Starting phenix.real_space_refine on Sun Aug 9 10:16:45 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9sc2_54747/08_2026/9sc2_54747.cif Found real_map, /net/cci-nas-00/data/ceres_data/9sc2_54747/08_2026/9sc2_54747.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.53 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9sc2_54747/08_2026/9sc2_54747.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9sc2_54747/08_2026/9sc2_54747.map" model { file = "/net/cci-nas-00/data/ceres_data/9sc2_54747/08_2026/9sc2_54747.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9sc2_54747/08_2026/9sc2_54747.cif" } resolution = 3.53 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.033 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 8 6.06 5 P 100 5.49 5 Mg 2 5.21 5 S 182 5.16 5 C 20561 2.51 5 N 5765 2.21 5 O 6465 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 33083 Number of models: 1 Model: "" Number of chains: 21 Chain: "A" Number of atoms: 10942 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1390, 10942 Classifications: {'peptide': 1390} Link IDs: {'PCIS': 1, 'PTRANS': 61, 'TRANS': 1327} Chain breaks: 6 Chain: "B" Number of atoms: 9155 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1150, 9155 Classifications: {'peptide': 1150} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 48, 'TRANS': 1100} Chain breaks: 6 Chain: "C" Number of atoms: 2095 Number of conformers: 1 Conformer: "" Number of residues, atoms: 266, 2095 Classifications: {'peptide': 266} Link IDs: {'PTRANS': 11, 'TRANS': 254} Chain: "D" Number of atoms: 1327 Number of conformers: 1 Conformer: "" Number of residues, atoms: 167, 1327 Classifications: {'peptide': 167} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 164} Chain breaks: 2 Chain: "E" Number of atoms: 1744 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1744 Classifications: {'peptide': 213} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 200} Chain: "F" Number of atoms: 670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 670 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 6, 'TRANS': 76} Chain: "G" Number of atoms: 1340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1340 Classifications: {'peptide': 171} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 162} Chain: "H" Number of atoms: 1077 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 1077 Classifications: {'peptide': 134} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 129} Chain breaks: 1 Chain: "I" Number of atoms: 909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 909 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 5, 'TRANS': 106} Chain: "J" Number of atoms: 532 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 532 Classifications: {'peptide': 65} Link IDs: {'PTRANS': 2, 'TRANS': 62} Chain: "K" Number of atoms: 904 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 904 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 5, 'TRANS': 106} Chain: "L" Number of atoms: 359 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 359 Classifications: {'peptide': 45} Modifications used: {'COO': 1} Link IDs: {'TRANS': 44} Chain: "N" Number of atoms: 905 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 905 Classifications: {'DNA': 44} Link IDs: {'rna3p': 43} Chain: "R" Number of atoms: 197 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 197 Classifications: {'RNA': 9} Modifications used: {'rna3p_pur': 6, 'rna3p_pyr': 2} Link IDs: {'rna3p': 8} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "T" Number of atoms: 886 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 886 Classifications: {'DNA': 44} Link IDs: {'rna3p': 43} Chain: "A" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 35 Unusual residues: {' MG': 2, ' ZN': 2, 'ATP': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 457 SG CYS A 67 105.614 69.405 94.999 1.00137.42 S ATOM 479 SG CYS A 70 105.069 65.924 93.568 1.00135.29 S ATOM 532 SG CYS A 77 102.414 68.653 93.132 1.00130.37 S ATOM 762 SG CYS A 107 80.358 75.633 135.307 1.00165.63 S ATOM 786 SG CYS A 110 81.841 72.248 135.959 1.00163.00 S ATOM 1091 SG CYS A 148 78.483 73.058 137.432 1.00182.44 S ATOM 1105 SG CYS A 167 81.610 74.860 138.784 1.00171.60 S ATOM 19603 SG CYS B1163 97.665 57.377 104.906 1.00129.75 S ATOM 19621 SG CYS B1166 95.754 60.559 105.196 1.00139.92 S ATOM 19746 SG CYS B1182 99.561 60.624 104.728 1.00141.62 S ATOM 19765 SG CYS B1185 97.954 59.606 108.075 1.00138.58 S ATOM 20753 SG CYS C 86 91.974 73.779 25.704 1.00168.12 S ATOM 20770 SG CYS C 88 93.709 76.164 27.975 1.00178.51 S ATOM 20803 SG CYS C 92 92.855 77.216 24.449 1.00158.61 S ATOM 20826 SG CYS C 95 90.112 76.850 27.159 1.00148.29 S ATOM 28411 SG CYS I 7 40.179 123.828 128.496 1.00223.45 S ATOM 28436 SG CYS I 10 43.839 123.178 128.057 1.00222.66 S ATOM 28602 SG CYS I 29 41.861 120.645 130.054 1.00234.20 S ATOM 28626 SG CYS I 32 42.611 123.999 131.519 1.00231.84 S ATOM 28953 SG CYS I 75 15.824 114.719 90.033 1.00221.20 S ATOM 28975 SG CYS I 78 15.620 118.324 89.091 1.00233.29 S ATOM 29191 SG CYS I 103 18.805 116.415 88.321 1.00220.82 S ATOM 29211 SG CYS I 106 17.956 117.198 91.942 1.00221.22 S ATOM 29313 SG CYS J 7 62.802 89.454 37.728 1.00118.04 S ATOM 29336 SG CYS J 10 62.385 87.220 34.663 1.00109.73 S ATOM 29616 SG CYS J 45 59.340 88.154 36.766 1.00120.66 S ATOM 29622 SG CYS J 46 61.029 90.575 34.415 1.00122.16 S ATOM 30745 SG CYS L 31 96.121 112.888 53.746 1.00197.93 S ATOM 30765 SG CYS L 34 97.168 114.778 50.622 1.00202.08 S ATOM 30869 SG CYS L 48 99.711 113.653 53.365 1.00204.82 S ATOM 30892 SG CYS L 51 97.392 116.576 53.872 1.00207.59 S Time building chain proxies: 5.77, per 1000 atoms: 0.17 Number of scatterers: 33083 At special positions: 0 Unit cell: (151.241, 153.417, 183.883, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 8 29.99 S 182 16.00 P 100 15.00 Mg 2 11.99 O 6465 8.00 N 5765 7.00 C 20561 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.28 Conformation dependent library (CDL) restraints added in 1.1 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 110 " pdb="ZN ZN A1805 " - pdb=" SG CYS A 148 " pdb="ZN ZN A1805 " - pdb=" SG CYS A 167 " pdb=" ZN B1301 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1166 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1163 " 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 86 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 92 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 95 " pdb=" ZN I 201 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 10 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 32 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 29 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 7 " pdb=" ZN I 202 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 75 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 78 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 103 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 106 " pdb=" ZN J 101 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 10 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 46 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 45 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 7 " pdb=" ZN L 101 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 48 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 31 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 51 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 34 " Number of angles added : 45 7708 Ramachandran restraints generated. 3854 Oldfield, 0 Emsley, 3854 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7340 Finding SS restraints... Secondary structure from input PDB file: 145 helices and 45 sheets defined 39.2% alpha, 19.8% beta 42 base pairs and 80 stacking pairs defined. Time for finding SS restraints: 3.51 Creating SS restraints... Processing helix chain 'A' and resid 23 through 31 Processing helix chain 'A' and resid 92 through 94 No H-bonds generated for 'chain 'A' and resid 92 through 94' Processing helix chain 'A' and resid 95 through 106 Processing helix chain 'A' and resid 119 through 127 removed outlier: 3.515A pdb=" N ALA A 127 " --> pdb=" O ARG A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 130 through 143 Processing helix chain 'A' and resid 203 through 212 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: 3.781A 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: 3.950A 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: 3.730A pdb=" N LEU A 528 " --> pdb=" O VAL A 524 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ARG A 532 " --> pdb=" O LEU A 528 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N LYS A 533 " --> pdb=" O CYS A 529 " (cutoff:3.500A) Processing helix chain 'A' and resid 542 through 553 removed outlier: 3.700A pdb=" N VAL A 553 " --> pdb=" O MET A 549 " (cutoff:3.500A) Processing helix chain 'A' and resid 574 through 579 Processing helix chain 'A' and resid 618 through 623 Processing helix chain 'A' and resid 628 through 637 Processing helix chain 'A' and resid 638 through 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 793 through 797 Processing helix chain 'A' and resid 809 through 829 removed outlier: 3.756A pdb=" N GLU A 822 " --> pdb=" O MET A 818 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N GLY A 823 " --> pdb=" O GLY A 819 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N LEU A 824 " --> pdb=" O GLY A 820 " (cutoff:3.500A) Processing helix chain 'A' and resid 830 through 845 removed outlier: 3.758A 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: 3.544A pdb=" N LEU A 920 " --> pdb=" O GLY A 916 " (cutoff:3.500A) Processing helix chain 'A' and resid 923 through 947 Processing helix chain 'A' and resid 959 through 972 Processing helix chain 'A' and resid 982 through 994 removed outlier: 3.539A pdb=" N GLN A 994 " --> pdb=" O VAL A 990 " (cutoff:3.500A) Processing helix chain 'A' and resid 1004 through 1015 Processing helix chain 'A' and resid 1015 through 1026 Processing helix chain 'A' and resid 1027 through 1034 Processing helix chain 'A' and resid 1038 through 1057 Processing helix chain 'A' and resid 1063 through 1083 removed outlier: 3.609A pdb=" N GLU A1074 " --> pdb=" O GLN A1070 " (cutoff:3.500A) Proline residue: A1075 - end of helix Processing helix chain 'A' and resid 1084 through 1086 No H-bonds generated for 'chain 'A' and resid 1084 through 1086' Processing helix chain 'A' and resid 1091 through 1106 removed outlier: 4.858A 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 1143 through 1145 No H-bonds generated for 'chain 'A' and resid 1143 through 1145' Processing helix chain 'A' and resid 1166 through 1174 removed outlier: 4.255A 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 1221 Processing helix chain 'A' and resid 1257 through 1270 Processing helix chain 'A' and resid 1312 through 1317 removed outlier: 3.755A pdb=" N MET A1317 " --> pdb=" O LEU A1313 " (cutoff:3.500A) Processing helix chain 'A' and resid 1331 through 1340 Processing helix chain 'A' and resid 1340 through 1357 Processing helix chain 'A' and resid 1364 through 1376 removed outlier: 3.956A pdb=" N MET A1368 " --> pdb=" O ASN A1364 " (cutoff:3.500A) Processing helix chain 'A' and resid 1388 through 1392 Processing helix chain 'A' and resid 1395 through 1400 Processing helix chain 'A' and resid 1404 through 1416 Processing helix chain 'A' and resid 1423 through 1431 removed outlier: 3.635A pdb=" N ASN A1427 " --> pdb=" O GLY A1423 " (cutoff:3.500A) Processing helix chain 'A' and resid 1436 through 1439 Processing helix chain 'A' and resid 1447 through 1452 removed outlier: 3.580A pdb=" N LYS A1452 " --> pdb=" O GLU A1448 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 37 removed outlier: 4.139A pdb=" N VAL B 33 " --> pdb=" O ASP B 29 " (cutoff:3.500A) Processing helix chain 'B' and resid 44 through 66 removed outlier: 4.695A pdb=" N LEU B 59 " --> pdb=" O VAL B 55 " (cutoff:3.500A) removed outlier: 5.446A pdb=" N GLN B 60 " --> pdb=" O ASP B 56 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N ASP B 66 " --> pdb=" O ILE B 62 " (cutoff:3.500A) Processing helix chain 'B' and resid 79 through 82 Processing helix chain 'B' and resid 113 through 120 Processing helix chain 'B' and resid 160 through 162 No H-bonds generated for 'chain 'B' and resid 160 through 162' Processing helix chain 'B' and resid 185 through 192 Processing helix chain 'B' and resid 282 through 290 Processing helix chain 'B' and resid 293 through 303 removed outlier: 3.625A pdb=" N ILE B 297 " --> pdb=" O PRO B 293 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LEU B 298 " --> pdb=" O ASP B 294 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N GLU B 299 " --> pdb=" O GLY B 295 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N TYR B 303 " --> pdb=" O GLU B 299 " (cutoff:3.500A) Processing helix chain 'B' and resid 308 through 321 Proline residue: B 316 - end of helix Processing helix chain 'B' and resid 326 through 338 Processing helix chain 'B' and resid 344 through 359 Processing helix chain 'B' and resid 370 through 390 Processing helix chain 'B' and resid 400 through 402 No H-bonds generated for 'chain 'B' and resid 400 through 402' Processing helix chain 'B' and resid 408 through 438 Processing helix chain 'B' and resid 443 through 448 Processing helix chain 'B' and resid 450 through 464 removed outlier: 3.783A pdb=" N THR B 454 " --> pdb=" O ALA B 450 " (cutoff:3.500A) Processing helix chain 'B' and resid 487 through 496 removed outlier: 3.627A pdb=" N ARG B 496 " --> pdb=" O LEU B 492 " (cutoff:3.500A) Processing helix chain 'B' and resid 515 through 519 Processing helix chain 'B' and resid 551 through 561 Processing helix chain 'B' and resid 567 through 569 No H-bonds generated for 'chain 'B' and resid 567 through 569' Processing helix chain 'B' and resid 592 through 607 Processing helix chain 'B' and resid 654 through 667 Processing helix chain 'B' and resid 680 through 687 Processing helix chain 'B' and resid 696 through 701 removed outlier: 3.829A pdb=" N ILE B 701 " --> pdb=" O GLU B 698 " (cutoff:3.500A) Processing helix chain 'B' and resid 706 through 710 Processing helix chain 'B' and resid 744 through 749 removed outlier: 3.610A 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: 3.702A pdb=" N ASN B 762 " --> pdb=" O PRO B 759 " (cutoff:3.500A) Processing helix chain 'B' and resid 763 through 775 removed outlier: 3.871A pdb=" N LYS B 775 " --> pdb=" O SER B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 784 through 788 removed outlier: 3.561A pdb=" N ARG B 788 " --> pdb=" O TYR B 785 " (cutoff:3.500A) Processing helix chain 'B' and resid 806 through 812 removed outlier: 3.661A pdb=" N GLU B 810 " --> pdb=" O ARG B 807 " (cutoff:3.500A) Processing helix chain 'B' and resid 843 through 849 Processing helix chain 'B' and resid 1015 