Starting phenix.real_space_refine on Thu Jun 19 00:07:03 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hmc_34895/06_2025/8hmc_34895.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hmc_34895/06_2025/8hmc_34895.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8hmc_34895/06_2025/8hmc_34895.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hmc_34895/06_2025/8hmc_34895.map" model { file = "/net/cci-nas-00/data/ceres_data/8hmc_34895/06_2025/8hmc_34895.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hmc_34895/06_2025/8hmc_34895.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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= 0.004 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: 5 Type Number sf(0) Gaussians Zn 2 6.06 5 S 117 5.16 5 C 13846 2.51 5 N 3684 2.21 5 O 4148 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 85 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 21797 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 5686 Number of conformers: 1 Conformer: "" Number of residues, atoms: 712, 5686 Classifications: {'peptide': 712} Link IDs: {'PTRANS': 17, 'TRANS': 694} Chain: "B" Number of atoms: 9690 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1195, 9690 Classifications: {'peptide': 1195} Link IDs: {'PTRANS': 39, 'TRANS': 1155} Chain: "C" Number of atoms: 5246 Number of conformers: 1 Conformer: "" Number of residues, atoms: 640, 5246 Classifications: {'peptide': 640} Link IDs: {'PTRANS': 20, 'TRANS': 619} Chain: "F" Number of atoms: 1173 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 1173 Classifications: {'peptide': 146} Link IDs: {'PTRANS': 6, 'TRANS': 139} Chain: "B" 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} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 14704 SG CYS B1111 66.497 141.939 71.176 1.00136.36 S ATOM 15022 SG CYS B1152 73.785 117.744 76.375 1.00133.59 S ATOM 15045 SG CYS B1155 72.263 118.555 73.143 1.00122.48 S ATOM 15190 SG CYS B1172 69.942 117.401 75.951 1.00123.08 S ATOM 15209 SG CYS B1175 72.343 114.895 74.385 1.00120.90 S Time building chain proxies: 11.51, per 1000 atoms: 0.53 Number of scatterers: 21797 At special positions: 0 Unit cell: (172.7, 169.4, 145.2, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 2 29.99 S 117 16.00 O 4148 8.00 N 3684 7.00 C 13846 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS B 857 " - pdb=" SG CYS B 876 " distance=2.03 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: 4.64 Conformation dependent library (CDL) restraints added in 2.7 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN B2001 " pdb="ZN ZN B2001 " - pdb=" SG CYS B1111 " pdb=" ZN B2002 " pdb="ZN ZN B2002 " - pdb=" SG CYS B1152 " pdb="ZN ZN B2002 " - pdb=" SG CYS B1155 " pdb="ZN ZN B2002 " - pdb=" SG CYS B1175 " pdb="ZN ZN B2002 " - pdb=" SG CYS B1172 " Number of angles added : 6 5370 Ramachandran restraints generated. 2685 Oldfield, 0 Emsley, 2685 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5146 Finding SS restraints... Secondary structure from input PDB file: 85 helices and 28 sheets defined 43.4% alpha, 17.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.53 Creating SS restraints... Processing helix chain 'A' and resid 245 through 247 No H-bonds generated for 'chain 'A' and resid 245 through 247' Processing helix chain 'A' and resid 582 through 592 removed outlier: 3.579A pdb=" N ARG A 592 " --> pdb=" O LYS A 588 " (cutoff:3.500A) Processing helix chain 'A' and resid 594 through 603 Processing helix chain 'A' and resid 607 through 621 Processing helix chain 'A' and resid 623 through 634 removed outlier: 3.888A pdb=" N ILE A 634 " --> pdb=" O CYS A 630 " (cutoff:3.500A) Processing helix chain 'A' and resid 637 through 653 removed outlier: 4.444A pdb=" N LYS A 651 " --> pdb=" O GLU A 647 " (cutoff:3.500A) removed outlier: 4.638A pdb=" N LYS A 652 " --> pdb=" O LYS A 648 " (cutoff:3.500A) Processing helix chain 'A' and resid 656 through 668 removed outlier: 3.859A pdb=" N TYR A 660 " --> pdb=" O VAL A 656 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N GLN A 668 " --> pdb=" O ILE A 664 " (cutoff:3.500A) Processing helix chain 'A' and resid 670 through 681 removed outlier: 3.677A pdb=" N ALA A 674 " --> pdb=" O LYS A 670 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N SER A 681 " --> pdb=" O ALA A 677 " (cutoff:3.500A) Processing helix chain 'A' and resid 683 through 693 removed outlier: 3.606A pdb=" N ILE A 693 " --> pdb=" O GLU A 689 " (cutoff:3.500A) Processing helix chain 'A' and resid 696 through 707 removed outlier: 4.216A pdb=" N THR A 706 " --> pdb=" O ARG A 702 " (cutoff:3.500A) Processing helix chain 'B' and resid 632 through 638 removed outlier: 3.650A pdb=" N ILE B 636 " --> pdb=" O TYR B 632 " (cutoff:3.500A) Processing helix chain 'B' and resid 655 through 668 Processing helix chain 'B' and resid 669 through 681 removed outlier: 3.753A pdb=" N MET B 673 " --> pdb=" O SER B 669 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N GLN B 679 " --> pdb=" O ILE B 675 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N HIS B 680 " --> pdb=" O VAL B 676 " (cutoff:3.500A) Processing helix chain 'B' and resid 682 through 696 Processing helix chain 'B' and resid 699 through 710 Processing helix chain 'B' and resid 711 through 723 removed outlier: 3.991A pdb=" N GLU B 723 " --> pdb=" O GLN B 719 " (cutoff:3.500A) Processing helix chain 'B' and resid 727 through 739 removed outlier: 3.955A pdb=" N ARG B 731 " --> pdb=" O ARG B 727 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ASN B 739 " --> pdb=" O GLN B 735 " (cutoff:3.500A) Processing helix chain 'B' and resid 740 through 752 removed outlier: 3.990A pdb=" N ALA B 744 " --> pdb=" O LYS B 740 " (cutoff:3.500A) Processing helix chain 'B' and resid 753 through 765 removed outlier: 4.252A pdb=" N SER B 757 " --> pdb=" O ARG B 753 " (cutoff:3.500A) Processing helix chain 'B' and resid 766 through 775 removed outlier: 3.996A pdb=" N VAL B 770 " --> pdb=" O ASP B 766 " (cutoff:3.500A) Processing helix chain 'B' and resid 780 through 798 Processing helix chain 'B' and resid 800 through 812 Processing helix chain 'B' and resid 813 through 825 Processing helix chain 'B' and resid 827 through 837 Processing helix chain 'B' and resid 841 through 855 removed outlier: 3.830A pdb=" N GLN B 845 " --> pdb=" O ASN B 841 " (cutoff:3.500A) Processing helix chain 'B' and resid 856 through 868 Processing helix chain 'B' and resid 870 through 880 Processing helix chain 'B' and resid 882 through 894 Processing helix chain 'B' and resid 896 through 912 removed outlier: 4.420A pdb=" N GLY B 900 " --> pdb=" O VAL B 896 " (cutoff:3.500A) Processing helix chain 'B' and resid 914 through 925 Processing helix chain 'B' and resid 927 through 944 removed outlier: 3.611A pdb=" N ALA B 931 " --> pdb=" O ARG B 927 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLU B 944 " --> pdb=" O ASP B 940 " (cutoff:3.500A) Processing helix chain 'B' and resid 948 through 976 removed outlier: 3.868A pdb=" N ILE B 952 " --> pdb=" O ASN B 948 " (cutoff:3.500A) Processing helix chain 'B' and resid 979 through 995 Processing helix chain 'B' and resid 997 through 1005 Processing helix chain 'B' and resid 1007 through 1025 Processing helix chain 'B' and resid 1027 through 1042 Processing helix chain 'B' and resid 1046 through 1061 Processing helix chain 'B' and resid 1063 through 1075 removed outlier: 3.677A pdb=" N CYS B1067 " --> pdb=" O SER B1063 " (cutoff:3.500A) Processing helix chain 'B' and resid 1081 through 1099 removed outlier: 4.038A pdb=" N HIS B1099 " --> pdb=" O ILE B1095 " (cutoff:3.500A) Processing helix chain 'B' and resid 1160 through 1168 Processing helix chain 'B' and resid 1180 through 1195 Processing helix chain 'C' and resid 697 through 711 removed outlier: 3.598A pdb=" N ASP C 711 " --> pdb=" O ASP C 707 " (cutoff:3.500A) Processing helix chain 'C' and resid 715 through 730 removed outlier: 3.949A pdb=" N TYR C 723 " --> pdb=" O TYR C 719 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LEU C 726 " --> pdb=" O CYS C 722 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ASP C 730 " --> pdb=" O LEU C 726 " (cutoff:3.500A) Processing helix chain 'C' and resid 734 through 747 Processing helix chain 'C' and resid 748 through 763 Processing helix chain 'C' and resid 766 through 780 Processing helix chain 'C' and resid 782 through 797 Processing helix chain 'C' and resid 800 through 814 Processing helix chain 'C' and resid 816 through 831 Proline residue: C 826 - end of helix Processing helix chain 'C' and resid 837 through 858 Processing helix chain 'C' and resid 867 through 891 removed outlier: 3.552A pdb=" N ARG C 871 " --> pdb=" O ILE C 867 " (cutoff:3.500A) Processing helix chain 'C' and resid 895 through 917 removed outlier: 3.671A pdb=" N TYR C 916 " --> pdb=" O TYR C 912 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLU C 917 " --> pdb=" O THR C 913 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 934 Processing helix chain 'C' and resid 944 through 962 Processing helix chain 'C' and resid 963 through 978 Processing helix chain 'C' and resid 981 through 996 removed outlier: 3.768A pdb=" N CYS C 985 " --> pdb=" O ASN C 981 " (cutoff:3.500A) Processing helix chain 'C' and resid 1000 through 1012 Processing helix chain 'C' and resid 1015 through 1029 Processing helix chain 'C' and resid 1031 through 1045 removed outlier: 3.949A pdb=" N LYS C1045 " --> pdb=" O ARG C1041 " (cutoff:3.500A) Processing helix chain 'C' and resid 1051 through 1064 Processing helix chain 'C' and resid 1067 through 1079 removed outlier: 3.771A pdb=" N ALA C1071 " --> pdb=" O SER C1067 " (cutoff:3.500A) Processing helix chain 'C' and resid 1084 through 1098 Processing helix chain 'C' and resid 1117 through 1134 removed outlier: 3.918A pdb=" N ILE C1132 " --> pdb=" O ARG C1128 " (cutoff:3.500A) Processing helix chain 'C' and resid 1136 through 1150 Processing helix chain 'C' and resid 1151 through 1154 removed outlier: 4.317A pdb=" N TYR C1154 " --> pdb=" O GLY C1151 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1151 through 1154' Processing helix chain 'C' and resid 1156 through 1172 Processing helix chain 'C' and resid 1175 through 1189 Processing helix chain 'C' and resid 1192 through 1204 