Starting phenix.real_space_refine on Wed Nov 20 18:36:00 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hmc_34895/11_2024/8hmc_34895.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hmc_34895/11_2024/8hmc_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hmc_34895/11_2024/8hmc_34895.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hmc_34895/11_2024/8hmc_34895.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hmc_34895/11_2024/8hmc_34895.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hmc_34895/11_2024/8hmc_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): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/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: 12.22, per 1000 atoms: 0.56 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: 4.88 Conformation dependent library (CDL) restraints added in 2.9 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: 2.58 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: 9.36 Time building geometry restraints manager: 5.74 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: 1.960 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.900 Check model and map are aligned: 0.160 Set scattering table: 0.200 Process input model: 51.930 Find NCS groups from input model: 0.280 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: 0.000 Load rotamer database and sin/cos tables:3.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 58.580 ------------------------------------------------------------------------------- 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 22212 Z= 0.206 Angle : 0.584 13.543 29989 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 *********************** 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 : 2.326 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: 0.2749 time to fit residues: 72.1621 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 : 2.368 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7412 moved from start: 0.1185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.100 22212 Z= 0.321 Angle : 0.590 8.739 29989 Z= 0.317 Chirality : 0.045 0.304 3282 Planarity : 0.004 0.063 3872 Dihedral : 4.244 23.581 2918 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 6.76 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 *********************** 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 : 2.716 Fit side-chains REVERT: A 240 ASP cc_start: 0.7637 (t0) cc_final: 0.7179 (t0) REVERT: B 459 PHE cc_start: 0.6069 (m-80) cc_final: 0.5826 (m-10) REVERT: B 760 MET cc_start: 0.7591 (tmm) cc_final: 0.7246 (tmm) REVERT: B 1089 GLU cc_start: 0.7361 (tp30) cc_final: 0.7140 (tm-30) REVERT: C 1331 GLN cc_start: 0.7897 (OUTLIER) cc_final: 0.7414 (mp10) outliers start: 52 outliers final: 21 residues processed: 184 average time/residue: 0.3087 time to fit residues: 94.0178 Evaluate side-chains 160 residues out of total 2396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 138 time to evaluate : 2.539 ------------------------------------------------------------------------------- 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 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 135 optimal weight: 4.9990 chunk 75 optimal weight: 4.9990 chunk 202 optimal weight: 2.9990 chunk 165 optimal weight: 10.0000 chunk 67 optimal weight: 4.9990 chunk 243 optimal weight: 5.9990 chunk 263 optimal weight: 4.9990 chunk 217 optimal weight: 10.0000 chunk 241 optimal weight: 6.9990 chunk 83 optimal weight: 0.0020 chunk 195 optimal weight: 7.9990 overall best weight: 3.5996 ------------------------------------------------------------------------------- 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** ** B1076 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1193 ASN C 879 GLN C1033 ASN C1050 ASN C1247 GLN F 35 GLN F 76 GLN ** F 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 145 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7516 moved from start: 0.2048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.066 22212 Z= 0.430 Angle : 0.677 9.330 29989 Z= 0.366 Chirality : 0.047 0.220 3282 Planarity : 0.004 0.067 3872 Dihedral : 4.800 23.882 2916 