through 1021 removed outlier: 4.292A pdb=" N SER B1019 " --> pdb=" O HIS B1015 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ARG B1020 " --> pdb=" O ALA B1016 " (cutoff:3.500A) Processing helix chain 'B' and resid 1022 through 1039 removed outlier: 3.716A pdb=" N LEU B1026 " --> pdb=" O THR B1022 " (cutoff:3.500A) Processing helix chain 'B' and resid 1051 through 1061 removed outlier: 3.514A 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 removed outlier: 3.512A pdb=" N ALA C 30 " --> pdb=" O ASP C 26 " (cutoff:3.500A) Processing helix chain 'C' and resid 59 through 69 removed outlier: 3.585A pdb=" N LEU C 69 " --> pdb=" O HIS C 65 " (cutoff:3.500A) Processing helix chain 'C' and resid 76 through 80 removed outlier: 3.543A pdb=" N GLN C 79 " --> pdb=" O ASP C 76 " (cutoff:3.500A) 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: 4.098A 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 'D' and resid 30 through 34 removed outlier: 3.656A pdb=" N GLN D 34 " --> pdb=" O GLN D 31 " (cutoff:3.500A) Processing helix chain 'D' and resid 51 through 73 Processing helix chain 'D' and resid 118 through 134 Processing helix chain 'D' and resid 138 through 151 Processing helix chain 'D' and resid 156 through 169 removed outlier: 3.800A pdb=" N VAL D 160 " --> pdb=" O ASP D 156 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N SER D 169 " --> pdb=" O GLN D 165 " (cutoff:3.500A) Processing helix chain 'D' and resid 173 through 183 removed outlier: 3.751A pdb=" N GLY D 181 " --> pdb=" O VAL D 177 " (cutoff:3.500A) Processing helix chain 'D' and resid 187 through 195 Processing helix chain 'D' and resid 196 through 199 Processing helix chain 'D' and resid 203 through 218 Processing helix chain 'E' and resid 5 through 27 removed outlier: 3.613A 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: 3.742A 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 92 through 104 Processing helix chain 'E' and resid 117 through 124 removed outlier: 3.510A pdb=" N MET E 121 " --> pdb=" O THR E 117 " (cutoff:3.500A) Processing helix chain 'E' and resid 138 through 141 removed outlier: 3.511A pdb=" N VAL E 141 " --> pdb=" O ALA E 138 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 138 through 141' Processing helix chain 'E' and resid 143 through 147 Processing helix chain 'E' and resid 157 through 168 Processing helix chain 'E' and resid 171 through 175 Processing helix chain 'E' and resid 182 through 189 Processing helix chain 'F' and resid 86 through 102 Processing helix chain 'F' and resid 116 through 127 Processing helix chain 'G' and resid 14 through 18 Processing helix chain 'G' and resid 21 through 35 Processing helix chain 'G' and resid 113 through 115 No H-bonds generated for 'chain 'G' and resid 113 through 115' Processing helix chain 'H' and resid 88 through 93 Processing helix chain 'I' and resid 59 through 65 removed outlier: 3.818A pdb=" N GLY I 63 " --> pdb=" O GLN I 60 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ASP I 65 " --> pdb=" O ILE I 62 " (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 52 removed outlier: 3.790A pdb=" N MET J 49 " --> pdb=" O CYS J 45 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ILE J 50 " --> pdb=" O CYS J 46 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N THR J 52 " --> pdb=" O ARG J 48 " (cutoff:3.500A) Processing helix chain 'J' and resid 56 through 61 Processing helix chain 'K' and resid 5 through 10 Processing helix chain 'K' and resid 39 through 52 removed outlier: 3.507A pdb=" N ASN K 44 " --> pdb=" O HIS K 40 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N LEU K 45 " --> pdb=" O THR K 41 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLU K 49 " --> pdb=" O LEU K 45 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ASN K 52 " --> pdb=" O ALA K 48 " (cutoff:3.500A) Processing helix chain 'K' and resid 82 through 110 Processing sheet with id=AA1, first strand: chain 'A' and resid 1418 through 1419 Processing sheet with id=AA2, first strand: chain 'A' and resid 82 through 90 removed outlier: 9.818A pdb=" N LEU A 86 " --> pdb=" O PRO A 240 " (cutoff:3.500A) removed outlier: 11.267A pdb=" N LYS A 88 " --> pdb=" O CYS A 238 " (cutoff:3.500A) removed outlier: 7.351A 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 Processing sheet with id=AA4, first strand: chain 'A' and resid 343 through 344 removed outlier: 3.531A pdb=" N LYS A 343 " --> pdb=" O PHE B1130 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 1104 through 1106 removed outlier: 3.987A pdb=" N THR A 351 " --> pdb=" O MET A 487 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N MET A 487 " --> pdb=" O THR A 351 " (cutoff:3.500A) removed outlier: 7.385A pdb=" N THR A 467 " --> pdb=" O PRO A 367 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LEU A 470 " --> pdb=" O SER A 354 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 375 through 379 removed outlier: 3.792A pdb=" N TYR A 404 " --> pdb=" O GLU A 433 " (cutoff:3.500A) removed outlier: 5.742A pdb=" N HIS A 435 " --> pdb=" O ALA A 402 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N ALA A 402 " --> pdb=" O HIS A 435 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 512 through 513 Processing sheet with id=AA8, first strand: chain 'A' and resid 540 through 541 Processing sheet with id=AA9, first strand: chain 'A' and resid 588 through 590 removed outlier: 7.079A pdb=" N LEU A 606 " --> pdb=" O ILE A 613 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 766 through 767 Processing sheet with id=AB2, first strand: chain 'A' and resid 849 through 850 Processing sheet with id=AB3, first strand: chain 'A' and resid 878 through 882 Processing sheet with id=AB4, first strand: chain 'A' and resid 1282 through 1292 removed outlier: 3.566A pdb=" N LEU A1116 " --> pdb=" O THR A1308 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 1224 through 1228 removed outlier: 4.239A pdb=" N LEU A1236 " --> pdb=" O LEU A1197 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N LEU A1192 " --> pdb=" O ILE A1152 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N ILE A1152 " --> pdb=" O LEU A1192 " (cutoff:3.500A) removed outlier: 6.927A 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: 6.433A pdb=" N GLU A1196 " --> pdb=" O ILE A1148 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N TYR I 44 " --> pdb=" O ILE A1152 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 48 through 50 removed outlier: 4.805A pdb=" N ILE D 48 " --> pdb=" O ILE G 4 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ILE G 4 " --> pdb=" O ILE D 48 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N PHE G 2 " --> pdb=" O LEU D 50 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLY G 59 " --> pdb=" O ILE A1445 " (cutoff:3.500A) removed outlier: 5.587A pdb=" N VAL A1443 " --> pdb=" O ILE G 61 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 48 through 50 removed outlier: 4.805A pdb=" N ILE D 48 " --> pdb=" O ILE G 4 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ILE G 4 " --> pdb=" O ILE D 48 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N PHE G 2 " --> pdb=" O LEU D 50 " (cutoff:3.500A) removed outlier: 7.172A pdb=" N ARG G 75 " --> pdb=" O VAL G 48 " (cutoff:3.500A) removed outlier: 5.244A pdb=" N VAL G 48 " --> pdb=" O ARG G 75 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N VAL G 77 " --> pdb=" O LEU G 46 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 69 through 73 removed outlier: 5.290A pdb=" N ARG B 86 " --> pdb=" O ALA B 139 " (cutoff:3.500A) removed outlier: 7.127A pdb=" N ALA B 139 " --> pdb=" O ARG B 86 " (cutoff:3.500A) removed outlier: 5.101A pdb=" N TYR B 88 " --> pdb=" O TYR B 137 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N TYR B 137 " --> pdb=" O TYR B 88 " (cutoff:3.500A) removed outlier: 4.770A pdb=" N ILE B 90 " --> pdb=" O ARG B 135 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N ARG B 135 " --> pdb=" O ILE B 90 " (cutoff:3.500A) removed outlier: 5.310A pdb=" N PHE B 92 " --> pdb=" O LYS B 133 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N LYS B 133 " --> pdb=" O PHE B 92 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N LYS B 94 " --> pdb=" O ASP B 131 " (cutoff:3.500A) removed outlier: 4.898A pdb=" N GLY B 127 " --> pdb=" O THR B 98 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N SER B 125 " --> pdb=" O PRO B 100 " (cutoff:3.500A) removed outlier: 8.278A pdb=" N VAL B 132 " --> pdb=" O SER B 156 " (cutoff:3.500A) removed outlier: 5.901A pdb=" N SER B 156 " --> pdb=" O VAL B 132 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N LYS B 134 " --> pdb=" O GLU B 154 " (cutoff:3.500A) removed outlier: 4.878A pdb=" N GLU B 154 " --> pdb=" O LYS B 134 " (cutoff:3.500A) removed outlier: 7.732A pdb=" N THR B 136 " --> pdb=" O ILE B 152 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ILE B 152 " --> pdb=" O THR B 136 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 109 through 111 removed outlier: 5.290A pdb=" N ARG B 86 " --> pdb=" O ALA B 139 " (cutoff:3.500A) removed outlier: 7.127A pdb=" N ALA B 139 " --> pdb=" O ARG B 86 " (cutoff:3.500A) removed outlier: 5.101A pdb=" N TYR B 88 " --> pdb=" O TYR B 137 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N TYR B 137 " --> pdb=" O TYR B 88 " (cutoff:3.500A) removed outlier: 4.770A pdb=" N ILE B 90 " --> pdb=" O ARG B 135 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N ARG B 135 " --> pdb=" O ILE B 90 " (cutoff:3.500A) removed outlier: 5.310A pdb=" N PHE B 92 " --> pdb=" O LYS B 133 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N LYS B 133 " --> pdb=" O PHE B 92 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N LYS B 94 " --> pdb=" O ASP B 131 " (cutoff:3.500A) removed outlier: 4.898A pdb=" N GLY B 127 " --> pdb=" O THR B 98 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N SER B 125 " --> pdb=" O PRO B 100 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N GLY B 168 " --> pdb=" O LEU B 128 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N VAL B 130 " --> pdb=" O PHE B 166 " (cutoff:3.500A) removed outlier: 5.738A pdb=" N PHE B 166 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 7.193A pdb=" N VAL B 132 " --> pdb=" O LYS B 164 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N LYS B 164 " --> pdb=" O VAL B 132 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 203 through 205 Processing sheet with id=AC2, first strand: chain 'B' and resid 404 through 407 removed outlier: 6.066A pdb=" N ALA B 214 " --> pdb=" O ASN B 499 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 224 through 227 removed outlier: 4.118A pdb=" N HIS B 236 " --> pdb=" O LEU B 258 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N GLN B 255 " --> pdb=" O THR B 272 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 544 through 545 Processing sheet with id=AC5, first strand: chain 'B' and resid 650 through 651 Processing sheet with id=AC6, first strand: chain 'B' and resid 564 through 565 removed outlier: 5.239A pdb=" N TRP B 586 " --> pdb=" O VAL B 582 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N VAL B 582 " --> pdb=" O TRP B 586 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N GLY B 588 " --> pdb=" O VAL B 580 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N ARG B 579 " --> pdb=" O LEU B 624 " (cutoff:3.500A) removed outlier: 7.699A pdb=" N ILE B 626 " --> pdb=" O ARG B 579 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N PHE B 581 " --> pdb=" O ILE B 626 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 792 through 796 removed outlier: 3.587A pdb=" N ILE B 795 " --> pdb=" O LEU B 854 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLN B 951 " --> pdb=" O ARG B 967 " (cutoff:3.500A) removed outlier: 5.940A pdb=" N ARG B 969 " --> pdb=" O VAL B 949 " (cutoff:3.500A) removed outlier: 5.494A pdb=" N VAL B 949 " --> pdb=" O ARG B 969 " (cutoff:3.500A) removed outlier: 8.488A pdb=" N THR B 971 " --> pdb=" O GLY B 947 " (cutoff:3.500A) removed outlier: 8.083A pdb=" N GLY B 947 " --> pdb=" O THR B 971 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 792 through 796 removed outlier: 3.587A pdb=" N ILE B 795 " --> pdb=" O LEU B 854 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLN B 951 " --> pdb=" O ARG B 967 " (cutoff:3.500A) removed outlier: 5.940A pdb=" N ARG B 969 " --> pdb=" O VAL B 949 " (cutoff:3.500A) removed outlier: 5.494A pdb=" N VAL B 949 " --> pdb=" O ARG B 969 " (cutoff:3.500A) removed outlier: 8.488A pdb=" N THR B 971 " --> pdb=" O GLY B 947 " (cutoff:3.500A) removed outlier: 8.083A pdb=" N GLY B 947 " --> pdb=" O THR B 971 " (cutoff:3.500A) removed outlier: 5.172A pdb=" N VAL B 952 " --> pdb=" O LYS L 58 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 804 through 805 Processing sheet with id=AD1, first strand: chain 'B' and resid 1069 through 1070 removed outlier: 7.164A pdb=" N MET B 839 " --> pdb=" O GLY B 991 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N THR B 993 " --> pdb=" O MET B 839 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N MET B 841 " --> pdb=" O THR B 993 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ILE B1012 " --> pdb=" O ALA B 826 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N PHE B1086 " --> pdb=" O ILE B 827 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 873 through 874 Processing sheet with id=AD3, first strand: chain 'B' and resid 910 through 912 removed outlier: 3.697A pdb=" N ILE B 912 " --> pdb=" O THR B 939 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 1158 through 1163 Processing sheet with id=AD5, first strand: chain 'B' and resid 1172 through 1174 removed outlier: 3.600A pdb=" N GLU B1181 " --> pdb=" O ILE B1172 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 10 through 13 removed outlier: 6.836A pdb=" N ASP C 19 " --> pdb=" O ARG C 11 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N ALA C 13 " --> pdb=" O ASN C 17 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N ASN C 17 " --> pdb=" O ALA C 13 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 119 through 120 removed outlier: 6.744A pdb=" N GLU C 152 " --> pdb=" O THR C 53 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N THR C 53 " --> pdb=" O GLU C 152 " (cutoff:3.500A) removed outlier: 7.557A pdb=" N LYS C 154 " --> pdb=" O VAL C 51 " (cutoff:3.500A) removed outlier: 4.807A pdb=" N VAL C 51 " --> pdb=" O LYS C 154 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N THR C 156 " --> pdb=" O VAL C 49 " (cutoff:3.500A) removed outlier: 4.648A pdb=" N VAL C 49 " --> pdb=" O THR C 156 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N VAL C 158 " --> pdb=" O ASP C 47 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ALA C 45 " --> pdb=" O LYS C 160 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N VAL C 51 " --> pdb=" O VAL L 65 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N