Processing helix chain 'C' and resid 1211 through 1228 removed outlier: 3.583A pdb=" N LEU C1215 " --> pdb=" O TYR C1211 " (cutoff:3.500A) Processing helix chain 'C' and resid 1231 through 1246 removed outlier: 3.658A pdb=" N ALA C1235 " --> pdb=" O LYS C1231 " (cutoff:3.500A) Processing helix chain 'C' and resid 1249 through 1263 removed outlier: 4.245A pdb=" N GLU C1253 " --> pdb=" O CYS C1249 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLU C1254 " --> pdb=" O GLY C1250 " (cutoff:3.500A) Processing helix chain 'C' and resid 1265 through 1280 Processing helix chain 'C' and resid 1285 through 1298 Processing helix chain 'C' and resid 1300 through 1315 Processing helix chain 'C' and resid 1319 through 1325 removed outlier: 3.696A pdb=" N LYS C1323 " --> pdb=" O PRO C1319 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ASP C1324 " --> pdb=" O LYS C1320 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N CYS C1325 " --> pdb=" O ILE C1321 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1319 through 1325' Processing helix chain 'C' and resid 1325 through 1334 removed outlier: 4.368A pdb=" N LYS C1334 " --> pdb=" O ARG C1330 " (cutoff:3.500A) Processing helix chain 'F' and resid 31 through 36 Processing helix chain 'F' and resid 37 through 40 removed outlier: 4.326A pdb=" N LEU F 40 " --> pdb=" O ASN F 37 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 37 through 40' Processing helix chain 'F' and resid 48 through 60 removed outlier: 3.534A pdb=" N GLU F 52 " --> pdb=" O GLN F 48 " (cutoff:3.500A) Processing helix chain 'F' and resid 77 through 81 Processing helix chain 'F' and resid 83 through 89 Processing helix chain 'F' and resid 93 through 98 Processing helix chain 'F' and resid 114 through 131 Processing helix chain 'F' and resid 132 through 139 Processing helix chain 'F' and resid 141 through 146 Processing sheet with id=AA1, first strand: chain 'A' and resid 2 through 10 removed outlier: 6.987A pdb=" N MET A 313 " --> pdb=" O LEU A 6 " (cutoff:3.500A) removed outlier: 4.993A pdb=" N THR A 8 " --> pdb=" O ILE A 311 " (cutoff:3.500A) removed outlier: 7.054A pdb=" N ILE A 311 " --> pdb=" O THR A 8 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N GLU A 310 " --> pdb=" O THR A 306 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ASN A 281 " --> pdb=" O THR A 305 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 36 through 40 removed outlier: 3.665A pdb=" N ILE A 44 " --> pdb=" O ILE A 59 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ILE A 59 " --> pdb=" O ILE A 44 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 67 through 71 removed outlier: 7.017A pdb=" N ALA A 82 " --> pdb=" O ASN A 68 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N ILE A 70 " --> pdb=" O ALA A 80 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N ALA A 80 " --> pdb=" O ILE A 70 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N THR A 87 " --> pdb=" O SER A 83 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N VAL A 88 " --> pdb=" O LYS A 106 " (cutoff:3.500A) removed outlier: 4.682A pdb=" N LYS A 106 " --> pdb=" O VAL A 88 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N VAL A 90 " --> pdb=" O GLU A 104 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 113 through 118 removed outlier: 3.682A pdb=" N ASP A 132 " --> pdb=" O GLY A 129 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 152 through 157 removed outlier: 6.711A pdb=" N GLY A 167 " --> pdb=" O ILE A 153 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N CYS A 155 " --> pdb=" O GLY A 165 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N GLY A 165 " --> pdb=" O CYS A 155 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ILE A 172 " --> pdb=" O THR A 168 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 192 through 197 removed outlier: 4.086A pdb=" N CYS A 194 " --> pdb=" O GLY A 212 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N SER A 217 " --> pdb=" O VAL A 213 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 238 through 243 removed outlier: 6.950A pdb=" N SER A 253 " --> pdb=" O ILE A 239 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N ILE A 241 " --> pdb=" O LEU A 251 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N LEU A 251 " --> pdb=" O ILE A 241 " (cutoff:3.500A) removed outlier: 5.092A pdb=" N PHE A 243 " --> pdb=" O PHE A 249 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N PHE A 249 " --> pdb=" O PHE A 243 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N GLY A 254 " --> pdb=" O LYS A 258 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N LYS A 258 " --> pdb=" O GLY A 254 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N CYS A 259 " --> pdb=" O VAL A 272 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N ILE A 270 " --> pdb=" O LEU A 261 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N THR A 263 " --> pdb=" O PHE A 268 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N PHE A 268 " --> pdb=" O THR A 263 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 322 through 324 Processing sheet with id=AA9, first strand: chain 'A' and resid 357 through 363 removed outlier: 7.059A pdb=" N HIS A 370 " --> pdb=" O LYS A 358 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N ILE A 360 " --> pdb=" O ALA A 368 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N ALA A 368 " --> pdb=" O ILE A 360 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N ILE A 362 " --> pdb=" O LYS A 366 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N LYS A 366 " --> pdb=" O ILE A 362 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ILE A 377 " --> pdb=" O LYS A 393 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N LYS A 393 " --> pdb=" O ILE A 377 " (cutoff:3.500A) removed outlier: 7.344A pdb=" N GLY A 379 " --> pdb=" O LEU A 391 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N LEU A 391 " --> pdb=" O GLY A 379 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 403 through 407 removed outlier: 3.640A pdb=" N ILE A 403 " --> pdb=" O CYS A 414 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N VAL A 419 " --> pdb=" O GLU A 431 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N GLU A 431 " --> pdb=" O VAL A 419 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N LEU A 421 " --> pdb=" O GLU A 429 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 438 through 443 removed outlier: 3.736A pdb=" N CYS A 440 " --> pdb=" O GLY A 456 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N ILE A 462 " --> pdb=" O ILE A 475 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 482 through 487 removed outlier: 6.923A pdb=" N VAL A 497 " --> pdb=" O LYS A 483 " (cutoff:3.500A) removed outlier: 4.640A pdb=" N ILE A 485 " --> pdb=" O ALA A 495 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N ALA A 495 " --> pdb=" O ILE A 485 " (cutoff:3.500A) removed outlier: 5.199A pdb=" N ALA A 487 " --> pdb=" O ARG A 493 " (cutoff:3.500A) removed outlier: 7.190A pdb=" N ARG A 493 " --> pdb=" O ALA A 487 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N PHE A 515 " --> pdb=" O VAL A 505 " (cutoff:3.500A) removed outlier: 7.592A pdb=" N ASP A 507 " --> pdb=" O GLN A 513 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N GLN A 513 " --> pdb=" O ASP A 507 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 522 through 525 Processing sheet with id=AB5, first strand: chain 'A' and resid 558 through 563 removed outlier: 5.838A pdb=" N VAL A 559 " --> pdb=" O LEU A 570 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N LEU A 570 " --> pdb=" O VAL A 559 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N GLY A 561 " --> pdb=" O PHE A 568 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 2 through 9 removed outlier: 5.052A pdb=" N PHE B 334 " --> pdb=" O SER B 6 " (cutoff:3.500A) removed outlier: 5.232A pdb=" N LYS B 8 " --> pdb=" O ILE B 332 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N ILE B 332 " --> pdb=" O LYS B 8 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 20 through 22 removed outlier: 3.545A pdb=" N VAL B 40 " --> pdb=" O ASN B 64 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ASN B 64 " --> pdb=" O VAL B 40 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 73 through 78 removed outlier: 4.397A pdb=" N LEU B 75 " --> pdb=" O VAL B 88 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N VAL B 96 " --> pdb=" O GLU B 109 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ALA B 98 " --> pdb=" O LYS B 107 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N LYS B 107 " --> pdb=" O ALA B 98 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N PHE B 100 " --> pdb=" O LEU B 105 " (cutoff:3.500A) removed outlier: 4.734A pdb=" N LEU B 105 " --> pdb=" O PHE B 100 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 119 through 124 removed outlier: 4.291A pdb=" N ASP B 121 " --> pdb=" O ALA B 134 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N ALA B 134 " --> pdb=" O ASP B 121 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N TRP B 151 " --> pdb=" O VAL B 142 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N SER B 144 " --> pdb=" O PRO B 149 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 161 through 164 removed outlier: 7.088A pdb=" N VAL B 180 " --> pdb=" O ARG B 192 " (cutoff:3.500A) removed outlier: 4.728A pdb=" N ARG B 192 " --> pdb=" O VAL B 180 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N VAL B 182 " --> pdb=" O MET B 190 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 214 through 219 removed outlier: 3.814A pdb=" N TYR B 238 " --> pdb=" O ARG B 242 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N ARG B 242 " --> pdb=" O TYR B 238 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 262 through 268 removed outlier: 5.617A pdb=" N ILE B 263 " --> pdb=" O THR B 280 " (cutoff:3.500A) removed outlier: 7.081A pdb=" N THR B 280 " --> pdb=" O ILE B 263 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N THR B 265 " --> pdb=" O SER B 278 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LYS B 302 " --> pdb=" O PHE B 293 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 343 through 345 Processing sheet with id=AC5, first strand: chain 'B' and resid 385 through 388 removed outlier: 3.733A pdb=" N LEU B 404 " --> pdb=" O LEU B 399 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N LEU B 409 " --> pdb=" O ASP B 418 " (cutoff:3.500A) removed outlier: 5.369A pdb=" N ASP B 418 " --> pdb=" O LEU B 409 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 428 through 431 Processing sheet with id=AC7, first strand: chain 'B' and resid 504 through 506 removed outlier: 3.700A pdb=" N VAL B 522 " --> pdb=" O ASN B 532 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N ASN B 532 " --> pdb=" O VAL B 522 " (cutoff:3.500A) removed outlier: 7.244A pdb=" N THR B 524 " --> pdb=" O LEU B 530 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N LEU B 530 " --> pdb=" O THR B 524 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 544 through 545 removed outlier: 3.532A pdb=" N ALA B 553 " --> pdb=" O SER B 544 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N ILE B 563 " --> pdb=" O LEU B 574 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N GLU B 572 " --> pdb=" O LYS B 565 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 583 through 586 Processing sheet with id=AD1, first strand: chain 'B' and resid 619 through 624 removed outlier: 6.629A pdb=" N LYS B 629 " --> pdb=" O CYS B 621 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N TYR B 623 " --> pdb=" O GLN B 627 " (cutoff:3.500A) removed outlier: 6.178A pdb=" N GLN B 627 " --> pdb=" O TYR B 623 " (cutoff:3.500A) 1065 hydrogen bonds defined for protein. 