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.07 % Allowed : 8.23 % Favored : 91.69 % Rotamer: Outliers : 3.42 % Allowed : 16.28 % Favored : 80.30 % 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: -0.52 (0.16), residues: 2685 helix: 1.16 (0.15), residues: 1124 sheet: -0.07 (0.22), residues: 583 loop : -2.37 (0.18), residues: 978 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 447 HIS 0.009 0.002 HIS A 301 PHE 0.028 0.002 PHE A 166 TYR 0.023 0.002 TYR B 68 ARG 0.004 0.001 ARG A 332 *********************** 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 225 residues out of total 2396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 143 time to evaluate : 2.596 Fit side-chains revert: symmetry clash REVERT: A 486 ASP cc_start: 0.8033 (t0) cc_final: 0.7829 (t70) REVERT: B 739 ASN cc_start: 0.7135 (t0) cc_final: 0.6737 (t0) REVERT: B 760 MET cc_start: 0.7570 (tmm) cc_final: 0.7285 (tmm) REVERT: B 823 ARG cc_start: 0.8653 (OUTLIER) cc_final: 0.7769 (mmp80) REVERT: B 1089 GLU cc_start: 0.7742 (tp30) cc_final: 0.7503 (tm-30) REVERT: C 838 TYR cc_start: 0.4613 (OUTLIER) cc_final: 0.3386 (m-80) REVERT: C 1179 MET cc_start: 0.6958 (mtm) cc_final: 0.6660 (mtm) REVERT: C 1331 GLN cc_start: 0.8052 (OUTLIER) cc_final: 0.7703 (mp10) REVERT: F 135 LEU cc_start: 0.8005 (OUTLIER) cc_final: 0.7782 (mm) outliers start: 82 outliers final: 40 residues processed: 208 average time/residue: 0.3150 time to fit residues: 106.9544 Evaluate side-chains 170 residues out of total 2396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 126 time to evaluate : 2.715 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 217 ILE Chi-restraints excluded: chain B residue 328 VAL Chi-restraints excluded: chain B residue 359 ASP 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 676 VAL Chi-restraints excluded: chain B residue 715 LEU Chi-restraints excluded: chain B residue 771 VAL 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 1077 LEU Chi-restraints excluded: chain C residue 761 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 1158 LEU Chi-restraints excluded: chain C residue 1199 LEU Chi-restraints excluded: chain C residue 1331 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 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 240 optimal weight: 1.9990 chunk 183 optimal weight: 7.9990 chunk 126 optimal weight: 3.9990 chunk 26 optimal weight: 1.9990 chunk 116 optimal weight: 0.5980 chunk 163 optimal weight: 6.9990 chunk 244 optimal weight: 0.5980 chunk 259 optimal weight: 0.0870 chunk 127 optimal weight: 0.9990 chunk 231 optimal weight: 5.9990 chunk 69 optimal weight: 0.9990 overall best weight: 0.6562 ------------------------------------------------------------------------------- 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 872 GLN F 48 GLN ** F 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7402 moved from start: 0.1847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 22212 Z= 0.151 Angle : 0.515 8.599 29989 Z= 0.278 Chirality : 0.042 0.172 3282 Planarity : 0.003 0.062 3872 Dihedral : 4.344 23.058 2916 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.00 % Favored : 93.97 % Rotamer: Outliers : 2.30 % Allowed : 18.36 % Favored : 79.34 % 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: 1124 sheet: 0.24 (0.22), residues: 580 loop : -2.21 (0.18), residues: 981 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 91 HIS 0.003 0.001 HIS B 443 PHE 0.013 0.001 PHE B 275 TYR 0.011 0.001 TYR B1059 ARG 0.004 0.000 ARG B 823 *********************** 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 201 residues out of total 2396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 146 time to evaluate : 2.654 Fit side-chains revert: symmetry clash REVERT: A 240 ASP cc_start: 0.7628 (t0) cc_final: 0.7159 (t0) REVERT: A 319 LEU cc_start: 0.8722 (OUTLIER) cc_final: 0.8515 (mt) REVERT: A 333 ASP cc_start: 0.7851 (t0) cc_final: 0.7638 (t0) REVERT: A 447 MET cc_start: 0.6430 (mmm) cc_final: 0.6118 (mmm) REVERT: A 486 ASP cc_start: 0.7964 (t0) cc_final: 0.7731 (t70) REVERT: A 590 LEU cc_start: 0.7783 (OUTLIER) cc_final: 0.7573 (mm) REVERT: B 739 ASN cc_start: 0.7253 (t0) cc_final: 0.6781 (t0) REVERT: B 1089 GLU cc_start: 0.7548 (tp30) cc_final: 0.7281 (tm-30) REVERT: C 977 LEU cc_start: 0.6227 (mt) cc_final: 0.5905 (mp) REVERT: C 1331 GLN cc_start: 0.7944 (OUTLIER) cc_final: 0.7508 (mp10) outliers start: 55 outliers final: 28 residues processed: 191 average time/residue: 0.3038 time to fit residues: 95.4147 Evaluate side-chains 166 residues out of total 2396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 135 time to evaluate : 2.571 ------------------------------------------------------------------------------- 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 319 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 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 590 LEU Chi-restraints excluded: chain A residue 638 ASP 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 503 THR Chi-restraints excluded: chain B residue 582 TRP 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 C residue 761 LEU Chi-restraints excluded: chain C residue 824 LEU Chi-restraints excluded: chain C residue 992 LEU Chi-restraints excluded: chain C residue 1199 LEU Chi-restraints excluded: chain C residue 1331 GLN Chi-restraints excluded: chain F residue 46 LEU 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 215 optimal weight: 2.9990 chunk 147 optimal weight: 3.9990 chunk 3 optimal weight: 2.9990 chunk 192 optimal weight: 9.9990 chunk 106 optimal weight: 0.4980 chunk 221 optimal weight: 1.9990 chunk 179 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 chunk 132 optimal weight: 0.5980 chunk 232 optimal weight: 0.8980 chunk 65 optimal weight: 3.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- 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** ** F 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7413 moved from start: 0.1922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 22212 Z= 0.167 Angle : 0.500 7.881 29989 Z= 0.269 Chirality : 0.042 0.205 3282 Planarity : 0.003 0.062 3872 Dihedral : 4.220 23.483 2916 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.48 % Favored : 93.48 % Rotamer: Outliers : 2.63 % Allowed : 18.57 % Favored : 78.80 % 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: 1.63 (0.16), residues: 1124 sheet: 0.25 (0.22), residues: 590 loop : -2.13 (0.18), residues: 971 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 91 HIS 0.004 0.001 HIS C1062 PHE 0.015 0.001 PHE B 275 TYR 0.021 0.001 TYR C 709 ARG 0.003 0.000 ARG B 823 *********************** 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 205 residues out of total 2396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 142 time to evaluate : 2.523 Fit side-chains revert: symmetry clash REVERT: A 240 ASP cc_start: 0.7725 (t0) cc_final: 0.7257 (t0) REVERT: A 319 LEU cc_start: 0.8723 (OUTLIER) cc_final: 0.8514 (mt) REVERT: A 333 ASP cc_start: 0.7896 (t0) cc_final: 0.7637 (t0) REVERT: A 486 ASP cc_start: 0.7979 (t0) cc_final: 0.7751 (t70) REVERT: A 590 LEU cc_start: 0.7806 (OUTLIER) cc_final: 0.7597 (mm) REVERT: B 466 ARG cc_start: 0.6710 (mmm160) cc_final: 0.5476 (mmt180) REVERT: B 673 MET cc_start: 0.6716 (OUTLIER) cc_final: 0.6462 (ttt) REVERT: B 739 ASN cc_start: 0.7278 (t0) cc_final: 0.6800 (t0) REVERT: B 1037 ARG cc_start: 0.6678 (tpt170) cc_final: 0.6379 (ttm-80) REVERT: B 1089 GLU cc_start: 0.7694 (tp30) cc_final: 0.7441 (tm-30) REVERT: B 1126 HIS cc_start: 0.7690 (OUTLIER) cc_final: 0.7434 (t-90) REVERT: C 769 ILE cc_start: 0.6846 (OUTLIER) cc_final: 0.6537 (tp) REVERT: C 838 TYR cc_start: 0.4261 (OUTLIER) cc_final: 0.3220 (m-80) REVERT: C 933 TYR cc_start: 0.6975 (OUTLIER) cc_final: 0.6238 (t80) REVERT: C 977 LEU cc_start: 0.6259 (mt) cc_final: 0.5960 (mp) REVERT: C 1331 GLN cc_start: 0.7912 (OUTLIER) cc_final: 0.7525 (mp10) outliers start: 63 outliers final: 38 residues processed: 194 average time/residue: 0.3525 time to fit residues: 114.5116 Evaluate side-chains 181 residues out of total 2396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 135 time to evaluate : 3.242 ------------------------------------------------------------------------------- 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 154 THR Chi-restraints excluded: chain A residue 302 VAL Chi-restraints