6726 (mtp85) REVERT: A 1217 LYS cc_start: 0.8690 (OUTLIER) cc_final: 0.8454 (mttp) REVERT: A 1228 TRP cc_start: 0.8077 (OUTLIER) cc_final: 0.7834 (m-10) REVERT: A 1239 ARG cc_start: 0.7376 (mtp-110) cc_final: 0.6881 (mtp-110) REVERT: A 1241 ARG cc_start: 0.6310 (mtt180) cc_final: 0.6043 (ttm-80) REVERT: A 1259 MET cc_start: 0.8230 (mmp) cc_final: 0.7864 (mpt) REVERT: A 1287 TYR cc_start: 0.8309 (m-10) cc_final: 0.8060 (m-80) REVERT: A 1315 GLU cc_start: 0.8408 (mt-10) cc_final: 0.7938 (mt-10) REVERT: A 1334 ASP cc_start: 0.8888 (m-30) cc_final: 0.8435 (m-30) REVERT: A 1393 ASN cc_start: 0.8360 (p0) cc_final: 0.8088 (m-40) REVERT: B 133 LYS cc_start: 0.8184 (tppp) cc_final: 0.7610 (tppp) REVERT: B 199 MET cc_start: 0.8781 (mtp) cc_final: 0.8522 (mtp) REVERT: B 328 GLU cc_start: 0.8600 (mm-30) cc_final: 0.8237 (mm-30) REVERT: B 336 ARG cc_start: 0.8632 (OUTLIER) cc_final: 0.7821 (mtt-85) REVERT: B 426 LYS cc_start: 0.8195 (mtpt) cc_final: 0.7899 (mttt) REVERT: B 637 LEU cc_start: 0.8668 (OUTLIER) cc_final: 0.8451 (pp) REVERT: B 652 LYS cc_start: 0.8684 (mttt) cc_final: 0.8354 (mtpp) REVERT: B 864 LYS cc_start: 0.7705 (mtmt) cc_final: 0.6424 (pptt) REVERT: B 887 HIS cc_start: 0.7907 (m90) cc_final: 0.7400 (m170) REVERT: C 195 GLN cc_start: 0.8681 (OUTLIER) cc_final: 0.8258 (mt0) REVERT: C 249 ASP cc_start: 0.8755 (t0) cc_final: 0.8395 (m-30) REVERT: E 54 GLN cc_start: 0.7924 (mm-40) cc_final: 0.7451 (mt0) REVERT: E 67 GLU cc_start: 0.7764 (tp30) cc_final: 0.7449 (tp30) REVERT: E 106 GLN cc_start: 0.8367 (tp-100) cc_final: 0.7874 (tp-100) REVERT: F 127 GLU cc_start: 0.8483 (mt-10) cc_final: 0.8222 (mt-10) REVERT: H 128 ASN cc_start: 0.8733 (t0) cc_final: 0.8352 (t0) REVERT: H 130 ARG cc_start: 0.8724 (mtt90) cc_final: 0.8134 (mmt-90) REVERT: I 1 MET cc_start: 0.5598 (OUTLIER) cc_final: 0.4581 (tpt) REVERT: J 19 GLU cc_start: 0.8694 (OUTLIER) cc_final: 0.8426 (mm-30) REVERT: J 26 GLN cc_start: 0.8600 (tt0) cc_final: 0.8076 (mt0) REVERT: K 54 ARG cc_start: 0.8642 (mmm160) cc_final: 0.8223 (tpt90) REVERT: L 28 LYS cc_start: 0.8599 (mmtt) cc_final: 0.7844 (mptt) outliers start: 84 outliers final: 38 residues processed: 414 average time/residue: 0.8268 time to fit residues: 395.8223 Evaluate side-chains 388 residues out of total 3133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 342 time to evaluate : 1.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 PHE Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 177 ASP Chi-restraints excluded: chain A residue 316 GLN Chi-restraints excluded: chain A residue 416 ARG Chi-restraints excluded: chain A residue 470 LEU Chi-restraints excluded: chain A residue 494 SER Chi-restraints excluded: chain A residue 883 LEU Chi-restraints excluded: chain A residue 912 LEU Chi-restraints excluded: chain A residue 992 ASP Chi-restraints excluded: chain A residue 998 LEU Chi-restraints excluded: chain A residue 1067 LEU Chi-restraints excluded: chain A residue 1124 HIS Chi-restraints excluded: chain A residue 1217 LYS Chi-restraints excluded: chain A residue 1228 TRP Chi-restraints excluded: chain A residue 1240 CYS Chi-restraints excluded: chain A residue 1263 ILE Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 323 VAL Chi-restraints excluded: chain B residue 336 ARG Chi-restraints excluded: chain B residue 367 LEU Chi-restraints excluded: chain B residue 598 GLU Chi-restraints excluded: chain B residue 637 LEU Chi-restraints excluded: chain B residue 903 VAL Chi-restraints excluded: chain B residue 943 SER Chi-restraints excluded: chain B residue 1162 ILE Chi-restraints excluded: chain B residue 1210 MET Chi-restraints excluded: chain C residue 83 SER Chi-restraints excluded: chain C residue 195 GLN Chi-restraints excluded: chain C residue 211 ASP Chi-restraints excluded: chain E residue 31 THR Chi-restraints excluded: chain E residue 91 LYS Chi-restraints excluded: chain F residue 74 ILE Chi-restraints excluded: chain F residue 104 ASN Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain H residue 100 THR Chi-restraints excluded: chain H residue 110 ASP Chi-restraints excluded: chain I residue 1 MET Chi-restraints excluded: chain I residue 90 GLN Chi-restraints excluded: chain J residue 19 GLU Chi-restraints excluded: chain J residue 52 THR Chi-restraints excluded: chain L residue 38 LEU Chi-restraints excluded: chain L residue 46 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 194 optimal weight: 2.9990 chunk 197 optimal weight: 5.9990 chunk 132 optimal weight: 0.5980 chunk 113 optimal weight: 9.9990 chunk 351 optimal weight: 9.9990 chunk 56 optimal weight: 4.9990 chunk 316 optimal weight: 2.9990 chunk 51 optimal weight: 0.6980 chunk 28 optimal weight: 0.9980 chunk 177 optimal weight: 3.9990 chunk 298 optimal weight: 1.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 451 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 838 GLN B 366 GLN ** H 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 87 GLN ** L 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.115001 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.074237 restraints weight = 42081.901| |-----------------------------------------------------------------------------| r_work (start): 0.2923 rms_B_bonded: 2.09 r_work: 0.2809 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2691 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.2691 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8583 moved from start: 0.2973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 31311 Z= 0.169 Angle : 0.564 9.665 42726 Z= 0.298 Chirality : 0.044 0.254 4794 Planarity : 0.004 0.049 5163 Dihedral : 16.885 153.656 5067 Min Nonbonded Distance : 1.725 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.09 % Favored : 96.79 % Rotamer: Outliers : 2.74 % Allowed : 13.82 % Favored : 83.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % 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: 3524 helix: 1.21 (0.15), residues: 1258 sheet: 0.17 (0.22), residues: 538 loop : -0.54 (0.14), residues: 1728 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 135 TYR 0.020 0.001 TYR J 63 PHE 0.029 0.002 PHE A 219 TRP 0.011 0.001 TRP B 31 HIS 0.012 0.001 HIS A 399 Details of bonding type rmsd/Z covalent geometry : bond 0.00399 / 0.17 (31279) covalent geometry : angle 0.55539 / 0.30 (42681) hydrogen bonds : bond 0.04106 / 2.75 ( 1293) hydrogen bonds : angle 4.56241 / 3.23 ( 3528) metal coordination : bond 0.00550 / 0.34 ( 32) metal coordination : angle 3.01572 / 2.03 ( 45) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7048 Ramachandran restraints generated. 3524 Oldfield, 0 Emsley, 3524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7048 Ramachandran restraints generated. 