3063 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 8.45 Time building geometry restraints manager: 5.59 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 6792 1.34 - 1.46: 3683 1.46 - 1.58: 11563 1.58 - 1.70: 0 1.70 - 1.82: 174 Bond restraints: 22212 Sorted by residual: bond pdb=" CG LEU C 710 " pdb=" CD1 LEU C 710 " ideal model delta sigma weight residual 1.521 1.342 0.179 3.30e-02 9.18e+02 2.93e+01 bond pdb=" N PRO F 85 " pdb=" CD PRO F 85 " ideal model delta sigma weight residual 1.473 1.540 -0.067 1.40e-02 5.10e+03 2.30e+01 bond pdb=" N PRO F 85 " pdb=" CA PRO F 85 " ideal model delta sigma weight residual 1.469 1.410 0.060 1.25e-02 6.40e+03 2.27e+01 bond pdb=" N PRO B 640 " pdb=" CA PRO B 640 " ideal model delta sigma weight residual 1.469 1.521 -0.052 1.28e-02 6.10e+03 1.65e+01 bond pdb=" CG GLN F 121 " pdb=" CD GLN F 121 " ideal model delta sigma weight residual 1.516 1.431 0.085 2.50e-02 1.60e+03 1.15e+01 ... (remaining 22207 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.71: 29780 2.71 - 5.42: 181 5.42 - 8.13: 24 8.13 - 10.83: 2 10.83 - 13.54: 2 Bond angle restraints: 29989 Sorted by residual: angle pdb=" C SER B1104 " pdb=" N PRO B1105 " pdb=" CA PRO B1105 " ideal model delta sigma weight residual 120.03 109.91 10.12 9.90e-01 1.02e+00 1.05e+02 angle pdb=" C LYS B 49 " pdb=" CA LYS B 49 " pdb=" CB LYS B 49 " ideal model delta sigma weight residual 116.54 110.04 6.50 1.15e+00 7.56e-01 3.19e+01 angle pdb=" N PRO B1105 " pdb=" CA PRO B1105 " pdb=" C PRO B1105 " ideal model delta sigma weight residual 111.41 119.77 -8.36 1.50e+00 4.44e-01 3.11e+01 angle pdb=" C GLN F 121 " pdb=" N ILE F 122 " pdb=" CA ILE F 122 " ideal model delta sigma weight residual 121.35 114.08 7.27 1.58e+00 4.01e-01 2.12e+01 angle pdb=" CB MET A 447 " pdb=" CG MET A 447 " pdb=" SD MET A 447 " ideal model delta sigma weight residual 112.70 99.16 13.54 3.00e+00 1.11e-01 2.04e+01 ... (remaining 29984 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.02: 11781 18.02 - 36.04: 1375 36.04 - 54.06: 342 54.06 - 72.08: 48 72.08 - 90.10: 29 Dihedral angle restraints: 13575 sinusoidal: 5618 harmonic: 7957 Sorted by residual: dihedral pdb=" CB CYS B 857 " pdb=" SG CYS B 857 " pdb=" SG CYS B 876 " pdb=" CB CYS B 876 " ideal model delta sinusoidal sigma weight residual 93.00 175.62 -82.62 1 1.00e+01 1.00e-02 8.37e+01 dihedral pdb=" CA GLN F 64 " pdb=" C GLN F 64 " pdb=" N PRO F 65 " pdb=" CA PRO F 65 " ideal model delta harmonic sigma weight residual -180.00 -156.62 -23.38 0 5.00e+00 4.00e-02 2.19e+01 dihedral pdb=" CA GLU B 839 " pdb=" C GLU B 839 " pdb=" N ARG B 840 " pdb=" CA ARG B 840 " ideal model delta harmonic sigma weight residual 180.00 157.63 22.37 0 5.00e+00 4.00e-02 2.00e+01 ... (remaining 13572 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.087: 3065 0.087 - 0.174: 208 0.174 - 0.261: 6 0.261 - 0.348: 1 0.348 - 0.435: 2 Chirality restraints: 3282 Sorted by residual: chirality pdb=" CG LEU C 710 " pdb=" CB LEU C 710 " pdb=" CD1 LEU C 710 " pdb=" CD2 LEU C 710 " both_signs ideal model delta sigma weight residual False -2.59 -2.15 -0.44 2.00e-01 2.50e+01 4.74e+00 chirality pdb=" CG LEU B 950 " pdb=" CB LEU B 950 " pdb=" CD1 LEU B 950 " pdb=" CD2 LEU B 950 " both_signs ideal model delta sigma weight residual False -2.59 -2.16 -0.43 2.00e-01 2.50e+01 4.69e+00 chirality pdb=" CG LEU C1201 " pdb=" CB LEU C1201 " pdb=" CD1 LEU C1201 " pdb=" CD2 LEU C1201 " both_signs ideal model delta sigma weight residual False -2.59 -2.30 -0.29 2.00e-01 2.50e+01 2.07e+00 ... (remaining 3279 not shown) Planarity restraints: 3872 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PRO B1105 " -0.023 2.00e-02 2.50e+03 4.68e-02 2.19e+01 pdb=" C PRO B1105 " 0.081 2.00e-02 2.50e+03 pdb=" O PRO B1105 " -0.031 2.00e-02 2.50e+03 pdb=" N CYS B1106 " -0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN F 121 " 0.021 2.00e-02 2.50e+03 4.16e-02 1.73e+01 pdb=" CD GLN F 121 " -0.072 2.00e-02 2.50e+03 pdb=" OE1 GLN F 121 " 0.027 2.00e-02 2.50e+03 pdb=" NE2 GLN F 121 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN F 117 " 0.019 2.00e-02 2.50e+03 3.86e-02 1.49e+01 pdb=" C GLN F 117 " -0.067 2.00e-02 2.50e+03 pdb=" O GLN F 117 " 0.025 2.00e-02 2.50e+03 pdb=" N LEU F 118 " 0.022 2.00e-02 2.50e+03 ... (remaining 3869 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 190 2.63 - 3.19: 18838 3.19 - 3.76: 31873 3.76 - 4.33: 41926 4.33 - 4.90: 71084 Nonbonded interactions: 163911 Sorted by model distance: nonbonded pdb=" OD1 ASP A 333 " pdb=" N ASN A 334 " model vdw 2.057 3.120 nonbonded pdb=" NH1 ARG B 47 " pdb=" OD2 ASP B 635 " model vdw 2.097 3.120 nonbonded pdb=" OG SER C1081 " pdb=" O GLN C1083 " model vdw 2.197 3.040 nonbonded pdb=" O LEU A 335 " pdb=" OG1 THR A 336 " model vdw 2.211 3.040 nonbonded pdb=" OG SER A 488 " pdb=" OD1 ASP A 530 " model vdw 2.217 3.040 ... (remaining 163906 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: 4.230 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.850 Check model and map are aligned: 0.150 Set scattering table: 0.180 Process input model: 50.000 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 58.590 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7242 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 : 0.003 0.179 22218 Z= 0.153 Angle : 0.586 13.543 29997 Z= 0.333 Chirality : 0.044 0.435 3282 Planarity : 0.004 0.093 3872 Dihedral : 16.345 90.097 8426 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.96 % Favored : 94.00 % Rotamer: Outliers : 0.13 % Allowed : 13.15 % Favored : 86.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.07 (0.16), residues: 2685 helix: 1.56 (0.16), residues: 1094 sheet: 0.27 (0.22), residues: 580 loop : -2.11 (0.18), residues: 1011 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 91 HIS 0.003 0.000 HIS B 443 PHE 0.009 0.001 PHE A 72 TYR 0.038 0.001 TYR B 445 ARG 0.006 0.000 ARG C 843 Details of bonding type rmsd hydrogen bonds : bond 0.12309 ( 1065) hydrogen bonds : angle 5.11445 ( 3063) metal coordination : bond 0.00320 ( 5) metal coordination : angle 2.98267 ( 6) SS BOND : bond 0.00347 ( 1) SS BOND : angle 0.90956 ( 2) covalent geometry : bond 0.00312 (22212) covalent geometry : angle 0.58408 (29989) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5370 Ramachandran restraints generated. 2685 Oldfield, 0 Emsley, 2685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5370 Ramachandran restraints generated. 2685 Oldfield, 0 Emsley, 2685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 2396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 158 time to evaluate : 2.692 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 67 ILE cc_start: 0.8558 (mm) cc_final: 0.8299 (mt) outliers start: 3 outliers final: 1 residues processed: 161 average time/residue: 0.3228 time to fit residues: 85.0716 Evaluate side-chains 145 residues out of total 2396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 144 time to evaluate : 2.538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 700 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 226 optimal weight: 4.9990 chunk 203 optimal weight: 0.9990 chunk 112 optimal weight: 2.9990 chunk 69 optimal weight: 0.9990 chunk 137 optimal weight: 5.9990 chunk 108 optimal weight: 5.9990 chunk 210 optimal weight: 8.9990 chunk 81 optimal weight: 4.9990 chunk 127 optimal weight: 4.9990 chunk 156 optimal weight: 4.9990 chunk 243 optimal weight: 1.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 402 HIS ** B 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 845 GLN B 872 GLN ** B 948 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1188 ASN B1190 ASN F 35 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.128827 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.100719 restraints weight = 43576.453| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.102812 restraints weight = 23842.112| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.104624 restraints weight = 17969.256| |-----------------------------------------------------------------------------| r_work (final): 0.3549 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7535 moved from start: 0.1184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.100 22218 Z= 0.209 Angle : 0.593 8.736 29997 Z= 0.318 Chirality : 0.045 0.302 3282 Planarity : 0.004 0.063 3872 Dihedral : 4.244 23.581 2918 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.34 % Favored : 92.59 % Rotamer: Outliers : 2.17 % Allowed : 13.48 % Favored : 84.