Starting phenix.real_space_refine on Fri Jul 3 00:07:47 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7rhq_24466/07_2026/7rhq_24466.cif Found real_map, /net/cci-nas-00/data/ceres_data/7rhq_24466/07_2026/7rhq_24466.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.53 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7rhq_24466/07_2026/7rhq_24466.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7rhq_24466/07_2026/7rhq_24466.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7rhq_24466/07_2026/7rhq_24466.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7rhq_24466/07_2026/7rhq_24466.map" model { file = "/net/cci-nas-00/data/ceres_data/7rhq_24466/07_2026/7rhq_24466.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7rhq_24466/07_2026/7rhq_24466.cif" } resolution = 3.53 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.007 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: 6 Type Number sf(0) Gaussians Ca 2 9.91 5 Zn 1 6.06 5 S 69 5.16 5 C 6768 2.51 5 N 1752 2.21 5 O 1907 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 10499 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 7680 Number of conformers: 1 Conformer: "" Number of residues, atoms: 974, 7680 Classifications: {'peptide': 974} Link IDs: {'PTRANS': 41, 'TRANS': 932} Chain breaks: 1 Chain: "C" Number of atoms: 1354 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1354 Classifications: {'peptide': 171} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 163} Chain breaks: 1 Chain: "G" Number of atoms: 1242 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 1242 Classifications: {'peptide': 160} Link IDs: {'PTRANS': 8, 'TRANS': 151} Chain breaks: 2 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 91 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 91 Unusual residues: {'CLR': 1, 'NAG': 2, 'Y01': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 48 Unusual residues: {' CA': 2, ' ZN': 1, 'CLR': 1, 'PLM': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'PLM:plan-1': 1} Unresolved non-hydrogen planarities: 1 Time building chain proxies: 2.14, per 1000 atoms: 0.20 Number of scatterers: 10499 At special positions: 0 Unit cell: (117.66, 85.86, 149.46, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 1 29.99 Ca 2 19.99 S 69 16.00 O 1907 8.00 N 1752 7.00 C 6768 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=13, symmetry=0 Simple disulfide: pdb=" SG CYS A 193 " - pdb=" SG CYS A 216 " distance=2.04 Simple disulfide: pdb=" SG CYS A 224 " - pdb=" SG CYS A 317 " distance=2.03 Simple disulfide: pdb=" SG CYS A 286 " - pdb=" SG CYS A 294 " distance=2.03 Simple disulfide: pdb=" SG CYS G 48 " - pdb=" SG CYS G 128 " distance=2.04 Simple disulfide: pdb=" SG CYS G 55 " - pdb=" SG CYS G 61 " distance=2.03 Simple disulfide: pdb=" SG CYS G 72 " - pdb=" SG CYS G 109 " distance=2.03 Simple disulfide: pdb=" SG CYS G 105 " - pdb=" SG CYS G 146 " distance=2.03 Simple disulfide: pdb=" SG CYS G 130 " - pdb=" SG CYS G 136 " distance=2.03 Simple disulfide: pdb=" SG CYS G 166 " - pdb=" SG CYS G 222 " distance=2.03 Simple disulfide: pdb=" SG CYS G 173 " - pdb=" SG CYS G 179 " distance=2.03 Simple disulfide: pdb=" SG CYS G 190 " - pdb=" SG CYS G 203 " distance=2.03 Simple disulfide: pdb=" SG CYS G 199 " - pdb=" SG CYS G 243 " distance=2.03 Simple disulfide: pdb=" SG CYS G 224 " - pdb=" SG CYS G 232 " 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=2, symmetry=0 Links applied BETA1-4 " NAG B 1 " - " NAG B 2 " " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " NAG-ASN " NAG A1503 " - " ASN A 339 " " NAG A1504 " - " ASN A 865 " " NAG B 1 " - " ASN A 302 " " NAG D 1 " - " ASN A 989 " " NAG E 1 " - " ASN G 117 " Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.63 Conformation dependent library (CDL) restraints added in 345.6 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN C 202 " pdb="ZN ZN C 202 " - pdb=" NE2 HIS C 140 " pdb="ZN ZN C 202 " - pdb=" ND1 HIS C 182 " pdb="ZN ZN C 202 " - pdb=" NE2 HIS C 134 " 2582 Ramachandran restraints generated. 1291 Oldfield, 0 Emsley, 1291 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2448 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 8 sheets defined 57.9% alpha, 5.