VAL L 65 " --> pdb=" O VAL C 51 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 111 through 114 removed outlier: 6.523A pdb=" N THR C 111 " --> pdb=" O LYS C 146 " (cutoff:3.500A) removed outlier: 4.701A pdb=" N LYS C 146 " --> pdb=" O THR C 111 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N VAL C 113 " --> pdb=" O ILE C 144 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'D' and resid 36 through 38 Processing sheet with id=AE1, first strand: chain 'E' and resid 47 through 48 removed outlier: 4.925A pdb=" N ARG E 52 " --> pdb=" O ASP E 48 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'E' and resid 60 through 62 removed outlier: 6.466A pdb=" N TRP E 79 " --> pdb=" O ILE E 109 " (cutoff:3.500A) removed outlier: 7.544A pdb=" N VAL E 111 " --> pdb=" O TRP E 79 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N GLU E 81 " --> pdb=" O VAL E 111 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'E' and resid 152 through 155 removed outlier: 3.755A pdb=" N LYS E 152 " --> pdb=" O ILE E 199 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'G' and resid 169 through 170 removed outlier: 6.281A pdb=" N ILE G 160 " --> pdb=" O GLU G 148 " (cutoff:3.500A) removed outlier: 4.775A pdb=" N CYS G 150 " --> pdb=" O HIS G 158 " (cutoff:3.500A) removed outlier: 7.167A pdb=" N HIS G 158 " --> pdb=" O CYS G 150 " (cutoff:3.500A) removed outlier: 7.470A pdb=" N LYS G 107 " --> pdb=" O ALA G 159 " (cutoff:3.500A) removed outlier: 8.058A pdb=" N GLY G 161 " --> pdb=" O LYS G 107 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N PHE G 109 " --> pdb=" O GLY G 161 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N GLY G 98 " --> pdb=" O CYS G 94 " (cutoff:3.500A) removed outlier: 4.801A pdb=" N CYS G 94 " --> pdb=" O GLY G 98 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N GLU G 100 " --> pdb=" O VAL G 92 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'G' and resid 120 through 122 removed outlier: 3.749A pdb=" N SER G 129 " --> pdb=" O ASN G 122 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N TYR G 130 " --> pdb=" O ILE G 137 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'H' and resid 4 through 16 removed outlier: 6.752A pdb=" N GLU H 27 " --> pdb=" O SER H 13 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N VAL H 15 " --> pdb=" O ARG H 25 " (cutoff:3.500A) removed outlier: 6.007A pdb=" N ARG H 25 " --> pdb=" O VAL H 15 " (cutoff:3.500A) removed outlier: 5.853A pdb=" N LEU H 122 " --> pdb=" O ASP H 41 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LYS H 103 " --> pdb=" O TYR H 115 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N SER H 117 " --> pdb=" O ALA H 101 " (cutoff:3.500A) removed outlier: 5.450A pdb=" N ALA H 101 " --> pdb=" O SER H 117 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLY H 99 " --> pdb=" O ALA H 140 " (cutoff:3.500A) removed outlier: 6.054A pdb=" N LEU H 55 " --> pdb=" O ILE H 9 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N ILE H 9 " --> pdb=" O LEU H 55 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N VAL H 57 " --> pdb=" O ASP H 7 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N ASP H 7 " --> pdb=" O VAL H 57 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N ILE H 59 " --> pdb=" O LEU H 5 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'I' and resid 15 through 19 Processing sheet with id=AE8, first strand: chain 'I' and resid 70 through 71 removed outlier: 4.216A pdb=" N ASN I 83 " --> pdb=" O SER I 71 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N HIS I 108 " --> pdb=" O CYS I 103 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'K' and resid 21 through 23 1336 hydrogen bonds defined for protein. 3660 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 108 hydrogen bonds 216 hydrogen bond angles 0 basepair planarities 42 basepair parallelities 80 stacking parallelities Total time for adding SS restraints: 9.41 Time building geometry restraints manager: 2.98 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: 5408 1.31 - 1.43: 8966 1.43 - 1.56: 19011 1.56 - 1.69: 196 1.69 - 1.81: 292 Bond restraints: 33873 Sorted by residual: bond pdb=" C4 ATP A1801 " pdb=" N9 ATP A1801 " ideal model delta sigma weight residual 1.374 1.182 0.192 1.00e-02 1.00e+04 3.70e+02 bond pdb=" C8 ATP A1801 " pdb=" N9 ATP A1801 " ideal model delta sigma weight residual 1.370 1.209 0.161 1.20e-02 6.94e+03 1.81e+02 bond pdb=" C6 ATP A1801 " pdb=" N6 ATP A1801 " ideal model delta sigma weight residual 1.337 1.446 -0.109 1.10e-02 8.26e+03 9.87e+01 bond pdb=" C5 ATP A1801 " pdb=" C6 ATP A1801 " ideal model delta sigma weight residual 1.409 1.331 0.078 1.00e-02 1.00e+04 6.13e+01 bond pdb=" C2' ATP A1801 " pdb=" C3' ATP A1801 " ideal model delta sigma weight residual 1.531 1.454 0.077 1.20e-02 6.94e+03 4.14e+01 ... (remaining 33868 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.34: 46051 4.34 - 8.69: 97 8.69 - 13.03: 2 13.03 - 17.37: 2 17.37 - 21.72: 1 Bond angle restraints: 46153 Sorted by residual: angle pdb=" PB ATP A1801 " pdb=" O3B ATP A1801 " pdb=" PG ATP A1801 " ideal model delta sigma weight residual 139.87 118.15 21.72 1.00e+00 1.00e+00 4.72e+02 angle pdb=" PA ATP A1801 " pdb=" O3A ATP A1801 " pdb=" PB ATP A1801 " ideal model delta sigma weight residual 136.83 121.61 15.22 1.00e+00 1.00e+00 2.32e+02 angle pdb=" C4 ATP A1801 " pdb=" N9 ATP A1801 " pdb=" C8 ATP A1801 " ideal model delta sigma weight residual 105.72 119.24 -13.52 1.00e+00 1.00e+00 1.83e+02 angle pdb=" N1 ATP A1801 " pdb=" C2 ATP A1801 " pdb=" N3 ATP A1801 " ideal model delta sigma weight residual 128.69 120.35 8.34 1.00e+00 1.00e+00 6.96e+01 angle pdb=" C GLN A 525 " pdb=" CA GLN A 525 " pdb=" CB GLN A 525 " ideal model delta sigma weight residual 116.63 110.28 6.35 1.16e+00 7.43e-01 2.99e+01 ... (remaining 46148 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.26: 19885 34.26 - 68.51: 539 68.51 - 102.77: 39 102.77 - 137.02: 3 137.02 - 171.28: 1 Dihedral angle restraints: 20467 sinusoidal: 9132 harmonic: 11335 Sorted by residual: dihedral pdb=" CA THR A 69 " pdb=" C THR A 69 " pdb=" N CYS A 70 " pdb=" CA CYS A 70 " ideal model delta harmonic sigma weight residual 180.00 155.92 24.08 0 5.00e+00 4.00e-02 2.32e+01 dihedral pdb=" CA HIS A1173 " pdb=" C HIS A1173 " pdb=" N PHE A1174 " pdb=" CA PHE A1174 " ideal model delta harmonic sigma weight residual 180.00 159.53 20.47 0 5.00e+00 4.00e-02 1.68e+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 31.28 -171.28 1 3.50e+01 8.16e-04 1.56e+01 ... (remaining 20464 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 3553 0.036 - 0.071: 1101 0.071 - 0.107: 393 0.107 - 0.143: 136 0.143 - 0.179: 7 Chirality restraints: 5190 Sorted by residual: chirality pdb=" C3' DG N 58 " pdb=" C4' DG N 58 " pdb=" O3' DG N 58 " pdb=" C2' DG N 58 " both_signs ideal model delta sigma weight residual False -2.73 -2.91 0.18 2.00e-01 2.50e+01 7.98e-01 chirality pdb=" C1' A R 1 " pdb=" O4' A R 1 " pdb=" C2' A R 1 " pdb=" N9 A R 1 " both_signs ideal model delta sigma weight residual False 2.47 2.30 0.17 2.00e-01 2.50e+01 7.40e-01 chirality pdb=" C2' G R 9 " pdb=" C3' G R 9 " pdb=" O2' G R 9 " pdb=" C1' G R 9 " both_signs ideal model delta sigma weight residual False -2.62 -2.78 0.16 2.00e-01 2.50e+01 6.77e-01 ... (remaining 5187 not shown) Planarity restraints: 5630 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU A 710 " -0.016 2.00e-02 2.50e+03 3.20e-02 1.02e+01 pdb=" C LEU A 710 " 0.055 2.00e-02 2.50e+03 pdb=" O LEU A 710 " -0.021 2.00e-02 2.50e+03 pdb=" N ARG A 711 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL A1098 " 0.039 5.00e-02 4.00e+02 5.91e-02 5.59e+00 pdb=" N PRO A1099 " -0.102 5.00e-02 4.00e+02 pdb=" CA PRO A1099 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO A1099 " 0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 809 " -0.033 5.00e-02 4.00e+02 5.05e-02 4.07e+00 pdb=" N PRO A 810 " 0.087 5.00e-02 4.00e+02 pdb=" CA PRO A 810 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 810 " -0.028 5.00e-02 4.00e+02 ... (remaining 5627 not shown) Histogram of nonbonded interaction distances: 1.74 - 2.37: 88 2.37 - 3.00: 17817 3.00 - 3.64: 49305 3.64 - 4.27: 75753 4.27 - 4.90: 127240 Nonbonded interactions: 270203 Sorted by model distance: nonbonded pdb=" O2A ATP A1801 " pdb="MG MG A1802 " model vdw 1.740 2.170 nonbonded pdb=" O2B ATP A1801 " pdb="MG MG A1802 " model vdw 1.826 2.170 nonbonded pdb=" OD2 ASP A 481 " pdb="MG MG A1802 " model vdw 1.907 2.170 nonbonded pdb=" O2G ATP A1801 " pdb="MG MG A1802 " model vdw 1.926 2.170 nonbonded pdb=" OD1 ASP A 483 " pdb="MG MG A1803 " model vdw 2.020 2.170 ... (remaining 270198 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.060 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.520 Check model and map are aligned: 0.110 Set scattering table: 0.080 Process input model: 34.960 Find NCS groups from input model: 0.130 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: 0.010 Load rotamer database and sin/cos tables:1.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8360 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 0.192 33905 Z= 0.307 Angle : 0.612 21.718 46198 Z= 0.416 Chirality : 0.042 0.179 5190 Planarity : 0.004 0.060 5630 Dihedral : 14.590 171.276 13127 Min Nonbonded Distance : 1.740 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.14 % Favored : 96.73 % Rotamer: Outliers : 0.00 % Allowed : 0.12 % Favored : 99.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.54 (0.14), residues: 3854 helix: 1.68 (0.15), residues: 1296 sheet: 0.01 (0.21), residues: 621 loop : -0.39 (0.15), residues: 1937 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A1366 TYR 0.028 0.001 TYR B 797 PHE 0.015 0.001 PHE A 219 TRP 0.011 0.001 TRP A1044 HIS 0.009 0.001 HIS A 287 Details of bonding type rmsd/Z covalent geometry : bond 0.00411 / 0.31 (33873) covalent geometry : angle 0.60610 / 0.42 (46153) hydrogen bonds : bond 0.18860 / 12.19 ( 1411) hydrogen bonds : angle 6.74916 / 4.83 ( 3876) metal coordination : bond 0.00434 / 0.28 ( 32) metal coordination : angle 2.67288 / 1.99 ( 45) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7708 Ramachandran restraints generated. 3854 Oldfield, 0 Emsley, 3854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7708 Ramachandran restraints generated. 3854 Oldfield, 0 Emsley, 3854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 757 residues out of total 3434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 757 time to evaluate : 1.254 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 109 HIS cc_start: 0.9004 (t-90) cc_final: 0.8772 (t-170) REVERT: A 542 GLU cc_start: 0.8376 (mt-10) cc_final: 0.8056 (mt-10) REVERT: A 681 GLU cc_start: 0.8359 (mt-10) cc_final: 0.8130 (pt0) REVERT: A 708 MET cc_start: 0.8954 (mtt) cc_final: 0.8663 (ttm) REVERT: A 880 LYS cc_start: 0.9413 (tttt) cc_final: 0.9147 (ttmm) REVERT: A 934 LYS cc_start: 0.8858 (tttm) cc_final: 0.8523 (mmtm) REVERT: A 961 ARG cc_start: 0.8551 (ttm-80) cc_final: 0.8302 (ttp-170) REVERT: A 1195 LEU cc_start: 0.8586 (mp) cc_final: 0.8297 (mt) REVERT: A 1196 GLU cc_start: 0.8957 (mt-10) cc_final: 0.8680 (mp0) REVERT: A 1205 LYS cc_start: 0.9014 (mtpp) cc_final: 0.8725 (tptp) REVERT: A 1267 MET cc_start: 0.8750 (mtm) cc_final: 0.8454 (mtp) REVERT: A 1411 GLU cc_start: 0.8439 (tp30) cc_final: 0.8159 (tp30) REVERT: B 71 LEU cc_start: 0.7755 (tp) cc_final: 0.7218 (tt) REVERT: B 216 GLU cc_start: 0.8805 (tt0) cc_final: 0.8206 (tt0) REVERT: B 244 LEU cc_start: 0.8609 (mp) cc_final: 0.8066 (tp) REVERT: B 278 GLN cc_start: 0.8434 (mp10) cc_final: 0.8139 (mt0) REVERT: B 326 ASP cc_start: 0.8434 (t70) cc_final: 0.7845 (t70) REVERT: B 347 LYS cc_start: 0.8725 (mmmm) cc_final: 0.8405 (tptt) REVERT: B 349 ILE cc_start: 0.7683 (mm) cc_final: 0.7146 (tt) REVERT: B 353 LYS cc_start: 0.8442 (mtpt) cc_final: 0.7988 (mtmm) REVERT: B 354 ASP cc_start: 0.8573 (m-30) cc_final: 0.8251 (m-30) REVERT: B 391 ASP cc_start: 0.8753 (m-30) cc_final: 0.8465 (m-30) REVERT: B 451 LYS cc_start: 0.9198 (mtmt) cc_final: 0.8950 (mtpp) REVERT: B 455 SER cc_start: 0.8736 (t) cc_final: 0.8463 (p) REVERT: B 476 ARG cc_start: 0.8118 (ttp-170) cc_final: 0.7491 (ptm160) REVERT: B 622 LYS cc_start: 0.9006 (mttt) cc_final: 0.8631 (mttm) REVERT: B 841 MET cc_start: 0.9409 (ttm) cc_final: 0.9180 (ttm) REVERT: B 863 GLU cc_start: 0.7354 (mt-10) cc_final: 0.7087 (mt-10) REVERT: B 939 THR cc_start: 0.8939 (m) cc_final: 0.8350 (p) REVERT: B 1049 ASP cc_start: 0.8596 (m-30) cc_final: 0.8256 (p0) REVERT: B 1152 MET cc_start: 0.8799 (mmm) cc_final: 0.8579 (mmm) REVERT: B 1206 GLU cc_start: 0.8996 (mt-10) cc_final: 0.8705 (mt-10) REVERT: C 224 GLN cc_start: 0.8283 (mt0) cc_final: 0.7906 (mm-40) REVERT: D 23 ASN cc_start: 0.8567 (t0) cc_final: 0.8300 (t0) REVERT: D 54 GLU cc_start: 0.9075 (tt0) cc_final: 0.8851 (mm-30) REVERT: D 68 ARG cc_start: 0.8803 (mtt180) cc_final: 0.8545 (tpt-90) REVERT: D 71 LYS cc_start: 0.7679 (mttt) cc_final: 0.7433 (mmtm) REVERT: D 139 LYS cc_start: 0.8039 (tttt) cc_final: 0.7730 (tptp) REVERT: D 145 MET cc_start: 0.8585 (mmm) cc_final: 0.8277 (mmm) REVERT: D 165 GLN cc_start: 0.8677 (tm-30) cc_final: 0.8316 (tp-100) REVERT: D 204 ASP cc_start: 0.8196 (m-30) cc_final: 0.7626 (t70) REVERT: E 8 ASN cc_start: 0.8974 (m-40) cc_final: 0.8688 (m-40) REVERT: E 31 THR cc_start: 0.8751 (p) cc_final: 0.8428 (p) REVERT: E 48 ASP cc_start: 0.7854 (t70) cc_final: 0.7524 (t70) REVERT: E 56 LYS cc_start: 0.9457 (tmmt) cc_final: 0.9177 (tppt) REVERT: E 57 MET cc_start: 0.9103 (mtm) cc_final: 0.8836 (ttt) REVERT: E 106 GLN cc_start: 0.8425 (mm-40) cc_final: 0.7862 (tt0) REVERT: E 179 GLN cc_start: 0.8956 (mt0) cc_final: 0.8620 (mt0) REVERT: E 192 ARG cc_start: 0.9013 (ttt180) cc_final: 0.8774 (ttm110) REVERT: E 201 LYS cc_start: 0.9217 (mtmt) cc_final: 0.8836 (ptpp) REVERT: F 77 ASP cc_start: 0.8857 (m-30) cc_final: 0.8646 (m-30) REVERT: F 78 GLN cc_start: 0.8725 (mt0) cc_final: 0.8516 (mt0) REVERT: F 89 GLU cc_start: 0.9146 (mt-10) cc_final: 0.8763 (mt-10) REVERT: F 109 VAL cc_start: 0.8792 (t) cc_final: 0.8582 (m) REVERT: F 110 ASP cc_start: 0.8640 (p0) cc_final: 0.7957 (p0) REVERT: F 127 GLU cc_start: 0.8409 (mt-10) cc_final: 0.8076 (mt-10) REVERT: F 143 PHE cc_start: 0.9277 (p90) cc_final: 0.8847 (p90) REVERT: F 150 GLU cc_start: 0.8793 (pt0) cc_final: 0.8583 (pt0) REVERT: F 152 ILE cc_start: 0.9045 (mt) cc_final: 0.8836 (mp) REVERT: G 4 ILE cc_start: 0.8648 (mt) cc_final: 0.8385 (tp) REVERT: G 25 TYR cc_start: 0.9171 (t80) cc_final: 0.8915 (t80) REVERT: G 28 THR cc_start: 0.8874 (m) cc_final: 0.8495 (p) REVERT: G 32 GLU cc_start: 0.8918 (mt-10) cc_final: 0.8540 (mt-10) REVERT: G 33 GLU cc_start: 0.8592 (mm-30) cc_final: 0.8386 (mm-30) REVERT: G 69 GLU cc_start: 0.8569 (tt0) cc_final: 0.8172 (tt0) REVERT: G 83 LYS cc_start: 0.7525 (tttt) cc_final: 0.6998 (mppt) REVERT: G 112 LYS cc_start: 0.5644 (ttmt) cc_final: 0.5206 (ptpp) REVERT: H 32 THR cc_start: 0.8837 (m) cc_final: 0.8605 (p) REVERT: H 33 GLN cc_start: 0.7733 (mm110) cc_final: 0.7383 (mm110) REVERT: H 37 LYS cc_start: 0.8870 (ptpt) cc_final: 0.8657 (pttm) REVERT: H 107 VAL cc_start: 0.8587 (t) cc_final: 0.8381 (t) REVERT: H 126 GLU cc_start: 0.8494 (tt0) cc_final: 0.8104 (tt0) REVERT: H 136 LYS cc_start: 0.8607 (mmtp) cc_final: 0.8061 (mttm) REVERT: H 138 GLU cc_start: 0.8671 (pt0) cc_final: 0.7821 (pm20) REVERT: I 22 ASN cc_start: 0.8414 (m110) cc_final: 0.8021 (p0) REVERT: I 34 TYR cc_start: 0.6704 (t80) cc_final: 0.6443 (t80) REVERT: J 26 GLN cc_start: 0.8746 (tt0) cc_final: 0.8024 (tm-30) REVERT: K 20 LYS cc_start: 0.9071 (tttp) cc_final: 0.8862 (ttmm) REVERT: K 36 GLU cc_start: 0.9301 (mm-30) cc_final: 0.9047 (tp30) REVERT: K 38 GLU cc_start: 0.8421 (mm-30) cc_final: 0.7928 (tp30) REVERT: K 54 ARG cc_start: 0.8866 (mtm180) cc_final: 0.8597 (mmm-85) REVERT: K 85 ASP cc_start: 0.8445 (m-30) cc_final: 0.8189 (m-30) REVERT: K 96 ASN cc_start: 0.8782 (m-40) cc_final: 0.8532 (m-40) outliers start: 0 outliers final: 0 residues processed: 757 average time/residue: 0.2293 time to fit residues: 269.5147 Evaluate side-chains 445 residues out of total 3434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 445 time to evaluate : 1.