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.16), residues: 2685 helix: 1.50 (0.16), residues: 1124 sheet: 0.20 (0.22), residues: 586 loop : -2.19 (0.18), residues: 975 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 447 HIS 0.006 0.001 HIS B1157 PHE 0.019 0.002 PHE B 275 TYR 0.021 0.001 TYR B 68 ARG 0.005 0.001 ARG A 332 Details of bonding type rmsd hydrogen bonds : bond 0.04576 ( 1065) hydrogen bonds : angle 4.38249 ( 3063) metal coordination : bond 0.00592 ( 5) metal coordination : angle 4.13762 ( 6) SS BOND : bond 0.00625 ( 1) SS BOND : angle 1.42041 ( 2) covalent geometry : bond 0.00493 (22212) covalent geometry : angle 0.58977 (29989) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5370 Ramachandran restraints generated. 2685 Oldfield, 0 Emsley, 2685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5370 Ramachandran restraints generated. 2685 Oldfield, 0 Emsley, 2685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 2396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 145 time to evaluate : 2.739 Fit side-chains REVERT: A 240 ASP cc_start: 0.7653 (t0) cc_final: 0.7215 (t0) REVERT: B 459 PHE cc_start: 0.6105 (m-80) cc_final: 0.5846 (m-10) REVERT: B 760 MET cc_start: 0.7519 (tmm) cc_final: 0.7147 (tmm) REVERT: C 1015 ASN cc_start: 0.6812 (OUTLIER) cc_final: 0.6421 (t0) REVERT: C 1331 GLN cc_start: 0.7898 (OUTLIER) cc_final: 0.7224 (mp10) outliers start: 52 outliers final: 21 residues processed: 184 average time/residue: 0.3284 time to fit residues: 100.2338 Evaluate side-chains 161 residues out of total 2396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 138 time to evaluate : 2.596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 362 ILE Chi-restraints excluded: chain A residue 377 ILE Chi-restraints excluded: chain A residue 392 HIS Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain A residue 530 ASP Chi-restraints excluded: chain A residue 543 ILE Chi-restraints excluded: chain A residue 638 ASP Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 217 ILE Chi-restraints excluded: chain B residue 328 VAL Chi-restraints excluded: chain B residue 503 THR Chi-restraints excluded: chain B residue 581 CYS Chi-restraints excluded: chain B residue 621 CYS Chi-restraints excluded: chain B residue 676 VAL Chi-restraints excluded: chain B residue 715 LEU Chi-restraints excluded: chain B residue 950 LEU Chi-restraints excluded: chain C residue 761 LEU Chi-restraints excluded: chain C residue 965 LEU Chi-restraints excluded: chain C residue 1015 ASN Chi-restraints excluded: chain C residue 1118 VAL Chi-restraints excluded: chain C residue 1331 GLN Chi-restraints excluded: chain F residue 125 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 230 optimal weight: 7.9990 chunk 229 optimal weight: 3.9990 chunk 196 optimal weight: 10.0000 chunk 114 optimal weight: 0.9980 chunk 120 optimal weight: 7.9990 chunk 167 optimal weight: 6.9990 chunk 4 optimal weight: 4.9990 chunk 198 optimal weight: 9.9990 chunk 113 optimal weight: 0.9990 chunk 110 optimal weight: 2.9990 chunk 112 optimal weight: 1.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 46 GLN ** B 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 336 ASN ** B 948 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1075 GLN ** B1076 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1119 GLN B1193 ASN C1033 ASN C1050 ASN C1247 GLN ** F 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 35 GLN F 76 GLN F 145 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.127592 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.099537 restraints weight = 43421.580| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.101288 restraints weight = 30356.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.102483 restraints weight = 21731.785| |-----------------------------------------------------------------------------| r_work (final): 0.3513 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7533 moved from start: 0.1610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 22218 Z= 0.185 Angle : 0.562 8.122 29997 Z= 0.303 Chirality : 0.044 0.209 3282 Planarity : 0.004 0.065 3872 Dihedral : 4.354 23.549 2916 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.82 % Favored : 93.11 % Rotamer: Outliers : 2.71 % Allowed : 15.69 % Favored : 81.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.15 (0.16), residues: 2685 helix: 1.51 (0.16), residues: 1124 sheet: 0.10 (0.22), residues: 581 loop : -2.22 (0.18), residues: 980 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 447 HIS 0.006 0.001 HIS B1157 PHE 0.017 0.002 PHE B 275 TYR 0.018 0.001 TYR B 68 ARG 0.003 0.000 ARG C 843 Details of bonding type rmsd hydrogen bonds : bond 0.04267 ( 1065) hydrogen bonds : angle 4.28699 ( 3063) metal coordination : bond 0.00426 ( 5) metal coordination : angle 3.97378 ( 6) SS BOND : bond 0.00636 ( 1) SS BOND : angle 1.51176 ( 2) covalent geometry : bond 0.00431 (22212) covalent geometry : angle 0.55874 (29989) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5370 Ramachandran restraints generated. 2685 Oldfield, 0 Emsley, 2685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5370 Ramachandran restraints generated. 2685 Oldfield, 0 Emsley, 2685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 2396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 144 time to evaluate : 2.747 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 40 VAL cc_start: 0.8126 (OUTLIER) cc_final: 0.7904 (m) REVERT: A 240 ASP cc_start: 0.7643 (t0) cc_final: 0.7198 (t0) REVERT: A 333 ASP cc_start: 0.7935 (t0) cc_final: 0.7720 (t0) REVERT: A 486 ASP cc_start: 0.8036 (t0) cc_final: 0.7834 (t70) REVERT: B 760 MET cc_start: 0.7487 (tmm) cc_final: 0.7112 (tmm) REVERT: B 950 LEU cc_start: 0.7999 (OUTLIER) cc_final: 0.7772 (pp) REVERT: B 1037 ARG cc_start: 0.6927 (OUTLIER) cc_final: 0.6503 (ttm-80) REVERT: C 838 TYR cc_start: 0.4558 (OUTLIER) cc_final: 0.3396 (m-80) REVERT: C 977 LEU cc_start: 0.6719 (mt) cc_final: 0.6261 (mp) REVERT: C 1015 ASN cc_start: 0.6914 (OUTLIER) cc_final: 0.6510 (t0) REVERT: C 1179 MET cc_start: 0.7665 (mtm) cc_final: 0.7438 (mtm) REVERT: C 1331 GLN cc_start: 0.8105 (OUTLIER) cc_final: 0.7489 (mp10) outliers start: 65 outliers final: 35 residues processed: 195 average time/residue: 0.3070 time to fit residues: 98.9225 Evaluate side-chains 173 residues out of total 2396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 132 time to evaluate : 2.624 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 362 ILE Chi-restraints excluded: chain A residue 377 ILE Chi-restraints excluded: chain A residue 392 HIS Chi-restraints excluded: chain A residue 530 ASP Chi-restraints excluded: chain A residue 543 ILE Chi-restraints excluded: chain A residue 638 ASP Chi-restraints excluded: chain A residue 688 LYS Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 29 ILE Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 74 TYR Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 121 ASP Chi-restraints excluded: chain B residue 217 ILE Chi-restraints excluded: chain B residue 328 VAL Chi-restraints excluded: chain B residue 503 THR Chi-restraints excluded: chain B residue 581 CYS Chi-restraints excluded: chain B residue 582 TRP Chi-restraints excluded: chain B residue 602 MET Chi-restraints excluded: chain B residue 676 VAL Chi-restraints excluded: chain B residue 715 LEU Chi-restraints excluded: chain B residue 823 ARG Chi-restraints excluded: chain B residue 833 LEU Chi-restraints excluded: chain B residue 839 GLU Chi-restraints excluded: chain B residue 950 LEU Chi-restraints excluded: chain B residue 1037 ARG Chi-restraints excluded: chain B residue 1077 LEU Chi-restraints excluded: chain C residue 761 LEU Chi-restraints excluded: chain C residue 838 TYR Chi-restraints excluded: chain C residue 992 LEU Chi-restraints excluded: chain C residue 1015 ASN Chi-restraints excluded: chain C residue 1158 LEU Chi-restraints excluded: chain C residue 1199 LEU Chi-restraints excluded: chain C residue 1331 GLN Chi-restraints excluded: chain F residue 36 ASN Chi-restraints excluded: chain F residue 94 SER Chi-restraints excluded: chain F residue 125 ILE Chi-restraints excluded: chain F residue 135 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 195 optimal weight: 9.9990 chunk 130 optimal weight: 5.9990 chunk 243 optimal weight: 4.9990 chunk 29 optimal weight: 10.0000 chunk 154 optimal weight: 6.9990 chunk 44 optimal weight: 5.9990 chunk 176 optimal weight: 3.9990 chunk 264 optimal weight: 8.9990 chunk 20 optimal weight: 0.9980 chunk 122 optimal weight: 5.9990 chunk 109 optimal weight: 2.9990 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 17 ASN ** B 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 69 HIS ** B1076 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 768 GLN C 879 GLN C1014 ASN C1033 ASN F 48 GLN ** F 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.122955 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.095876 restraints weight = 44601.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.096918 restraints weight = 35933.221| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.098021 restraints weight = 24096.653| |-----------------------------------------------------------------------------| r_work (final): 0.3452 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7662 moved from start: 0.2329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.067 22218 Z= 0.295 Angle : 0.691 9.376 29997 Z= 0.370 Chirality : 0.048 0.225 3282 Planarity : 0.004 0.069 3872 Dihedral : 4.866 23.673 2916 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.11 % Allowed : 8.60 % Favored : 91.28 % Rotamer: Outliers : 4.13 % Allowed : 17.15 % Favored : 78.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.61 (0.16), residues: 2685 helix: 1.07 (0.15), residues: 1125 sheet: -0.11 (0.22), residues: 582 loop : -2.40 (0.17), residues: 978 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 447 HIS 0.007 0.002 HIS B1157 PHE 0.027 0.003 PHE A 166 TYR 0.022 0.002 TYR A 133 ARG 0.005 0.001 ARG A 394 Details of bonding type rmsd hydrogen bonds : bond 0.05445 ( 1065) hydrogen bonds : angle 4.65555 ( 3063) metal coordination : bond 0.00509 ( 5) metal coordination : angle 4.47096 ( 6) SS BOND : bond 0.00788 ( 1) SS BOND : angle 1.99278 ( 2) covalent geometry : bond 0.00698 (22212) covalent geometry : angle 0.68826 (29989) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5370 Ramachandran restraints generated. 2685 Oldfield, 0 Emsley, 2685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5370 Ramachandran restraints generated. 