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.23 Creating SS restraints... Processing helix chain 'A' and resid 69 through 87 removed outlier: 3.840A pdb=" N ILE A 84 " --> pdb=" O LEU A 80 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N LYS A 86 " --> pdb=" O CYS A 82 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ASN A 87 " --> pdb=" O TYR A 83 " (cutoff:3.500A) Processing helix chain 'A' and resid 87 through 105 removed outlier: 4.307A pdb=" N LEU A 92 " --> pdb=" O CYS A 88 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N VAL A 93 " --> pdb=" O GLY A 89 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N LEU A 97 " --> pdb=" O VAL A 93 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N PHE A 102 " --> pdb=" O ILE A 98 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ALA A 103 " --> pdb=" O PHE A 99 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N GLY A 105 " --> pdb=" O ALA A 101 " (cutoff:3.500A) Processing helix chain 'A' and resid 106 through 108 No H-bonds generated for 'chain 'A' and resid 106 through 108' Processing helix chain 'A' and resid 114 through 118 removed outlier: 3.564A pdb=" N GLU A 117 " --> pdb=" O ASN A 114 " (cutoff:3.500A) Processing helix chain 'A' and resid 124 through 131 Processing helix chain 'A' and resid 138 through 141 Processing helix chain 'A' and resid 163 through 176 removed outlier: 3.613A pdb=" N GLN A 167 " --> pdb=" O GLU A 163 " (cutoff:3.500A) Processing helix chain 'A' and resid 188 through 192 Processing helix chain 'A' and resid 206 through 211 Processing helix chain 'A' and resid 220 through 232 removed outlier: 3.778A pdb=" N ASP A 223 " --> pdb=" O THR A 220 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N CYS A 224 " --> pdb=" O PRO A 221 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N TRP A 226 " --> pdb=" O ASP A 223 " (cutoff:3.500A) removed outlier: 7.051A pdb=" N GLU A 227 " --> pdb=" O CYS A 224 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLY A 228 " --> pdb=" O PHE A 225 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LYS A 230 " --> pdb=" O GLU A 227 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LEU A 231 " --> pdb=" O GLY A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 259 removed outlier: 3.528A pdb=" N LEU A 255 " --> pdb=" O PRO A 251 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 276 removed outlier: 3.511A pdb=" N ALA A 275 " --> pdb=" O MET A 271 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 313 removed outlier: 3.727A pdb=" N ILE A 312 " --> pdb=" O ASP A 308 " (cutoff:3.500A) Processing helix chain 'A' and resid 358 through 366 Processing helix chain 'A' and resid 378 through 400 removed outlier: 3.585A pdb=" N ALA A 384 " --> pdb=" O ASP A 380 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N THR A 392 " --> pdb=" O ALA A 388 " (cutoff:3.500A) Processing helix chain 'A' and resid 413 through 423 removed outlier: 3.728A pdb=" N LEU A 417 " --> pdb=" O THR A 413 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N LEU A 421 " --> pdb=" O LEU A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 428 through 446 removed outlier: 3.583A pdb=" N LEU A 438 " --> pdb=" O SER A 434 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N LEU A 445 " --> pdb=" O ALA A 441 " (cutoff:3.500A) Processing helix chain 'A' and resid 456 through 481 removed outlier: 3.587A pdb=" N LEU A 461 " --> pdb=" O GLY A 457 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LEU A 465 " --> pdb=" O LEU A 461 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N ALA A 472 " --> pdb=" O ALA A 468 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LEU A 480 " --> pdb=" O GLY A 476 " (cutoff:3.500A) Processing helix chain 'A' and resid 492 through 516 removed outlier: 3.966A pdb=" N LEU A 498 " --> pdb=" O PRO A 494 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N GLY A 499 " --> pdb=" O PHE A 495 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N ASP A 503 " --> pdb=" O GLY A 499 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N ASP A 504 " --> pdb=" O VAL A 500 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N VAL A 505 " --> pdb=" O GLY A 501 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N LEU A 507 " --> pdb=" O ASP A 503 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU A 508 " --> pdb=" O ASP A 504 " (cutoff:3.500A) Processing helix chain 'A' and resid 526 through 550 removed outlier: 3.731A pdb=" N THR A 534 " --> pdb=" O CYS A 530 " (cutoff:3.500A) removed outlier: 