3524 Oldfield, 0 Emsley, 3524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 436 residues out of total 3133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 350 time to evaluate : 1.246 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 75 ASN cc_start: 0.8833 (t0) cc_final: 0.8463 (t0) REVERT: A 393 ARG cc_start: 0.9016 (mpt180) cc_final: 0.8783 (mmt180) REVERT: A 601 LYS cc_start: 0.8901 (mtmt) cc_final: 0.8337 (mmtp) REVERT: A 677 ARG cc_start: 0.8070 (ptt90) cc_final: 0.7761 (ptp90) REVERT: A 895 LYS cc_start: 0.8549 (ttmm) cc_final: 0.8031 (tptp) REVERT: A 909 ASP cc_start: 0.8548 (t0) cc_final: 0.8331 (t0) REVERT: A 912 LEU cc_start: 0.8196 (OUTLIER) cc_final: 0.7975 (pp) REVERT: A 934 LYS cc_start: 0.7958 (tttm) cc_final: 0.7379 (mmmt) REVERT: A 977 LYS cc_start: 0.9073 (tttp) cc_final: 0.8497 (mmpt) REVERT: A 1199 ARG cc_start: 0.7116 (mtp-110) cc_final: 0.6903 (mtp85) REVERT: A 1209 MET cc_start: 0.7952 (tpp) cc_final: 0.7278 (tmm) REVERT: A 1217 LYS cc_start: 0.8683 (OUTLIER) cc_final: 0.8447 (mttp) REVERT: A 1239 ARG cc_start: 0.7356 (mtp-110) cc_final: 0.6899 (mtp85) REVERT: A 1241 ARG cc_start: 0.6264 (mtt180) cc_final: 0.5596 (mtp-110) REVERT: A 1259 MET cc_start: 0.8209 (mmp) cc_final: 0.7842 (mpt) REVERT: A 1287 TYR cc_start: 0.8317 (m-10) cc_final: 0.8086 (m-80) REVERT: A 1315 GLU cc_start: 0.8434 (mt-10) cc_final: 0.7945 (mt-10) REVERT: A 1334 ASP cc_start: 0.8898 (m-30) cc_final: 0.8454 (m-30) REVERT: A 1393 ASN cc_start: 0.8380 (p0) cc_final: 0.8106 (m-40) REVERT: B 133 LYS cc_start: 0.8131 (tppp) cc_final: 0.7918 (tptm) REVERT: B 199 MET cc_start: 0.8757 (OUTLIER) cc_final: 0.8325 (mtp) REVERT: B 328 GLU cc_start: 0.8605 (mm-30) cc_final: 0.8205 (mm-30) REVERT: B 426 LYS cc_start: 0.8239 (mtpt) cc_final: 0.7978 (mttt) REVERT: B 637 LEU cc_start: 0.8539 (OUTLIER) cc_final: 0.8072 (pt) REVERT: B 652 LYS cc_start: 0.8666 (mttt) cc_final: 0.8315 (mtpp) REVERT: C 249 ASP cc_start: 0.8764 (t0) cc_final: 0.8435 (m-30) REVERT: E 54 GLN cc_start: 0.7879 (mm-40) cc_final: 0.7469 (mt0) REVERT: E 67 GLU cc_start: 0.7853 (tp30) cc_final: 0.7505 (tp30) REVERT: E 106 GLN cc_start: 0.8472 (tp-100) cc_final: 0.7992 (tp-100) REVERT: F 119 ARG cc_start: 0.8392 (mtp85) cc_final: 0.8117 (mtp85) REVERT: F 127 GLU cc_start: 0.8489 (mt-10) cc_final: 0.8203 (mt-10) REVERT: H 128 ASN cc_start: 0.8712 (t0) cc_final: 0.8458 (t0) REVERT: I 1 MET cc_start: 0.5587 (OUTLIER) cc_final: 0.4484 (tpt) REVERT: J 26 GLN cc_start: 0.8608 (tt0) cc_final: 0.8076 (mt0) REVERT: K 54 ARG cc_start: 0.8666 (mmm160) cc_final: 0.8254 (tpt90) REVERT: L 28 LYS cc_start: 0.8596 (mmtt) cc_final: 0.7856 (mptt) outliers start: 86 outliers final: 48 residues processed: 398 average time/residue: 0.8355 time to fit residues: 382.5908 Evaluate side-chains 393 residues out of total 3133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 340 time to evaluate : 1.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 PHE Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 177 ASP Chi-restraints excluded: chain A residue 257 ARG Chi-restraints excluded: chain A residue 316 GLN Chi-restraints excluded: chain A residue 416 ARG Chi-restraints excluded: chain A residue 470 LEU Chi-restraints excluded: chain A residue 494 SER Chi-restraints excluded: chain A residue 516 SER Chi-restraints excluded: chain A residue 883 LEU Chi-restraints excluded: chain A residue 901 LEU Chi-restraints excluded: chain A residue 912 LEU Chi-restraints excluded: chain A residue 919 ILE Chi-restraints excluded: chain A residue 965 GLN Chi-restraints excluded: chain A residue 992 ASP Chi-restraints excluded: chain A residue 998 LEU Chi-restraints excluded: chain A residue 1067 LEU Chi-restraints excluded: chain A residue 1124 HIS Chi-restraints excluded: chain A residue 1130 GLN Chi-restraints excluded: chain A residue 1217 LYS Chi-restraints excluded: chain A residue 1240 CYS Chi-restraints excluded: chain A residue 1263 ILE Chi-restraints excluded: chain A residue 1268 LEU Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 199 MET Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 323 VAL Chi-restraints excluded: chain B residue 367 LEU Chi-restraints excluded: chain B residue 415 GLN Chi-restraints excluded: chain B residue 598 GLU Chi-restraints excluded: chain B residue 637 LEU Chi-restraints excluded: chain B residue 903 VAL Chi-restraints excluded: chain B residue 943 SER Chi-restraints excluded: chain B residue 961 LEU Chi-restraints excluded: chain B residue 1162 ILE Chi-restraints excluded: chain C residue 26 ASP Chi-restraints excluded: chain C residue 29 MET Chi-restraints excluded: chain C residue 83 SER Chi-restraints excluded: chain E residue 31 THR Chi-restraints excluded: chain E residue 91 LYS Chi-restraints excluded: chain F residue 104 ASN Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain H residue 78 SER Chi-restraints excluded: chain H residue 100 THR Chi-restraints excluded: chain H residue 110 ASP Chi-restraints excluded: chain I residue 1 MET Chi-restraints excluded: chain I residue 90 GLN Chi-restraints excluded: chain J residue 52 THR Chi-restraints excluded: chain L residue 46 VAL Chi-restraints excluded: chain L residue 66 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 202 optimal weight: 2.9990 chunk 331 optimal weight: 6.9990 chunk 81 optimal weight: 0.9980 chunk 236 optimal weight: 2.9990 chunk 201 optimal weight: 1.9990 chunk 195 optimal weight: 1.9990 chunk 295 optimal weight: 3.9990 chunk 255 optimal weight: 0.9990 chunk 321 optimal weight: 5.9990 chunk 93 optimal weight: 10.0000 chunk 13 optimal weight: 3.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 451 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1203 ASN H 128 ASN I 87 GLN ** L 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.114552 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.073747 restraints weight = 42034.305| |-----------------------------------------------------------------------------| r_work (start): 0.2931 rms_B_bonded: 2.09 r_work: 0.2817 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2700 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.2700 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8593 moved from start: 0.3093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 31311 Z= 0.187 Angle : 0.569 7.759 42726 Z= 0.300 Chirality : 0.044 0.240 4794 Planarity : 0.004 0.048 5163 Dihedral : 16.825 150.615 5067 Min Nonbonded Distance : 1.490 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.04 % Favored : 96.85 % Rotamer: Outliers : 2.87 % Allowed : 14.01 % Favored : 83.