excluded: chain A residue 319 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 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 577 THR Chi-restraints excluded: chain A residue 590 LEU 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 74 TYR 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 493 VAL 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 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 739 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 838 TYR Chi-restraints excluded: chain C residue 933 TYR Chi-restraints excluded: chain C residue 992 LEU 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 125 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 87 optimal weight: 0.5980 chunk 233 optimal weight: 6.9990 chunk 51 optimal weight: 0.5980 chunk 152 optimal weight: 0.7980 chunk 63 optimal weight: 3.9990 chunk 259 optimal weight: 0.7980 chunk 215 optimal weight: 1.9990 chunk 120 optimal weight: 2.9990 chunk 21 optimal weight: 3.9990 chunk 85 optimal weight: 2.9990 chunk 136 optimal weight: 2.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7405 moved from start: 0.2009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 22212 Z= 0.160 Angle : 0.495 8.239 29989 Z= 0.266 Chirality : 0.042 0.182 3282 Planarity : 0.003 0.062 3872 Dihedral : 4.135 23.425 2916 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.41 % Favored : 93.56 % Rotamer: Outliers : 2.71 % Allowed : 19.16 % Favored : 78.13 % 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: 0.11 (0.16), residues: 2685 helix: 1.69 (0.16), residues: 1124 sheet: 0.26 (0.22), residues: 594 loop : -2.07 (0.18), residues: 967 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 97 HIS 0.002 0.001 HIS B1157 PHE 0.014 0.001 PHE B 275 TYR 0.018 0.001 TYR C 709 ARG 0.003 0.000 ARG B 823 *********************** 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 210 residues out of total 2396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 145 time to evaluate : 2.594 Fit side-chains revert: symmetry clash REVERT: A 240 ASP cc_start: 0.7723 (t0) cc_final: 0.7258 (t0) REVERT: A 319 LEU cc_start: 0.8743 (OUTLIER) cc_final: 0.8520 (mt) REVERT: A 486 ASP cc_start: 0.7963 (t0) cc_final: 0.7753 (t70) REVERT: A 590 LEU cc_start: 0.7700 (OUTLIER) cc_final: 0.7496 (mm) REVERT: B 466 ARG cc_start: 0.6714 (mmm160) cc_final: 0.5665 (mmt180) REVERT: B 673 MET cc_start: 0.6672 (OUTLIER) cc_final: 0.6433 (ttt) REVERT: B 1037 ARG cc_start: 0.6681 (tpt170) cc_final: 0.6398 (ttm-80) REVERT: B 1089 GLU cc_start: 0.7669 (tp30) cc_final: 0.7435 (tm-30) REVERT: B 1126 HIS cc_start: 0.7687 (OUTLIER) cc_final: 0.7448 (t-90) REVERT: B 1159 MET cc_start: 0.7001 (tpp) cc_final: 0.6709 (tpp) REVERT: C 769 ILE cc_start: 0.6902 (OUTLIER) cc_final: 0.6612 (tp) REVERT: C 796 MET cc_start: 0.4989 (tmm) cc_final: 0.4676 (tmm) REVERT: C 838 TYR cc_start: 0.4276 (OUTLIER) cc_final: 0.3185 (m-80) REVERT: C 933 TYR cc_start: 0.7057 (OUTLIER) cc_final: 0.6846 (t80) REVERT: C 977 LEU cc_start: 0.6250 (mt) cc_final: 0.5954 (mp) REVERT: C 1015 ASN cc_start: 0.7111 (OUTLIER) cc_final: 0.6902 (t0) REVERT: C 1331 GLN cc_start: 0.7912 (OUTLIER) cc_final: 0.7469 (mp10) outliers start: 65 outliers final: 39 residues processed: 201 average time/residue: 0.3109 time to fit residues: 103.6509 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 : 2.670 ------------------------------------------------------------------------------- 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 154 THR Chi-restraints excluded: chain A residue 319 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 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 577 THR Chi-restraints excluded: chain A residue 590 LEU 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 74 TYR 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 493 VAL Chi-restraints excluded: chain B residue 503 THR Chi-restraints excluded: chain B residue 582 TRP Chi-restraints excluded: chain B residue 673 MET 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 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 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 1141 VAL Chi-restraints excluded: chain