Starting phenix.real_space_refine on Sun Aug 24 18:03:30 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hmc_34895/08_2025/8hmc_34895.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hmc_34895/08_2025/8hmc_34895.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8hmc_34895/08_2025/8hmc_34895.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hmc_34895/08_2025/8hmc_34895.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8hmc_34895/08_2025/8hmc_34895.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hmc_34895/08_2025/8hmc_34895.map" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: 4.15, per 1000 atoms: 0.19 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: 1.53 Conformation dependent library (CDL) restraints added in 783.6 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 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: 1.01 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: 3.40 Time building geometry restraints manager: 1.99 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: 2.360 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: 0.030 Extract box with map and model: 0.250 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 19.230 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.040 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:1.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7242 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.179 22218 Z= 0.153 Angle : 0.586 13.543 29997 Z= 0.333 Chirality : 0.044 0.435 3282 Planarity : 0.004 0.093 3872 Dihedral : 16.345 90.097 8426 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.96 % Favored : 94.00 % Rotamer: Outliers : 0.13 % Allowed : 13.15 % Favored : 86.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.006 0.000 ARG C 843 TYR 0.038 0.001 TYR B 445 PHE 0.009 0.001 PHE A 72 TRP 0.015 0.001 TRP A 91 HIS 0.003 0.000 HIS B 443 Details of bonding type rmsd covalent geometry : bond 0.00312 (22212) covalent geometry : angle 0.58408 (29989) SS BOND : bond 0.00347 ( 1) SS BOND : angle 0.90956 ( 2) hydrogen bonds : bond 0.12309 ( 1065) hydrogen bonds : angle 5.11445 ( 3063) metal coordination : bond 0.00320 ( 5) metal coordination : angle 2.98267 ( 6) *********************** 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 : 0.571 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: 0.1109 time to fit residues: 29.1872 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 : 0.646 ------------------------------------------------------------------------------- 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 197 optimal weight: 6.9990 chunk 215 optimal weight: 8.9990 chunk 20 optimal weight: 3.9990 chunk 132 optimal weight: 1.9990 chunk 261 optimal weight: 6.9990 chunk 248 optimal weight: 2.9990 chunk 207 optimal weight: 7.9990 chunk 155 optimal weight: 5.9990 chunk 244 optimal weight: 1.9990 chunk 183 optimal weight: 0.7980 chunk 111 optimal weight: 4.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- 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 948 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1188 ASN B1190 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.128584 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.100283 restraints weight = 43666.492| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.102372 restraints weight = 24137.548| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.103933 restraints weight = 17669.451| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.104298 restraints weight = 15773.143| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.104602 restraints weight = 13646.389| |-----------------------------------------------------------------------------| r_work (final): 0.3539 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7508 moved from start: 0.1259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.093 22218 Z= 0.203 Angle : 0.599 8.836 29997 Z= 0.320 Chirality : 0.045 0.235 3282 Planarity : 0.004 0.064 3872 Dihedral : 4.288 23.602 2918 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.41 % Favored : 92.51 % Rotamer: Outliers : 2.30 % Allowed : 13.48 % Favored : 84.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.13 (0.16), residues: 2685 helix: 1.47 (0.16), residues: 1124 sheet: 0.16 (0.22), residues: 589 loop : -2.18 (0.18), residues: 972 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 332 TYR 0.021 0.002 TYR B 68 PHE 0.020 0.002 PHE B 275 TRP 0.025 0.002 TRP B 447 HIS 0.006 0.001 HIS B1157 Details of bonding type rmsd covalent geometry : bond 0.00476 (22212) covalent geometry : angle 0.59658 (29989) SS BOND : bond 0.00698 ( 1) SS BOND : angle 1.49126 ( 2) hydrogen bonds : bond 0.04608 ( 1065) hydrogen bonds : angle 4.38646 ( 3063) metal coordination : bond 0.00504 ( 5) metal coordination : angle 4.08702 ( 6) *********************** 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 199 residues out of total 2396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 144 time to evaluate : 0.643 Fit side-chains REVERT: A 240 ASP cc_start: 0.7577 (t0) cc_final: 0.7073 (t0) REVERT: B 760 MET cc_start: 0.7487 (tmm) cc_final: 0.7107 (tmm) REVERT: B 823 ARG cc_start: 0.8554 (OUTLIER) cc_final: 0.8180 (mmp80) REVERT: C 1015 ASN cc_start: 0.6796 (OUTLIER) cc_final: 0.6364 (t0) REVERT: C 1331 GLN cc_start: 0.7905 (OUTLIER) cc_final: 0.7239 (mp10) outliers start: 55 outliers final: 23 residues processed: 186 average time/residue: 0.1354 time to fit residues: 41.3393 Evaluate side-chains 161 residues out of total 2396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 135 time to evaluate : 0.994 ------------------------------------------------------------------------------- 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 582 TRP 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 823 ARG Chi-restraints excluded: chain B residue 950 LEU Chi-restraints excluded: chain C residue 761 LEU Chi-restraints excluded: chain C residue 965 LEU Chi-restraints excluded: chain C residue 1015 ASN Chi-restraints excluded: chain C residue 1201 LEU 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 61 optimal weight: 0.9980 chunk 30 optimal weight: 1.9990 chunk 136 optimal weight: 2.9990 chunk 36 optimal weight: 3.9990 chunk 80 optimal weight: 4.9990 chunk 120 optimal weight: 7.9990 chunk 247 optimal weight: 7.9990 chunk 126 optimal weight: 4.9990 chunk 69 optimal weight: 3.9990 chunk 177 optimal weight: 6.9990 chunk 15 optimal weight: 0.