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % 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: 3524 helix: 1.23 (0.15), residues: 1256 sheet: 0.21 (0.22), residues: 538 loop : -0.54 (0.14), residues: 1730 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 52 TYR 0.020 0.001 TYR J 63 PHE 0.028 0.002 PHE A 219 TRP 0.010 0.001 TRP B 31 HIS 0.012 0.001 HIS A 399 Details of bonding type rmsd/Z covalent geometry : bond 0.00447 / 0.19 (31279) covalent geometry : angle 0.56028 / 0.30 (42681) hydrogen bonds : bond 0.04120 / 2.76 ( 1293) hydrogen bonds : angle 4.51940 / 3.20 ( 3528) metal coordination : bond 0.00630 / 0.40 ( 32) metal coordination : angle 3.06739 / 2.03 ( 45) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7048 Ramachandran restraints generated. 3524 Oldfield, 0 Emsley, 3524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7048 Ramachandran restraints generated. 3524 Oldfield, 0 Emsley, 3524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 441 residues out of total 3133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 351 time to evaluate : 1.200 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 ARG cc_start: 0.7659 (ptm160) cc_final: 0.7380 (ptm160) REVERT: A 75 ASN cc_start: 0.8851 (t0) cc_final: 0.8480 (t0) REVERT: A 256 GLN cc_start: 0.8082 (mt0) cc_final: 0.7652 (mt0) REVERT: A 393 ARG cc_start: 0.9025 (mpt180) cc_final: 0.8777 (mmt180) REVERT: A 601 LYS cc_start: 0.8925 (mtmt) cc_final: 0.8400 (mmtm) REVERT: A 677 ARG cc_start: 0.8092 (ptt90) cc_final: 0.7780 (ptp90) REVERT: A 895 LYS cc_start: 0.8498 (ttmm) cc_final: 0.7988 (tptp) REVERT: A 909 ASP cc_start: 0.8593 (t0) cc_final: 0.8370 (t0) REVERT: A 912 LEU cc_start: 0.8212 (OUTLIER) cc_final: 0.7987 (pp) REVERT: A 934 LYS cc_start: 0.7952 (tttm) cc_final: 0.7386 (mmmt) REVERT: A 977 LYS cc_start: 0.9023 (tttp) cc_final: 0.8473 (mmpt) REVERT: A 1199 ARG cc_start: 0.7080 (mtp-110) cc_final: 0.6878 (mtp85) REVERT: A 1239 ARG cc_start: 0.7344 (mtp-110) cc_final: 0.6924 (mtp85) REVERT: A 1241 ARG cc_start: 0.6187 (mtt180) cc_final: 0.5906 (mtt-85) REVERT: A 1259 MET cc_start: 0.8188 (mmp) cc_final: 0.7687 (mpt) REVERT: A 1287 TYR cc_start: 0.8315 (m-10) cc_final: 0.8093 (m-80) REVERT: A 1334 ASP cc_start: 0.8898 (m-30) cc_final: 0.8451 (m-30) REVERT: A 1393 ASN cc_start: 0.8380 (p0) cc_final: 0.8095 (m-40) REVERT: B 133 LYS cc_start: 0.8264 (tppp) cc_final: 0.7666 (tppp) REVERT: B 135 ARG cc_start: 0.6881 (mtt90) cc_final: 0.6460 (mtt90) REVERT: B 199 MET cc_start: 0.8743 (OUTLIER) cc_final: 0.8309 (mtp) REVERT: B 328 GLU cc_start: 0.8597 (mm-30) cc_final: 0.8203 (mm-30) REVERT: B 426 LYS cc_start: 0.8275 (mtpt) cc_final: 0.8013 (mttt) REVERT: B 451 LYS cc_start: 0.8678 (OUTLIER) cc_final: 0.8059 (mtmp) REVERT: B 573 GLN cc_start: 0.8497 (tt0) cc_final: 0.8026 (tm130) REVERT: B 637 LEU cc_start: 0.8544 (OUTLIER) cc_final: 0.8067 (pt) REVERT: B 652 LYS cc_start: 0.8677 (mttt) cc_final: 0.8326 (mtpp) REVERT: B 862 GLN cc_start: 0.8509 (OUTLIER) cc_final: 0.8198 (tt0) REVERT: B 864 LYS cc_start: 0.7741 (mtmt) cc_final: 0.6540 (pptt) REVERT: C 249 ASP cc_start: 0.8785 (t0) cc_final: 0.8453 (m-30) REVERT: E 54 GLN cc_start: 0.7897 (mm-40) cc_final: 0.7456 (mt0) REVERT: E 67 GLU cc_start: 0.7915 (tp30) cc_final: 0.7546 (tp30) REVERT: E 106 GLN cc_start: 0.8533 (tp-100) cc_final: 0.8057 (tp-100) REVERT: F 119 ARG cc_start: 0.8365 (mtp85) cc_final: 0.8126 (mtp85) REVERT: F 127 GLU cc_start: 0.8477 (mt-10) cc_final: 0.8173 (mt-10) REVERT: H 130 ARG cc_start: 0.8791 (mmt90) cc_final: 0.8366 (mmt-90) REVERT: H 136 LYS cc_start: 0.8430 (mmtp) cc_final: 0.8060 (ptmt) REVERT: I 1 MET cc_start: 0.5625 (OUTLIER) cc_final: 0.4523 (tpt) REVERT: I 47 GLU cc_start: 0.7525 (OUTLIER) cc_final: 0.6216 (mm-30) REVERT: I 48 LEU cc_start: 0.7997 (OUTLIER) cc_final: 0.7431 (mm) REVERT: J 19 GLU cc_start: 0.8729 (OUTLIER) cc_final: 0.8456 (mm-30) REVERT: J 26 GLN cc_start: 0.8604 (tt0) cc_final: 0.8071 (mt0) REVERT: K 54 ARG cc_start: 0.8629 (mmm160) cc_final: 0.8216 (tpt90) REVERT: L 28 LYS cc_start: 0.8596 (mmtt) cc_final: 0.7857 (mptt) outliers start: 90 outliers final: 51 residues processed: 404 average time/residue: 0.8302 time to fit residues: 386.7683 Evaluate side-chains 397 residues out of total 3133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 337 time to evaluate : 1.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 PHE Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 177 ASP Chi-restraints excluded: chain A residue 257 ARG Chi-restraints excluded: chain A residue 291 GLU Chi-restraints excluded: chain A residue 316 GLN Chi-restraints excluded: chain A residue 416 ARG Chi-restraints excluded: chain A residue 470 LEU Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 494 SER Chi-restraints excluded: chain A residue 516 SER Chi-restraints excluded: chain A residue 883 LEU Chi-restraints excluded: chain A residue 901 LEU Chi-restraints excluded: chain A residue 912 LEU Chi-restraints excluded: chain A residue 919 ILE Chi-restraints excluded: chain A residue 965 GLN Chi-restraints excluded: chain A residue 975 HIS Chi-restraints excluded: chain A residue 992 ASP Chi-restraints excluded: chain A residue 998 LEU Chi-restraints excluded: chain A residue 1067 LEU Chi-restraints excluded: chain A residue 1124 HIS Chi-restraints excluded: chain A residue 1207 LEU Chi-restraints excluded: chain A residue 1228 TRP Chi-restraints excluded: chain A residue 1240 CYS Chi-restraints excluded: chain A residue 1263 ILE Chi-restraints excluded: chain A residue 1433 MET Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 199 MET Chi-restraints excluded: chain B residue 272 THR Chi-restraints excluded: chain B residue 323 VAL Chi-restraints excluded: chain B residue 367 LEU Chi-restraints excluded: chain B residue 415 GLN Chi-restraints excluded: chain B residue 451 LYS Chi-restraints excluded: chain B residue 455 SER Chi-restraints excluded: chain B residue 598 GLU Chi-restraints excluded: chain B residue 637 LEU Chi-restraints excluded: chain B residue 862 GLN Chi-restraints excluded: chain B residue 903 VAL Chi-restraints excluded: chain B residue 943 SER Chi-restraints excluded: chain B residue 1162 ILE Chi-restraints excluded: chain C residue 12 GLU Chi-restraints excluded: chain C residue 26 ASP Chi-restraints excluded: chain C residue 83 SER Chi-restraints excluded: chain E residue 31 THR Chi-restraints excluded: chain F residue 104 ASN Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain H residue 78 SER Chi-restraints excluded: chain H residue 100 THR Chi-restraints excluded: chain H residue 110 ASP Chi-restraints excluded: chain I residue 1 MET Chi-restraints excluded: chain I residue 47 GLU Chi-restraints excluded: chain I residue 48 LEU Chi-restraints excluded: chain I residue 90 GLN Chi-restraints excluded: chain J residue 19 GLU Chi-restraints excluded: chain J residue 52 THR Chi-restraints excluded: chain K residue 17 SER Chi-restraints excluded: chain L residue 46 VAL Chi-restraints excluded: chain L residue 66 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 258 optimal weight: 4.9990 chunk 298 optimal weight: 0.9990 chunk 144 optimal weight: 0.9990 chunk 220 optimal weight: 0.7980 chunk 323 optimal weight: 1.9990 chunk 290 optimal weight: 1.9990 chunk 139 optimal weight: 1.9990 chunk 90 optimal weight: 0.8980 chunk 297 optimal weight: 4.9990 chunk 318 optimal weight: 0.9990 chunk 234 optimal weight: 2.9990 overall best weight: 0.