C residue 1158 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 Chi-restraints excluded: chain F residue 135 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 249 optimal weight: 4.9990 chunk 29 optimal weight: 9.9990 chunk 147 optimal weight: 5.9990 chunk 189 optimal weight: 0.0370 chunk 146 optimal weight: 0.7980 chunk 218 optimal weight: 0.9990 chunk 144 optimal weight: 1.9990 chunk 258 optimal weight: 7.9990 chunk 161 optimal weight: 10.0000 chunk 157 optimal weight: 5.9990 chunk 119 optimal weight: 2.9990 overall best weight: 1.3664 ------------------------------------------------------------------------------- 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** B1119 GLN F 76 GLN ** F 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7429 moved from start: 0.2126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 22212 Z= 0.198 Angle : 0.524 8.768 29989 Z= 0.280 Chirality : 0.043 0.215 3282 Planarity : 0.003 0.062 3872 Dihedral : 4.152 23.412 2916 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.89 % Favored : 93.07 % Rotamer: Outliers : 2.63 % Allowed : 19.70 % Favored : 77.67 % 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: 0.11 (0.16), residues: 2685 helix: 1.67 (0.16), residues: 1124 sheet: 0.26 (0.22), residues: 591 loop : -2.05 (0.18), residues: 970 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 97 HIS 0.003 0.001 HIS B1157 PHE 0.016 0.001 PHE B 275 TYR 0.014 0.001 TYR C 709 ARG 0.004 0.000 ARG B 823 *********************** 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 196 residues out of total 2396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 133 time to evaluate : 2.708 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 240 ASP cc_start: 0.7774 (t0) cc_final: 0.7281 (t0) REVERT: A 319 LEU cc_start: 0.8758 (OUTLIER) cc_final: 0.8533 (mt) REVERT: A 486 ASP cc_start: 0.7981 (t0) cc_final: 0.7762 (t70) REVERT: B 466 ARG cc_start: 0.6637 (mmm160) cc_final: 0.5629 (mmt180) REVERT: B 673 MET cc_start: 0.6690 (OUTLIER) cc_final: 0.6438 (ttt) REVERT: B 1089 GLU cc_start: 0.7740 (tp30) cc_final: 0.7529 (tm-30) REVERT: B 1126 HIS cc_start: 0.7710 (OUTLIER) cc_final: 0.7463 (t-90) REVERT: B 1159 MET cc_start: 0.7049 (tpp) cc_final: 0.6712 (tpp) REVERT: C 769 ILE cc_start: 0.6926 (OUTLIER) cc_final: 0.6628 (tp) REVERT: C 796 MET cc_start: 0.5020 (tmm) cc_final: 0.4702 (tmm) REVERT: C 838 TYR cc_start: 0.4315 (OUTLIER) cc_final: 0.3267 (m-80) REVERT: C 977 LEU cc_start: 0.6246 (mt) cc_final: 0.5945 (mp) REVERT: C 1331 GLN cc_start: 0.7870 (OUTLIER) cc_final: 0.7492 (mp10) outliers start: 63 outliers final: 48 residues processed: 187 average time/residue: 0.3177 time to fit residues: 98.5592 Evaluate side-chains 184 residues out of total 2396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 130 time to evaluate : 2.673 ------------------------------------------------------------------------------- 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 55 VAL Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 154 THR Chi-restraints excluded: chain A residue 302 VAL Chi-restraints excluded: chain A residue 319 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 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 577 THR 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 74 TYR Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 121 ASP Chi-restraints excluded: chain B residue 167 ASP Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 328 VAL Chi-restraints excluded: chain B residue 493 VAL 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 715 LEU 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 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 992 LEU Chi-restraints excluded: chain C residue 1141 VAL Chi-restraints excluded: chain C residue 1158 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 Chi-restraints excluded: chain F residue 135 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 159 optimal weight: 4.9990 chunk 103 optimal weight: 6.9990 chunk 154 optimal weight: 5.9990 chunk 77 optimal weight: 10.0000 chunk 50 optimal weight: 0.9980 chunk 164 optimal weight: 5.9990 chunk 175 optimal weight: 1.9990 chunk 127 optimal weight: 3.9990 chunk 24 optimal weight: 3.9990 chunk 203 optimal weight: 2.9990 chunk 234 optimal weight: 3.