2685 Oldfield, 0 Emsley, 2685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 2396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 137 time to evaluate : 2.419 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 739 ASN cc_start: 0.7665 (t0) cc_final: 0.7245 (t0) REVERT: B 950 LEU cc_start: 0.8249 (OUTLIER) cc_final: 0.8001 (pp) REVERT: B 1089 GLU cc_start: 0.7667 (tm-30) cc_final: 0.7464 (tm-30) REVERT: C 838 TYR cc_start: 0.4924 (OUTLIER) cc_final: 0.3685 (m-80) REVERT: C 1015 ASN cc_start: 0.7339 (OUTLIER) cc_final: 0.6497 (t0) REVERT: C 1331 GLN cc_start: 0.8166 (OUTLIER) cc_final: 0.7665 (mp10) outliers start: 99 outliers final: 58 residues processed: 224 average time/residue: 0.3052 time to fit residues: 111.2266 Evaluate side-chains 190 residues out of total 2396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 128 time to evaluate : 2.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 ILE Chi-restraints excluded: chain A residue 29 PHE Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 139 ASP Chi-restraints excluded: chain A residue 154 THR Chi-restraints excluded: chain A residue 302 VAL Chi-restraints excluded: chain A residue 362 ILE Chi-restraints excluded: chain A residue 377 ILE Chi-restraints excluded: chain A residue 392 HIS Chi-restraints excluded: chain A residue 399 VAL Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 530 ASP Chi-restraints excluded: chain A residue 543 ILE Chi-restraints excluded: chain A residue 555 ILE Chi-restraints excluded: chain A residue 577 THR Chi-restraints excluded: chain A residue 638 ASP Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 29 ILE Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 121 ASP Chi-restraints excluded: chain B residue 217 ILE Chi-restraints excluded: chain B residue 328 VAL Chi-restraints excluded: chain B residue 359 ASP Chi-restraints excluded: chain B residue 397 THR Chi-restraints excluded: chain B residue 438 VAL Chi-restraints excluded: chain B residue 503 THR Chi-restraints excluded: chain B residue 581 CYS Chi-restraints excluded: chain B residue 582 TRP Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 602 MET Chi-restraints excluded: chain B residue 621 CYS Chi-restraints excluded: chain B residue 673 MET Chi-restraints excluded: chain B residue 676 VAL Chi-restraints excluded: chain B residue 715 LEU Chi-restraints excluded: chain B residue 771 VAL Chi-restraints excluded: chain B residue 814 ASN Chi-restraints excluded: chain B residue 823 ARG Chi-restraints excluded: chain B residue 833 LEU Chi-restraints excluded: chain B residue 839 GLU Chi-restraints excluded: chain B residue 887 VAL Chi-restraints excluded: chain B residue 950 LEU Chi-restraints excluded: chain B residue 1077 LEU Chi-restraints excluded: chain C residue 761 LEU Chi-restraints excluded: chain C residue 824 LEU Chi-restraints excluded: chain C residue 838 TYR Chi-restraints excluded: chain C residue 901 THR Chi-restraints excluded: chain C residue 965 LEU Chi-restraints excluded: chain C residue 992 LEU Chi-restraints excluded: chain C residue 1015 ASN Chi-restraints excluded: chain C residue 1141 VAL Chi-restraints excluded: chain C residue 1158 LEU Chi-restraints excluded: chain C residue 1199 LEU Chi-restraints excluded: chain C residue 1331 GLN Chi-restraints excluded: chain F residue 30 GLN Chi-restraints excluded: chain F residue 32 ILE Chi-restraints excluded: chain F residue 89 GLU Chi-restraints excluded: chain F residue 94 SER Chi-restraints excluded: chain F residue 125 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 107 optimal weight: 0.9980 chunk 150 optimal weight: 3.9990 chunk 158 optimal weight: 1.9990 chunk 232 optimal weight: 6.9990 chunk 116 optimal weight: 2.9990 chunk 65 optimal weight: 2.9990 chunk 83 optimal weight: 3.9990 chunk 48 optimal weight: 0.8980 chunk 264 optimal weight: 2.9990 chunk 244 optimal weight: 0.9980 chunk 64 optimal weight: 0.7980 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1076 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 946 ASN ** F 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.126764 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.099581 restraints weight = 43621.527| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.100953 restraints weight = 30550.301| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.101868 restraints weight = 22157.571| |-----------------------------------------------------------------------------| r_work (final): 0.3511 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7562 moved from start: 0.2193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 22218 Z= 0.127 Angle : 0.532 9.468 29997 Z= 0.285 Chirality : 0.043 0.179 3282 Planarity : 0.003 0.064 3872 Dihedral : 4.505 23.763 2916 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.44 % Favored : 93.45 % Rotamer: Outliers : 2.46 % Allowed : 19.62 % Favored : 77.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.25 (0.16), residues: 2685 helix: 1.38 (0.16), residues: 1125 sheet: 0.06 (0.22), residues: 590 loop : -2.23 (0.18), residues: 970 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 91 HIS 0.004 0.001 HIS B 69 PHE 0.016 0.001 PHE B 275 TYR 0.027 0.001 TYR C 709 ARG 0.006 0.000 ARG C 899 Details of bonding type rmsd hydrogen bonds : bond 0.03801 ( 1065) hydrogen bonds : angle 4.25517 ( 3063) metal coordination : bond 0.00250 ( 5) metal coordination : angle 4.06858 ( 6) SS BOND : bond 0.00607 ( 1) SS BOND : angle 1.26958 ( 2) covalent geometry : bond 0.00283 (22212) covalent geometry : angle 0.52856 (29989) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5370 Ramachandran restraints generated. 2685 Oldfield, 0 Emsley, 2685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5370 Ramachandran restraints generated. 2685 Oldfield, 0 Emsley, 2685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 2396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 141 time to evaluate : 2.448 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 240 ASP cc_start: 0.7680 (t0) cc_final: 0.7205 (t0) REVERT: A 690 MET cc_start: 0.7470 (tmm) cc_final: 0.7265 (tmm) REVERT: B 466 ARG cc_start: 0.6813 (mmm160) cc_final: 0.5576 (mmt180) REVERT: B 739 ASN cc_start: 0.7599 (t0) cc_final: 0.7110 (t0) REVERT: B 950 LEU cc_start: 0.8067 (OUTLIER) cc_final: 0.7818 (pp) REVERT: B 1089 GLU cc_start: 0.7622 (tm-30) cc_final: 0.7392 (tm-30) REVERT: B 1126 HIS cc_start: 0.8013 (OUTLIER) cc_final: 0.7725 (t-90) REVERT: B 1155 CYS cc_start: 0.8136 (OUTLIER) cc_final: 0.7914 (p) REVERT: C 838 TYR cc_start: 0.4676 (OUTLIER) cc_final: 0.3616 (m-80) REVERT: C 933 TYR cc_start: 0.7191 (OUTLIER) cc_final: 0.6754 (t80) REVERT: C 977 LEU cc_start: 0.6563 (mt) cc_final: 0.6137 (mp) REVERT: C 1015 ASN cc_start: 0.6899 (OUTLIER) cc_final: 0.6385 (t0) REVERT: C 1253 GLU cc_start: 0.7335 (mt-10) cc_final: 0.7076 (mt-10) REVERT: C 1331 GLN cc_start: 0.8053 (OUTLIER) cc_final: 0.7432 (mp10) outliers start: 59 outliers final: 34 residues processed: 190 average time/residue: 0.3053 time to fit residues: 96.1473 Evaluate side-chains 173 residues out of total 2396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 132 time to evaluate : 2.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 ILE Chi-restraints excluded: chain A residue 29 PHE Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 362 ILE Chi-restraints excluded: chain A residue 377 ILE Chi-restraints excluded: chain A residue 392 HIS Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain A residue 530 ASP Chi-restraints excluded: chain A residue 543 ILE Chi-restraints excluded: chain A residue 638 ASP Chi-restraints excluded: chain B residue 29 ILE Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 121 ASP Chi-restraints excluded: chain B residue 328 VAL Chi-restraints excluded: chain B residue 486 TYR Chi-restraints excluded: chain B residue 503 THR Chi-restraints excluded: chain B residue 582 TRP Chi-restraints excluded: chain B residue 602 MET Chi-restraints excluded: chain B residue 673 MET Chi-restraints excluded: chain B residue 814 ASN Chi-restraints excluded: chain B residue 833 LEU Chi-restraints excluded: chain B residue 839 GLU Chi-restraints excluded: chain B residue 879 LEU Chi-restraints excluded: chain B residue 943 THR Chi-restraints excluded: chain B residue 950 LEU Chi-restraints excluded: chain B residue 1077 LEU Chi-restraints excluded: chain B residue 1126 HIS Chi-restraints excluded: chain B residue 1155 CYS Chi-restraints excluded: chain C residue 761 LEU Chi-restraints excluded: chain C residue 824 LEU Chi-restraints excluded: chain C residue 838 TYR Chi-restraints excluded: chain C residue 933 TYR Chi-restraints excluded: chain C residue 992 LEU Chi-restraints excluded: chain C residue 1015 ASN Chi-restraints excluded: chain C residue 1032 ILE Chi-restraints excluded: chain C residue 1158 LEU Chi-restraints excluded: chain C residue 1199 LEU Chi-restraints excluded: chain C residue 1331 GLN Chi-restraints excluded: chain F residue 83 THR Chi-restraints excluded: chain F residue 125 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 212 optimal weight: 8.9990 chunk 154 optimal weight: 0.0170 chunk 173 optimal weight: 0.9980 chunk 93 optimal weight: 0.0030 chunk 30 optimal weight: 0.7980 chunk 188 optimal weight: 0.5980 chunk 213 optimal weight: 10.0000 chunk 127 optimal weight: 0.4980 chunk 230 optimal weight: 7.9990 chunk 123 optimal weight: 5.9990 chunk 51 optimal weight: 10.0000 overall best weight: 0.3828 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 112 ASN B 872 GLN C 946 ASN ** F 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.129415 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.101587 restraints weight = 43312.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.103131 restraints weight = 29293.360| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.104069 restraints weight = 20723.065| |-----------------------------------------------------------------------------| r_work (final): 0.3536 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7517 moved from start: 0.2098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 22218 Z= 0.097 Angle : 0.496 8.176 29997 Z= 0.265 Chirality : 0.042 0.180 3282 Planarity : 0.003 0.062 3872 Dihedral : 4.165 23.500 2916 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.41 % Favored : 93.52 % Rotamer: Outliers : 2.05 % Allowed : 20.78 % Favored : 77.