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 46 GLN ** B 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 336 ASN ** B 948 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1075 GLN ** B1076 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1119 GLN B1193 ASN C1033 ASN C1050 ASN C1247 GLN ** F 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 76 GLN F 145 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.127577 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.099424 restraints weight = 43885.031| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.101264 restraints weight = 30856.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.102517 restraints weight = 21726.721| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.102921 restraints weight = 18676.346| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.103251 restraints weight = 16533.190| |-----------------------------------------------------------------------------| r_work (final): 0.3525 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7523 moved from start: 0.1574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 22218 Z= 0.184 Angle : 0.560 8.032 29997 Z= 0.301 Chirality : 0.044 0.205 3282 Planarity : 0.004 0.065 3872 Dihedral : 4.335 23.693 2916 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.00 % Favored : 92.92 % Rotamer: Outliers : 2.63 % Allowed : 15.44 % Favored : 81.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.14 (0.16), residues: 2685 helix: 1.52 (0.16), residues: 1125 sheet: 0.11 (0.22), residues: 581 loop : -2.21 (0.18), residues: 979 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 466 TYR 0.018 0.001 TYR B 68 PHE 0.018 0.002 PHE B 275 TRP 0.014 0.001 TRP B 447 HIS 0.005 0.001 HIS B1157 Details of bonding type rmsd covalent geometry : bond 0.00427 (22212) covalent geometry : angle 0.55718 (29989) SS BOND : bond 0.00653 ( 1) SS BOND : angle 1.52717 ( 2) hydrogen bonds : bond 0.04313 ( 1065) hydrogen bonds : angle 4.28766 ( 3063) metal coordination : bond 0.00431 ( 5) metal coordination : angle 3.95707 ( 6) *********************** 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 204 residues out of total 2396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 141 time to evaluate : 0.888 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 40 VAL cc_start: 0.8080 (OUTLIER) cc_final: 0.7874 (m) REVERT: A 240 ASP cc_start: 0.7647 (t0) cc_final: 0.7209 (t0) REVERT: B 760 MET cc_start: 0.7485 (tmm) cc_final: 0.7115 (tmm) REVERT: B 950 LEU cc_start: 0.7999 (OUTLIER) cc_final: 0.7765 (pp) REVERT: B 1037 ARG cc_start: 0.6918 (OUTLIER) cc_final: 0.6498 (ttm-80) REVERT: C 838 TYR cc_start: 0.4573 (OUTLIER) cc_final: 0.3418 (m-80) REVERT: C 1015 ASN cc_start: 0.6966 (OUTLIER) cc_final: 0.6572 (t0) REVERT: C 1179 MET cc_start: 0.7657 (mtm) cc_final: 0.7417 (mtm) REVERT: C 1331 GLN cc_start: 0.8064 (OUTLIER) cc_final: 0.7446 (mp10) outliers start: 63 outliers final: 35 residues processed: 191 average time/residue: 0.1268 time to fit residues: 39.7487 Evaluate side-chains 172 residues out of total 2396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 131 time to evaluate : 0.788 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 362 ILE Chi-restraints excluded: chain A residue 377 ILE Chi-restraints excluded: chain A residue 392 HIS Chi-restraints excluded: chain A residue 530 ASP Chi-restraints excluded: chain A residue 543 ILE Chi-restraints excluded: chain A residue 638 ASP Chi-restraints excluded: chain A residue 688 LYS Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 29 ILE Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 74 TYR Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 121 ASP Chi-restraints excluded: chain B residue 217 ILE Chi-restraints excluded: chain B residue 328 VAL Chi-restraints excluded: chain B residue 503 THR Chi-restraints excluded: chain B residue 581 CYS Chi-restraints excluded: chain B residue 582 TRP Chi-restraints excluded: chain B residue 602 MET Chi-restraints excluded: chain B residue 676 VAL Chi-restraints excluded: chain B residue 715 LEU Chi-restraints excluded: chain B residue 823 ARG Chi-restraints excluded: chain B residue 833 LEU Chi-restraints excluded: chain B residue 839 GLU Chi-restraints excluded: chain B residue 950 LEU Chi-restraints excluded: chain B residue 1037 ARG Chi-restraints excluded: chain B residue 1077 LEU Chi-restraints excluded: chain C residue 705 LEU Chi-restraints excluded: chain C residue 761 LEU Chi-restraints excluded: chain C residue 838 TYR Chi-restraints excluded: chain C residue 992 LEU Chi-restraints excluded: chain C residue 1015 ASN Chi-restraints excluded: chain C residue 1158 LEU Chi-restraints excluded: chain C residue 1199 LEU Chi-restraints excluded: chain C residue 1331 GLN Chi-restraints excluded: chain F residue 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 163 optimal weight: 10.0000 chunk 10 optimal weight: 3.9990 chunk 51 optimal weight: 0.9980 chunk 195 optimal weight: 10.0000 chunk 19 optimal weight: 1.9990 chunk 29 optimal weight: 10.0000 chunk 172 optimal weight: 3.9990 chunk 131 optimal weight: 0.9980 chunk 48 optimal weight: 7.9990 chunk 63 optimal weight: 1.9990 chunk 84 optimal weight: 3.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- 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 948 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1076 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1033 ASN F 48 GLN ** F 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.126998 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.099743 restraints weight = 43778.290| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.100642 restraints weight = 31775.452| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.101721 restraints weight = 22964.