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- 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 946 ASN C1014 ASN F 76 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7506 moved from start: 0.2490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 22212 Z= 0.346 Angle : 0.619 12.135 29989 Z= 0.329 Chirality : 0.045 0.201 3282 Planarity : 0.004 0.066 3872 Dihedral : 4.510 23.892 2916 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.93 % Favored : 91.99 % Rotamer: Outliers : 3.34 % Allowed : 19.45 % Favored : 77.21 % 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: -0.19 (0.16), residues: 2685 helix: 1.43 (0.16), residues: 1122 sheet: 0.09 (0.22), residues: 590 loop : -2.20 (0.18), residues: 973 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 447 HIS 0.005 0.001 HIS B 435 PHE 0.022 0.002 PHE B 275 TYR 0.020 0.002 TYR A 133 ARG 0.006 0.001 ARG C 899 *********************** 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 211 residues out of total 2396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 131 time to evaluate : 2.658 Fit side-chains revert: symmetry clash REVERT: A 240 ASP cc_start: 0.7759 (t0) cc_final: 0.7256 (t0) REVERT: A 486 ASP cc_start: 0.8014 (t0) cc_final: 0.7807 (t70) REVERT: B 466 ARG cc_start: 0.6701 (mmm160) cc_final: 0.5719 (mmt180) REVERT: B 557 HIS cc_start: 0.7378 (OUTLIER) cc_final: 0.6448 (t70) REVERT: B 673 MET cc_start: 0.6847 (OUTLIER) cc_final: 0.6557 (ttt) REVERT: B 739 ASN cc_start: 0.7299 (t0) cc_final: 0.6727 (t0) REVERT: B 1159 MET cc_start: 0.7306 (tpp) cc_final: 0.6947 (tpp) REVERT: C 769 ILE cc_start: 0.6949 (OUTLIER) cc_final: 0.6653 (tp) REVERT: C 838 TYR cc_start: 0.4781 (OUTLIER) cc_final: 0.3633 (m-80) REVERT: C 977 LEU cc_start: 0.6293 (mt) cc_final: 0.5965 (mp) REVERT: C 1015 ASN cc_start: 0.7343 (OUTLIER) cc_final: 0.7077 (t0) REVERT: C 1331 GLN cc_start: 0.7873 (OUTLIER) cc_final: 0.7437 (mp10) REVERT: F 135 LEU cc_start: 0.7916 (OUTLIER) cc_final: 0.7650 (mm) outliers start: 80 outliers final: 52 residues processed: 200 average time/residue: 0.3115 time to fit residues: 103.1517 Evaluate side-chains 182 residues out of total 2396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 123 time to evaluate : 2.718 ------------------------------------------------------------------------------- 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 79 PHE Chi-restraints excluded: chain A residue 101 LEU 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 514 VAL Chi-restraints excluded: chain A residue 530 ASP Chi-restraints excluded: chain A residue 543 ILE Chi-restraints excluded: chain A residue 577 THR 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 74 TYR 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 217 ILE Chi-restraints excluded: chain B residue 243 VAL 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 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 814 ASN 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 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 838 TYR 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 1141 VAL 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 Chi-restraints excluded: chain F residue 125 ILE Chi-restraints excluded: chain F residue 135 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 247 optimal weight: 6.9990 chunk 225 optimal weight: 10.0000 chunk 240 optimal weight: 3.9990 chunk 144 optimal weight: 2.9990 chunk 104 optimal weight: 2.9990 chunk 189 optimal weight: 6.9990 chunk 73 optimal weight: 1.9990 chunk 217 optimal weight: 10.0000 chunk 227 optimal weight: 2.9990 chunk 239 optimal weight: 0.6980 chunk 158 optimal weight: 3.