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.07 (0.16), residues: 2685 helix: 1.66 (0.16), residues: 1126 sheet: 0.17 (0.22), residues: 595 loop : -2.06 (0.18), residues: 964 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 91 HIS 0.006 0.001 HIS C1062 PHE 0.012 0.001 PHE B 275 TYR 0.018 0.001 TYR C 709 ARG 0.002 0.000 ARG B 823 Details of bonding type rmsd hydrogen bonds : bond 0.03115 ( 1065) hydrogen bonds : angle 3.99501 ( 3063) metal coordination : bond 0.00165 ( 5) metal coordination : angle 3.27325 ( 6) SS BOND : bond 0.00543 ( 1) SS BOND : angle 1.13300 ( 2) covalent geometry : bond 0.00202 (22212) covalent geometry : angle 0.49424 (29989) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5370 Ramachandran restraints generated. 2685 Oldfield, 0 Emsley, 2685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5370 Ramachandran restraints generated. 2685 Oldfield, 0 Emsley, 2685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 2396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 149 time to evaluate : 2.738 Fit side-chains revert: symmetry clash REVERT: A 240 ASP cc_start: 0.7693 (t0) cc_final: 0.7223 (t0) REVERT: A 486 ASP cc_start: 0.7672 (t0) cc_final: 0.7463 (t70) REVERT: B 117 SER cc_start: 0.4158 (OUTLIER) cc_final: 0.3888 (t) REVERT: B 466 ARG cc_start: 0.6775 (mmm160) cc_final: 0.5783 (mmt180) REVERT: B 739 ASN cc_start: 0.7618 (t0) cc_final: 0.7100 (t0) REVERT: B 1037 ARG cc_start: 0.6422 (tpt170) cc_final: 0.6164 (ttm-80) REVERT: B 1089 GLU cc_start: 0.7589 (tm-30) cc_final: 0.7344 (tm-30) REVERT: B 1126 HIS cc_start: 0.7921 (OUTLIER) cc_final: 0.7560 (t-90) REVERT: C 744 MET cc_start: 0.6895 (mmm) cc_final: 0.5618 (mtt) REVERT: C 769 ILE cc_start: 0.6498 (OUTLIER) cc_final: 0.6218 (tp) REVERT: C 977 LEU cc_start: 0.6618 (mt) cc_final: 0.6183 (mp) REVERT: C 1015 ASN cc_start: 0.6834 (OUTLIER) cc_final: 0.6388 (t0) REVERT: C 1253 GLU cc_start: 0.7203 (mt-10) cc_final: 0.6932 (mt-10) outliers start: 49 outliers final: 25 residues processed: 191 average time/residue: 0.3588 time to fit residues: 113.4371 Evaluate side-chains 169 residues out of total 2396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 140 time to evaluate : 2.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 PHE Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 362 ILE Chi-restraints excluded: chain A residue 377 ILE Chi-restraints excluded: chain A residue 392 HIS Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain A residue 530 ASP Chi-restraints excluded: chain A residue 638 ASP Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 117 SER Chi-restraints excluded: chain B residue 121 ASP Chi-restraints excluded: chain B residue 328 VAL Chi-restraints excluded: chain B residue 503 THR Chi-restraints excluded: chain B residue 715 LEU Chi-restraints excluded: chain B residue 814 ASN Chi-restraints excluded: chain B residue 833 LEU Chi-restraints excluded: chain B residue 839 GLU Chi-restraints excluded: chain B residue 943 THR Chi-restraints excluded: chain B residue 1077 LEU Chi-restraints excluded: chain B residue 1126 HIS Chi-restraints excluded: chain C residue 761 LEU Chi-restraints excluded: chain C residue 769 ILE Chi-restraints excluded: chain C residue 824 LEU Chi-restraints excluded: chain C residue 901 THR Chi-restraints excluded: chain C residue 992 LEU Chi-restraints excluded: chain C residue 1015 ASN Chi-restraints excluded: chain F residue 83 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 168 optimal weight: 7.9990 chunk 253 optimal weight: 0.7980 chunk 145 optimal weight: 6.9990 chunk 137 optimal weight: 0.9980 chunk 212 optimal weight: 6.9990 chunk 234 optimal weight: 5.9990 chunk 143 optimal weight: 0.0060 chunk 5 optimal weight: 7.9990 chunk 61 optimal weight: 0.3980 chunk 195 optimal weight: 10.0000 chunk 206 optimal weight: 4.9990 overall best weight: 1.4398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 946 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.127236 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.099471 restraints weight = 43873.612| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.100847 restraints weight = 30563.776| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.101745 restraints weight = 21380.447| |-----------------------------------------------------------------------------| r_work (final): 0.3509 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7594 moved from start: 0.2246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 22218 Z= 0.138 Angle : 0.531 9.161 29997 Z= 0.283 Chirality : 0.043 0.183 3282 Planarity : 0.003 0.063 3872 Dihedral : 4.194 23.630 2916 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.74 % Favored : 93.18 % Rotamer: Outliers : 2.55 % Allowed : 20.62 % Favored : 76.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (0.16), residues: 2685 helix: 1.63 (0.16), residues: 1126 sheet: 0.19 (0.22), residues: 591 loop : -2.05 (0.18), residues: 968 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 151 HIS 0.005 0.001 HIS B 69 PHE 0.017 0.001 PHE B 275 TYR 0.015 0.001 TYR B 68 ARG 0.003 0.000 ARG B 823 Details of bonding type rmsd hydrogen bonds : bond 0.03630 ( 1065) hydrogen bonds : angle 4.05077 ( 3063) metal coordination : bond 0.00268 ( 5) metal coordination : angle 3.47555 ( 6) SS BOND : bond 0.00639 ( 1) SS BOND : angle 1.47034 ( 2) covalent geometry : bond 0.00317 (22212) covalent geometry : angle 0.52885 (29989) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5370 Ramachandran restraints generated. 2685 Oldfield, 0 Emsley, 2685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5370 Ramachandran restraints generated. 2685 Oldfield, 0 Emsley, 2685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 2396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 138 time to evaluate : 2.449 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 164 LEU cc_start: 0.8505 (OUTLIER) cc_final: 0.8293 (tp) REVERT: A 240 ASP cc_start: 0.7749 (t0) cc_final: 0.7290 (t0) REVERT: B 11 MET cc_start: 0.6934 (pmm) cc_final: 0.6675 (pmm) REVERT: B 466 ARG cc_start: 0.6744 (mmm160) cc_final: 0.5830 (mmt180) REVERT: B 557 HIS cc_start: 0.7560 (OUTLIER) cc_final: 0.6686 (t70) REVERT: B 673 MET cc_start: 0.6850 (OUTLIER) cc_final: 0.6624 (ttt) REVERT: B 739 ASN cc_start: 0.7639 (t0) cc_final: 0.7126 (t0) REVERT: B 1089 GLU cc_start: 0.7683 (tm-30) cc_final: 0.7454 (tm-30) REVERT: C 769 ILE cc_start: 0.6589 (OUTLIER) cc_final: 0.6314 (tp) REVERT: C 977 LEU cc_start: 0.6628 (mt) cc_final: 0.6180 (mp) REVERT: C 1015 ASN cc_start: 0.7043 (OUTLIER) cc_final: 0.6523 (t0) REVERT: C 1253 GLU cc_start: 0.7367 (mt-10) cc_final: 0.7138 (mt-10) REVERT: C 1331 GLN cc_start: 0.7950 (OUTLIER) cc_final: 0.7361 (mp10) outliers start: 61 outliers final: 42 residues processed: 189 average time/residue: 0.3437 time to fit residues: 108.2269 Evaluate side-chains 180 residues out of total 2396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 132 time to evaluate : 2.703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 LEU Chi-restraints excluded: chain A residue 20 ILE Chi-restraints excluded: chain A residue 29 PHE Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 154 THR Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 362 ILE Chi-restraints excluded: chain A residue 377 ILE Chi-restraints excluded: chain A residue 392 HIS Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 530 ASP Chi-restraints excluded: chain A residue 638 ASP Chi-restraints excluded: chain B residue 20 VAL Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 121 ASP Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain B residue 328 VAL Chi-restraints excluded: chain B residue 503 THR Chi-restraints excluded: chain B residue 557 HIS Chi-restraints excluded: chain B residue 582 TRP Chi-restraints excluded: chain B residue 602 MET Chi-restraints excluded: chain B residue 673 MET Chi-restraints excluded: chain B residue 715 LEU Chi-restraints excluded: chain B residue 771 VAL Chi-restraints excluded: chain B residue 814 ASN Chi-restraints excluded: chain B residue 823 ARG Chi-restraints excluded: chain B residue 833 LEU Chi-restraints excluded: chain B residue 839 GLU Chi-restraints excluded: chain B residue 904 GLN Chi-restraints excluded: chain B residue 943 THR Chi-restraints excluded: chain B residue 1038 LEU Chi-restraints excluded: chain B residue 1077 LEU Chi-restraints excluded: chain C residue 761 LEU Chi-restraints excluded: chain C residue 769 ILE Chi-restraints excluded: chain C residue 824 LEU Chi-restraints excluded: chain C residue 901 THR Chi-restraints excluded: chain C residue 992 LEU Chi-restraints excluded: chain C residue 1015 ASN Chi-restraints excluded: chain C residue 1018 ILE Chi-restraints excluded: chain C residue 1158 LEU Chi-restraints excluded: chain C residue 1331 GLN Chi-restraints excluded: chain F residue 32 ILE Chi-restraints excluded: chain F residue 83 THR Chi-restraints excluded: chain F residue 94 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 162 optimal weight: 3.9990 chunk 138 optimal weight: 3.9990 chunk 154 optimal weight: 6.9990 chunk 204 optimal weight: 0.9990 chunk 206 optimal weight: 0.0270 chunk 144 optimal weight: 4.9990 chunk 78 optimal weight: 5.9990 chunk 136 optimal weight: 2.9990 chunk 69 optimal weight: 2.9990 chunk 122 optimal weight: 4.9990 chunk 94 optimal weight: 0.0670 overall best weight: 1.4182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1076 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 121 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.127110 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.099026 restraints weight = 43778.443| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.101880 restraints weight = 23665.287| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.102912 restraints weight = 16258.335| |-----------------------------------------------------------------------------| r_work (final): 0.3522 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7580 moved from start: 0.2325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 22218 Z= 0.135 Angle : 0.533 10.821 29997 Z= 0.282 Chirality : 0.043 0.281 3282 Planarity : 0.003 0.062 3872 Dihedral : 4.203 23.558 2916 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.82 % Favored : 93.11 % Rotamer: Outliers : 2.88 % Allowed : 20.53 % Favored : 76.