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.102502 restraints weight = 17592.245| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.102767 restraints weight = 15939.375| |-----------------------------------------------------------------------------| r_work (final): 0.3518 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7539 moved from start: 0.1815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 22218 Z= 0.171 Angle : 0.549 7.425 29997 Z= 0.295 Chirality : 0.043 0.183 3282 Planarity : 0.003 0.065 3872 Dihedral : 4.353 23.483 2916 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.37 % Favored : 92.55 % Rotamer: Outliers : 2.96 % Allowed : 17.32 % Favored : 79.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.12 (0.16), residues: 2685 helix: 1.52 (0.16), residues: 1125 sheet: 0.14 (0.22), residues: 578 loop : -2.20 (0.18), residues: 982 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 823 TYR 0.016 0.001 TYR B 68 PHE 0.018 0.002 PHE B 275 TRP 0.011 0.001 TRP B 343 HIS 0.005 0.001 HIS B1157 Details of bonding type rmsd covalent geometry : bond 0.00396 (22212) covalent geometry : angle 0.54677 (29989) SS BOND : bond 0.00652 ( 1) SS BOND : angle 1.52845 ( 2) hydrogen bonds : bond 0.04078 ( 1065) hydrogen bonds : angle 4.22747 ( 3063) metal coordination : bond 0.00353 ( 5) metal coordination : angle 3.66749 ( 6) *********************** 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 219 residues out of total 2396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 148 time to evaluate : 0.636 Fit side-chains revert: symmetry clash REVERT: A 40 VAL cc_start: 0.8073 (OUTLIER) cc_final: 0.7865 (m) REVERT: A 240 ASP cc_start: 0.7671 (t0) cc_final: 0.7213 (t0) REVERT: A 590 LEU cc_start: 0.7932 (OUTLIER) cc_final: 0.7731 (mm) REVERT: B 739 ASN cc_start: 0.7516 (t0) cc_final: 0.7053 (t0) REVERT: B 950 LEU cc_start: 0.8068 (OUTLIER) cc_final: 0.7851 (pp) REVERT: B 1037 ARG cc_start: 0.6913 (OUTLIER) cc_final: 0.6523 (ttm-80) REVERT: C 838 TYR cc_start: 0.4700 (OUTLIER) cc_final: 0.3598 (m-80) REVERT: C 977 LEU cc_start: 0.6682 (mt) cc_final: 0.6227 (mp) REVERT: C 1015 ASN cc_start: 0.6928 (OUTLIER) cc_final: 0.6451 (t0) REVERT: C 1196 LYS cc_start: 0.7238 (mttp) cc_final: 0.7007 (mttp) REVERT: C 1331 GLN cc_start: 0.8103 (OUTLIER) cc_final: 0.7523 (mp10) outliers start: 71 outliers final: 42 residues processed: 204 average time/residue: 0.1255 time to fit residues: 42.2151 Evaluate side-chains 177 residues out of total 2396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 128 time to evaluate : 0.792 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 PHE Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 362 ILE Chi-restraints excluded: chain A residue 377 ILE Chi-restraints excluded: chain A residue 392 HIS Chi-restraints excluded: chain A residue 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 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 503 THR Chi-restraints excluded: chain B residue 581 CYS Chi-restraints excluded: chain B residue 582 TRP Chi-restraints excluded: chain B residue 602 MET Chi-restraints excluded: chain B residue 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 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 950 LEU Chi-restraints excluded: chain B residue 1037 ARG Chi-restraints excluded: chain B residue 1077 LEU Chi-restraints excluded: chain C residue 761 LEU Chi-restraints excluded: chain C residue 824 LEU Chi-restraints excluded: chain C residue 838 TYR Chi-restraints excluded: chain C residue 901 THR Chi-restraints excluded: chain C residue 965 LEU Chi-restraints excluded: chain C residue 992 LEU Chi-restraints excluded: chain C residue 1015 ASN Chi-restraints excluded: chain C residue 1158 LEU Chi-restraints excluded: chain C residue 1199 LEU Chi-restraints excluded: chain C residue 1331 GLN Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 30 GLN 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 118 optimal weight: 5.9990 chunk 40 optimal weight: 3.9990 chunk 260 optimal weight: 1.9990 chunk 59 optimal weight: 3.9990 chunk 250 optimal weight: 5.9990 chunk 3 optimal weight: 1.9990 chunk 109 optimal weight: 2.9990 chunk 225 optimal weight: 9.9990 chunk 76 optimal weight: 20.0000 chunk 133 optimal weight: 4.9990 chunk 87 optimal weight: 0.3980 overall best weight: 2.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1076 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 768 GLN C 946 ASN ** F 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.125803 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.098525 restraints weight = 43871.675| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.099194 restraints weight = 32204.527| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.100183 restraints weight = 23303.640| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.100976 restraints weight = 18642.380| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.101383 restraints weight = 16718.100| |-----------------------------------------------------------------------------| r_work (final): 0.3499 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7606 moved from start: 0.2079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 22218 Z= 0.190 Angle : 0.570 7.948 29997 Z= 0.306 Chirality : 0.044 0.182 3282 Planarity : 0.004 0.066 3872 Dihedral : 4.459 23.899 2916 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.64 % Favored : 92.29 % Rotamer: Outliers : 3.51 % Allowed : 18.61 % Favored : 77.