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 395 random chunks: chunk 197 optimal weight: 2.9990 chunk 388 optimal weight: 40.0000 chunk 215 optimal weight: 4.9990 chunk 20 optimal weight: 0.0970 chunk 132 optimal weight: 6.9990 chunk 261 optimal weight: 8.9990 chunk 248 optimal weight: 3.9990 chunk 207 optimal weight: 0.6980 chunk 155 optimal weight: 7.9990 chunk 244 optimal weight: 7.9990 chunk 183 optimal weight: 1.9990 overall best weight: 1.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 281 HIS ** A 603 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 851 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 975 HIS ** A1128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1173 HIS ** A1188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1270 ASN B 115 GLN ** B 740 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 984 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1093 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 31 GLN D 143 ASN ** D 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 89 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.109481 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.075653 restraints weight = 64185.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.079153 restraints weight = 30529.515| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.079699 restraints weight = 16392.325| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.079792 restraints weight = 15022.782| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.079928 restraints weight = 14593.021| |-----------------------------------------------------------------------------| r_work (final): 0.3001 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8596 moved from start: 0.1675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 33905 Z= 0.181 Angle : 0.620 11.939 46198 Z= 0.327 Chirality : 0.046 0.249 5190 Planarity : 0.005 0.063 5630 Dihedral : 16.799 168.793 5346 Min Nonbonded Distance : 1.876 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.53 % Favored : 96.32 % Rotamer: Outliers : 1.34 % Allowed : 6.58 % Favored : 92.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.40 (0.14), residues: 3854 helix: 1.49 (0.15), residues: 1336 sheet: -0.07 (0.21), residues: 597 loop : -0.46 (0.14), residues: 1921 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 119 TYR 0.022 0.001 TYR D 147 PHE 0.021 0.001 PHE A 219 TRP 0.011 0.001 TRP A1044 HIS 0.007 0.001 HIS A1173 Details of bonding type rmsd/Z covalent geometry : bond 0.00406 / 0.18 (33873) covalent geometry : angle 0.61186 / 0.33 (46153) hydrogen bonds : bond 0.04923 / 3.29 ( 1411) hydrogen bonds : angle 5.17761 / 3.70 ( 3876) metal coordination : bond 0.00742 / 0.48 ( 32) metal coordination : angle 3.34613 / 2.58 ( 45) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7708 Ramachandran restraints generated. 3854 Oldfield, 0 Emsley, 3854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7708 Ramachandran restraints generated. 3854 Oldfield, 0 Emsley, 3854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 516 residues out of total 3434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 470 time to evaluate : 1.229 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 MET cc_start: 0.8493 (mmm) cc_final: 0.8291 (mmm) REVERT: A 108 MET cc_start: 0.8755 (mmm) cc_final: 0.8497 (mmm) REVERT: A 109 HIS cc_start: 0.8687 (t-90) cc_final: 0.8448 (t-170) REVERT: A 800 VAL cc_start: 0.9396 (t) cc_final: 0.9187 (p) REVERT: A 1267 MET cc_start: 0.8592 (mtm) cc_final: 0.8278 (mtp) REVERT: B 71 LEU cc_start: 0.7702 (tp) cc_final: 0.7388 (tt) REVERT: B 216 GLU cc_start: 0.8193 (tt0) cc_final: 0.7597 (tt0) REVERT: B 244 LEU cc_start: 0.8639 (mp) cc_final: 0.8405 (tp) REVERT: B 313 MET cc_start: 0.9166 (mmm) cc_final: 0.8903 (mmm) REVERT: B 349 ILE cc_start: 0.7707 (mm) cc_final: 0.7488 (tt) REVERT: B 353 LYS cc_start: 0.8592 (mtpt) cc_final: 0.8273 (mtmm) REVERT: B 354 ASP cc_start: 0.8238 (m-30) cc_final: 0.7922 (m-30) REVERT: B 391 ASP cc_start: 0.8692 (m-30) cc_final: 0.8349 (m-30) REVERT: B 476 ARG cc_start: 0.8183 (ttp-170) cc_final: 0.7584 (ptm160) REVERT: B 764 SER cc_start: 0.8925 (m) cc_final: 0.8546 (t) REVERT: B 939 THR cc_start: 0.9152 (m) cc_final: 0.8647 (p) REVERT: B 1136 ASP cc_start: 0.8571 (m-30) cc_final: 0.8347 (m-30) REVERT: B 1152 MET cc_start: 0.8703 (mmm) cc_final: 0.8497 (mmm) REVERT: D 23 ASN cc_start: 0.8639 (t0) cc_final: 0.8330 (t0) REVERT: D 71 LYS cc_start: 0.7984 (mttt) cc_final: 0.7630 (mmtm) REVERT: D 119 ARG cc_start: 0.6975 (mmp80) cc_final: 0.6381 (mmp-170) REVERT: D 204 ASP cc_start: 0.8068 (m-30) cc_final: 0.7471 (t0) REVERT: E 8 ASN cc_start: 0.8794 (m-40) cc_final: 0.8537 (m-40) REVERT: E 74 ASP cc_start: 0.8041 (t0) cc_final: 0.7593 (t0) REVERT: E 84 ASP cc_start: 0.8212 (t0) cc_final: 0.7983 (t0) REVERT: E 179 GLN cc_start: 0.8807 (mt0) cc_final: 0.8493 (mt0) REVERT: F 89 GLU cc_start: 0.8796 (mt-10) cc_final: 0.8575 (mt-10) REVERT: F 109 VAL cc_start: 0.8786 (t) cc_final: 0.8445 (m) REVERT: F 110 ASP cc_start: 0.8491 (p0) cc_final: 0.7811 (p0) REVERT: F 127 GLU cc_start: 0.7917 (mt-10) cc_final: 0.7607 (mt-10) REVERT: F 143 PHE cc_start: 0.9336 (p90) cc_final: 0.8983 (p90) REVERT: G 28 THR cc_start: 0.8769 (m) cc_final: 0.8460 (p) REVERT: G 32 GLU cc_start: 0.8532 (mt-10) cc_final: 0.8247 (mt-10) REVERT: G 69 GLU cc_start: 0.7871 (tt0) cc_final: 0.7659 (tt0) REVERT: G 83 LYS cc_start: 0.7344 (tttt) cc_final: 0.6957 (mppt) REVERT: H 33 GLN cc_start: 0.7691 (mm110) cc_final: 0.7465 (mm110) REVERT: H 107 VAL cc_start: 0.8742 (t) cc_final: 0.8450 (t) REVERT: H 126 GLU cc_start: 0.7857 (tt0) cc_final: 0.7313 (tt0) REVERT: H 136 LYS cc_start: 0.8543 (mmtp) cc_final: 0.8102 (mmtt) REVERT: H 138 GLU cc_start: 0.8430 (pt0) cc_final: 0.7945 (pm20) REVERT: H 139 ASN cc_start: 0.9135 (m-40) cc_final: 0.8849 (m110) REVERT: K 38 GLU cc_start: 0.7820 (mm-30) cc_final: 0.7473 (tp30) REVERT: K 96 ASN cc_start: 0.8639 (m-40) cc_final: 0.8370 (m-40) outliers start: 46 outliers final: 31 residues processed: 501 average time/residue: 0.2241 time to fit residues: 177.4439 Evaluate side-chains 432 residues out of total 3434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 401 time to evaluate : 1.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 620 LYS Chi-restraints excluded: chain A residue 710 LEU Chi-restraints excluded: chain A residue 842 VAL Chi-restraints excluded: chain A residue 907 THR Chi-restraints excluded: chain A residue 1067 LEU Chi-restraints excluded: chain A residue 1174 PHE Chi-restraints excluded: chain A residue 1240 CYS Chi-restraints excluded: chain A residue 1381 LEU Chi-restraints excluded: chain A residue 1420 ASP Chi-restraints excluded: chain A residue 1428 VAL Chi-restraints excluded: chain B residue 70 ILE Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 337 ARG Chi-restraints excluded: chain B residue 339 THR Chi-restraints excluded: chain B residue 415 GLN Chi-restraints excluded: chain B residue 771 SER Chi-restraints excluded: chain B residue 963 PHE Chi-restraints excluded: chain B residue 1210 MET Chi-restraints excluded: chain C residue 163 ILE Chi-restraints excluded: chain D residue 4 SER Chi-restraints excluded: chain F residue 101 ILE Chi-restraints excluded: chain G residue 24 GLN Chi-restraints excluded: chain G residue 26 LEU Chi-restraints excluded: chain G residue 54 ILE Chi-restraints excluded: chain G residue 93 SER Chi-restraints excluded: chain H residue 44 VAL Chi-restraints excluded: chain I residue 1 MET Chi-restraints excluded: chain J residue 37 SER Chi-restraints excluded: chain K residue 5 ASP Chi-restraints excluded: chain K residue 77 THR Chi-restraints excluded: chain K residue 88 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 395 random chunks: chunk 242 optimal weight: 7.9990 chunk 191 optimal weight: 1.9990 chunk 5 optimal weight: 7.9990 chunk 373 optimal weight: 8.9990 chunk 22 optimal weight: 2.9990 chunk 333 optimal weight: 0.0570 chunk 304 optimal weight: 0.6980 chunk 239 optimal weight: 8.9990 chunk 7 optimal weight: 3.9990 chunk 249 optimal weight: 8.9990 chunk 222 optimal weight: 7.9990 overall best weight: 1.9504 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 603 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 757 ASN A 851 HIS A 996 ASN ** A1188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1203 ASN B 740 HIS B 763 GLN ** B 984 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1093 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 138 ASN D 173 HIS J 26 GLN ** K 2 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.111600 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.077803 restraints weight = 63882.612| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.081424 restraints weight = 30210.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.081731 restraints weight = 16130.439| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.081894 restraints weight = 14965.451| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.081966 restraints weight = 14504.369| |-----------------------------------------------------------------------------| r_work (final): 0.3038 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8615 moved from start: 0.2047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 33905 Z= 0.172 Angle : 0.583 11.608 46198 Z= 0.306 Chirality : 0.045 0.236 5190 Planarity : 0.004 0.049 5630 Dihedral : 16.677 168.722 5346 Min Nonbonded Distance : 1.876 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.66 % Favored : 96.21 % Rotamer: Outliers : 1.46 % Allowed : 8.91 % Favored : 89.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.38 (0.14), residues: 3854 helix: 1.47 (0.14), residues: 1332 sheet: -0.08 (0.21), residues: 601 loop : -0.47 (0.14), residues: 1921 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 21 TYR 0.018 0.001 TYR A 383 PHE 0.022 0.001 PHE A 219 TRP 0.010 0.001 TRP B 561 HIS 0.011 0.001 HIS D 173 Details of bonding type rmsd/Z covalent geometry : bond 0.00392 / 0.17 (33873) covalent geometry : angle 0.57439 / 0.31 (46153) hydrogen bonds : bond 0.04224 / 2.81 ( 1411) hydrogen bonds : angle 4.86842 / 3.47 ( 3876) metal coordination : bond 0.00722 / 0.48 ( 32) metal coordination : angle 3.24109 / 2.51 ( 45) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7708 Ramachandran restraints generated. 3854 Oldfield, 0 Emsley, 3854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7708 Ramachandran restraints generated. 3854 Oldfield, 0 Emsley, 3854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 474 residues out of total 3434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 424 time to evaluate : 1.182 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 108 MET cc_start: 0.8745 (mmm) cc_final: 0.8432 (mmm) REVERT: A 109 HIS cc_start: 0.8747 (t-90) cc_final: 0.8503 (t-170) REVERT: A 122 MET cc_start: 0.9061 (tpp) cc_final: 0.8356 (tpp) REVERT: B 71 LEU cc_start: 0.7917 (tp) cc_final: 0.7617 (tt) REVERT: B 216 GLU cc_start: 0.8172 (tt0) cc_final: 0.7601 (tt0) REVERT: B 244 LEU cc_start: 0.8629 (mp) cc_final: 0.8361 (tp) REVERT: B 313 MET cc_start: 0.9164 (mmm) cc_final: 0.8906 (mmm) REVERT: B 349 ILE cc_start: 0.7802 (mm) cc_final: 0.7416 (tt) REVERT: B 353 LYS cc_start: 0.8602 (mtpt) cc_final: 0.8208 (mtmm) REVERT: B 354 ASP cc_start: 0.8151 (m-30) cc_final: 0.7763 (m-30) REVERT: B 391 ASP cc_start: 0.8640 (m-30) cc_final: 0.8278 (m-30) REVERT: B 455 SER cc_start: 0.8885 (t) cc_final: 0.8378 (p) REVERT: B 476 ARG cc_start: 0.8206 (ttp-170) cc_final: 0.7762 (ptm160) REVERT: B 531 GLN cc_start: 0.8048 (pm20) cc_final: 0.7788 (pm20) REVERT: B 939 THR cc_start: 0.9258 (m) cc_final: 0.8745 (p) REVERT: B 1136 ASP cc_start: 0.8486 (m-30) cc_final: 0.8280 (m-30) REVERT: B 1152 MET cc_start: 0.8655 (mmm) cc_final: 0.8423 (mmm) REVERT: B 1202 LEU cc_start: 0.9548 (tp) cc_final: 0.9320 (tt) REVERT: B 1206 GLU cc_start: 0.8389 (mt-10) cc_final: 0.7983 (mt-10) REVERT: D 23 ASN cc_start: 0.8655 (t0) cc_final: 0.8171 (t0) REVERT: D 71 LYS cc_start: 0.8179 (mttt) cc_final: 0.7806 (mmtm) REVERT: D 119 ARG cc_start: 0.6882 (mmp80) cc_final: 0.6364 (mmp-170) REVERT: D 138 ASN cc_start: 0.7902 (p0) cc_final: 0.7560 (p0) REVERT: D 204 ASP cc_start: 0.7890 (m-30) cc_final: 0.7264 (t0) REVERT: E 8 ASN cc_start: 0.8787 (m-40) cc_final: 0.8500 (m-40) REVERT: E 84 ASP cc_start: 0.8359 (t0) cc_final: 0.8072 (t0) REVERT: E 179 GLN cc_start: 0.8849 (mt0) cc_final: 0.8545 (mt0) REVERT: E 192 ARG cc_start: 0.8247 (ttm-80) cc_final: 0.8029 (ttm110) REVERT: F 89 GLU cc_start: 0.8831 (mt-10) cc_final: 0.8572 (mt-10) REVERT: F 109 VAL cc_start: 0.8785 (t) cc_final: 0.8497 (m) REVERT: F 110 ASP cc_start: 0.8496 (p0) cc_final: 0.7905 (p0) REVERT: F 127 GLU cc_start: 0.7927 (mt-10) cc_final: 0.7602 (mt-10) REVERT: F 143 PHE cc_start: 0.9317 (p90) cc_final: 0.8924 (p90) REVERT: F 144 GLU cc_start: 0.7825 (mt-10) cc_final: 0.7345 (mt-10) REVERT: G 28 THR cc_start: 0.8802 (m) cc_final: 0.8466 (p) REVERT: G 32 GLU cc_start: 0.8575 (mt-10) cc_final: 0.8232 (mt-10) REVERT: G 33 GLU cc_start: 0.8287 (mm-30) cc_final: 0.7799 (mm-30) REVERT: G 67 SER cc_start: 0.8960 (m) cc_final: 0.8715 (p) REVERT: G 69 GLU cc_start: 0.7845 (tt0) cc_final: 0.7638 (tt0) REVERT: G 79 PHE cc_start: 0.8303 (t80) cc_final: 0.7516 (t80) REVERT: G 83 LYS cc_start: 0.7506 (tttt) cc_final: 0.6923 (tmmt) REVERT: H 136 LYS cc_start: 0.8556 (mmtp) cc_final: 0.8132 (mmtt) REVERT: H 138 GLU cc_start: 0.8412 (pt0) cc_final: 0.7991 (pm20) REVERT: I 13 MET cc_start: 0.7718 (ptp) cc_final: 0.7008 (ppp) REVERT: K 38 GLU cc_start: 0.7729 (mm-30) cc_final: 0.7294 (tp30) REVERT: K 96 ASN cc_start: 0.8646 (m-40) cc_final: 0.8376 (m-40) outliers start: 50 outliers final: 37 residues processed: 455 average time/residue: 0.2064 time to fit residues: 150.1478 Evaluate side-chains 425 residues out of total 3434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 388 time to evaluate : 1.