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.04 (0.16), residues: 2685 helix: 1.61 (0.16), residues: 1127 sheet: 0.19 (0.22), residues: 591 loop : -2.06 (0.18), residues: 967 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 582 HIS 0.004 0.001 HIS B 69 PHE 0.016 0.001 PHE B 275 TYR 0.020 0.001 TYR B 68 ARG 0.006 0.000 ARG C1121 Details of bonding type rmsd hydrogen bonds : bond 0.03599 ( 1065) hydrogen bonds : angle 4.04183 ( 3063) metal coordination : bond 0.00219 ( 5) metal coordination : angle 3.40422 ( 6) SS BOND : bond 0.00619 ( 1) SS BOND : angle 1.38340 ( 2) covalent geometry : bond 0.00307 (22212) covalent geometry : angle 0.53077 (29989) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5370 Ramachandran restraints generated. 2685 Oldfield, 0 Emsley, 2685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5370 Ramachandran restraints generated. 2685 Oldfield, 0 Emsley, 2685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 2396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 138 time to evaluate : 2.635 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 164 LEU cc_start: 0.8472 (OUTLIER) cc_final: 0.8210 (tp) REVERT: A 240 ASP cc_start: 0.7748 (t0) cc_final: 0.7286 (t0) REVERT: B 11 MET cc_start: 0.6989 (pmm) cc_final: 0.6787 (pmm) REVERT: B 466 ARG cc_start: 0.6732 (mmm160) cc_final: 0.5828 (mmt180) REVERT: B 557 HIS cc_start: 0.7532 (OUTLIER) cc_final: 0.6656 (t70) REVERT: B 571 ASP cc_start: 0.8260 (OUTLIER) cc_final: 0.7841 (t0) REVERT: B 673 MET cc_start: 0.6829 (OUTLIER) cc_final: 0.6593 (ttt) REVERT: B 739 ASN cc_start: 0.7557 (t0) cc_final: 0.6889 (t0) REVERT: B 950 LEU cc_start: 0.7840 (OUTLIER) cc_final: 0.7623 (pp) REVERT: B 1089 GLU cc_start: 0.7656 (tm-30) cc_final: 0.7420 (tm-30) REVERT: B 1126 HIS cc_start: 0.7767 (OUTLIER) cc_final: 0.7419 (t-90) REVERT: C 744 MET cc_start: 0.6632 (mmm) cc_final: 0.5527 (mtt) REVERT: C 769 ILE cc_start: 0.6508 (OUTLIER) cc_final: 0.6240 (tp) REVERT: C 821 GLU cc_start: 0.7663 (tm-30) cc_final: 0.7435 (tm-30) REVERT: C 838 TYR cc_start: 0.4619 (OUTLIER) cc_final: 0.3535 (m-80) REVERT: C 977 LEU cc_start: 0.6671 (mt) cc_final: 0.6220 (mp) REVERT: C 1015 ASN cc_start: 0.6862 (OUTLIER) cc_final: 0.6326 (t0) REVERT: C 1253 GLU cc_start: 0.7396 (mt-10) cc_final: 0.7183 (mt-10) REVERT: C 1318 TYR cc_start: 0.5394 (OUTLIER) cc_final: 0.4119 (m-80) REVERT: C 1331 GLN cc_start: 0.7927 (OUTLIER) cc_final: 0.7321 (mp10) outliers start: 69 outliers final: 48 residues processed: 195 average time/residue: 0.3587 time to fit residues: 115.0019 Evaluate side-chains 191 residues out of total 2396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 132 time to evaluate : 2.806 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 LEU Chi-restraints excluded: chain A residue 20 ILE Chi-restraints excluded: chain A residue 29 PHE Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 154 THR Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 302 VAL Chi-restraints excluded: chain A residue 362 ILE Chi-restraints excluded: chain A residue 377 ILE Chi-restraints excluded: chain A residue 392 HIS Chi-restraints excluded: chain A residue 399 VAL Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 530 ASP Chi-restraints excluded: chain A residue 543 ILE Chi-restraints excluded: chain A residue 638 ASP Chi-restraints excluded: chain B residue 20 VAL Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 121 ASP Chi-restraints excluded: chain B residue 328 VAL Chi-restraints excluded: chain B residue 486 TYR Chi-restraints excluded: chain B residue 493 VAL Chi-restraints excluded: chain B residue 503 THR Chi-restraints excluded: chain B residue 557 HIS Chi-restraints excluded: chain B residue 571 ASP Chi-restraints excluded: chain B residue 582 TRP Chi-restraints excluded: chain B residue 673 MET Chi-restraints excluded: chain B residue 715 LEU Chi-restraints excluded: chain B residue 771 VAL Chi-restraints excluded: chain B residue 814 ASN Chi-restraints excluded: chain B residue 823 ARG Chi-restraints excluded: chain B residue 833 LEU Chi-restraints excluded: chain B residue 839 GLU Chi-restraints excluded: chain B residue 904 GLN Chi-restraints excluded: chain B residue 943 THR Chi-restraints excluded: chain B residue 950 LEU Chi-restraints excluded: chain B residue 1038 LEU Chi-restraints excluded: chain B residue 1077 LEU Chi-restraints excluded: chain B residue 1126 HIS Chi-restraints excluded: chain C residue 761 LEU Chi-restraints excluded: chain C residue 769 ILE Chi-restraints excluded: chain C residue 824 LEU Chi-restraints excluded: chain C residue 838 TYR Chi-restraints excluded: chain C residue 901 THR Chi-restraints excluded: chain C residue 933 TYR Chi-restraints excluded: chain C residue 992 LEU Chi-restraints excluded: chain C residue 1015 ASN Chi-restraints excluded: chain C residue 1018 ILE Chi-restraints excluded: chain C residue 1158 LEU Chi-restraints excluded: chain C residue 1318 TYR Chi-restraints excluded: chain C residue 1331 GLN Chi-restraints excluded: chain F residue 32 ILE Chi-restraints excluded: chain F residue 83 THR Chi-restraints excluded: chain F residue 94 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 116 optimal weight: 3.9990 chunk 38 optimal weight: 0.4980 chunk 214 optimal weight: 20.0000 chunk 203 optimal weight: 1.9990 chunk 55 optimal weight: 2.9990 chunk 53 optimal weight: 0.7980 chunk 79 optimal weight: 7.9990 chunk 250 optimal weight: 5.9990 chunk 157 optimal weight: 3.9990 chunk 59 optimal weight: 3.9990 chunk 197 optimal weight: 4.9990 overall best weight: 2.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1076 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 813 GLN F 76 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.125440 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.096468 restraints weight = 44079.034| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.100184 restraints weight = 24408.256| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.102871 restraints weight = 14720.011| |-----------------------------------------------------------------------------| r_work (final): 0.3527 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7576 moved from start: 0.2502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 22218 Z= 0.176 Angle : 0.565 8.457 29997 Z= 0.301 Chirality : 0.044 0.296 3282 Planarity : 0.003 0.064 3872 Dihedral : 4.344 23.586 2916 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.67 % Favored : 92.25 % Rotamer: Outliers : 2.80 % Allowed : 20.70 % Favored : 76.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.09 (0.16), residues: 2685 helix: 1.52 (0.16), residues: 1127 sheet: 0.11 (0.22), residues: 591 loop : -2.14 (0.18), residues: 967 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 447 HIS 0.004 0.001 HIS B 435 PHE 0.031 0.002 PHE B1184 TYR 0.018 0.001 TYR B 68 ARG 0.004 0.000 ARG B 823 Details of bonding type rmsd hydrogen bonds : bond 0.04061 ( 1065) hydrogen bonds : angle 4.15729 ( 3063) metal coordination : bond 0.00208 ( 5) metal coordination : angle 2.65550 ( 6) SS BOND : bond 0.00678 ( 1) SS BOND : angle 1.61531 ( 2) covalent geometry : bond 0.00410 (22212) covalent geometry : angle 0.56346 (29989) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5370 Ramachandran restraints generated. 2685 Oldfield, 0 Emsley, 2685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5370 Ramachandran restraints generated. 2685 Oldfield, 0 Emsley, 2685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 2396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 132 time to evaluate : 4.973 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 164 LEU cc_start: 0.8436 (OUTLIER) cc_final: 0.8231 (tp) REVERT: A 240 ASP cc_start: 0.7707 (t0) cc_final: 0.7228 (t0) REVERT: A 690 MET cc_start: 0.7749 (tmm) cc_final: 0.7522 (tmm) REVERT: B 466 ARG cc_start: 0.6676 (mmm160) cc_final: 0.5759 (mmt180) REVERT: B 557 HIS cc_start: 0.7573 (OUTLIER) cc_final: 0.6704 (t70) REVERT: B 571 ASP cc_start: 0.8247 (OUTLIER) cc_final: 0.7827 (t0) REVERT: B 673 MET cc_start: 0.6884 (OUTLIER) cc_final: 0.6649 (ttt) REVERT: B 739 ASN cc_start: 0.7485 (t0) cc_final: 0.6873 (t0) REVERT: B 950 LEU cc_start: 0.7802 (OUTLIER) cc_final: 0.7579 (pp) REVERT: B 1089 GLU cc_start: 0.7670 (tm-30) cc_final: 0.7439 (tm-30) REVERT: B 1126 HIS cc_start: 0.7895 (OUTLIER) cc_final: 0.7406 (t-90) REVERT: C 769 ILE cc_start: 0.6486 (OUTLIER) cc_final: 0.6224 (tp) REVERT: C 838 TYR cc_start: 0.4770 (OUTLIER) cc_final: 0.3670 (m-80) REVERT: C 977 LEU cc_start: 0.6699 (mt) cc_final: 0.6236 (mp) REVERT: C 1015 ASN cc_start: 0.6947 (OUTLIER) cc_final: 0.6289 (t0) REVERT: C 1253 GLU cc_start: 0.7414 (mt-10) cc_final: 0.7189 (mt-10) REVERT: C 1318 TYR cc_start: 0.5494 (OUTLIER) cc_final: 0.4296 (m-80) REVERT: C 1331 GLN cc_start: 0.7919 (OUTLIER) cc_final: 0.7272 (mp10) outliers start: 67 outliers final: 48 residues processed: 188 average time/residue: 0.4924 time to fit residues: 160.8725 Evaluate side-chains 187 residues out of total 2396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 128 time to evaluate : 3.