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.18 (0.16), residues: 2685 helix: 1.48 (0.16), residues: 1124 sheet: 0.06 (0.22), residues: 585 loop : -2.21 (0.18), residues: 976 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 823 TYR 0.016 0.001 TYR B 68 PHE 0.020 0.002 PHE B 275 TRP 0.011 0.001 TRP A 691 HIS 0.005 0.001 HIS B1157 Details of bonding type rmsd covalent geometry : bond 0.00443 (22212) covalent geometry : angle 0.56740 (29989) SS BOND : bond 0.00677 ( 1) SS BOND : angle 1.61050 ( 2) hydrogen bonds : bond 0.04273 ( 1065) hydrogen bonds : angle 4.27376 ( 3063) metal coordination : bond 0.00354 ( 5) metal coordination : angle 3.73907 ( 6) *********************** 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 221 residues out of total 2396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 137 time to evaluate : 0.628 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 40 VAL cc_start: 0.8125 (OUTLIER) cc_final: 0.7921 (m) REVERT: A 240 ASP cc_start: 0.7718 (t0) cc_final: 0.7266 (t0) REVERT: B 673 MET cc_start: 0.6946 (OUTLIER) cc_final: 0.6651 (ttt) REVERT: B 739 ASN cc_start: 0.7475 (t0) cc_final: 0.6914 (t0) REVERT: B 950 LEU cc_start: 0.8041 (OUTLIER) cc_final: 0.7828 (pp) REVERT: B 1126 HIS cc_start: 0.7976 (OUTLIER) cc_final: 0.7711 (t-90) REVERT: C 769 ILE cc_start: 0.6553 (OUTLIER) cc_final: 0.6265 (tp) REVERT: C 838 TYR cc_start: 0.4653 (OUTLIER) cc_final: 0.3574 (m-80) REVERT: C 977 LEU cc_start: 0.6591 (mt) cc_final: 0.6166 (mp) REVERT: C 1015 ASN cc_start: 0.7014 (OUTLIER) cc_final: 0.6440 (t0) REVERT: C 1331 GLN cc_start: 0.8086 (OUTLIER) cc_final: 0.7527 (mp10) outliers start: 84 outliers final: 52 residues processed: 210 average time/residue: 0.1199 time to fit residues: 41.6899 Evaluate side-chains 193 residues out of total 2396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 133 time to evaluate : 0.626 ------------------------------------------------------------------------------- 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 40 VAL 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 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 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 1 MET Chi-restraints excluded: chain B residue 29 ILE Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 74 TYR Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 121 ASP Chi-restraints excluded: chain B residue 217 ILE Chi-restraints excluded: chain B residue 328 VAL Chi-restraints excluded: chain B residue 397 THR Chi-restraints excluded: chain B residue 438 VAL Chi-restraints excluded: chain B residue 503 THR Chi-restraints excluded: chain B residue 582 TRP Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 602 MET Chi-restraints excluded: chain B residue 621 CYS Chi-restraints excluded: chain B residue 673 MET Chi-restraints excluded: chain B residue 676 VAL Chi-restraints excluded: chain B residue 715 LEU Chi-restraints excluded: chain B residue 771 VAL Chi-restraints excluded: chain B residue 814 ASN Chi-restraints excluded: chain B residue 823 ARG Chi-restraints excluded: chain B residue 833 LEU Chi-restraints excluded: chain B residue 839 GLU Chi-restraints excluded: chain B residue 950 LEU Chi-restraints excluded: chain B residue 1077 LEU Chi-restraints excluded: chain B residue 1126 HIS Chi-restraints excluded: chain C residue 709 TYR Chi-restraints excluded: chain C residue 761 LEU Chi-restraints excluded: chain C residue 769 ILE Chi-restraints excluded: chain C residue 824 LEU Chi-restraints excluded: chain C residue 838 TYR Chi-restraints excluded: chain C residue 901 THR Chi-restraints excluded: chain C residue 965 LEU Chi-restraints excluded: chain C residue 992 LEU Chi-restraints excluded: chain C residue 1015 ASN Chi-restraints excluded: chain C residue 1018 ILE Chi-restraints excluded: chain C residue 1032 ILE Chi-restraints excluded: chain C residue 1141 VAL Chi-restraints excluded: chain C residue 1158 LEU Chi-restraints excluded: chain C residue 1199 LEU Chi-restraints excluded: chain C residue 1331 GLN Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 32 ILE Chi-restraints excluded: chain F residue 89 GLU 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 231 optimal weight: 5.9990 chunk 186 optimal weight: 0.3980 chunk 120 optimal weight: 7.9990 chunk 174 optimal weight: 3.9990 chunk 250 optimal weight: 5.9990 chunk 163 optimal weight: 8.9990 chunk 160 optimal weight: 8.9990 chunk 258 optimal weight: 7.9990 chunk 134 optimal weight: 0.9980 chunk 92 optimal weight: 0.8980 chunk 190 optimal weight: 0.3980 overall best weight: 1.3382 ------------------------------------------------------------------------------- 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 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1076 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 946 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.127317 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.100277 restraints weight = 43545.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.101264 restraints weight = 30829.098| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.102122 restraints weight = 22837.231| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.102629 restraints weight = 18476.909| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.103715 restraints weight = 16877.835| |-----------------------------------------------------------------------------| r_work (final): 0.3529 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7522 moved from start: 0.2101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 22218 Z= 0.131 Angle : 0.528 8.495 29997 Z= 0.281 Chirality : 0.043 0.231 3282 Planarity : 0.003 0.064 3872 Dihedral : 4.315 23.799 2916 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.63 % Favored : 93.33 % Rotamer: Outliers : 3.13 % Allowed : 19.32 % Favored : 77.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.04 (0.16), residues: 2685 helix: 1.57 (0.16), residues: 1126 sheet: 0.16 (0.22), residues: 591 loop : -2.15 (0.18), residues: 968 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 823 TYR 0.012 0.001 TYR A 133 PHE 0.016 0.001 PHE B 275 TRP 0.014 0.001 TRP B 97 HIS 0.003 0.001 HIS C1062 Details of bonding type rmsd covalent geometry : bond 0.00298 (22212) covalent geometry : angle 0.52517 (29989) SS BOND : bond 0.00609 ( 1) SS BOND : angle 1.32962 ( 2) hydrogen bonds : bond 0.03673 ( 1065) hydrogen bonds : angle 4.12939 ( 3063) metal coordination : bond 0.00182 ( 5) metal coordination : angle 3.56342 ( 6) *********************** 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 221 residues out of total 2396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 146 time to evaluate : 0.874 Fit side-chains revert: symmetry clash REVERT: A 240 ASP cc_start: 0.7733 (t0) cc_final: 0.7234 (t0) REVERT: B 466 ARG cc_start: 0.6807 (mmm160) cc_final: 0.5592 (mmt180) REVERT: B 673 MET cc_start: 0.6816 (OUTLIER) cc_final: 0.6541 (ttt) REVERT: B 739 ASN cc_start: 0.7536 (t0) cc_final: 0.6936 (t0) REVERT: B 950 LEU cc_start: 0.7968 (OUTLIER) cc_final: 0.7731 (pp) REVERT: B 1037 ARG cc_start: 0.6607 (tpt170) cc_final: 0.6160 (ttm-80) REVERT: B 1126 HIS cc_start: 0.7955 (OUTLIER) cc_final: 0.7670 (t-90) REVERT: C 769 ILE cc_start: 0.6438 (OUTLIER) cc_final: 0.6147 (tp) REVERT: C 838 TYR cc_start: 0.4613 (OUTLIER) cc_final: 0.3549 (m-80) REVERT: C 933 TYR cc_start: 0.7091 (OUTLIER) cc_final: 0.6680 (t80) REVERT: C 977 LEU cc_start: 0.6666 (mt) cc_final: 0.6217 (mp) REVERT: C 1015 ASN cc_start: 0.6860 (OUTLIER) cc_final: 0.6362 (t0) REVERT: C 1253 GLU cc_start: 0.7286 (mt-10) cc_final: 0.7078 (mt-10) REVERT: C 1331 GLN cc_start: 0.8007 (OUTLIER) cc_final: 0.7396 (mp10) outliers start: 75 outliers final: 42 residues processed: 209 average time/residue: 0.1063 time to fit residues: 37.0975 Evaluate side-chains 183 residues out of total 2396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 133 time to evaluate : 0.819 ------------------------------------------------------------------------------- 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 362 ILE Chi-restraints excluded: chain A residue 377 ILE Chi-restraints excluded: chain A residue 392 HIS Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 530 ASP Chi-restraints excluded: chain A residue 543 ILE Chi-restraints excluded: chain A residue 638 ASP Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 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 217 ILE 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 673 MET Chi-restraints excluded: chain B residue 771 VAL Chi-restraints excluded: chain B residue 814 ASN Chi-restraints excluded: chain B residue 823 ARG Chi-restraints excluded: chain B residue 833 LEU Chi-restraints excluded: chain B residue 839 GLU Chi-restraints excluded: chain B residue 879 LEU Chi-restraints excluded: chain B residue 887 VAL Chi-restraints excluded: chain B residue 950 LEU Chi-restraints excluded: chain B residue 1077 LEU Chi-restraints excluded: chain B residue 1126 HIS Chi-restraints excluded: chain C residue 761 LEU Chi-restraints excluded: chain C residue 769 ILE Chi-restraints excluded: chain C residue 824 LEU Chi-restraints excluded: chain C residue 838 TYR Chi-restraints excluded: chain C residue 901 THR Chi-restraints excluded: chain C residue 933 TYR Chi-restraints excluded: chain C residue 965 LEU Chi-restraints excluded: chain C residue 992 LEU Chi-restraints excluded: chain C residue 1015 ASN Chi-restraints excluded: chain C residue 1158 LEU Chi-restraints excluded: chain C residue 1199 LEU Chi-restraints excluded: chain C residue 1331 GLN Chi-restraints excluded: chain F residue 1 MET 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 165 optimal weight: 7.9990 chunk 255 optimal weight: 0.0070 chunk 68 optimal weight: 0.9990 chunk 213 optimal weight: 0.6980 chunk 101 optimal weight: 4.9990 chunk 180 optimal weight: 4.9990 chunk 168 optimal weight: 0.0050 chunk 233 optimal weight: 6.9990 chunk 265 optimal weight: 0.4980 chunk 254 optimal weight: 0.8980 chunk 242 optimal weight: 6.9990 overall best weight: 0.4212 ------------------------------------------------------------------------------- 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 948 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 121 GLN ** 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 = 0.3921 r_free = 0.3921 target = 0.129884 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.099284 restraints weight = 43384.756| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 57)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.102757 restraints weight = 24030.825| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.105128 restraints weight = 16300.687| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 59)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.106760 restraints weight = 12481.742| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.107801 restraints weight = 10337.601| |-----------------------------------------------------------------------------| r_work (final): 0.3598 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7451 moved from start: 0.2061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 22218 Z= 0.098 Angle : 0.501 8.660 29997 Z= 0.266 Chirality : 0.042 0.180 3282 Planarity : 0.003 0.061 3872 Dihedral : 4.106 23.555 2916 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.18 % Favored : 93.78 % Rotamer: Outliers : 2.09 % Allowed : 20.74 % Favored : 77.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.14 (0.17), residues: 2685 helix: 1.71 (0.16), residues: 1125 sheet: 0.23 (0.22), residues: 595 loop : -2.02 (0.18), residues: 965 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 823 TYR 0.013 0.001 TYR C 709 PHE 0.013 0.001 PHE B 275 TRP 0.013 0.001 TRP A 91 HIS 0.002 0.001 HIS B 443 Details of bonding type rmsd covalent geometry : bond 0.00203 (22212) covalent geometry : angle 0.49875 (29989) SS BOND : bond 0.00552 ( 1) SS BOND : angle 1.08663 ( 2) hydrogen bonds : bond 0.03136 ( 1065) hydrogen bonds : angle 3.96068 ( 3063) metal coordination : bond 0.00167 ( 5) metal coordination : angle 3.15091 ( 6) *********************** 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 197 residues out of total 2396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 147 time to evaluate : 0.678 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 240 ASP cc_start: 0.7861 (t0) cc_final: 0.7371 (t0) REVERT: A 271 ASP cc_start: 0.7745 (p0) cc_final: 0.7502 (p0) REVERT: B 117 SER cc_start: 0.4216 (OUTLIER) cc_final: 0.3968 (t) REVERT: B 466 ARG cc_start: 0.6677 (mmm160) cc_final: 0.5412 (mmt180) REVERT: B 1037 ARG cc_start: 0.6380 (tpt170) cc_final: 0.5970 (ttm-80) REVERT: B 1126 HIS cc_start: 0.7859 (OUTLIER) cc_final: 0.7471 (t-90) REVERT: C 744 MET cc_start: 0.6654 (mmm) cc_final: 0.5577 (mtt) REVERT: C 769 ILE cc_start: 0.6422 (OUTLIER) cc_final: 0.6138 (tp) REVERT: C 933 TYR cc_start: 0.7067 (OUTLIER) cc_final: 0.6757 (t80) REVERT: C 977 LEU cc_start: 0.6614 (mt) cc_final: 0.6190 (mp) REVERT: C 1015 ASN cc_start: 0.6783 (OUTLIER) cc_final: 