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 451 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 762 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 862 GLN B 957 ASN I 87 GLN ** L 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.114960 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.074202 restraints weight = 42021.416| |-----------------------------------------------------------------------------| r_work (start): 0.2955 rms_B_bonded: 2.09 r_work: 0.2842 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2725 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.2725 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8573 moved from start: 0.3142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 31311 Z= 0.130 Angle : 0.534 7.774 42726 Z= 0.284 Chirality : 0.043 0.236 4794 Planarity : 0.004 0.048 5163 Dihedral : 16.710 148.456 5067 Min Nonbonded Distance : 1.390 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.06 % Favored : 96.82 % Rotamer: Outliers : 2.59 % Allowed : 14.62 % Favored : 82.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % 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: 0.38 (0.14), residues: 3524 helix: 1.32 (0.15), residues: 1255 sheet: 0.23 (0.22), residues: 538 loop : -0.49 (0.14), residues: 1731 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG H 87 TYR 0.018 0.001 TYR I 44 PHE 0.025 0.001 PHE A 219 TRP 0.011 0.001 TRP C 201 HIS 0.010 0.001 HIS A1258 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.13 (31279) covalent geometry : angle 0.52724 / 0.28 (42681) hydrogen bonds : bond 0.03736 / 2.50 ( 1293) hydrogen bonds : angle 4.42599 / 3.14 ( 3528) metal coordination : bond 0.00454 / 0.28 ( 32) metal coordination : angle 2.70710 / 1.82 ( 45) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7048 Ramachandran restraints generated. 3524 Oldfield, 0 Emsley, 3524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7048 Ramachandran restraints generated. 3524 Oldfield, 0 Emsley, 3524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 433 residues out of total 3133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 352 time to evaluate : 1.183 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 ARG cc_start: 0.7665 (ptm160) cc_final: 0.7398 (ptm160) REVERT: A 75 ASN cc_start: 0.8808 (t0) cc_final: 0.8447 (t0) REVERT: A 256 GLN cc_start: 0.8127 (mt0) cc_final: 0.7776 (mt0) REVERT: A 393 ARG cc_start: 0.9008 (mpt180) cc_final: 0.8769 (mmt180) REVERT: A 494 SER cc_start: 0.8367 (OUTLIER) cc_final: 0.8103 (p) REVERT: A 601 LYS cc_start: 0.8915 (mtmt) cc_final: 0.8311 (mmtp) REVERT: A 895 LYS cc_start: 0.8488 (ttmm) cc_final: 0.7985 (tptp) REVERT: A 909 ASP cc_start: 0.8591 (t0) cc_final: 0.8363 (t0) REVERT: A 912 LEU cc_start: 0.8263 (OUTLIER) cc_final: 0.8033 (pp) REVERT: A 934 LYS cc_start: 0.7935 (tttm) cc_final: 0.7375 (mmmt) REVERT: A 961 ARG cc_start: 0.8271 (ttm-80) cc_final: 0.7933 (ttm110) REVERT: A 977 LYS cc_start: 0.9018 (tttp) cc_final: 0.8421 (mmmt) REVERT: A 1209 MET cc_start: 0.7898 (tpp) cc_final: 0.7281 (tmm) REVERT: A 1239 ARG cc_start: 0.7387 (mtp-110) cc_final: 0.7066 (mtp-110) REVERT: A 1259 MET cc_start: 0.8276 (mmp) cc_final: 0.7807 (mpt) REVERT: A 1287 TYR cc_start: 0.8296 (m-10) cc_final: 0.8079 (m-80) REVERT: A 1315 GLU cc_start: 0.8435 (mp0) cc_final: 0.8084 (mt-10) REVERT: A 1334 ASP cc_start: 0.8865 (m-30) cc_final: 0.8424 (m-30) REVERT: A 1393 ASN cc_start: 0.8364 (p0) cc_final: 0.8067 (m-40) REVERT: B 199 MET cc_start: 0.8758 (OUTLIER) cc_final: 0.8470 (mtp) REVERT: B 328 GLU cc_start: 0.8594 (mm-30) cc_final: 0.8200 (mm-30) REVERT: B 394 ASP cc_start: 0.9112 (OUTLIER) cc_final: 0.8890 (m-30) REVERT: B 426 LYS cc_start: 0.8277 (mtpt) cc_final: 0.8003 (mttt) REVERT: B 451 LYS cc_start: 0.8672 (OUTLIER) cc_final: 0.8048 (mtmp) REVERT: B 573 GLN cc_start: 0.8435 (tt0) cc_final: 0.7990 (tm130) REVERT: B 637 LEU cc_start: 0.8640 (OUTLIER) cc_final: 0.8138 (pt) REVERT: B 652 LYS cc_start: 0.8710 (mttt) cc_final: 0.8336 (mtpp) REVERT: B 864 LYS cc_start: 0.7802 (mtmt) cc_final: 0.6533 (pptt) REVERT: B 887 HIS cc_start: 0.7908 (m90) cc_final: 0.7376 (m170) REVERT: C 249 ASP cc_start: 0.8767 (t0) cc_final: 0.8447 (m-30) REVERT: E 54 GLN cc_start: 0.7840 (mm-40) cc_final: 0.7437 (mt0) REVERT: E 67 GLU cc_start: 0.7913 (tp30) cc_final: 0.7548 (tp30) REVERT: E 106 GLN cc_start: 0.8570 (tp-100) cc_final: 0.8076 (tp-100) REVERT: F 127 GLU cc_start: 0.8462 (mt-10) cc_final: 0.8148 (mt-10) REVERT: H 130 ARG cc_start: 0.8761 (mmt90) cc_final: 0.8356 (mmt-90) REVERT: H 136 LYS cc_start: 0.8231 (mmtp) cc_final: 0.7906 (ptmt) REVERT: J 19 GLU cc_start: 0.8713 (OUTLIER) cc_final: 0.8441 (mm-30) REVERT: J 26 GLN cc_start: 0.8539 (tt0) cc_final: 0.7995 (mt0) REVERT: K 54 ARG cc_start: 0.8613 (mmm160) cc_final: 0.8211 (tpt90) REVERT: L 28 LYS cc_start: 0.8611 (mmtt) cc_final: 0.7871 (mptt) REVERT: L 47 ARG cc_start: 0.7934 (mtp85) cc_final: 0.7400 (mtt-85) outliers start: 81 outliers final: 48 residues processed: 401 average time/residue: 0.8091 time to fit residues: 375.0819 Evaluate side-chains 394 residues out of total 3133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 339 time to evaluate : 1.