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- 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** B1075 GLN ** B1076 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 768 GLN C 946 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7494 moved from start: 0.2571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 22212 Z= 0.293 Angle : 0.599 11.106 29989 Z= 0.317 Chirality : 0.044 0.258 3282 Planarity : 0.004 0.064 3872 Dihedral : 4.512 23.891 2916 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.56 % Favored : 92.33 % Rotamer: Outliers : 2.96 % Allowed : 20.08 % Favored : 76.96 % 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: -0.22 (0.16), residues: 2685 helix: 1.40 (0.16), residues: 1125 sheet: 0.10 (0.22), residues: 589 loop : -2.21 (0.18), residues: 971 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 447 HIS 0.004 0.001 HIS B1126 PHE 0.018 0.002 PHE B 275 TYR 0.016 0.001 TYR A 133 ARG 0.005 0.000 ARG B 823 *********************** 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 204 residues out of total 2396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 133 time to evaluate : 2.331 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 240 ASP cc_start: 0.7744 (t0) cc_final: 0.7238 (t0) REVERT: A 486 ASP cc_start: 0.7993 (t0) cc_final: 0.7777 (t70) REVERT: B 466 ARG cc_start: 0.6705 (mmm160) cc_final: 0.5769 (mmt180) REVERT: B 557 HIS cc_start: 0.7422 (OUTLIER) cc_final: 0.6560 (t70) REVERT: B 571 ASP cc_start: 0.8279 (OUTLIER) cc_final: 0.7870 (t0) REVERT: B 673 MET cc_start: 0.6772 (OUTLIER) cc_final: 0.6490 (ttt) REVERT: B 739 ASN cc_start: 0.7301 (t0) cc_final: 0.6687 (t0) REVERT: B 1159 MET cc_start: 0.7266 (tpp) cc_final: 0.6875 (tpp) REVERT: C 769 ILE cc_start: 0.6913 (OUTLIER) cc_final: 0.6622 (tp) REVERT: C 838 TYR cc_start: 0.4685 (OUTLIER) cc_final: 0.4031 (m-10) REVERT: C 977 LEU cc_start: 0.6194 (mt) cc_final: 0.5893 (mp) REVERT: C 1015 ASN cc_start: 0.7435 (OUTLIER) cc_final: 0.7156 (t0) REVERT: C 1331 GLN cc_start: 0.7810 (OUTLIER) cc_final: 0.7417 (mp10) outliers start: 71 outliers final: 53 residues processed: 192 average time/residue: 0.3186 time to fit residues: 100.0866 Evaluate side-chains 188 residues out of total 2396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 128 time to evaluate : 2.676 ------------------------------------------------------------------------------- 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 79 PHE Chi-restraints excluded: chain A residue 101 LEU 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 514 VAL Chi-restraints excluded: chain A residue 530 ASP Chi-restraints excluded: chain A residue 543 ILE Chi-restraints excluded: chain A residue 577 THR 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 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 243 VAL 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 557 HIS Chi-restraints excluded: chain B residue 571 ASP 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 887 VAL 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 838 TYR Chi-restraints excluded: chain C residue 933 TYR 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 1141 VAL 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 Chi-restraints excluded: chain F residue 125 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 254 optimal weight: 2.9990 chunk 155 optimal weight: 0.9990 chunk 120 optimal weight: 0.9990 chunk 176 optimal weight: 2.9990 chunk 266 optimal weight: 8.9990 chunk 245 optimal weight: 3.9990 chunk 212 optimal weight: 5.9990 chunk 22 optimal weight: 1.9990 chunk 164 optimal weight: 2.9990 chunk 130 optimal weight: 3.9990 chunk 168 optimal weight: 5.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- 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 ** B1076 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7485 moved from start: 0.2631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 22212 Z= 0.261 Angle : 0.586 13.352 29989 Z= 0.311 Chirality : 0.044 0.257 3282 Planarity : 0.003 0.064 3872 Dihedral : 4.472 23.818 2916 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.75 % Favored : 92.14 % Rotamer: Outliers : 2.71 % Allowed : 20.33 % Favored : 76.96 % 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: -0.18 (0.16), residues: 2685 helix: 1.47 (0.16), residues: 1116 sheet: 0.12 (0.22), residues: 589 loop : -2.22 (0.18), residues: 980 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 447 HIS 0.006 0.001 HIS B 69 PHE 0.018 0.001 PHE B 275 TYR 0.015 0.001 TYR A 133 ARG 0.005 0.000 ARG B 823 ********************** 