0.6489 (t0) REVERT: C 1253 GLU cc_start: 0.7136 (mt-10) cc_final: 0.6922 (mt-10) REVERT: C 1331 GLN cc_start: 0.7945 (OUTLIER) cc_final: 0.7265 (mp10) REVERT: F 1 MET cc_start: 0.1812 (OUTLIER) cc_final: 0.0051 (mpp) outliers start: 50 outliers final: 32 residues processed: 191 average time/residue: 0.1204 time to fit residues: 37.6688 Evaluate side-chains 173 residues out of total 2396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 134 time to evaluate : 0.627 ------------------------------------------------------------------------------- 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 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 638 ASP 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 117 SER Chi-restraints excluded: chain B residue 121 ASP Chi-restraints excluded: chain B residue 328 VAL Chi-restraints excluded: chain B residue 438 VAL Chi-restraints excluded: chain B residue 503 THR Chi-restraints excluded: chain B residue 715 LEU Chi-restraints excluded: chain B residue 814 ASN Chi-restraints excluded: chain B residue 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 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 933 TYR Chi-restraints excluded: chain C residue 992 LEU Chi-restraints excluded: chain C residue 1015 ASN Chi-restraints excluded: chain C residue 1158 LEU Chi-restraints excluded: chain C residue 1331 GLN Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 94 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 78 optimal weight: 6.9990 chunk 87 optimal weight: 0.0980 chunk 157 optimal weight: 4.9990 chunk 214 optimal weight: 10.0000 chunk 172 optimal weight: 4.9990 chunk 76 optimal weight: 0.4980 chunk 35 optimal weight: 4.9990 chunk 228 optimal weight: 10.0000 chunk 128 optimal weight: 0.9980 chunk 264 optimal weight: 20.0000 chunk 79 optimal weight: 0.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- 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 948 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1076 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 946 ASN F 121 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.127105 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.098745 restraints weight = 43862.569| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.101582 restraints weight = 23836.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.102651 restraints weight = 16370.892| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.103119 restraints weight = 14916.576| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.103224 restraints weight = 12770.046| |-----------------------------------------------------------------------------| r_work (final): 0.3524 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7551 moved from start: 0.2215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 22218 Z= 0.143 Angle : 0.540 11.958 29997 Z= 0.284 Chirality : 0.043 0.183 3282 Planarity : 0.003 0.063 3872 Dihedral : 4.146 23.706 2916 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.74 % Favored : 93.22 % Rotamer: Outliers : 2.34 % Allowed : 20.87 % Favored : 76.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.11 (0.17), residues: 2685 helix: 1.69 (0.16), residues: 1125 sheet: 0.20 (0.22), residues: 594 loop : -2.05 (0.18), residues: 966 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C1121 TYR 0.022 0.001 TYR C 709 PHE 0.017 0.001 PHE B 275 TRP 0.008 0.001 TRP B 151 HIS 0.003 0.001 HIS B 69 Details of bonding type rmsd covalent geometry : bond 0.00330 (22212) covalent geometry : angle 0.53775 (29989) SS BOND : bond 0.00643 ( 1) SS BOND : angle 1.47261 ( 2) hydrogen bonds : bond 0.03635 ( 1065) hydrogen bonds : angle 4.03343 ( 3063) metal coordination : bond 0.00229 ( 5) metal coordination : angle 3.29250 ( 6) *********************** 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 190 residues out of total 2396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 134 time to evaluate : 0.820 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 164 LEU cc_start: 0.8472 (OUTLIER) cc_final: 0.8232 (tp) REVERT: A 240 ASP cc_start: 0.7836 (t0) cc_final: 0.7335 (t0) REVERT: A 271 ASP cc_start: 0.7710 (p0) cc_final: 0.7484 (p0) REVERT: B 11 MET cc_start: 0.6955 (pmm) cc_final: 0.6750 (pmm) REVERT: B 466 ARG cc_start: 0.6827 (mmm160) cc_final: 0.5882 (mmt180) REVERT: B 557 HIS cc_start: 0.7522 (OUTLIER) cc_final: 0.6639 (t70) REVERT: B 1037 ARG cc_start: 0.6586 (tpt170) cc_final: 0.6114 (ttm-80) REVERT: B 1126 HIS cc_start: 0.7947 (OUTLIER) cc_final: 0.7677 (t-90) REVERT: C 769 ILE cc_start: 0.6475 (OUTLIER) cc_final: 0.6217 (tp) REVERT: C 977 LEU cc_start: 0.6638 (mt) cc_final: 0.6207 (mp) REVERT: C 1015 ASN cc_start: 0.6921 (OUTLIER) cc_final: 0.6412 (t0) REVERT: C 1253 GLU cc_start: 0.7322 (mt-10) cc_final: 0.7087 (mt-10) REVERT: C 1331 GLN cc_start: 0.7819 (OUTLIER) cc_final: 0.7106 (mp10) outliers start: 56 outliers final: 40 residues processed: 182 average time/residue: 0.1166 time to fit residues: 35.1801 Evaluate side-chains 176 residues out of total 2396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 130 time to evaluate : 0.621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 LEU Chi-restraints excluded: chain A residue 20 ILE Chi-restraints excluded: chain A residue 29 PHE Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 154 THR Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 362 ILE Chi-restraints excluded: chain A residue 377 ILE Chi-restraints excluded: chain A residue 392 HIS Chi-restraints excluded: chain A residue 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 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 328 VAL Chi-restraints excluded: chain B residue 438 VAL Chi-restraints excluded: chain B residue 503 THR Chi-restraints excluded: chain B residue 557 HIS 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 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 992 LEU Chi-restraints excluded: chain C residue 1015 ASN Chi-restraints excluded: chain C residue 1018 ILE Chi-restraints excluded: chain C residue 1158 LEU Chi-restraints excluded: chain C residue 1331 GLN Chi-restraints excluded: chain F residue 32 ILE Chi-restraints excluded: chain F residue 83 THR Chi-restraints excluded: chain F residue 94 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 264 optimal weight: 6.9990 chunk 62 optimal weight: 5.9990 chunk 22 optimal weight: 5.9990 chunk 248 optimal weight: 0.6980 chunk 41 optimal weight: 4.9990 chunk 78 optimal weight: 0.9980 chunk 150 optimal weight: 2.9990 chunk 130 optimal weight: 3.9990 chunk 103 optimal weight: 7.9990 chunk 98 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1076 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 879 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.126338 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.096132 restraints weight = 44085.