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 281 HIS Chi-restraints excluded: chain A residue 470 LEU Chi-restraints excluded: chain A residue 620 LYS Chi-restraints excluded: chain A residue 710 LEU Chi-restraints excluded: chain A residue 756 ILE Chi-restraints excluded: chain A residue 842 VAL Chi-restraints excluded: chain A residue 920 LEU Chi-restraints excluded: chain A residue 948 VAL Chi-restraints excluded: chain A residue 1067 LEU Chi-restraints excluded: chain A residue 1174 PHE Chi-restraints excluded: chain A residue 1381 LEU Chi-restraints excluded: chain A residue 1420 ASP Chi-restraints excluded: chain A residue 1428 VAL Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 70 ILE Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 415 GLN Chi-restraints excluded: chain B residue 637 LEU Chi-restraints excluded: chain B residue 771 SER Chi-restraints excluded: chain B residue 935 ARG Chi-restraints excluded: chain B residue 963 PHE Chi-restraints excluded: chain B residue 1210 MET Chi-restraints excluded: chain C residue 163 ILE Chi-restraints excluded: chain F residue 77 ASP Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 101 ILE Chi-restraints excluded: chain F residue 147 SER Chi-restraints excluded: chain G residue 1 MET Chi-restraints excluded: chain G residue 26 LEU Chi-restraints excluded: chain G residue 54 ILE Chi-restraints excluded: chain H residue 123 MET Chi-restraints excluded: chain I residue 1 MET Chi-restraints excluded: chain I residue 110 PHE Chi-restraints excluded: chain J residue 37 SER Chi-restraints excluded: chain K residue 77 THR Chi-restraints excluded: chain K residue 88 LYS Chi-restraints excluded: chain L residue 61 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 395 random chunks: chunk 0 optimal weight: 10.0000 chunk 345 optimal weight: 8.9990 chunk 138 optimal weight: 0.7980 chunk 183 optimal weight: 3.9990 chunk 169 optimal weight: 8.9990 chunk 216 optimal weight: 5.9990 chunk 286 optimal weight: 8.9990 chunk 108 optimal weight: 0.0060 chunk 251 optimal weight: 0.9990 chunk 308 optimal weight: 0.0980 chunk 352 optimal weight: 3.9990 overall best weight: 1.1800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 603 ASN ** A1188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 984 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1093 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 89 GLN J 53 HIS ** K 2 ASN ** 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 = 0.3576 r_free = 0.3576 target = 0.112336 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.078626 restraints weight = 63477.096| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.082118 restraints weight = 29187.758| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.082639 restraints weight = 15873.803| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.082857 restraints weight = 14505.486| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.082984 restraints weight = 14109.049| |-----------------------------------------------------------------------------| r_work (final): 0.3061 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8592 moved from start: 0.2239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 33905 Z= 0.128 Angle : 0.544 8.906 46198 Z= 0.288 Chirality : 0.043 0.234 5190 Planarity : 0.004 0.050 5630 Dihedral : 16.597 168.728 5346 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.19 % Favored : 96.68 % Rotamer: Outliers : 1.60 % Allowed : 9.26 % Favored : 89.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.43 (0.14), residues: 3854 helix: 1.54 (0.15), residues: 1339 sheet: -0.04 (0.21), residues: 585 loop : -0.47 (0.14), residues: 1930 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG K 54 TYR 0.014 0.001 TYR D 147 PHE 0.023 0.001 PHE A 219 TRP 0.009 0.001 TRP B 561 HIS 0.005 0.001 HIS A1367 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.13 (33873) covalent geometry : angle 0.53660 / 0.29 (46153) hydrogen bonds : bond 0.03705 / 2.48 ( 1411) hydrogen bonds : angle 4.61021 / 3.29 ( 3876) metal coordination : bond 0.00547 / 0.35 ( 32) metal coordination : angle 2.97446 / 2.26 ( 45) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7708 Ramachandran restraints generated. 3854 Oldfield, 0 Emsley, 3854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7708 Ramachandran restraints generated. 3854 Oldfield, 0 Emsley, 3854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 475 residues out of total 3434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 420 time to evaluate : 1.188 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 108 MET cc_start: 0.8721 (mmm) cc_final: 0.8439 (mmm) REVERT: A 109 HIS cc_start: 0.8725 (t-90) cc_final: 0.8476 (t-170) REVERT: A 708 MET cc_start: 0.9093 (ttm) cc_final: 0.8581 (ttm) REVERT: A 1267 MET cc_start: 0.8120 (mtp) cc_final: 0.7909 (mtp) REVERT: A 1284 MET cc_start: 0.8047 (ttm) cc_final: 0.7830 (ttm) REVERT: B 71 LEU cc_start: 0.7916 (tp) cc_final: 0.7629 (tt) REVERT: B 216 GLU cc_start: 0.8162 (tt0) cc_final: 0.7592 (tt0) REVERT: B 244 LEU cc_start: 0.8604 (mp) cc_final: 0.8348 (tp) REVERT: B 313 MET cc_start: 0.9141 (mmm) cc_final: 0.8900 (mmm) REVERT: B 349 ILE cc_start: 0.7798 (mm) cc_final: 0.7560 (tt) REVERT: B 353 LYS cc_start: 0.8603 (mtpt) cc_final: 0.8238 (mtmm) REVERT: B 354 ASP cc_start: 0.8165 (m-30) cc_final: 0.7780 (m-30) REVERT: B 391 ASP cc_start: 0.8634 (m-30) cc_final: 0.8401 (m-30) REVERT: B 444 MET cc_start: 0.8880 (mmt) cc_final: 0.8656 (mmp) REVERT: B 455 SER cc_start: 0.8850 (t) cc_final: 0.8369 (p) REVERT: B 476 ARG cc_start: 0.8188 (ttp-170) cc_final: 0.7755 (ptm160) REVERT: B 531 GLN cc_start: 0.7992 (pm20) cc_final: 0.7759 (pm20) REVERT: B 939 THR cc_start: 0.9260 (m) cc_final: 0.8767 (p) REVERT: B 1202 LEU cc_start: 0.9532 (tp) cc_final: 0.9295 (tt) REVERT: B 1206 GLU cc_start: 0.8347 (mt-10) cc_final: 0.7914 (mt-10) REVERT: D 23 ASN cc_start: 0.8565 (t0) cc_final: 0.8315 (t0) REVERT: D 70 PHE cc_start: 0.8021 (m-80) cc_final: 0.7812 (m-80) REVERT: D 119 ARG cc_start: 0.6998 (mmp80) cc_final: 0.6349 (mmp-170) REVERT: D 204 ASP cc_start: 0.7809 (m-30) cc_final: 0.7105 (t70) REVERT: E 8 ASN cc_start: 0.8790 (m-40) cc_final: 0.8527 (m-40) REVERT: E 54 GLN cc_start: 0.8851 (mm-40) cc_final: 0.8181 (pt0) REVERT: E 84 ASP cc_start: 0.8339 (t0) cc_final: 0.8034 (t0) REVERT: E 179 GLN cc_start: 0.8839 (mt0) cc_final: 0.8530 (mt0) REVERT: E 192 ARG cc_start: 0.8236 (ttm-80) cc_final: 0.8018 (ttm110) REVERT: F 89 GLU cc_start: 0.8839 (mt-10) cc_final: 0.8589 (mt-10) REVERT: F 109 VAL cc_start: 0.8790 (t) cc_final: 0.8441 (m) REVERT: F 110 ASP cc_start: 0.8517 (p0) cc_final: 0.7927 (p0) REVERT: F 127 GLU cc_start: 0.7917 (mt-10) cc_final: 0.7590 (mt-10) REVERT: F 143 PHE cc_start: 0.9290 (p90) cc_final: 0.8949 (p90) REVERT: G 28 THR cc_start: 0.8805 (m) cc_final: 0.8426 (p) REVERT: G 32 GLU cc_start: 0.8566 (mt-10) cc_final: 0.8235 (mt-10) REVERT: G 69 GLU cc_start: 0.7844 (tt0) cc_final: 0.7591 (tt0) REVERT: I 6 PHE cc_start: 0.6145 (m-80) cc_final: 0.5823 (m-80) REVERT: I 13 MET cc_start: 0.7488 (ptp) cc_final: 0.6852 (ppp) REVERT: J 26 GLN cc_start: 0.7498 (tm130) cc_final: 0.7009 (tm-30) REVERT: K 38 GLU cc_start: 0.7701 (mm-30) cc_final: 0.7300 (tp30) REVERT: K 54 ARG cc_start: 0.8100 (mmm-85) cc_final: 0.7822 (tpt90) REVERT: K 96 ASN cc_start: 0.8660 (m-40) cc_final: 0.8407 (m-40) outliers start: 55 outliers final: 35 residues processed: 455 average time/residue: 0.2121 time to fit residues: 156.3235 Evaluate side-chains 423 residues out of total 3434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 388 time to evaluate : 1.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 470 LEU Chi-restraints excluded: chain A residue 620 LYS Chi-restraints excluded: chain A residue 710 LEU Chi-restraints excluded: chain A residue 756 ILE Chi-restraints excluded: chain A residue 842 VAL Chi-restraints excluded: chain A residue 907 THR Chi-restraints excluded: chain A residue 983 ILE Chi-restraints excluded: chain A residue 1067 LEU Chi-restraints excluded: chain A residue 1148 ILE Chi-restraints excluded: chain A residue 1174 PHE Chi-restraints excluded: chain A residue 1314 SER Chi-restraints excluded: chain A residue 1381 LEU Chi-restraints excluded: chain A residue 1420 ASP Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 70 ILE Chi-restraints excluded: chain B residue 173 MET Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 612 GLU Chi-restraints excluded: chain B residue 637 LEU Chi-restraints excluded: chain B residue 771 SER Chi-restraints excluded: chain B residue 1156 ASP Chi-restraints excluded: chain C residue 163 ILE Chi-restraints excluded: chain D residue 4 SER Chi-restraints excluded: chain E residue 75 MET Chi-restraints excluded: chain E residue 115 ASN Chi-restraints excluded: chain F residue 147 SER Chi-restraints excluded: chain G residue 1 MET Chi-restraints excluded: chain G residue 54 ILE Chi-restraints excluded: chain H residue 123 MET Chi-restraints excluded: chain I residue 1 MET Chi-restraints excluded: chain I residue 110 PHE Chi-restraints excluded: chain J residue 37 SER Chi-restraints excluded: chain K residue 77 THR Chi-restraints excluded: chain K residue 88 LYS Chi-restraints excluded: chain L residue 61 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 395 random chunks: chunk 46 optimal weight: 0.0980 chunk 140 optimal weight: 3.9990 chunk 136 optimal weight: 3.9990 chunk 106 optimal weight: 4.9990 chunk 95 optimal weight: 4.9990 chunk 105 optimal weight: 0.6980 chunk 111 optimal weight: 7.9990 chunk 182 optimal weight: 7.9990 chunk 71 optimal weight: 0.7980 chunk 138 optimal weight: 6.9990 chunk 103 optimal weight: 4.9990 overall best weight: 1.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A1188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 110 HIS ** B 984 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1093 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 53 HIS ** K 2 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.111288 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.077729 restraints weight = 63964.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.081694 restraints weight = 29729.251| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.081819 restraints weight = 15860.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.081964 restraints weight = 14400.702| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.082117 restraints weight = 14503.043| |-----------------------------------------------------------------------------| r_work (final): 0.3066 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8613 moved from start: 0.2382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 33905 Z= 0.162 Angle : 0.557 12.453 46198 Z= 0.291 Chirality : 0.044 0.230 5190 Planarity : 0.004 0.050 5630 Dihedral : 16.587 169.165 5346 Min Nonbonded Distance : 1.829 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.50 % Favored : 96.34 % Rotamer: Outliers : 1.75 % Allowed : 10.25 % Favored : 88.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.42 (0.14), residues: 3854 helix: 1.59 (0.15), residues: 1332 sheet: -0.13 (0.20), residues: 598 loop : -0.49 (0.14), residues: 1924 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 135 TYR 0.013 0.001 TYR G 167 PHE 0.023 0.001 PHE A 219 TRP 0.009 0.001 TRP B 561 HIS 0.005 0.001 HIS A 659 Details of bonding type rmsd/Z covalent geometry : bond 0.00370 / 0.16 (33873) covalent geometry : angle 0.54931 / 0.29 (46153) hydrogen bonds : bond 0.03651 / 2.45 ( 1411) hydrogen bonds : angle 4.54356 / 3.23 ( 3876) metal coordination : bond 0.00650 / 0.42 ( 32) metal coordination : angle 3.02761 / 2.31 ( 45) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7708 Ramachandran restraints generated. 3854 Oldfield, 0 Emsley, 3854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7708 Ramachandran restraints generated. 3854 Oldfield, 0 Emsley, 3854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 449 residues out of total 3434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 389 time to evaluate : 1.270 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 108 MET cc_start: 0.8729 (mmm) cc_final: 0.8433 (mmm) REVERT: A 109 HIS cc_start: 0.8735 (t-90) cc_final: 0.8487 (t-170) REVERT: A 122 MET cc_start: 0.9032 (tpp) cc_final: 0.8401 (tpp) REVERT: A 708 MET cc_start: 0.9006 (ttm) cc_final: 0.8532 (ttm) REVERT: A 919 ILE cc_start: 0.9273 (OUTLIER) cc_final: 0.9066 (mm) REVERT: A 1267 MET cc_start: 0.8123 (mtp) cc_final: 0.7905 (mtp) REVERT: A 1284 MET cc_start: 0.8060 (ttm) cc_final: 0.7828 (ttm) REVERT: A 1336 MET cc_start: 0.9075 (tmm) cc_final: 0.8638 (ttt) REVERT: B 71 LEU cc_start: 0.8045 (tp) cc_final: 0.7767 (tt) REVERT: B 135 ARG cc_start: 0.7143 (mtt90) cc_final: 0.6667 (mtm-85) REVERT: B 216 GLU cc_start: 0.8174 (tt0) cc_final: 0.7594 (tt0) REVERT: B 244 LEU cc_start: 0.8600 (mp) cc_final: 0.8306 (tp) REVERT: B 313 MET cc_start: 0.9186 (mmm) cc_final: 0.8941 (mmm) REVERT: B 349 ILE cc_start: 0.7817 (mm) cc_final: 0.7580 (tt) REVERT: B 353 LYS cc_start: 0.8601 (mtpt) cc_final: 0.8243 (mtmm) REVERT: B 354 ASP cc_start: 0.8136 (m-30) cc_final: 0.7718 (m-30) REVERT: B 391 ASP cc_start: 0.8654 (m-30) cc_final: 0.8420 (m-30) REVERT: B 444 MET cc_start: 0.8875 (mmt) cc_final: 0.8670 (mmp) REVERT: B 455 SER cc_start: 0.8848 (t) cc_final: 0.8369 (p) REVERT: B 476 ARG cc_start: 0.8219 (ttp-170) cc_final: 0.7772 (ptm160) REVERT: B 531 GLN cc_start: 0.8031 (pm20) cc_final: 0.7797 (pm20) REVERT: B 939 THR cc_start: 0.9260 (m) cc_final: 0.8761 (p) REVERT: B 1202 LEU cc_start: 0.9557 (tp) cc_final: 0.9313 (tt) REVERT: B 1206 GLU cc_start: 0.8370 (mt-10) cc_final: 0.7948 (mt-10) REVERT: D 126 ILE cc_start: 0.8655 (tt) cc_final: 0.8142 (mt) REVERT: D 145 MET cc_start: 0.8622 (mmm) cc_final: 0.7991 (ppp) REVERT: D 204 ASP cc_start: 0.7922 (m-30) cc_final: 0.7174 (t70) REVERT: E 8 ASN cc_start: 0.8788 (m-40) cc_final: 0.8510 (m-40) REVERT: E 50 MET cc_start: 0.8352 (ppp) cc_final: 0.7516 (ppp) REVERT: E 54 GLN cc_start: 0.8863 (mm-40) cc_final: 0.8197 (pt0) REVERT: E 84 ASP cc_start: 0.8338 (t0) cc_final: 0.8060 (t0) REVERT: E 179 GLN cc_start: 0.8886 (mt0) cc_final: 0.8603 (mt0) REVERT: F 89 GLU cc_start: 0.8819 (mt-10) cc_final: 0.8530 (mt-10) REVERT: F 109 VAL cc_start: 0.8812 (t) cc_final: 0.8475 (m) REVERT: F 110 ASP cc_start: 0.8522 (p0) cc_final: 0.7934 (p0) REVERT: F 127 GLU cc_start: 0.7927 (mt-10) cc_final: 0.7598 (mt-10) REVERT: G 28 THR cc_start: 0.8826 (m) cc_final: 0.8340 (p) REVERT: G 32 GLU cc_start: 0.8552 (mt-10) cc_final: 0.8154 (mt-10) REVERT: G 33 GLU cc_start: 0.8327 (mm-30) cc_final: 0.7947 (mm-30) REVERT: G 69 GLU cc_start: 0.7866 (tt0) cc_final: 0.7639 (tt0) REVERT: G 79 PHE cc_start: 0.8162 (t80) cc_final: 0.7641 (t80) REVERT: H 138 GLU cc_start: 0.8299 (pt0) cc_final: 0.7982 (pm20) REVERT: I 6 PHE cc_start: 0.6116 (m-80) cc_final: 0.5805 (m-80) REVERT: K 38 GLU cc_start: 0.7712 (mm-30) cc_final: 0.7358 (tp30) REVERT: K 54 ARG cc_start: 0.8092 (mmm-85) cc_final: 0.7788 (tpt90) REVERT: K 96 ASN cc_start: 0.8669 (m-40) cc_final: 0.8417 (m-40) REVERT: L 54 ARG cc_start: 0.8101 (mtt180) cc_final: 0.7780 (mtt180) outliers start: 60 outliers final: 49 residues processed: 428 average time/residue: 0.1969 time to fit residues: 135.9022 Evaluate side-chains 426 residues out of total 3434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 376 time to evaluate : 1.