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 PHE Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 177 ASP Chi-restraints excluded: chain A residue 291 GLU Chi-restraints excluded: chain A residue 316 GLN Chi-restraints excluded: chain A residue 470 LEU Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 494 SER Chi-restraints excluded: chain A residue 516 SER Chi-restraints excluded: chain A residue 702 LEU Chi-restraints excluded: chain A residue 883 LEU Chi-restraints excluded: chain A residue 901 LEU Chi-restraints excluded: chain A residue 912 LEU Chi-restraints excluded: chain A residue 919 ILE Chi-restraints excluded: chain A residue 975 HIS Chi-restraints excluded: chain A residue 992 ASP Chi-restraints excluded: chain A residue 998 LEU Chi-restraints excluded: chain A residue 1067 LEU Chi-restraints excluded: chain A residue 1124 HIS Chi-restraints excluded: chain A residue 1130 GLN Chi-restraints excluded: chain A residue 1228 TRP Chi-restraints excluded: chain A residue 1240 CYS Chi-restraints excluded: chain A residue 1263 ILE Chi-restraints excluded: chain A residue 1433 MET Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 199 MET Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 272 THR Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 323 VAL Chi-restraints excluded: chain B residue 367 LEU Chi-restraints excluded: chain B residue 394 ASP Chi-restraints excluded: chain B residue 415 GLN Chi-restraints excluded: chain B residue 451 LYS Chi-restraints excluded: chain B residue 637 LEU Chi-restraints excluded: chain B residue 903 VAL Chi-restraints excluded: chain B residue 943 SER Chi-restraints excluded: chain B residue 1162 ILE Chi-restraints excluded: chain C residue 12 GLU Chi-restraints excluded: chain C residue 26 ASP Chi-restraints excluded: chain C residue 83 SER Chi-restraints excluded: chain C residue 211 ASP Chi-restraints excluded: chain E residue 31 THR Chi-restraints excluded: chain F residue 104 ASN Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain H residue 78 SER Chi-restraints excluded: chain H residue 100 THR Chi-restraints excluded: chain H residue 110 ASP Chi-restraints excluded: chain I residue 90 GLN Chi-restraints excluded: chain I residue 110 PHE Chi-restraints excluded: chain J residue 19 GLU Chi-restraints excluded: chain J residue 52 THR Chi-restraints excluded: chain L residue 46 VAL Chi-restraints excluded: chain L residue 66 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 75 optimal weight: 0.8980 chunk 98 optimal weight: 0.9980 chunk 117 optimal weight: 3.9990 chunk 147 optimal weight: 5.9990 chunk 133 optimal weight: 0.7980 chunk 43 optimal weight: 1.9990 chunk 229 optimal weight: 0.7980 chunk 0 optimal weight: 6.9990 chunk 34 optimal weight: 0.6980 chunk 177 optimal weight: 4.9990 chunk 293 optimal weight: 4.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 762 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 87 GLN ** L 53 HIS ** 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 = 0.3582 r_free = 0.3582 target = 0.116075 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.075609 restraints weight = 42082.998| |-----------------------------------------------------------------------------| r_work (start): 0.2964 rms_B_bonded: 2.09 r_work: 0.2852 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2736 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.2736 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8568 moved from start: 0.3192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 31311 Z= 0.124 Angle : 0.530 7.951 42726 Z= 0.281 Chirality : 0.042 0.230 4794 Planarity : 0.004 0.048 5163 Dihedral : 16.602 146.179 5067 Min Nonbonded Distance : 1.268 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.92 % Favored : 96.96 % Rotamer: Outliers : 2.39 % Allowed : 15.67 % Favored : 81.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.44 (0.14), residues: 3524 helix: 1.40 (0.15), residues: 1254 sheet: 0.22 (0.22), residues: 537 loop : -0.46 (0.15), residues: 1733 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG H 87 TYR 0.015 0.001 TYR I 15 PHE 0.025 0.001 PHE A 219 TRP 0.011 0.001 TRP C 201 HIS 0.011 0.001 HIS I 46 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.12 (31279) covalent geometry : angle 0.52383 / 0.28 (42681) hydrogen bonds : bond 0.03591 / 2.40 ( 1293) hydrogen bonds : angle 4.33229 / 3.07 ( 3528) metal coordination : bond 0.00386 / 0.25 ( 32) metal coordination : angle 2.49289 / 1.70 ( 45) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7048 Ramachandran restraints generated. 3524 Oldfield, 0 Emsley, 3524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7048 Ramachandran restraints generated. 3524 Oldfield, 0 Emsley, 3524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 424 residues out of total 3133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 349 time to evaluate : 1.176 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 ARG cc_start: 0.7668 (ptm160) cc_final: 0.7357 (ptm160) REVERT: A 75 ASN cc_start: 0.8791 (t0) cc_final: 0.8430 (t0) REVERT: A 256 GLN cc_start: 0.8124 (mt0) cc_final: 0.7761 (mt0) REVERT: A 393 ARG cc_start: 0.9005 (mpt180) cc_final: 0.8774 (mmt180) REVERT: A 494 SER cc_start: 0.8394 (OUTLIER) cc_final: 0.8136 (p) REVERT: A 601 LYS cc_start: 0.8928 (mtmt) cc_final: 0.8326 (mmtp) REVERT: A 677 ARG cc_start: 0.7982 (ptt90) cc_final: 0.7710 (ptp90) REVERT: A 895 LYS cc_start: 0.8490 (ttmm) cc_final: 0.7988 (tptp) REVERT: A 909 ASP cc_start: 0.8574 (t0) cc_final: 0.8341 (t0) REVERT: A 912 LEU cc_start: 0.8240 (OUTLIER) cc_final: 0.8025 (pp) REVERT: A 934 LYS cc_start: 0.7935 (tttm) cc_final: 0.7323 (mmmt) REVERT: A 961 ARG cc_start: 0.8273 (ttm-80) cc_final: 0.7941 (ttm110) REVERT: A 977 LYS cc_start: 0.9020 (tttp) cc_final: 0.8433 (mmmt) REVERT: A 1209 MET cc_start: 0.7906 (tpp) cc_final: 0.7417 (tmm) REVERT: A 1259 MET cc_start: 0.8267 (mmp) cc_final: 0.7828 (mpt) REVERT: A 1287 TYR cc_start: 0.8308 (m-10) cc_final: 0.8091 (m-80) REVERT: A 1315 GLU cc_start: 0.8453 (mt-10) cc_final: 0.8113 (mt-10) REVERT: A 1334 ASP cc_start: 0.8876 (m-30) cc_final: 0.8436 (m-30) REVERT: A 1393 ASN cc_start: 0.8353 (p0) cc_final: 0.8044 (m-40) REVERT: B 199 MET cc_start: 0.8686 (OUTLIER) cc_final: 0.8394 (mtp) REVERT: B 328 GLU cc_start: 0.8588 (mm-30) cc_final: 0.8190 (mm-30) REVERT: B 394 ASP cc_start: 0.9135 (OUTLIER) cc_final: 0.8912 (m-30) REVERT: B 426 LYS cc_start: 0.8252 (mtpt) cc_final: 0.7984 (mttt) REVERT: B 573 GLN cc_start: 0.8433 (tt0) cc_final: 0.7999 (tm130) REVERT: B 637 LEU cc_start: 0.8620 (OUTLIER) cc_final: 0.8111 (pt) REVERT: B 652 LYS cc_start: 0.8701 (mttt) cc_final: 0.8330 (mtpp) REVERT: B 682 SER cc_start: 0.8888 (t) cc_final: 0.8670 (m) REVERT: B 864 LYS cc_start: 0.7837 (mtmt) cc_final: 0.6598 (pptt) REVERT: B 887 HIS cc_start: 0.7911 (m90) cc_final: 0.7374 (m170) REVERT: C 211 ASP cc_start: 0.8935 (m-30) cc_final: 0.8685 (m-30) REVERT: C 249 ASP cc_start: 0.8768 (t0) cc_final: 0.8459 (m-30) REVERT: E 54 GLN cc_start: 0.7845 (mm-40) cc_final: 0.7471 (mt0) REVERT: E 67 GLU cc_start: 0.7937 (tp30) cc_final: 0.7565 (tp30) REVERT: E 106 GLN cc_start: 0.8589 (tp-100) cc_final: 0.8097 (tp-100) REVERT: F 127 GLU cc_start: 0.8443 (mt-10) cc_final: 0.8118 (mt-10) REVERT: H 130 ARG cc_start: 0.8760 (mmt90) cc_final: 0.8380 (mmt-90) REVERT: H 136 LYS cc_start: 0.8219 (mmtp) cc_final: 0.7758 (ptmt) REVERT: H 138 GLU cc_start: 0.8243 (pm20) cc_final: 0.7539 (pm20) REVERT: I 1 MET cc_start: 0.5917 (tpt) cc_final: 0.4243 (tpt) REVERT: J 19 GLU cc_start: 0.8711 (OUTLIER) cc_final: 0.8438 (mm-30) REVERT: J 26 GLN cc_start: 0.8513 (tt0) cc_final: 0.7974 (mt0) REVERT: K 54 ARG cc_start: 0.8555 (mmm160) cc_final: 0.8160 (tpt90) REVERT: L 28 LYS