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 200 residues out of total 2396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 135 time to evaluate : 2.463 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 240 ASP cc_start: 0.7789 (t0) cc_final: 0.7274 (t0) REVERT: A 486 ASP cc_start: 0.7983 (t0) cc_final: 0.7761 (t70) REVERT: B 466 ARG cc_start: 0.6684 (mmm160) cc_final: 0.5791 (mmt180) REVERT: B 557 HIS cc_start: 0.7415 (OUTLIER) cc_final: 0.6570 (t70) REVERT: B 571 ASP cc_start: 0.8266 (OUTLIER) cc_final: 0.7854 (t0) REVERT: B 673 MET cc_start: 0.6729 (OUTLIER) cc_final: 0.6456 (ttt) REVERT: B 739 ASN cc_start: 0.7319 (t0) cc_final: 0.6712 (t0) REVERT: B 1126 HIS cc_start: 0.7683 (OUTLIER) cc_final: 0.7125 (t-90) REVERT: B 1159 MET cc_start: 0.7319 (tpp) cc_final: 0.6918 (tpp) REVERT: C 769 ILE cc_start: 0.6880 (OUTLIER) cc_final: 0.6601 (tp) REVERT: C 838 TYR cc_start: 0.4684 (OUTLIER) cc_final: 0.4035 (m-10) REVERT: C 977 LEU cc_start: 0.6197 (mt) cc_final: 0.5892 (mp) REVERT: C 1015 ASN cc_start: 0.7290 (OUTLIER) cc_final: 0.7009 (t0) REVERT: C 1331 GLN cc_start: 0.7829 (OUTLIER) cc_final: 0.7366 (mp10) outliers start: 65 outliers final: 53 residues processed: 190 average time/residue: 0.3205 time to fit residues: 99.2997 Evaluate side-chains 192 residues out of total 2396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 131 time to evaluate : 2.699 ------------------------------------------------------------------------------- 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 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 577 THR Chi-restraints excluded: chain A residue 590 LEU 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 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 243 VAL 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 557 HIS Chi-restraints excluded: chain B residue 571 ASP 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 887 VAL 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 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 965 LEU Chi-restraints excluded: chain C residue 992 LEU Chi-restraints excluded: chain C residue 1015 ASN Chi-restraints excluded: chain C residue 1092 MET Chi-restraints excluded: chain C residue 1141 VAL 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 36 ASN Chi-restraints excluded: chain F residue 83 THR Chi-restraints excluded: chain F residue 94 SER Chi-restraints excluded: chain F residue 125 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 226 optimal weight: 4.9990 chunk 65 optimal weight: 0.5980 chunk 196 optimal weight: 6.9990 chunk 31 optimal weight: 3.9990 chunk 59 optimal weight: 3.9990 chunk 212 optimal weight: 3.9990 chunk 89 optimal weight: 1.9990 chunk 218 optimal weight: 3.9990 chunk 26 optimal weight: 4.9990 chunk 39 optimal weight: 4.9990 chunk 186 optimal weight: 0.8980 overall best weight: 2.2986 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.124421 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.095442 restraints weight = 44349.004| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.099333 restraints weight = 25147.133| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.100880 restraints weight = 15320.280| |-----------------------------------------------------------------------------| r_work (final): 0.3498 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7631 moved from start: 0.2716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 22212 Z= 0.292 Angle : 0.601 11.235 29989 Z= 0.319 Chirality : 0.044 0.255 3282 Planarity : 0.004 0.064 3872 Dihedral : 4.526 23.850 2916 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.11 % Allowed : 8.01 % Favored : 91.88 % Rotamer: Outliers : 2.84 % Allowed : 20.49 % Favored : 76.67 % 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: 1.42 (0.16), residues: 1117 sheet: 0.08 (0.22), residues: 589 loop : -2.27 (0.18), residues: 979 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 447 HIS 0.006 0.001 HIS B 69 PHE 0.019 0.002 PHE B 275 TYR 0.018 0.001 TYR B 68 ARG 0.007 0.000 ARG B 823 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3565.33 seconds wall clock time: 68 minutes 42.90 seconds (4122.90 seconds total)