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 PHE Chi-restraints excluded: chain A residue 454 SER Chi-restraints excluded: chain A residue 470 LEU Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 620 LYS Chi-restraints excluded: chain A residue 710 LEU Chi-restraints excluded: chain A residue 747 VAL Chi-restraints excluded: chain A residue 756 ILE Chi-restraints excluded: chain A residue 842 VAL Chi-restraints excluded: chain A residue 907 THR Chi-restraints excluded: chain A residue 919 ILE Chi-restraints excluded: chain A residue 920 LEU Chi-restraints excluded: chain A residue 983 ILE Chi-restraints excluded: chain A residue 1067 LEU Chi-restraints excluded: chain A residue 1174 PHE Chi-restraints excluded: chain A residue 1420 ASP Chi-restraints excluded: chain A residue 1428 VAL Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 70 ILE Chi-restraints excluded: chain B residue 173 MET Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 415 GLN Chi-restraints excluded: chain B residue 612 GLU Chi-restraints excluded: chain B residue 637 LEU Chi-restraints excluded: chain B residue 771 SER Chi-restraints excluded: chain B residue 1156 ASP Chi-restraints excluded: chain C residue 163 ILE Chi-restraints excluded: chain D residue 4 SER Chi-restraints excluded: chain D residue 138 ASN Chi-restraints excluded: chain D residue 215 SER Chi-restraints excluded: chain E residue 75 MET Chi-restraints excluded: chain E residue 115 ASN Chi-restraints excluded: chain F residue 77 ASP Chi-restraints excluded: chain F residue 101 ILE Chi-restraints excluded: chain F residue 147 SER Chi-restraints excluded: chain G residue 1 MET Chi-restraints excluded: chain G residue 26 LEU Chi-restraints excluded: chain G residue 54 ILE Chi-restraints excluded: chain H residue 33 GLN Chi-restraints excluded: chain H residue 100 THR Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain H residue 123 MET Chi-restraints excluded: chain I residue 1 MET Chi-restraints excluded: chain I residue 98 VAL Chi-restraints excluded: chain I residue 110 PHE Chi-restraints excluded: chain J residue 37 SER Chi-restraints excluded: chain J residue 53 HIS Chi-restraints excluded: chain K residue 77 THR Chi-restraints excluded: chain K residue 88 LYS Chi-restraints excluded: chain L residue 61 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 395 random chunks: chunk 317 optimal weight: 0.4980 chunk 101 optimal weight: 0.0370 chunk 159 optimal weight: 7.9990 chunk 89 optimal weight: 7.9990 chunk 65 optimal weight: 0.9990 chunk 143 optimal weight: 0.0070 chunk 114 optimal weight: 5.9990 chunk 150 optimal weight: 7.9990 chunk 144 optimal weight: 10.0000 chunk 31 optimal weight: 0.9980 chunk 293 optimal weight: 9.9990 overall best weight: 0.5078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 92 HIS ** A 757 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 224 GLN ** B 984 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1093 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 39 ASN J 53 HIS ** K 2 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.112993 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.079589 restraints weight = 63435.671| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.083262 restraints weight = 29497.525| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.083676 restraints weight = 15755.421| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.083773 restraints weight = 14305.678| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.083948 restraints weight = 14027.700| |-----------------------------------------------------------------------------| r_work (final): 0.3076 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8581 moved from start: 0.2507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 33905 Z= 0.106 Angle : 0.526 10.224 46198 Z= 0.278 Chirality : 0.043 0.236 5190 Planarity : 0.004 0.044 5630 Dihedral : 16.516 169.164 5346 Min Nonbonded Distance : 1.825 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.30 % Favored : 96.55 % Rotamer: Outliers : 1.40 % Allowed : 11.24 % Favored : 87.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.50 (0.14), residues: 3854 helix: 1.65 (0.15), residues: 1339 sheet: -0.08 (0.20), residues: 611 loop : -0.44 (0.15), residues: 1904 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 135 TYR 0.019 0.001 TYR G 51 PHE 0.023 0.001 PHE A 219 TRP 0.009 0.001 TRP J 18 HIS 0.017 0.001 HIS J 53 Details of bonding type rmsd/Z covalent geometry : bond 0.00220 / 0.11 (33873) covalent geometry : angle 0.51884 / 0.28 (46153) hydrogen bonds : bond 0.03362 / 2.26 ( 1411) hydrogen bonds : angle 4.38862 / 3.13 ( 3876) metal coordination : bond 0.00388 / 0.23 ( 32) metal coordination : angle 2.74225 / 2.03 ( 45) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7708 Ramachandran restraints generated. 3854 Oldfield, 0 Emsley, 3854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7708 Ramachandran restraints generated. 3854 Oldfield, 0 Emsley, 3854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 467 residues out of total 3434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 419 time to evaluate : 0.945 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 108 MET cc_start: 0.8705 (mmm) cc_final: 0.8393 (mmm) REVERT: A 109 HIS cc_start: 0.8726 (t-90) cc_final: 0.8482 (t-170) REVERT: A 175 ARG cc_start: 0.8173 (ttp-110) cc_final: 0.7262 (ptt90) REVERT: A 455 MET cc_start: 0.8284 (OUTLIER) cc_final: 0.7969 (ttm) REVERT: A 708 MET cc_start: 0.8961 (ttm) cc_final: 0.8660 (ttm) REVERT: A 919 ILE cc_start: 0.9250 (OUTLIER) cc_final: 0.9042 (mm) REVERT: A 983 ILE cc_start: 0.9253 (OUTLIER) cc_final: 0.8955 (mm) REVERT: A 1267 MET cc_start: 0.8108 (mtp) cc_final: 0.7853 (mtp) REVERT: B 71 LEU cc_start: 0.7919 (tp) cc_final: 0.7678 (tt) REVERT: B 135 ARG cc_start: 0.7197 (mtt90) cc_final: 0.6784 (mtm-85) REVERT: B 216 GLU cc_start: 0.8149 (tt0) cc_final: 0.7559 (tt0) REVERT: B 244 LEU cc_start: 0.8590 (mp) cc_final: 0.8345 (tp) REVERT: B 313 MET cc_start: 0.9156 (mmm) cc_final: 0.8941 (mmm) REVERT: B 353 LYS cc_start: 0.8543 (mtpt) cc_final: 0.8181 (mtmm) REVERT: B 354 ASP cc_start: 0.8178 (m-30) cc_final: 0.7799 (m-30) REVERT: B 391 ASP cc_start: 0.8579 (m-30) cc_final: 0.8361 (m-30) REVERT: B 455 SER cc_start: 0.8791 (t) cc_final: 0.8357 (p) REVERT: B 476 ARG cc_start: 0.8187 (ttp-170) cc_final: 0.7760 (ptm160) REVERT: B 531 GLN cc_start: 0.7980 (pm20) cc_final: 0.7734 (pm20) REVERT: B 939 THR cc_start: 0.9247 (m) cc_final: 0.8762 (p) REVERT: B 1202 LEU cc_start: 0.9514 (tp) cc_final: 0.9249 (tt) REVERT: B 1206 GLU cc_start: 0.8329 (mt-10) cc_final: 0.7846 (mt-10) REVERT: D 126 ILE cc_start: 0.8637 (tt) cc_final: 0.8177 (mt) REVERT: D 145 MET cc_start: 0.8480 (mmm) cc_final: 0.7835 (ppp) REVERT: D 204 ASP cc_start: 0.7897 (m-30) cc_final: 0.7168 (t70) REVERT: E 8 ASN cc_start: 0.8772 (m-40) cc_final: 0.8494 (m-40) REVERT: E 50 MET cc_start: 0.8373 (ppp) cc_final: 0.7499 (ppp) REVERT: E 54 GLN cc_start: 0.8864 (mm-40) cc_final: 0.8233 (pt0) REVERT: E 84 ASP cc_start: 0.8287 (t0) cc_final: 0.8015 (t0) REVERT: E 179 GLN cc_start: 0.8867 (mt0) cc_final: 0.8563 (mt0) REVERT: F 89 GLU cc_start: 0.8820 (mt-10) cc_final: 0.8565 (mt-10) REVERT: F 110 ASP cc_start: 0.8512 (p0) cc_final: 0.7924 (p0) REVERT: G 2 PHE cc_start: 0.8877 (m-80) cc_final: 0.8520 (m-10) REVERT: G 13 LEU cc_start: 0.8698 (OUTLIER) cc_final: 0.8472 (tp) REVERT: G 28 THR cc_start: 0.8796 (m) cc_final: 0.8383 (p) REVERT: G 32 GLU cc_start: 0.8531 (mt-10) cc_final: 0.8124 (mt-10) REVERT: G 33 GLU cc_start: 0.8299 (mm-30) cc_final: 0.7869 (mm-30) REVERT: G 69 GLU cc_start: 0.7852 (tt0) cc_final: 0.7624 (tt0) REVERT: G 79 PHE cc_start: 0.8091 (t80) cc_final: 0.7732 (t80) REVERT: H 138 GLU cc_start: 0.8297 (pt0) cc_final: 0.7989 (pm20) REVERT: I 6 PHE cc_start: 0.6171 (m-80) cc_final: 0.5875 (m-80) REVERT: K 38 GLU cc_start: 0.7638 (mm-30) cc_final: 0.7376 (tp30) REVERT: K 54 ARG cc_start: 0.8096 (mmm-85) cc_final: 0.7754 (tpt90) REVERT: K 96 ASN cc_start: 0.8657 (m-40) cc_final: 0.8400 (m-40) outliers start: 48 outliers final: 32 residues processed: 444 average time/residue: 0.2052 time to fit residues: 145.8942 Evaluate side-chains 421 residues out of total 3434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 385 time to evaluate : 1.053 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 455 MET Chi-restraints excluded: chain A residue 470 LEU Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 710 LEU Chi-restraints excluded: chain A residue 907 THR Chi-restraints excluded: chain A residue 919 ILE Chi-restraints excluded: chain A residue 920 LEU Chi-restraints excluded: chain A residue 983 ILE Chi-restraints excluded: chain A residue 1067 LEU Chi-restraints excluded: chain A residue 1174 PHE Chi-restraints excluded: chain A residue 1420 ASP Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 70 ILE Chi-restraints excluded: chain B residue 173 MET Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 415 GLN Chi-restraints excluded: chain B residue 612 GLU Chi-restraints excluded: chain B residue 637 LEU Chi-restraints excluded: chain B residue 1169 MET Chi-restraints excluded: chain B residue 1213 THR Chi-restraints excluded: chain D residue 4 SER Chi-restraints excluded: chain D residue 39 ASN Chi-restraints excluded: chain D residue 138 ASN Chi-restraints excluded: chain D residue 215 SER Chi-restraints excluded: chain E residue 115 ASN Chi-restraints excluded: chain F residue 122 MET Chi-restraints excluded: chain G residue 1 MET Chi-restraints excluded: chain G residue 13 LEU Chi-restraints excluded: chain H residue 9 ILE Chi-restraints excluded: chain H residue 33 GLN Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain H residue 123 MET Chi-restraints excluded: chain I residue 98 VAL Chi-restraints excluded: chain I residue 110 PHE Chi-restraints excluded: chain K residue 77 THR Chi-restraints excluded: chain L residue 61 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 395 random chunks: chunk 382 optimal weight: 5.9990 chunk 3 optimal weight: 9.9990 chunk 200 optimal weight: 2.9990 chunk 306 optimal weight: 8.9990 chunk 78 optimal weight: 0.8980 chunk 354 optimal weight: 6.9990 chunk 270 optimal weight: 3.9990 chunk 70 optimal weight: 3.9990 chunk 357 optimal weight: 20.0000 chunk 254 optimal weight: 0.9980 chunk 351 optimal weight: 9.9990 overall best weight: 2.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 659 HIS ** A 757 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 984 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 39 ASN ** D 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 26 GLN ** K 2 ASN ** 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 = 0.3557 r_free = 0.3557 target = 0.110760 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.077484 restraints weight = 64071.444| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.080790 restraints weight = 29952.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.081371 restraints weight = 16305.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.081582 restraints weight = 14772.673| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.081677 restraints weight = 14426.232| |-----------------------------------------------------------------------------| r_work (final): 0.3034 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8627 moved from start: 0.2574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 33905 Z= 0.199 Angle : 0.572 12.541 46198 Z= 0.298 Chirality : 0.044 0.229 5190 Planarity : 0.004 0.044 5630 Dihedral : 16.549 169.623 5346 Min Nonbonded Distance : 1.833 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.61 % Favored : 96.24 % Rotamer: Outliers : 1.63 % Allowed : 11.74 % Favored : 86.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.45 (0.14), residues: 3854 helix: 1.64 (0.15), residues: 1334 sheet: -0.18 (0.20), residues: 604 loop : -0.46 (0.14), residues: 1916 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG F 135 TYR 0.016 0.001 TYR I 34 PHE 0.024 0.001 PHE A 219 TRP 0.010 0.001 TRP B 561 HIS 0.007 0.001 HIS D 40 Details of bonding type rmsd/Z covalent geometry : bond 0.00461 / 0.20 (33873) covalent geometry : angle 0.56474 / 0.30 (46153) hydrogen bonds : bond 0.03565 / 2.38 ( 1411) hydrogen bonds : angle 4.43750 / 3.16 ( 3876) metal coordination : bond 0.00745 / 0.48 ( 32) metal coordination : angle 2.92397 / 2.24 ( 45) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7708 Ramachandran restraints generated. 3854 Oldfield, 0 Emsley, 3854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7708 Ramachandran restraints generated. 