cc_start: 0.8616 (mmtt) cc_final: 0.7873 (mptt) REVERT: L 47 ARG cc_start: 0.7893 (mtp85) cc_final: 0.7382 (mtt-85) outliers start: 75 outliers final: 44 residues processed: 397 average time/residue: 0.7103 time to fit residues: 326.8908 Evaluate side-chains 391 residues out of total 3133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 341 time to evaluate : 1.067 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 PHE Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 291 GLU Chi-restraints excluded: chain A residue 316 GLN Chi-restraints excluded: chain A residue 470 LEU Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 494 SER Chi-restraints excluded: chain A residue 516 SER Chi-restraints excluded: chain A residue 702 LEU Chi-restraints excluded: chain A residue 883 LEU Chi-restraints excluded: chain A residue 901 LEU Chi-restraints excluded: chain A residue 912 LEU Chi-restraints excluded: chain A residue 919 ILE Chi-restraints excluded: chain A residue 975 HIS Chi-restraints excluded: chain A residue 1067 LEU Chi-restraints excluded: chain A residue 1124 HIS Chi-restraints excluded: chain A residue 1130 GLN Chi-restraints excluded: chain A residue 1228 TRP Chi-restraints excluded: chain A residue 1240 CYS Chi-restraints excluded: chain A residue 1263 ILE Chi-restraints excluded: chain A residue 1433 MET Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 199 MET Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 272 THR Chi-restraints excluded: chain B residue 323 VAL Chi-restraints excluded: chain B residue 337 ARG Chi-restraints excluded: chain B residue 343 ILE Chi-restraints excluded: chain B residue 367 LEU Chi-restraints excluded: chain B residue 394 ASP Chi-restraints excluded: chain B residue 637 LEU Chi-restraints excluded: chain B residue 903 VAL Chi-restraints excluded: chain B residue 943 SER Chi-restraints excluded: chain B residue 1162 ILE Chi-restraints excluded: chain C residue 12 GLU Chi-restraints excluded: chain C residue 26 ASP Chi-restraints excluded: chain C residue 83 SER Chi-restraints excluded: chain E residue 31 THR Chi-restraints excluded: chain F residue 104 ASN Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain H residue 78 SER Chi-restraints excluded: chain H residue 88 SER Chi-restraints excluded: chain H residue 100 THR Chi-restraints excluded: chain H residue 110 ASP Chi-restraints excluded: chain I residue 90 GLN Chi-restraints excluded: chain I residue 110 PHE Chi-restraints excluded: chain J residue 19 GLU Chi-restraints excluded: chain J residue 52 THR Chi-restraints excluded: chain L residue 46 VAL Chi-restraints excluded: chain L residue 66 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 275 optimal weight: 0.0010 chunk 266 optimal weight: 3.9990 chunk 320 optimal weight: 0.9990 chunk 356 optimal weight: 9.9990 chunk 359 optimal weight: 40.0000 chunk 279 optimal weight: 0.6980 chunk 302 optimal weight: 0.9980 chunk 67 optimal weight: 0.8980 chunk 304 optimal weight: 3.9990 chunk 18 optimal weight: 3.9990 chunk 288 optimal weight: 2.9990 overall best weight: 0.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 762 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 87 GLN ** L 53 HIS ** 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 = 0.3589 r_free = 0.3589 target = 0.116606 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.076273 restraints weight = 42005.392| |-----------------------------------------------------------------------------| r_work (start): 0.2977 rms_B_bonded: 2.08 r_work: 0.2864 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2749 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.2749 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8559 moved from start: 0.3250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 31311 Z= 0.116 Angle : 0.526 7.369 42726 Z= 0.279 Chirality : 0.042 0.221 4794 Planarity : 0.004 0.054 5163 Dihedral : 16.491 143.854 5067 Min Nonbonded Distance : 1.159 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.84 % Favored : 97.05 % Rotamer: Outliers : 2.01 % Allowed : 16.25 % Favored : 81.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.49 (0.14), residues: 3524 helix: 1.42 (0.15), residues: 1266 sheet: 0.30 (0.22), residues: 523 loop : -0.44 (0.15), residues: 1735 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG A1239 TYR 0.020 0.001 TYR I 44 PHE 0.024 0.001 PHE A 219 TRP 0.013 0.001 TRP B 308 HIS 0.012 0.001 HIS I 46 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.12 (31279) covalent geometry : angle 0.51989 / 0.28 (42681) hydrogen bonds : bond 0.03450 / 2.31 ( 1293) hydrogen bonds : angle 4.29185 / 3.04 ( 3528) metal coordination : bond 0.00409 / 0.24 ( 32) metal coordination : angle 2.49878 / 1.70 ( 45) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7048 Ramachandran restraints generated. 3524 Oldfield, 0 Emsley, 3524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7048 Ramachandran restraints generated. 3524 Oldfield, 0 Emsley, 3524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 413 residues out of total 3133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 350 time to evaluate : 1.110 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 ARG cc_start: 0.7683 (ptm160) cc_final: 0.7325 (ptm160) REVERT: A 75 ASN cc_start: 0.8778 (t0) cc_final: 0.8429 (t0) REVERT: A 256 GLN cc_start: 0.8121 (mt0) cc_final: 0.7787 (mt0) REVERT: A 393 ARG cc_start: 0.9014 (mpt180) cc_final: 0.8784 (mmt180) REVERT: A 494 SER cc_start: 0.8407 (OUTLIER) cc_final: 0.8164 (p) REVERT: A 601 LYS cc_start: 0.8922 (mtmt) cc_final: 0.8316 (mmtp) REVERT: A 895 LYS cc_start: 0.8563 (ttmm) cc_final: 0.8060 (tptp) REVERT: A 909 ASP cc_start: 0.8561 (t0) cc_final: 0.8336 (t0) REVERT: A 912 LEU cc_start: 0.8232 (OUTLIER) cc_final: 0.8023 (pp) REVERT: A 934 LYS cc_start: 0.7930 (tttm) cc_final: 0.7310 (mmmt) REVERT: A 961 ARG cc_start: 0.8261 (ttm-80) cc_final: 0.7939 (ttm110) REVERT: A 977 LYS cc_start: 0.8988 (tttp) cc_final: 0.8405 (mmmt) REVERT: A 1239 ARG cc_start: 0.7151 (mtp-110) cc_final: 0.6861 (mtp-110) REVERT: A 1259 MET cc_start: 0.8242 (mmp) cc_final: 0.7808 (mpt) REVERT: A 1287 TYR cc_start: 0.8305 (m-10) cc_final: 0.8088 (m-80) REVERT: A 1315 GLU cc_start: 0.8499 (mt-10) cc_final: 0.8160 (mt-10) REVERT: A 1334 ASP cc_start: 0.8852 (m-30) cc_final: 0.8426 (m-30) REVERT: A 1393 ASN cc_start: 0.8352 (p0) cc_final: 0.8030 (m-40) REVERT: B 199 MET cc_start: 0.8697 (OUTLIER) cc_final: 0.8403 (mtp) REVERT: B 328 GLU cc_start: 0.8588 (mm-30) cc_final: 0.8214 (mm-30) REVERT: B 337 ARG cc_start: 0.8305 (OUTLIER) cc_final: 0.7401 (mtt90) REVERT: B 394 ASP cc_start: 0.9121 (OUTLIER) cc_final: 0.8887 (m-30) REVERT: B 426 LYS cc_start: 0.8234 (mtpt) cc_final: 0.7976 (mttt) REVERT: B 573 GLN cc_start: 0.8408 (tt0) cc_final: 0.8061 (tm-30) REVERT: B 637 LEU cc_start: 0.8572 (OUTLIER) cc_final: 0.8063 (pt) REVERT: B 652 LYS cc_start: 0.8694 (mttt) cc_final: 0.8329 (mtpp) REVERT: B 682 SER cc_start: 0.8906 (t) cc_final: 0.8699 (m) REVERT: B 864 LYS cc_start: 0.7799 (mtmt) cc_final: 0.6501 (pptt) REVERT: B 887 HIS cc_start: 0.7936 (m90) cc_final: 0.7393 (m170) REVERT: C 211 ASP cc_start: 0.8943 (m-30) cc_final: 0.8700 (m-30) REVERT: C 249 ASP cc_start: 0.8729 (t0) cc_final: 0.8419 (m-30) REVERT: E 54 GLN cc_start: 0.7842 (mm-40) cc_final: 0.7472 (mt0) REVERT: E 67 GLU cc_start: 0.7941 (tp30) cc_final: 0.7567 (tp30) REVERT: E 106 GLN cc_start: 0.8624 (tp-100) cc_final: 0.8174 (tp-100) REVERT: E 159 ASP cc_start: 0.8827 (OUTLIER) cc_final: 0.8625 (m-30) REVERT: F 127 GLU cc_start: 0.8438 (mt-10) cc_final: 0.8114 (mt-10) REVERT: H 136 LYS cc_start: 0.8228 (mmtp) cc_final: 0.7756 (ptmt) REVERT: H 138 GLU cc_start: 0.8170 (OUTLIER) cc_final: 0.7438 (pm20) REVERT: J 19 GLU cc_start: 0.8709 (OUTLIER) cc_final: 0.8432 (mm-30) REVERT: J 26 GLN cc_start: 0.8505 (tt0) cc_final: 0.7969 (mt0) REVERT: K 54 ARG cc_start: 0.8545 (mmm160) cc_final: 0.8169 (tpt90) REVERT: L 28 LYS cc_start: 0.8591 (mmtt) cc_final: 0.7867 (mptt) REVERT: L 47 ARG cc_start: 0.7749 (mtp85) cc_final: 0.7094 (mtt180) REVERT: L 54 ARG cc_start: 0.8614 (mtp85) cc_final: 0.8114 (mtp85) outliers start: 63 outliers final: 36 residues processed: 388 average time/residue: 0.7085 time to fit residues: 318.2780 Evaluate side-chains 391 residues out of total 3133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 346 time to evaluate : 0.970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 PHE Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 470 LEU Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 494 SER Chi-restraints excluded: chain A residue 516 SER Chi-restraints excluded: chain A residue 702 LEU Chi-restraints excluded: chain A residue 883 LEU Chi-restraints excluded: chain A residue 912 LEU Chi-restraints excluded: chain A residue 975 HIS Chi-restraints excluded: chain A residue 1124 HIS Chi-restraints excluded: chain A residue 1130 GLN Chi-restraints excluded: chain A residue 1207 LEU Chi-restraints excluded: chain A residue 1228 TRP Chi-restraints excluded: chain A residue 1263 ILE Chi-restraints excluded: chain A residue 1433 MET Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 199 MET Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 272 THR Chi-restraints excluded: chain B residue 323 VAL Chi-restraints excluded: chain B residue 337 ARG Chi-restraints excluded: chain B residue 343 ILE Chi-restraints excluded: chain B residue 367 LEU Chi-restraints excluded: chain B residue 394 ASP Chi-restraints excluded: chain B residue 637 LEU Chi-restraints excluded: chain B residue 943 SER Chi-restraints excluded: chain B residue 1162 ILE Chi-restraints excluded: chain C residue 12 GLU Chi-restraints excluded: chain C residue 26 ASP Chi-restraints excluded: chain C residue 83 SER Chi-restraints excluded: chain E residue 31 THR Chi-restraints excluded: chain E residue 159 ASP Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain H residue 88 SER Chi-restraints excluded: chain H residue 100 THR Chi-restraints excluded: chain H residue 110 ASP Chi-restraints excluded: chain H residue 138 GLU Chi-restraints excluded: chain I residue 90 GLN Chi-restraints excluded: chain I residue 110 PHE Chi-restraints excluded: chain J residue 19 GLU Chi-restraints excluded: chain J residue 52 THR Chi-restraints excluded: chain K residue 17 SER Chi-restraints excluded: chain L residue 46 VAL Chi-restraints excluded: chain L residue 66 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 56 optimal weight: 5.9990 chunk 139 optimal weight: 3.9990 chunk 218 optimal weight: 4.9990 chunk 146 optimal weight: 0.9980 chunk 261 optimal weight: 2.9990 chunk 206 optimal weight: 1.9990 chunk 68 optimal weight: 8.9990 chunk 90 optimal weight: 0.6980 chunk 39 optimal weight: 2.9990 chunk 228 optimal weight: 4.9990 chunk 109 optimal weight: 0.8980 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 887 HIS I 87 GLN ** L 53 HIS ** 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 = 0.3569 r_free = 0.3569 target = 0.115207 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.074727 restraints weight = 41905.726| |-----------------------------------------------------------------------------| r_work (start): 0.2948 rms_B_bonded: 2.08 r_work: 0.2836 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2719 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.2719 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8581 moved from start: 0.3305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 31311 Z= 0.166 Angle : 0.559 9.648 42726 Z= 0.294 Chirality : 0.044 0.211 4794 Planarity : 0.004 0.055 5163 Dihedral : 16.473 142.528 5067 Min Nonbonded Distance : 1.072 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.26 % Favored : 96.62 % Rotamer: Outliers : 1.82 % Allowed : 16.47 % Favored : 81.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.41 (0.14), residues: 3524 helix: 1.33 (0.15), residues: 1266 sheet: 0.22 (0.22), residues: 539 loop : -0.46 (0.15), residues: 1719 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A1239 TYR 0.016 0.001 TYR J 63 PHE 0.028 0.001 PHE A 219 TRP 0.017 0.001 TRP B 308 HIS 0.011 0.001 HIS I 46 Details of bonding type rmsd/Z covalent geometry : bond 0.00395 / 0.17 (31279) covalent geometry : angle 0.55270 / 0.29 (42681) hydrogen bonds : bond 0.03754 / 2.51 ( 1293) hydrogen bonds : angle 4.34062 / 3.07 ( 3528) metal coordination : bond 0.00531 / 0.33 ( 32) metal coordination : angle 2.65859 / 1.77 ( 45) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7048 Ramachandran restraints generated. 3524 Oldfield, 0 Emsley, 3524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7048 Ramachandran restraints generated. 