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 LEU Chi-restraints excluded: chain A residue 20 ILE Chi-restraints excluded: chain A residue 29 PHE Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 154 THR Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 302 VAL Chi-restraints excluded: chain A residue 362 ILE Chi-restraints excluded: chain A residue 377 ILE Chi-restraints excluded: chain A residue 392 HIS Chi-restraints excluded: chain A residue 399 VAL Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 530 ASP Chi-restraints excluded: chain A residue 543 ILE Chi-restraints excluded: chain A residue 638 ASP Chi-restraints excluded: chain B residue 20 VAL Chi-restraints excluded: chain B residue 29 ILE Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 121 ASP Chi-restraints excluded: chain B residue 328 VAL Chi-restraints excluded: chain B residue 486 TYR Chi-restraints excluded: chain B residue 493 VAL Chi-restraints excluded: chain B residue 503 THR Chi-restraints excluded: chain B residue 535 HIS Chi-restraints excluded: chain B residue 557 HIS Chi-restraints excluded: chain B residue 571 ASP Chi-restraints excluded: chain B residue 582 TRP Chi-restraints excluded: chain B residue 673 MET Chi-restraints excluded: chain B residue 771 VAL Chi-restraints excluded: chain B residue 814 ASN Chi-restraints excluded: chain B residue 833 LEU Chi-restraints excluded: chain B residue 839 GLU Chi-restraints excluded: chain B residue 904 GLN Chi-restraints excluded: chain B residue 943 THR Chi-restraints excluded: chain B residue 950 LEU Chi-restraints excluded: chain B residue 1038 LEU Chi-restraints excluded: chain B residue 1077 LEU Chi-restraints excluded: chain B residue 1126 HIS Chi-restraints excluded: chain C residue 761 LEU Chi-restraints excluded: chain C residue 769 ILE Chi-restraints excluded: chain C residue 824 LEU Chi-restraints excluded: chain C residue 838 TYR Chi-restraints excluded: chain C residue 901 THR Chi-restraints excluded: chain C residue 965 LEU Chi-restraints excluded: chain C residue 992 LEU Chi-restraints excluded: chain C residue 1015 ASN Chi-restraints excluded: chain C residue 1018 ILE Chi-restraints excluded: chain C residue 1158 LEU Chi-restraints excluded: chain C residue 1318 TYR Chi-restraints excluded: chain C residue 1331 GLN Chi-restraints excluded: chain F residue 32 ILE Chi-restraints excluded: chain F residue 83 THR Chi-restraints excluded: chain F residue 94 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 36 optimal weight: 2.9990 chunk 139 optimal weight: 1.9990 chunk 181 optimal weight: 0.6980 chunk 194 optimal weight: 9.9990 chunk 51 optimal weight: 4.9990 chunk 170 optimal weight: 3.9990 chunk 223 optimal weight: 7.9990 chunk 138 optimal weight: 0.9990 chunk 125 optimal weight: 0.6980 chunk 38 optimal weight: 7.9990 chunk 148 optimal weight: 0.5980 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 76 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.127326 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.098906 restraints weight = 43840.990| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.102098 restraints weight = 23907.659| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.103155 restraints weight = 15835.535| |-----------------------------------------------------------------------------| r_work (final): 0.3532 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7566 moved from start: 0.2454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 22218 Z= 0.117 Angle : 0.532 10.278 29997 Z= 0.283 Chirality : 0.042 0.287 3282 Planarity : 0.003 0.061 3872 Dihedral : 4.213 23.330 2916 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.67 % Favored : 93.26 % Rotamer: Outliers : 2.59 % Allowed : 21.12 % Favored : 76.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (0.16), residues: 2685 helix: 1.64 (0.16), residues: 1126 sheet: 0.20 (0.22), residues: 591 loop : -2.06 (0.18), residues: 968 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 91 HIS 0.004 0.001 HIS B 69 PHE 0.040 0.001 PHE B1184 TYR 0.013 0.001 TYR B 68 ARG 0.006 0.000 ARG C1121 Details of bonding type rmsd hydrogen bonds : bond 0.03423 ( 1065) hydrogen bonds : angle 4.02997 ( 3063) metal coordination : bond 0.00137 ( 5) metal coordination : angle 2.50376 ( 6) SS BOND : bond 0.00580 ( 1) SS BOND : angle 1.25546 ( 2) covalent geometry : bond 0.00261 (22212) covalent geometry : angle 0.53033 (29989) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5370 Ramachandran restraints generated. 2685 Oldfield, 0 Emsley, 2685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5370 Ramachandran restraints generated. 2685 Oldfield, 0 Emsley, 2685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 2396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 140 time to evaluate : 3.331 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 164 LEU cc_start: 0.8457 (OUTLIER) cc_final: 0.8194 (tp) REVERT: A 240 ASP cc_start: 0.7723 (t0) cc_final: 0.7243 (t0) REVERT: A 690 MET cc_start: 0.7707 (tmm) cc_final: 0.7418 (tmm) REVERT: B 466 ARG cc_start: 0.6738 (mmm160) cc_final: 0.5864 (mmt180) REVERT: B 557 HIS cc_start: 0.7528 (OUTLIER) cc_final: 0.6671 (t70) REVERT: B 571 ASP cc_start: 0.8236 (OUTLIER) cc_final: 0.7815 (t0) REVERT: B 673 MET cc_start: 0.6767 (OUTLIER) cc_final: 0.6535 (ttt) REVERT: B 723 GLU cc_start: 0.7329 (OUTLIER) cc_final: 0.6554 (pt0) REVERT: B 739 ASN cc_start: 0.7483 (t0) cc_final: 0.6887 (t0) REVERT: B 950 LEU cc_start: 0.7856 (OUTLIER) cc_final: 0.7612 (pp) REVERT: B 1089 GLU cc_start: 0.7621 (tm-30) cc_final: 0.7387 (tm-30) REVERT: B 1126 HIS cc_start: 0.7914 (OUTLIER) cc_final: 0.7399 (t-90) REVERT: C 744 MET cc_start: 0.6741 (mmm) cc_final: 0.5557 (mtt) REVERT: C 769 ILE cc_start: 0.6480 (OUTLIER) cc_final: 0.6203 (tp) REVERT: C 821 GLU cc_start: 0.7656 (tm-30) cc_final: 0.7445 (tm-30) REVERT: C 927 LEU cc_start: 0.6555 (tp) cc_final: 0.6325 (tp) REVERT: C 977 LEU cc_start: 0.6678 (mt) cc_final: 0.6221 (mp) REVERT: C 1015 ASN cc_start: 0.6844 (OUTLIER) cc_final: 0.6268 (t0) REVERT: C 1253 GLU cc_start: 0.7368 (mt-10) cc_final: 0.7147 (mt-10) REVERT: C 1318 TYR cc_start: 0.5430 (OUTLIER) cc_final: 0.4216 (m-80) REVERT: C 1331 GLN cc_start: 0.7884 (OUTLIER) cc_final: 0.7282 (mp10) outliers start: 62 outliers final: 48 residues processed: 193 average time/residue: 0.3207 time to fit residues: 102.3981 Evaluate side-chains 190 residues out of total 2396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 131 time to evaluate : 3.108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 LEU Chi-restraints excluded: chain A residue 20 ILE Chi-restraints excluded: chain A residue 29 PHE Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 154 THR Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 302 VAL Chi-restraints excluded: chain A residue 362 ILE Chi-restraints excluded: chain A residue 377 ILE Chi-restraints excluded: chain A residue 392 HIS Chi-restraints excluded: chain A residue 399 VAL Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 530 ASP Chi-restraints excluded: chain A residue 543 ILE Chi-restraints excluded: chain A residue 638 ASP Chi-restraints excluded: chain B residue 20 VAL Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 121 ASP Chi-restraints excluded: chain B residue 328 VAL Chi-restraints excluded: chain B residue 486 TYR Chi-restraints excluded: chain B residue 493 VAL Chi-restraints excluded: chain B residue 503 THR Chi-restraints excluded: chain B residue 535 HIS Chi-restraints excluded: chain B residue 557 HIS Chi-restraints excluded: chain B residue 571 ASP Chi-restraints excluded: chain B residue 673 MET Chi-restraints excluded: chain B residue 715 LEU Chi-restraints excluded: chain B residue 723 GLU Chi-restraints excluded: chain B residue 771 VAL Chi-restraints excluded: chain B residue 814 ASN Chi-restraints excluded: chain B residue 823 ARG Chi-restraints excluded: chain B residue 833 LEU Chi-restraints excluded: chain B residue 839 GLU Chi-restraints excluded: chain B residue 904 GLN Chi-restraints excluded: chain B residue 943 THR Chi-restraints excluded: chain B residue 950 LEU Chi-restraints excluded: chain B residue 1038 LEU Chi-restraints excluded: chain B residue 1077 LEU Chi-restraints excluded: chain B residue 1126 HIS Chi-restraints excluded: chain C residue 761 LEU Chi-restraints excluded: chain C residue 769 ILE Chi-restraints excluded: chain C residue 824 LEU Chi-restraints excluded: chain C residue 901 THR Chi-restraints excluded: chain C residue 965 LEU Chi-restraints excluded: chain C residue 992 LEU Chi-restraints excluded: chain C residue 1015 ASN Chi-restraints excluded: chain C residue 1018 ILE Chi-restraints excluded: chain C residue 1158 LEU Chi-restraints excluded: chain C residue 1318 TYR Chi-restraints excluded: chain C residue 1331 GLN Chi-restraints excluded: chain F residue 32 ILE Chi-restraints excluded: chain F residue 83 THR Chi-restraints excluded: chain F residue 94 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 252 optimal weight: 0.9980 chunk 19 optimal weight: 1.9990 chunk 110 optimal weight: 3.9990 chunk 8 optimal weight: 4.9990 chunk 262 optimal weight: 3.9990 chunk 7 optimal weight: 0.9990 chunk 41 optimal weight: 1.9990 chunk 167 optimal weight: 10.0000 chunk 241 optimal weight: 0.9980 chunk 222 optimal weight: 6.9990 chunk 136 optimal weight: 1.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B1076 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 946 ASN C1062 HIS F 76 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.126623 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.097654 restraints weight = 44103.429| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.101346 restraints weight = 24278.249| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.103865 restraints weight = 14600.612| |-----------------------------------------------------------------------------| r_work (final): 0.3543 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7551 moved from start: 0.2534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 22218 Z= 0.135 Angle : 0.539 9.555 29997 Z= 0.287 Chirality : 0.043 0.267 3282 Planarity : 0.003 0.063 3872 Dihedral : 4.218 23.290 2916 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.19 % Favored : 92.74 % Rotamer: Outliers : 2.71 % Allowed : 20.91 % Favored : 76.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.03 (0.16), residues: 2685 helix: 1.64 (0.16), residues: 1124 sheet: 0.18 (0.22), residues: 591 loop : -2.09 (0.18), residues: 970 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 91 HIS 0.007 0.001 HIS C1062 PHE 0.035 0.001 PHE B1184 TYR 0.015 0.001 TYR B 68 ARG 0.008 0.000 ARG C1121 Details of bonding type rmsd hydrogen bonds : bond 0.03609 ( 1065) hydrogen bonds : angle 4.04266 ( 3063) metal coordination : bond 0.00137 ( 5) metal coordination : angle 2.38759 ( 6) SS BOND : bond 0.00636 ( 1) SS BOND : angle 1.40872 ( 2) covalent geometry : bond 0.00309 (22212) covalent geometry : angle 0.53756 (29989) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7685.09 seconds wall clock time: 139 minutes 9.61 seconds (8349.61 seconds total)