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.099446 restraints weight = 24765.041| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 56)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.101685 restraints weight = 16909.905| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 55)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.103209 restraints weight = 13054.266| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.104203 restraints weight = 10878.507| |-----------------------------------------------------------------------------| r_work (final): 0.3556 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7546 moved from start: 0.2367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 22218 Z= 0.154 Angle : 0.561 13.383 29997 Z= 0.294 Chirality : 0.043 0.183 3282 Planarity : 0.003 0.063 3872 Dihedral : 4.255 23.447 2916 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.23 % Favored : 92.74 % Rotamer: Outliers : 2.63 % Allowed : 20.58 % Favored : 76.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.04 (0.16), residues: 2685 helix: 1.63 (0.16), residues: 1125 sheet: 0.17 (0.22), residues: 591 loop : -2.06 (0.18), residues: 969 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 899 TYR 0.017 0.001 TYR C 709 PHE 0.017 0.001 PHE B 275 TRP 0.009 0.001 TRP B 447 HIS 0.003 0.001 HIS B 435 Details of bonding type rmsd covalent geometry : bond 0.00357 (22212) covalent geometry : angle 0.55860 (29989) SS BOND : bond 0.00660 ( 1) SS BOND : angle 1.50503 ( 2) hydrogen bonds : bond 0.03812 ( 1065) hydrogen bonds : angle 4.10045 ( 3063) metal coordination : bond 0.00230 ( 5) metal coordination : angle 3.51452 ( 6) *********************** 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 197 residues out of total 2396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 134 time to evaluate : 0.737 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 164 LEU cc_start: 0.8469 (OUTLIER) cc_final: 0.8251 (tp) REVERT: A 240 ASP cc_start: 0.7762 (t0) cc_final: 0.7295 (t0) REVERT: B 454 GLU cc_start: 0.7900 (mm-30) cc_final: 0.7609 (tp30) REVERT: B 466 ARG cc_start: 0.6532 (mmm160) cc_final: 0.5557 (mmt180) REVERT: B 557 HIS cc_start: 0.7528 (OUTLIER) cc_final: 0.6660 (t70) REVERT: B 739 ASN cc_start: 0.7569 (t0) cc_final: 0.6922 (t0) REVERT: B 1126 HIS cc_start: 0.7891 (OUTLIER) cc_final: 0.7665 (t-90) REVERT: C 744 MET cc_start: 0.6666 (mmm) cc_final: 0.5611 (mtt) REVERT: C 769 ILE cc_start: 0.6506 (OUTLIER) cc_final: 0.6229 (tp) REVERT: C 838 TYR cc_start: 0.4670 (OUTLIER) cc_final: 0.3522 (m-80) REVERT: C 977 LEU cc_start: 0.6621 (mt) cc_final: 0.6180 (mp) REVERT: C 1015 ASN cc_start: 0.7122 (OUTLIER) cc_final: 0.6589 (t0) REVERT: C 1253 GLU cc_start: 0.7279 (mt-10) cc_final: 0.7075 (mt-10) REVERT: C 1318 TYR cc_start: 0.5385 (OUTLIER) cc_final: 0.4109 (m-80) REVERT: C 1331 GLN cc_start: 0.7819 (OUTLIER) cc_final: 0.7120 (mp10) outliers start: 63 outliers final: 46 residues processed: 186 average time/residue: 0.1154 time to fit residues: 35.2220 Evaluate side-chains 183 residues out of total 2396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 129 time to evaluate : 0.580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 LEU Chi-restraints excluded: chain A residue 20 ILE Chi-restraints excluded: chain A residue 29 PHE Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 154 THR Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 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 29 ILE Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain B residue 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 217 ILE Chi-restraints excluded: chain B residue 328 VAL Chi-restraints excluded: chain B residue 438 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 771 VAL Chi-restraints excluded: chain B residue 814 ASN Chi-restraints excluded: chain B residue 823 ARG Chi-restraints excluded: chain B residue 833 LEU Chi-restraints excluded: chain B residue 839 GLU Chi-restraints excluded: chain B residue 904 GLN Chi-restraints excluded: chain B residue 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 838 TYR Chi-restraints excluded: chain C residue 901 THR Chi-restraints excluded: chain C residue 992 LEU Chi-restraints excluded: chain C residue 1015 ASN Chi-restraints excluded: chain C residue 1018 ILE Chi-restraints excluded: chain C residue 1158 LEU Chi-restraints excluded: chain C residue 1318 TYR Chi-restraints excluded: chain C residue 1331 GLN Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 32 ILE Chi-restraints excluded: chain F residue 83 THR Chi-restraints excluded: chain F residue 94 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 218 optimal weight: 4.9990 chunk 156 optimal weight: 5.9990 chunk 36 optimal weight: 1.9990 chunk 74 optimal weight: 10.0000 chunk 243 optimal weight: 1.9990 chunk 251 optimal weight: 0.8980 chunk 215 optimal weight: 0.9980 chunk 226 optimal weight: 3.9990 chunk 236 optimal weight: 8.9990 chunk 188 optimal weight: 0.9990 chunk 114 optimal weight: 0.0370 overall best weight: 0.9862 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 112 ASN C 946 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.127918 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.097642 restraints weight = 44034.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.101028 restraints weight = 24504.855| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.103319 restraints weight = 16671.