3524 Oldfield, 0 Emsley, 3524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 403 residues out of total 3133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 346 time to evaluate : 1.230 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 ARG cc_start: 0.7696 (ptm160) cc_final: 0.7313 (ptm160) REVERT: A 75 ASN cc_start: 0.8779 (t0) cc_final: 0.8432 (t0) REVERT: A 256 GLN cc_start: 0.8094 (mt0) cc_final: 0.7742 (mt0) REVERT: A 393 ARG cc_start: 0.9016 (mpt180) cc_final: 0.8780 (mmt-90) REVERT: A 494 SER cc_start: 0.8460 (OUTLIER) cc_final: 0.8208 (p) REVERT: A 601 LYS cc_start: 0.8916 (mtmt) cc_final: 0.8304 (mmtp) REVERT: A 677 ARG cc_start: 0.8100 (ptt90) cc_final: 0.7846 (ptt90) REVERT: A 895 LYS cc_start: 0.8578 (ttmm) cc_final: 0.8067 (tptp) REVERT: A 909 ASP cc_start: 0.8674 (t0) cc_final: 0.8410 (t0) REVERT: A 912 LEU cc_start: 0.8262 (OUTLIER) cc_final: 0.8049 (pp) REVERT: A 934 LYS cc_start: 0.7933 (tttm) cc_final: 0.7357 (mmmt) REVERT: A 961 ARG cc_start: 0.8277 (ttm-80) cc_final: 0.7952 (ttm110) REVERT: A 969 GLN cc_start: 0.7946 (mm-40) cc_final: 0.7338 (tm-30) REVERT: A 977 LYS cc_start: 0.9025 (tttp) cc_final: 0.8418 (mmmt) REVERT: A 1259 MET cc_start: 0.8277 (mmp) cc_final: 0.7836 (mpt) REVERT: A 1287 TYR cc_start: 0.8297 (m-10) cc_final: 0.8093 (m-80) REVERT: A 1315 GLU cc_start: 0.8500 (mt-10) cc_final: 0.8125 (mt-10) REVERT: A 1334 ASP cc_start: 0.8870 (m-30) cc_final: 0.8465 (m-30) REVERT: A 1393 ASN cc_start: 0.8362 (p0) cc_final: 0.8017 (m-40) REVERT: B 199 MET cc_start: 0.8706 (OUTLIER) cc_final: 0.8452 (mtp) REVERT: B 328 GLU cc_start: 0.8605 (mm-30) cc_final: 0.8191 (mm-30) REVERT: B 426 LYS cc_start: 0.8248 (mtpt) cc_final: 0.7994 (mttt) REVERT: B 573 GLN cc_start: 0.8406 (tt0) cc_final: 0.8055 (tm-30) REVERT: B 637 LEU cc_start: 0.8636 (OUTLIER) cc_final: 0.8124 (pt) REVERT: B 652 LYS cc_start: 0.8699 (mttt) cc_final: 0.8323 (mtpp) REVERT: B 682 SER cc_start: 0.8894 (t) cc_final: 0.8682 (m) REVERT: B 864 LYS cc_start: 0.7819 (mtmt) cc_final: 0.6634 (pptt) REVERT: C 211 ASP cc_start: 0.8940 (m-30) cc_final: 0.8712 (m-30) REVERT: C 249 ASP cc_start: 0.8750 (t0) cc_final: 0.8440 (m-30) REVERT: E 54 GLN cc_start: 0.7840 (mm-40) cc_final: 0.7471 (mt0) REVERT: E 67 GLU cc_start: 0.7966 (tp30) cc_final: 0.7540 (tp30) REVERT: E 106 GLN cc_start: 0.8643 (tp-100) cc_final: 0.8198 (tp-100) REVERT: F 127 GLU cc_start: 0.8433 (mt-10) cc_final: 0.8073 (mt-10) REVERT: H 130 ARG cc_start: 0.8527 (mmt-90) cc_final: 0.8252 (mmt-90) REVERT: H 136 LYS cc_start: 0.8232 (mmtp) cc_final: 0.7770 (ptmt) REVERT: H 138 GLU cc_start: 0.8154 (OUTLIER) cc_final: 0.7415 (pm20) REVERT: J 19 GLU cc_start: 0.8711 (OUTLIER) cc_final: 0.8429 (mm-30) REVERT: J 26 GLN cc_start: 0.8514 (tt0) cc_final: 0.7976 (mt0) REVERT: K 54 ARG cc_start: 0.8558 (mmm160) cc_final: 0.8153 (tpt90) REVERT: L 28 LYS cc_start: 0.8603 (mmtt) cc_final: 0.7871 (mptt) REVERT: L 47 ARG cc_start: 0.7747 (mtp85) cc_final: 0.7122 (mtt180) REVERT: L 54 ARG cc_start: 0.8568 (mtp85) cc_final: 0.8104 (mtp85) outliers start: 57 outliers final: 38 residues processed: 380 average time/residue: 0.8052 time to fit residues: 352.8480 Evaluate side-chains 387 residues out of total 3133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 343 time to evaluate : 0.957 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 PHE Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 257 ARG Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 470 LEU Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 494 SER Chi-restraints excluded: chain A residue 516 SER Chi-restraints excluded: chain A residue 702 LEU Chi-restraints excluded: chain A residue 883 LEU Chi-restraints excluded: chain A residue 912 LEU Chi-restraints excluded: chain A residue 1124 HIS Chi-restraints excluded: chain A residue 1130 GLN Chi-restraints excluded: chain A residue 1207 LEU Chi-restraints excluded: chain A residue 1228 TRP Chi-restraints excluded: chain A residue 1263 ILE Chi-restraints excluded: chain A residue 1433 MET Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 199 MET Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 272 THR Chi-restraints excluded: chain B residue 323 VAL Chi-restraints excluded: chain B residue 343 ILE Chi-restraints excluded: chain B residue 367 LEU Chi-restraints excluded: chain B residue 455 SER Chi-restraints excluded: chain B residue 637 LEU Chi-restraints excluded: chain B residue 943 SER Chi-restraints excluded: chain B residue 1162 ILE Chi-restraints excluded: chain C residue 12 GLU Chi-restraints excluded: chain C residue 26 ASP Chi-restraints excluded: chain C residue 83 SER Chi-restraints excluded: chain E residue 31 THR Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain H residue 88 SER Chi-restraints excluded: chain H residue 100 THR Chi-restraints excluded: chain H residue 110 ASP Chi-restraints excluded: chain H residue 138 GLU Chi-restraints excluded: chain I residue 90 GLN Chi-restraints excluded: chain I residue 110 PHE Chi-restraints excluded: chain J residue 19 GLU Chi-restraints excluded: chain J residue 52 THR Chi-restraints excluded: chain K residue 17 SER Chi-restraints excluded: chain L residue 46 VAL Chi-restraints excluded: chain L residue 66 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 1 optimal weight: 3.9990 chunk 113 optimal weight: 7.9990 chunk 68 optimal weight: 8.9990 chunk 361 optimal weight: 10.0000 chunk 139 optimal weight: 4.9990 chunk 49 optimal weight: 3.9990 chunk 267 optimal weight: 1.9990 chunk 318 optimal weight: 2.9990 chunk 147 optimal weight: 5.9990 chunk 203 optimal weight: 4.9990 chunk 242 optimal weight: 0.3980 overall best weight: 2.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 451 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 443 ASN B 887 HIS B1193 GLN F 104 ASN I 87 GLN ** L 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.112222 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2908 r_free = 0.2908 target = 0.071306 restraints weight = 42139.456| |-----------------------------------------------------------------------------| r_work (start): 0.2905 rms_B_bonded: 2.09 r_work: 0.2791 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2674 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.2674 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8614 moved from start: 0.3440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.095 31311 Z= 0.260 Angle : 0.636 9.791 42726 Z= 0.331 Chirality : 0.047 0.204 4794 Planarity : 0.005 0.057 5163 Dihedral : 16.577 141.032 5067 Min Nonbonded Distance : 1.028 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.38 % Favored : 96.51 % Rotamer: Outliers : 1.79 % Allowed : 16.85 % Favored : 81.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % 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: 0.26 (0.14), residues: 3524 helix: 1.15 (0.15), residues: 1258 sheet: 0.17 (0.22), residues: 537 loop : -0.50 (0.14), residues: 1729 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG A1239 TYR 0.021 0.002 TYR B 113 PHE 0.032 0.002 PHE A 219 TRP 0.025 0.002 TRP B 308 HIS 0.013 0.002 HIS A 399 Details of bonding type rmsd/Z covalent geometry : bond 0.00636 / 0.26 (31279) covalent geometry : angle 0.62648 / 0.33 (42681) hydrogen bonds : bond 0.04482 / 2.98 ( 1293) hydrogen bonds : angle 4.54785 / 3.22 ( 3528) metal coordination : bond 0.00820 / 0.53 ( 32) metal coordination : angle 3.37168 / 2.18 ( 45) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14023.00 seconds wall clock time: 238 minutes 51.10 seconds (14331.10 seconds total)