3854 Oldfield, 0 Emsley, 3854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 434 residues out of total 3434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 378 time to evaluate : 1.154 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 108 MET cc_start: 0.8729 (mmm) cc_final: 0.8438 (mmm) REVERT: A 122 MET cc_start: 0.8842 (tpp) cc_final: 0.8413 (tpp) REVERT: A 708 MET cc_start: 0.8982 (ttm) cc_final: 0.8716 (ttm) REVERT: A 983 ILE cc_start: 0.9305 (OUTLIER) cc_final: 0.9021 (mm) REVERT: A 1336 MET cc_start: 0.9058 (tmm) cc_final: 0.8720 (ttt) REVERT: B 71 LEU cc_start: 0.7963 (tp) cc_final: 0.7715 (tt) REVERT: B 135 ARG cc_start: 0.7271 (mtt90) cc_final: 0.6768 (mtm-85) REVERT: B 216 GLU cc_start: 0.8175 (tt0) cc_final: 0.7602 (tt0) REVERT: B 244 LEU cc_start: 0.8609 (mp) cc_final: 0.8334 (tp) REVERT: B 313 MET cc_start: 0.9208 (mmm) cc_final: 0.8970 (mmm) REVERT: B 353 LYS cc_start: 0.8559 (mtpt) cc_final: 0.8185 (mtmm) REVERT: B 354 ASP cc_start: 0.8116 (m-30) cc_final: 0.7707 (m-30) REVERT: B 391 ASP cc_start: 0.8605 (m-30) cc_final: 0.8365 (m-30) REVERT: B 455 SER cc_start: 0.8840 (t) cc_final: 0.8373 (p) REVERT: B 476 ARG cc_start: 0.8242 (ttp-170) cc_final: 0.7788 (ptm160) REVERT: B 531 GLN cc_start: 0.8019 (pm20) cc_final: 0.7814 (pm20) REVERT: B 939 THR cc_start: 0.9265 (m) cc_final: 0.8775 (p) REVERT: B 1072 MET cc_start: 0.9223 (mtp) cc_final: 0.9022 (mtp) REVERT: B 1202 LEU cc_start: 0.9561 (tp) cc_final: 0.9301 (tt) REVERT: B 1206 GLU cc_start: 0.8366 (mt-10) cc_final: 0.7950 (mt-10) REVERT: D 145 MET cc_start: 0.8340 (mmm) cc_final: 0.8066 (mmm) REVERT: D 204 ASP cc_start: 0.7924 (m-30) cc_final: 0.7161 (t70) REVERT: E 8 ASN cc_start: 0.8767 (m-40) cc_final: 0.8484 (m-40) REVERT: E 50 MET cc_start: 0.8494 (ppp) cc_final: 0.7646 (ppp) REVERT: E 54 GLN cc_start: 0.8882 (mm-40) cc_final: 0.8244 (pt0) REVERT: E 84 ASP cc_start: 0.8332 (t0) cc_final: 0.8065 (t0) REVERT: E 179 GLN cc_start: 0.8908 (mt0) cc_final: 0.8617 (mt0) REVERT: F 89 GLU cc_start: 0.8857 (mt-10) cc_final: 0.8441 (mt-10) REVERT: F 127 GLU cc_start: 0.7978 (mt-10) cc_final: 0.7619 (mt-10) REVERT: G 28 THR cc_start: 0.8845 (m) cc_final: 0.8323 (p) REVERT: G 32 GLU cc_start: 0.8541 (mt-10) cc_final: 0.8143 (mt-10) REVERT: G 33 GLU cc_start: 0.8352 (mm-30) cc_final: 0.7887 (mm-30) REVERT: G 69 GLU cc_start: 0.7866 (tt0) cc_final: 0.7616 (tt0) REVERT: G 79 PHE cc_start: 0.8129 (t80) cc_final: 0.7680 (t80) REVERT: G 148 GLU cc_start: 0.6481 (pm20) cc_final: 0.6139 (pm20) REVERT: H 138 GLU cc_start: 0.8379 (pt0) cc_final: 0.8022 (pm20) REVERT: H 139 ASN cc_start: 0.9125 (m-40) cc_final: 0.8910 (m-40) REVERT: I 6 PHE cc_start: 0.6292 (m-80) cc_final: 0.5988 (m-80) REVERT: J 49 MET cc_start: 0.8805 (tpp) cc_final: 0.8324 (tpp) REVERT: K 96 ASN cc_start: 0.8675 (m-40) cc_final: 0.8419 (m-40) outliers start: 56 outliers final: 44 residues processed: 412 average time/residue: 0.1951 time to fit residues: 130.8612 Evaluate side-chains 416 residues out of total 3434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 371 time to evaluate : 1.043 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 PHE Chi-restraints excluded: chain A residue 454 SER Chi-restraints excluded: chain A residue 470 LEU Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 710 LEU Chi-restraints excluded: chain A residue 756 ILE Chi-restraints excluded: chain A residue 907 THR Chi-restraints excluded: chain A residue 920 LEU Chi-restraints excluded: chain A residue 983 ILE Chi-restraints excluded: chain A residue 1057 VAL Chi-restraints excluded: chain A residue 1067 LEU Chi-restraints excluded: chain A residue 1174 PHE Chi-restraints excluded: chain A residue 1420 ASP Chi-restraints excluded: chain A residue 1428 VAL Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 70 ILE Chi-restraints excluded: chain B residue 173 MET Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 339 THR Chi-restraints excluded: chain B residue 415 GLN Chi-restraints excluded: chain B residue 612 GLU Chi-restraints excluded: chain B residue 637 LEU Chi-restraints excluded: chain B residue 1169 MET Chi-restraints excluded: chain B residue 1210 MET Chi-restraints excluded: chain B residue 1213 THR Chi-restraints excluded: chain D residue 4 SER Chi-restraints excluded: chain D residue 138 ASN Chi-restraints excluded: chain D residue 215 SER Chi-restraints excluded: chain E residue 204 THR Chi-restraints excluded: chain F residue 77 ASP Chi-restraints excluded: chain F residue 101 ILE Chi-restraints excluded: chain G residue 1 MET Chi-restraints excluded: chain G residue 54 ILE Chi-restraints excluded: chain H residue 9 ILE Chi-restraints excluded: chain H residue 33 GLN Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain H residue 123 MET Chi-restraints excluded: chain I residue 1 MET Chi-restraints excluded: chain I residue 98 VAL Chi-restraints excluded: chain I residue 110 PHE Chi-restraints excluded: chain J residue 37 SER Chi-restraints excluded: chain J residue 42 LYS Chi-restraints excluded: chain K residue 77 THR Chi-restraints excluded: chain K residue 88 LYS Chi-restraints excluded: chain L residue 61 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 395 random chunks: chunk 20 optimal weight: 0.9990 chunk 80 optimal weight: 3.9990 chunk 121 optimal weight: 0.9990 chunk 363 optimal weight: 7.9990 chunk 243 optimal weight: 0.4980 chunk 331 optimal weight: 0.8980 chunk 139 optimal weight: 8.9990 chunk 56 optimal weight: 0.9990 chunk 12 optimal weight: 7.9990 chunk 126 optimal weight: 3.9990 chunk 275 optimal weight: 0.0870 overall best weight: 0.6962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 659 HIS A 757 ASN A 975 HIS ** A1188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 984 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1025 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1093 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 2 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.112598 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.078937 restraints weight = 63430.628| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.082666 restraints weight = 29631.298| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.082873 restraints weight = 15995.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.083122 restraints weight = 14419.219| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.083266 restraints weight = 14438.188| |-----------------------------------------------------------------------------| r_work (final): 0.3072 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8585 moved from start: 0.2675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 33905 Z= 0.109 Angle : 0.528 9.592 46198 Z= 0.278 Chirality : 0.043 0.236 5190 Planarity : 0.004 0.044 5630 Dihedral : 16.481 169.508 5346 Min Nonbonded Distance : 1.866 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.30 % Favored : 96.55 % Rotamer: Outliers : 1.25 % Allowed : 12.35 % Favored : 86.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.54 (0.14), residues: 3854 helix: 1.73 (0.15), residues: 1333 sheet: -0.12 (0.20), residues: 606 loop : -0.42 (0.15), residues: 1915 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 72 TYR 0.019 0.001 TYR G 51 PHE 0.022 0.001 PHE A 219 TRP 0.007 0.001 TRP C 170 HIS 0.006 0.001 HIS A1173 Details of bonding type rmsd/Z covalent geometry : bond 0.00234 / 0.11 (33873) covalent geometry : angle 0.52108 / 0.28 (46153) hydrogen bonds : bond 0.03275 / 2.20 ( 1411) hydrogen bonds : angle 4.30845 / 3.08 ( 3876) metal coordination : bond 0.00393 / 0.23 ( 32) metal coordination : angle 2.68644 / 2.00 ( 45) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7708 Ramachandran restraints generated. 3854 Oldfield, 0 Emsley, 3854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7708 Ramachandran restraints generated. 3854 Oldfield, 0 Emsley, 3854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 444 residues out of total 3434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 401 time to evaluate : 1.104 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 108 MET cc_start: 0.8717 (mmm) cc_final: 0.8418 (mmm) REVERT: A 122 MET cc_start: 0.8810 (tpp) cc_final: 0.8378 (tpp) REVERT: A 175 ARG cc_start: 0.8202 (ttp-110) cc_final: 0.7295 (ptt90) REVERT: A 455 MET cc_start: 0.8267 (ttp) cc_final: 0.7964 (ttm) REVERT: A 983 ILE cc_start: 0.9248 (OUTLIER) cc_final: 0.8945 (mm) REVERT: A 1071 SER cc_start: 0.9330 (m) cc_final: 0.9103 (m) REVERT: A 1267 MET cc_start: 0.8196 (mtp) cc_final: 0.7964 (mtp) REVERT: A 1336 MET cc_start: 0.9027 (tmm) cc_final: 0.8684 (ttt) REVERT: B 71 LEU cc_start: 0.7952 (tp) cc_final: 0.7666 (tt) REVERT: B 135 ARG cc_start: 0.7352 (mtt90) cc_final: 0.7005 (mtm-85) REVERT: B 216 GLU cc_start: 0.8152 (tt0) cc_final: 0.7612 (tt0) REVERT: B 244 LEU cc_start: 0.8590 (mp) cc_final: 0.8340 (tp) REVERT: B 313 MET cc_start: 0.9227 (mmm) cc_final: 0.8992 (mmm) REVERT: B 353 LYS cc_start: 0.8533 (mtpt) cc_final: 0.8158 (mtmm) REVERT: B 354 ASP cc_start: 0.8147 (m-30) cc_final: 0.7760 (m-30) REVERT: B 391 ASP cc_start: 0.8607 (m-30) cc_final: 0.8375 (m-30) REVERT: B 444 MET cc_start: 0.8843 (mmt) cc_final: 0.8605 (mmp) REVERT: B 455 SER cc_start: 0.8776 (t) cc_final: 0.8356 (p) REVERT: B 476 ARG cc_start: 0.8203 (ttp-170) cc_final: 0.7757 (ptm160) REVERT: B 531 GLN cc_start: 0.7972 (pm20) cc_final: 0.7740 (pm20) REVERT: B 860 MET cc_start: 0.8930 (tmm) cc_final: 0.8672 (tmm) REVERT: B 939 THR cc_start: 0.9233 (m) cc_final: 0.8743 (p) REVERT: B 1202 LEU cc_start: 0.9508 (tp) cc_final: 0.9234 (tt) REVERT: B 1206 GLU cc_start: 0.8353 (mt-10) cc_final: 0.7878 (mt-10) REVERT: D 202 ILE cc_start: 0.5314 (mm) cc_final: 0.4810 (mt) REVERT: D 204 ASP cc_start: 0.7919 (m-30) cc_final: 0.7158 (t70) REVERT: E 8 ASN cc_start: 0.8786 (m-40) cc_final: 0.8491 (m-40) REVERT: E 50 MET cc_start: 0.8465 (ppp) cc_final: 0.7613 (ppp) REVERT: E 54 GLN cc_start: 0.8855 (mm-40) cc_final: 0.8244 (pt0) REVERT: E 84 ASP cc_start: 0.8360 (t0) cc_final: 0.8133 (t0) REVERT: E 179 GLN cc_start: 0.8889 (mt0) cc_final: 0.8587 (mt0) REVERT: F 89 GLU cc_start: 0.8831 (mt-10) cc_final: 0.8561 (mt-10) REVERT: F 119 ARG cc_start: 0.8772 (ttm-80) cc_final: 0.8509 (mtp85) REVERT: F 127 GLU cc_start: 0.8016 (mt-10) cc_final: 0.7648 (mt-10) REVERT: G 2 PHE cc_start: 0.8883 (m-80) cc_final: 0.8528 (m-10) REVERT: G 28 THR cc_start: 0.8835 (m) cc_final: 0.8314 (p) REVERT: G 32 GLU cc_start: 0.8554 (mt-10) cc_final: 0.8162 (mt-10) REVERT: G 33 GLU cc_start: 0.8372 (mm-30) cc_final: 0.7942 (mm-30) REVERT: G 69 GLU cc_start: 0.7861 (tt0) cc_final: 0.7583 (tt0) REVERT: G 79 PHE cc_start: 0.8094 (t80) cc_final: 0.7768 (t80) REVERT: H 138 GLU cc_start: 0.8311 (pt0) cc_final: 0.7983 (pm20) REVERT: I 6 PHE cc_start: 0.6142 (m-80) cc_final: 0.5866 (m-80) REVERT: K 54 ARG cc_start: 0.8142 (mmm-85) cc_final: 0.7880 (tpt90) REVERT: K 96 ASN cc_start: 0.8650 (m-40) cc_final: 0.8385 (m-40) outliers start: 43 outliers final: 32 residues processed: 423 average time/residue: 0.2019 time to fit residues: 137.3150 Evaluate side-chains 405 residues out of total 3434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 372 time to evaluate : 1.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 287 HIS Chi-restraints excluded: chain A residue 454 SER Chi-restraints excluded: chain A residue 470 LEU Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 710 LEU Chi-restraints excluded: chain A residue 907 THR Chi-restraints excluded: chain A residue 920 LEU Chi-restraints excluded: chain A residue 983 ILE Chi-restraints excluded: chain A residue 1174 PHE Chi-restraints excluded: chain A residue 1420 ASP Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 70 ILE Chi-restraints excluded: chain B residue 173 MET Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 415 GLN Chi-restraints excluded: chain B residue 612 GLU Chi-restraints excluded: chain B residue 637 LEU Chi-restraints excluded: chain B residue 1169 MET Chi-restraints excluded: chain B residue 1213 THR Chi-restraints excluded: chain D residue 4 SER Chi-restraints excluded: chain D residue 138 ASN Chi-restraints excluded: chain D residue 215 SER Chi-restraints excluded: chain E residue 75 MET Chi-restraints excluded: chain E residue 115 ASN Chi-restraints excluded: chain E residue 204 THR Chi-restraints excluded: chain G residue 1 MET Chi-restraints excluded: chain G residue 26 LEU Chi-restraints excluded: chain H residue 9 ILE Chi-restraints excluded: chain I residue 98 VAL Chi-restraints excluded: chain I residue 110 PHE Chi-restraints excluded: chain K residue 77 THR Chi-restraints excluded: chain K residue 88 LYS Chi-restraints excluded: chain L residue 61 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 395 random chunks: chunk 58 optimal weight: 7.9990 chunk 377 optimal weight: 6.9990 chunk 167 optimal weight: 9.9990 chunk 196 optimal weight: 1.9990 chunk 62 optimal weight: 0.8980 chunk 6 optimal weight: 3.9990 chunk 99 optimal weight: 6.9990 chunk 331 optimal weight: 2.9990 chunk 134 optimal weight: 0.9990 chunk 247 optimal weight: 7.9990 chunk 163 optimal weight: 7.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 659 HIS ** A1188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 984 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.111225 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.078017 restraints weight = 63767.120| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.081482 restraints weight = 29877.056| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.081652 restraints weight = 16720.736| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.082074 restraints weight = 15502.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.082165 restraints weight = 14150.975| |-----------------------------------------------------------------------------| r_work (final): 0.3045 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8621 moved from start: 0.2715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 33905 Z= 0.174 Angle : 0.565 11.617 46198 Z= 0.294 Chirality : 0.044 0.234 5190 Planarity : 0.004 0.044 5630 Dihedral : 16.510 169.799 5346 Min Nonbonded Distance : 1.857 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.74 % Favored : 96.13 % Rotamer: Outliers : 1.31 % Allowed : 12.55 % Favored : 86.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.53 (0.14), residues: 3854 helix: 1.75 (0.15), residues: 1333 sheet: -0.20 (0.20), residues: 610 loop : -0.42 (0.15), residues: 1911 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 72 TYR 0.021 0.001 TYR G 51 PHE 0.023 0.001 PHE A 219 TRP 0.010 0.001 TRP B 561 HIS 0.006 0.001 HIS A1173 Details of bonding type rmsd/Z covalent geometry : bond 0.00402 / 0.17 (33873) covalent geometry : angle 0.55854 / 0.29 (46153) hydrogen bonds : bond 0.03460 / 2.31 ( 1411) hydrogen bonds : angle 4.36328 / 3.11 ( 3876) metal coordination : bond 0.00655 / 0.41 ( 32) metal coordination : angle 2.79684 / 2.15 ( 45) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7708 Ramachandran restraints generated. 3854 Oldfield, 0 Emsley, 3854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7708 Ramachandran restraints generated. 