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 61)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.104858 restraints weight = 12799.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.105861 restraints weight = 10672.099| |-----------------------------------------------------------------------------| r_work (final): 0.3580 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7508 moved from start: 0.2363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 22218 Z= 0.116 Angle : 0.526 11.755 29997 Z= 0.277 Chirality : 0.042 0.182 3282 Planarity : 0.003 0.061 3872 Dihedral : 4.156 23.419 2916 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.52 % Favored : 93.45 % Rotamer: Outliers : 2.17 % Allowed : 21.08 % Favored : 76.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.13 (0.16), residues: 2685 helix: 1.69 (0.16), residues: 1124 sheet: 0.23 (0.22), residues: 591 loop : -2.00 (0.18), residues: 970 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 823 TYR 0.015 0.001 TYR B 827 PHE 0.014 0.001 PHE B 275 TRP 0.011 0.001 TRP A 91 HIS 0.002 0.001 HIS B 69 Details of bonding type rmsd covalent geometry : bond 0.00258 (22212) covalent geometry : angle 0.52411 (29989) SS BOND : bond 0.00583 ( 1) SS BOND : angle 1.27209 ( 2) hydrogen bonds : bond 0.03359 ( 1065) hydrogen bonds : angle 4.01034 ( 3063) metal coordination : bond 0.00176 ( 5) metal coordination : angle 3.31458 ( 6) ********************** 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 186 residues out of total 2396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 134 time to evaluate : 0.693 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 164 LEU cc_start: 0.8441 (OUTLIER) cc_final: 0.8231 (tp) REVERT: A 240 ASP cc_start: 0.7729 (t0) cc_final: 0.7272 (t0) REVERT: A 271 ASP cc_start: 0.7732 (p0) cc_final: 0.7510 (p0) REVERT: B 466 ARG cc_start: 0.6537 (mmm160) cc_final: 0.5610 (mmt180) REVERT: B 557 HIS cc_start: 0.7500 (OUTLIER) cc_final: 0.6647 (t70) REVERT: B 1126 HIS cc_start: 0.7875 (OUTLIER) cc_final: 0.7573 (t-90) REVERT: C 744 MET cc_start: 0.6762 (mmm) cc_final: 0.5623 (mtt) REVERT: C 769 ILE cc_start: 0.6497 (OUTLIER) cc_final: 0.6224 (tp) REVERT: C 977 LEU cc_start: 0.6614 (mt) cc_final: 0.6171 (mp) REVERT: C 1015 ASN cc_start: 0.7006 (OUTLIER) cc_final: 0.6541 (t0) REVERT: C 1253 GLU cc_start: 0.7370 (mt-10) cc_final: 0.7132 (mt-10) REVERT: C 1318 TYR cc_start: 0.5321 (OUTLIER) cc_final: 0.4126 (m-80) REVERT: C 1331 GLN cc_start: 0.7799 (OUTLIER) cc_final: 0.7117 (mp10) outliers start: 52 outliers final: 41 residues processed: 181 average time/residue: 0.1171 time to fit residues: 35.0490 Evaluate side-chains 178 residues out of total 2396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 130 time to evaluate : 0.668 ------------------------------------------------------------------------------- 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 164 LEU Chi-restraints excluded: chain A residue 362 ILE Chi-restraints excluded: chain A residue 377 ILE Chi-restraints excluded: chain A residue 392 HIS Chi-restraints excluded: chain A residue 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 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 66 LEU 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 438 VAL Chi-restraints excluded: chain B residue 503 THR Chi-restraints excluded: chain B residue 557 HIS 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 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 901 THR Chi-restraints excluded: chain C residue 965 LEU Chi-restraints excluded: chain C residue 992 LEU Chi-restraints excluded: chain C residue 1015 ASN Chi-restraints excluded: chain C residue 1158 LEU Chi-restraints excluded: chain C residue 1199 LEU Chi-restraints excluded: chain C residue 1318 TYR Chi-restraints excluded: chain C residue 1331 GLN Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 83 THR Chi-restraints excluded: chain F residue 94 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 97 optimal weight: 3.9990 chunk 240 optimal weight: 3.9990 chunk 25 optimal weight: 0.0770 chunk 120 optimal weight: 0.4980 chunk 117 optimal weight: 0.0070 chunk 60 optimal weight: 0.9980 chunk 213 optimal weight: 0.9980 chunk 183 optimal weight: 10.0000 chunk 226 optimal weight: 3.9990 chunk 34 optimal weight: 4.9990 chunk 220 optimal weight: 6.9990 overall best weight: 0.5156 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.129523 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.100930 restraints weight = 43797.673| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.104414 restraints weight = 24008.885| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.105630 restraints weight = 15142.052| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.106170 restraints weight = 13113.609| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.106556 restraints weight = 11739.783| |-----------------------------------------------------------------------------| r_work (final): 0.3576 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7482 moved from start: 0.2354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 22218 Z= 0.099 Angle : 0.509 10.802 29997 Z= 0.267 Chirality : 0.041 0.181 3282 Planarity : 0.003 0.060 3872 Dihedral : 4.005 23.266 2916 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.00 % Favored : 93.97 % Rotamer: Outliers : 2.21 % Allowed : 21.20 % Favored : 76.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.24 (0.17), residues: 2685 helix: 1.80 (0.16), residues: 1126 sheet: 0.23 (0.22), residues: 597 loop : -1.96 (0.18), residues: 962 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 823 TYR 0.011 0.001 TYR C 709 PHE 0.012 0.001 PHE B 275 TRP 0.011 0.001 TRP A 91 HIS 0.003 0.001 HIS B 299 Details of bonding type rmsd covalent geometry : bond 0.00214 (22212) covalent geometry : angle 0.50724 (29989) SS BOND : bond 0.00541 ( 1) SS BOND : angle 1.12423 ( 2) hydrogen bonds : bond 0.03017 ( 1065) hydrogen bonds : angle 3.90556 ( 3063) metal coordination : bond 0.00153 ( 5) metal coordination : angle 3.06178 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3079.37 seconds wall clock time: 54 minutes 8.38 seconds (3248.38 seconds total)