3854 Oldfield, 0 Emsley, 3854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 422 residues out of total 3434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 377 time to evaluate : 1.083 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 122 MET cc_start: 0.8883 (tpp) cc_final: 0.8410 (tpp) REVERT: A 175 ARG cc_start: 0.8166 (ttp-110) cc_final: 0.7242 (ptt90) REVERT: A 983 ILE cc_start: 0.9291 (OUTLIER) cc_final: 0.9002 (mm) REVERT: A 1267 MET cc_start: 0.8163 (mtp) cc_final: 0.7924 (mtp) REVERT: A 1269 GLU cc_start: 0.8777 (mm-30) cc_final: 0.8467 (mt-10) REVERT: A 1336 MET cc_start: 0.9060 (tmm) cc_final: 0.8675 (ttt) REVERT: B 71 LEU cc_start: 0.8005 (tp) cc_final: 0.7699 (tt) REVERT: B 135 ARG cc_start: 0.7244 (mtt90) cc_final: 0.6773 (mtm-85) REVERT: B 216 GLU cc_start: 0.8178 (tt0) cc_final: 0.7599 (tt0) REVERT: B 244 LEU cc_start: 0.8604 (mp) cc_final: 0.8369 (tp) REVERT: B 313 MET cc_start: 0.9263 (mmm) cc_final: 0.9011 (mmm) REVERT: B 353 LYS cc_start: 0.8557 (mtpt) cc_final: 0.8139 (mtmm) REVERT: B 354 ASP cc_start: 0.8107 (m-30) cc_final: 0.7695 (m-30) REVERT: B 391 ASP cc_start: 0.8639 (m-30) cc_final: 0.8398 (m-30) REVERT: B 444 MET cc_start: 0.8814 (mmt) cc_final: 0.8551 (mmp) REVERT: B 455 SER cc_start: 0.8803 (t) cc_final: 0.8360 (p) REVERT: B 476 ARG cc_start: 0.8236 (ttp-170) cc_final: 0.7774 (ptm160) REVERT: B 531 GLN cc_start: 0.8028 (pm20) cc_final: 0.7810 (pm20) REVERT: B 939 THR cc_start: 0.9253 (m) cc_final: 0.8770 (p) REVERT: B 1072 MET cc_start: 0.9230 (mtp) cc_final: 0.9025 (mtp) REVERT: B 1202 LEU cc_start: 0.9552 (tp) cc_final: 0.9282 (tt) REVERT: B 1206 GLU cc_start: 0.8367 (mt-10) cc_final: 0.7943 (mt-10) REVERT: D 145 MET cc_start: 0.8381 (mmm) cc_final: 0.8028 (mmm) REVERT: D 204 ASP cc_start: 0.7900 (m-30) cc_final: 0.7110 (t70) REVERT: E 8 ASN cc_start: 0.8788 (m-40) cc_final: 0.8487 (m-40) REVERT: E 50 MET cc_start: 0.8532 (ppp) cc_final: 0.7676 (ppp) REVERT: E 54 GLN cc_start: 0.8865 (mm-40) cc_final: 0.8241 (pt0) REVERT: E 84 ASP cc_start: 0.8400 (t0) cc_final: 0.8173 (t0) REVERT: E 113 GLN cc_start: 0.8191 (pt0) cc_final: 0.7869 (pm20) REVERT: E 179 GLN cc_start: 0.8934 (mt0) cc_final: 0.8650 (mt0) REVERT: F 89 GLU cc_start: 0.8879 (mt-10) cc_final: 0.8586 (mt-10) REVERT: F 119 ARG cc_start: 0.8755 (ttm-80) cc_final: 0.8485 (mtp85) REVERT: F 127 GLU cc_start: 0.8032 (mt-10) cc_final: 0.7673 (mt-10) REVERT: G 2 PHE cc_start: 0.8896 (m-80) cc_final: 0.8516 (m-10) REVERT: G 25 TYR cc_start: 0.9181 (t80) cc_final: 0.8823 (t80) REVERT: G 28 THR cc_start: 0.8847 (m) cc_final: 0.8314 (p) REVERT: G 32 GLU cc_start: 0.8537 (mt-10) cc_final: 0.8148 (mt-10) REVERT: G 33 GLU cc_start: 0.8390 (mm-30) cc_final: 0.7976 (mm-30) REVERT: G 69 GLU cc_start: 0.7864 (tt0) cc_final: 0.7609 (tt0) REVERT: G 79 PHE cc_start: 0.8126 (t80) cc_final: 0.7806 (t80) REVERT: G 114 LEU cc_start: 0.6609 (mt) cc_final: 0.6380 (tp) REVERT: G 148 GLU cc_start: 0.5363 (pm20) cc_final: 0.5100 (pm20) REVERT: H 138 GLU cc_start: 0.8263 (pt0) cc_final: 0.8029 (pm20) REVERT: I 6 PHE cc_start: 0.6218 (m-80) cc_final: 0.5938 (m-80) REVERT: J 49 MET cc_start: 0.8774 (tpp) cc_final: 0.8286 (tpp) REVERT: K 54 ARG cc_start: 0.8132 (mmm-85) cc_final: 0.7863 (tpt90) REVERT: K 96 ASN cc_start: 0.8650 (m-40) cc_final: 0.8389 (m-40) REVERT: L 54 ARG cc_start: 0.7488 (mtt180) cc_final: 0.7225 (mtt180) outliers start: 45 outliers final: 37 residues processed: 405 average time/residue: 0.2005 time to fit residues: 130.3633 Evaluate side-chains 409 residues out of total 3434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 371 time to evaluate : 1.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 PHE Chi-restraints excluded: chain A residue 454 SER Chi-restraints excluded: chain A residue 470 LEU Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 710 LEU Chi-restraints excluded: chain A residue 907 THR Chi-restraints excluded: chain A residue 920 LEU Chi-restraints excluded: chain A residue 983 ILE Chi-restraints excluded: chain A residue 1057 VAL Chi-restraints excluded: chain A residue 1174 PHE Chi-restraints excluded: chain A residue 1420 ASP Chi-restraints excluded: chain A residue 1428 VAL Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 70 ILE Chi-restraints excluded: chain B residue 173 MET Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 415 GLN Chi-restraints excluded: chain B residue 612 GLU Chi-restraints excluded: chain B residue 637 LEU Chi-restraints excluded: chain B residue 1169 MET Chi-restraints excluded: chain B residue 1213 THR Chi-restraints excluded: chain C residue 163 ILE Chi-restraints excluded: chain D residue 4 SER Chi-restraints excluded: chain D residue 138 ASN Chi-restraints excluded: chain D residue 215 SER Chi-restraints excluded: chain E residue 115 ASN Chi-restraints excluded: chain F residue 77 ASP Chi-restraints excluded: chain F residue 101 ILE Chi-restraints excluded: chain G residue 1 MET Chi-restraints excluded: chain G residue 26 LEU Chi-restraints excluded: chain H residue 33 GLN Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain I residue 98 VAL Chi-restraints excluded: chain I residue 110 PHE Chi-restraints excluded: chain J residue 37 SER Chi-restraints excluded: chain K residue 77 THR Chi-restraints excluded: chain K residue 88 LYS Chi-restraints excluded: chain L residue 61 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 395 random chunks: chunk 308 optimal weight: 7.9990 chunk 268 optimal weight: 6.9990 chunk 200 optimal weight: 0.9980 chunk 176 optimal weight: 6.9990 chunk 232 optimal weight: 0.0270 chunk 49 optimal weight: 0.9990 chunk 314 optimal weight: 4.9990 chunk 73 optimal weight: 6.9990 chunk 164 optimal weight: 1.9990 chunk 321 optimal weight: 9.9990 chunk 241 optimal weight: 5.9990 overall best weight: 1.8044 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 736 ASN ** A1188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 984 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1025 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 = 0.3564 r_free = 0.3564 target = 0.111288 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.077232 restraints weight = 64070.911| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.080798 restraints weight = 31501.418| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.081229 restraints weight = 17097.677| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.081753 restraints weight = 15427.024| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.081867 restraints weight = 14343.155| |-----------------------------------------------------------------------------| r_work (final): 0.3045 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8615 moved from start: 0.2763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 33905 Z= 0.154 Angle : 0.557 11.226 46198 Z= 0.290 Chirality : 0.043 0.235 5190 Planarity : 0.004 0.047 5630 Dihedral : 16.496 169.854 5346 Min Nonbonded Distance : 1.869 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.66 % Favored : 96.21 % Rotamer: Outliers : 1.14 % Allowed : 12.67 % Favored : 86.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.51 (0.14), residues: 3854 helix: 1.73 (0.15), residues: 1333 sheet: -0.23 (0.20), residues: 598 loop : -0.43 (0.14), residues: 1923 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 72 TYR 0.022 0.001 TYR G 51 PHE 0.031 0.001 PHE G 82 TRP 0.011 0.001 TRP B 561 HIS 0.007 0.001 HIS A 816 Details of bonding type rmsd/Z covalent geometry : bond 0.00353 / 0.15 (33873) covalent geometry : angle 0.55069 / 0.29 (46153) hydrogen bonds : bond 0.03424 / 2.29 ( 1411) hydrogen bonds : angle 4.33173 / 3.09 ( 3876) metal coordination : bond 0.00593 / 0.37 ( 32) metal coordination : angle 2.83606 / 2.17 ( 45) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7708 Ramachandran restraints generated. 3854 Oldfield, 0 Emsley, 3854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7708 Ramachandran restraints generated. 3854 Oldfield, 0 Emsley, 3854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 419 residues out of total 3434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 380 time to evaluate : 1.098 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 122 MET cc_start: 0.8845 (tpp) cc_final: 0.8374 (tpp) REVERT: A 175 ARG cc_start: 0.8165 (ttp-110) cc_final: 0.7245 (ptt90) REVERT: A 218 ASP cc_start: 0.8741 (m-30) cc_final: 0.8504 (m-30) REVERT: A 983 ILE cc_start: 0.9280 (OUTLIER) cc_final: 0.8991 (mm) REVERT: A 1071 SER cc_start: 0.9345 (m) cc_final: 0.9129 (m) REVERT: A 1267 MET cc_start: 0.8178 (mtp) cc_final: 0.7935 (mtp) REVERT: B 71 LEU cc_start: 0.7980 (tp) cc_final: 0.7692 (tt) REVERT: B 135 ARG cc_start: 0.7340 (mtt90) cc_final: 0.6952 (mtm-85) REVERT: B 216 GLU cc_start: 0.8187 (tt0) cc_final: 0.7600 (tt0) REVERT: B 244 LEU cc_start: 0.8579 (mp) cc_final: 0.8220 (tp) REVERT: B 313 MET cc_start: 0.9275 (mmm) cc_final: 0.9002 (mmm) REVERT: B 353 LYS cc_start: 0.8554 (mtpt) cc_final: 0.8131 (mtmm) REVERT: B 354 ASP cc_start: 0.8156 (m-30) cc_final: 0.7734 (m-30) REVERT: B 391 ASP cc_start: 0.8684 (m-30) cc_final: 0.8469 (m-30) REVERT: B 444 MET cc_start: 0.8854 (mmt) cc_final: 0.8613 (mmp) REVERT: B 455 SER cc_start: 0.8802 (t) cc_final: 0.8374 (p) REVERT: B 476 ARG cc_start: 0.8231 (ttp-170) cc_final: 0.7764 (ptm160) REVERT: B 531 GLN cc_start: 0.8031 (pm20) cc_final: 0.7811 (pm20) REVERT: B 885 MET cc_start: 0.6032 (tpp) cc_final: 0.5672 (mmt) REVERT: B 939 THR cc_start: 0.9244 (m) cc_final: 0.8759 (p) REVERT: B 1202 LEU cc_start: 0.9545 (tp) cc_final: 0.9270 (tt) REVERT: B 1206 GLU cc_start: 0.8374 (mt-10) cc_final: 0.7932 (mt-10) REVERT: D 202 ILE cc_start: 0.4912 (mm) cc_final: 0.4345 (mt) REVERT: D 204 ASP cc_start: 0.7822 (m-30) cc_final: 0.7022 (t70) REVERT: E 8 ASN cc_start: 0.8800 (m-40) cc_final: 0.8485 (m-40) REVERT: E 50 MET cc_start: 0.8564 (ppp) cc_final: 0.7683 (ppp) REVERT: E 54 GLN cc_start: 0.8870 (mm-40) cc_final: 0.8243 (pt0) REVERT: E 113 GLN cc_start: 0.8170 (pt0) cc_final: 0.7850 (pm20) REVERT: E 179 GLN cc_start: 0.8930 (mt0) cc_final: 0.8640 (mt0) REVERT: F 89 GLU cc_start: 0.8890 (mt-10) cc_final: 0.8584 (mt-10) REVERT: F 119 ARG cc_start: 0.8761 (ttm-80) cc_final: 0.8498 (mtp85) REVERT: F 127 GLU cc_start: 0.8032 (mt-10) cc_final: 0.7659 (mt-10) REVERT: G 25 TYR cc_start: 0.9219 (t80) cc_final: 0.8852 (t80) REVERT: G 28 THR cc_start: 0.8844 (m) cc_final: 0.8313 (p) REVERT: G 32 GLU cc_start: 0.8535 (mt-10) cc_final: 0.8145 (mt-10) REVERT: G 33 GLU cc_start: 0.8403 (mm-30) cc_final: 0.7982 (mm-30) REVERT: G 69 GLU cc_start: 0.7872 (tt0) cc_final: 0.7622 (tt0) REVERT: G 79 PHE cc_start: 0.8178 (t80) cc_final: 0.7696 (t80) REVERT: G 114 LEU cc_start: 0.6676 (mt) cc_final: 0.6442 (tp) REVERT: G 148 GLU cc_start: 0.5376 (pm20) cc_final: 0.5162 (pm20) REVERT: H 138 GLU cc_start: 0.8237 (pt0) cc_final: 0.7989 (pm20) REVERT: I 6 PHE cc_start: 0.6244 (m-80) cc_final: 0.5973 (m-80) REVERT: J 49 MET cc_start: 0.8775 (tpp) cc_final: 0.8271 (tpp) REVERT: K 54 ARG cc_start: 0.8143 (mmm-85) cc_final: 0.7857 (tpt90) REVERT: K 96 ASN cc_start: 0.8671 (m-40) cc_final: 0.8404 (m-40) REVERT: L 54 ARG cc_start: 0.7575 (mtt180) cc_final: 0.7372 (mtt180) outliers start: 39 outliers final: 37 residues processed: 406 average time/residue: 0.1911 time to fit residues: 125.5945 Evaluate side-chains 408 residues out of total 3434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 370 time to evaluate : 0.943 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 PHE Chi-restraints excluded: chain A residue 287 HIS Chi-restraints excluded: chain A residue 454 SER Chi-restraints excluded: chain A residue 470 LEU Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 710 LEU Chi-restraints excluded: chain A residue 907 THR Chi-restraints excluded: chain A residue 920 LEU Chi-restraints excluded: chain A residue 983 ILE Chi-restraints excluded: chain A residue 1057 VAL Chi-restraints excluded: chain A residue 1067 LEU Chi-restraints excluded: chain A residue 1174 PHE Chi-restraints excluded: chain A residue 1420 ASP Chi-restraints excluded: chain A residue 1428 VAL Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 70 ILE Chi-restraints excluded: chain B residue 173 MET Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 415 GLN Chi-restraints excluded: chain B residue 612 GLU Chi-restraints excluded: chain B residue 637 LEU Chi-restraints excluded: chain B residue 1169 MET Chi-restraints excluded: chain B residue 1213 THR Chi-restraints excluded: chain D residue 4 SER Chi-restraints excluded: chain D residue 138 ASN Chi-restraints excluded: chain D residue 215 SER Chi-restraints excluded: chain E residue 115 ASN Chi-restraints excluded: chain F residue 101 ILE Chi-restraints excluded: chain G residue 1 MET Chi-restraints excluded: chain G residue 26 LEU Chi-restraints excluded: chain H residue 33 GLN Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain I residue 98 VAL Chi-restraints excluded: chain I residue 110 PHE Chi-restraints excluded: chain J residue 37 SER Chi-restraints excluded: chain K residue 77 THR Chi-restraints excluded: chain K residue 88 LYS Chi-restraints excluded: chain L residue 61 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 395 random chunks: chunk 352 optimal weight: 0.8980 chunk 284 optimal weight: 0.6980 chunk 354 optimal weight: 0.9980 chunk 214 optimal weight: 3.9990 chunk 374 optimal weight: 6.9990 chunk 155 optimal weight: 5.9990 chunk 56 optimal weight: 4.9990 chunk 343 optimal weight: 5.9990 chunk 296 optimal weight: 2.9990 chunk 250 optimal weight: 4.9990 chunk 10 optimal weight: 5.9990 overall best weight: 1.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A1188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 984 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1025 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 179 GLN L 53 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.110944 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.077309 restraints weight = 63641.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.081397 restraints weight = 29934.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.081642 restraints weight = 15699.828| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.081633 restraints weight = 13711.937| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.081740 restraints weight = 13801.531| |-----------------------------------------------------------------------------| r_work (final): 0.3043 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8617 moved from start: 0.2818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 33905 Z= 0.162 Angle : 0.568 11.557 46198 Z= 0.294 Chirality : 0.043 0.237 5190 Planarity : 0.004 0.053 5630 Dihedral : 16.486 169.756 5346 Min Nonbonded Distance : 1.842 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.81 % Favored : 96.06 % Rotamer: Outliers : 1.37 % Allowed : 12.64 % Favored : 85.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.51 (0.14), residues: 3854 helix: 1.75 (0.15), residues: 1333 sheet: -0.25 (0.20), residues: 608 loop : -0.44 (0.14), residues: 1913 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 72 TYR 0.022 0.001 TYR G 51 PHE 0.023 0.001 PHE A 219 TRP 0.012 0.001 TRP B 561 HIS 0.007 0.001 HIS A 816 Details of bonding type rmsd/Z covalent geometry : bond 0.00375 / 0.16 (33873) covalent geometry : angle 0.56146 / 0.29 (46153) hydrogen bonds : bond 0.03462 / 2.31 ( 1411) hydrogen bonds : angle 4.32331 / 3.08 ( 3876) metal coordination : bond 0.00633 / 0.40 ( 32) metal coordination : angle 2.82841 / 2.19 ( 45) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4950.44 seconds wall clock time: 86 minutes 38.05 seconds (5198.05 seconds total)