5.308A pdb=" N ALA A 536 " --> pdb=" O LYS A 532 " (cutoff:3.500A) removed outlier: 5.198A pdb=" N SER A 537 " --> pdb=" O ARG A 533 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ILE A 543 " --> pdb=" O ALA A 539 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N SER A 544 " --> pdb=" O LEU A 540 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ALA A 548 " --> pdb=" O SER A 544 " (cutoff:3.500A) Processing helix chain 'A' and resid 557 through 581 removed outlier: 3.663A pdb=" N SER A 564 " --> pdb=" O LEU A 560 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N GLN A 566 " --> pdb=" O ALA A 562 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N VAL A 578 " --> pdb=" O ASN A 574 " (cutoff:3.500A) Processing helix chain 'A' and resid 581 through 592 removed outlier: 3.514A pdb=" N ILE A 585 " --> pdb=" O ILE A 581 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ARG A 592 " --> pdb=" O MET A 588 " (cutoff:3.500A) Processing helix chain 'A' and resid 726 through 731 removed outlier: 3.582A pdb=" N TYR A 730 " --> pdb=" O ALA A 726 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N ALA A 731 " --> pdb=" O GLU A 727 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 726 through 731' Processing helix chain 'A' and resid 732 through 734 No H-bonds generated for 'chain 'A' and resid 732 through 734' Processing helix chain 'A' and resid 736 through 758 removed outlier: 3.761A pdb=" N ALA A 742 " --> pdb=" O LYS A 738 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N VAL A 743 " --> pdb=" O THR A 739 " (cutoff:3.500A) Processing helix chain 'A' and resid 766 through 770 Processing helix chain 'A' and resid 776 through 785 removed outlier: 3.514A pdb=" N ILE A 781 " --> pdb=" O GLU A 777 " (cutoff:3.500A) Processing helix chain 'A' and resid 806 through 815 Processing helix chain 'A' and resid 816 through 818 No H-bonds generated for 'chain 'A' and resid 816 through 818' Processing helix chain 'A' and resid 833 through 855 removed outlier: 3.638A pdb=" N TYR A 837 " --> pdb=" O MET A 833 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ARG A 839 " --> pdb=" O LEU A 835 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N LEU A 842 " --> pdb=" O PHE A 838 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N THR A 848 " --> pdb=" O GLY A 844 " (cutoff:3.500A) Processing helix chain 'A' and resid 867 through 879 removed outlier: 3.508A pdb=" N LEU A 877 " --> pdb=" O ALA A 873 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ILE A 878 " --> pdb=" O TYR A 874 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N GLN A 879 " --> pdb=" O LYS A 875 " (cutoff:3.500A) Processing helix chain 'A' and resid 908 through 920 removed outlier: 3.601A pdb=" N SER A 918 " --> pdb=" O THR A 914 " (cutoff:3.500A) Processing helix chain 'A' and resid 920 through 927 removed outlier: 3.504A pdb=" N ALA A 925 " --> pdb=" O PRO A 921 " (cutoff:3.500A) Processing helix chain 'A' and resid 972 through 991 removed outlier: 3.513A pdb=" N ALA A 985 " --> pdb=" O GLU A 981 " (cutoff:3.500A) Processing helix chain 'A' and resid 1001 through 1005 removed outlier: 3.535A pdb=" N PHE A1004 " --> pdb=" O GLY A1001 " (cutoff:3.500A) Processing helix chain 'A' and resid 1013 through 1037 removed outlier: 3.781A pdb=" N LEU A1019 " --> pdb=" O HIS A1015 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N SER A1022 " --> pdb=" O LEU A1018 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N VAL A1023 " --> pdb=" O LEU A1019 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ALA A1026 " --> pdb=" O SER A1022 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LEU A1034 " --> pdb=" O LEU A1030 " (cutoff:3.500A) Processing helix chain 'A' and resid 1038 through 1064 removed outlier: 3.510A pdb=" N VAL A1046 " --> pdb=" O ALA A1042 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N LEU A1051 " --> pdb=" O MET A1047 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N VAL A1054 " --> pdb=" O ALA A1050 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N MET A1059 " --> pdb=" O GLU A1055 " (cutoff:3.500A) Processing helix chain 'A' and resid 1068 through 1096 removed outlier: 3.627A pdb=" N VAL A1072 " --> pdb=" O SER A1068 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N VAL A1073 " --> pdb=" O ALA A1069 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N ILE A1074 " --> pdb=" O VAL A1070 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N VAL A1079 " --> pdb=" O LEU A1075 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N GLY A1080 " --> pdb=" O ILE A1076 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N GLU A1084 " --> pdb=" O GLY A1080 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N PHE A1085 " --> pdb=" O ILE A1081 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N THR A1086 " --> pdb=" O GLY A1082 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N HIS A1088 " --> pdb=" O GLU A1084 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N VAL A1089 " --> pdb=" O PHE A1085 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ALA A1096 " --> pdb=" O ALA A1092 " (cutoff:3.500A) Processing helix chain 'A' and resid 1099 through 1112 Processing helix chain 'A' and resid 1112 through 1126 Processing helix chain 'A' and resid 1127 through 1130 Processing helix chain 'A' and resid 1134 through 1141 removed outlier: 3.941A pdb=" N VAL A1138 " --> pdb=" O PHE A1134 " (cutoff:3.500A) Processing helix chain 'A' and resid 1141 through 1157 removed outlier: 4.205A pdb=" N ILE A1147 " --> pdb=" O ALA A1143 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LEU A1154 " --> pdb=" O LEU A1150 " (cutoff:3.500A) Processing helix chain 'A' and resid 1158 through 1167 removed outlier: 3.651A pdb=" N VAL A1162 " --> pdb=" O VAL A1158 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N PHE A1166 " --> pdb=" O VAL A1162 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N PHE A1167 " --> pdb=" O LEU A1163 " (cutoff:3.500A) Processing helix chain 'C' and resid 99 through 117 removed outlier: 3.828A pdb=" N ALA C 108 " --> pdb=" O ASP C 104 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LEU C 109 " --> pdb=" O LYS C 105 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N MET C 114 " --> pdb=" O ALA C 110 " (cutoff:3.500A) Processing helix chain 'C' and resid 138 through 143 removed outlier: 3.643A pdb=" N TYR C 141 " --> pdb=" O SER C 138 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N GLU C 142 " --> pdb=" O LEU C 139 " (cutoff:3.500A) Processing helix chain 'C' and resid 154 through 156 No H-bonds generated for 'chain 'C' and resid 154 through 156' Processing helix chain 'C' and resid 157 through 168 Processing helix chain 'G' and resid 47 through 56 removed outlier: 3.736A pdb=" N CYS G 55 " --> pdb=" O ALA G 51 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLN G 56 " --> pdb=" O LEU G 52 " (cutoff:3.500A) Processing helix chain 'G' and resid 60 through 72 Processing helix chain 'G' and resid 72 through 80 removed outlier: 3.527A pdb=" N LEU G 76 " --> pdb=" O CYS G 72 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N HIS G 79 " --> pdb=" O VAL G 75 " (cutoff:3.500A) Processing helix chain 'G' and resid 108 through 119 removed outlier: 3.562A pdb=" N HIS G 118 " --> pdb=" O ILE G 114 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N THR G 119 " --> pdb=" O GLN G 115 " (cutoff:3.500A) Processing helix chain 'G' and resid 122 through 126 Processing helix chain 'G' and resid 136 through 144 Processing helix chain 'G' and resid 167 through 176 Processing helix chain 'G' and resid 176 through 190 Processing helix chain 'G' and resid 190 through 195 removed outlier: 3.680A pdb=" N PHE G 194 " --> pdb=" O CYS G 190 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N ASN G 195 " --> pdb=" O GLY G 191 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 190 through 195' Processing helix chain 'G' and resid 200 through 211 removed outlier: 3.600A pdb=" N THR G 205 " --> pdb=" O ASP G 201 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N VAL G 206 " --> pdb=" O GLU G 202 " (cutoff:3.500A) Processing helix chain 'G' and resid 213 through 221 removed outlier: 4.002A pdb=" N LEU G 219 " --> pdb=" O LYS G 215 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ASN G 220 " --> pdb=" O ALA G 216 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ASP G 221 " --> pdb=" O ALA G 217 " (cutoff:3.500A) Processing helix chain 'G' and resid 228 through 243 removed outlier: 3.680A pdb=" N ALA G 240 " --> pdb=" O LYS G 236 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 218 through 219 Processing sheet with id=AA2, first strand: chain 'A' and resid 218 through 219 Processing sheet with id=AA3, first strand: chain 'A' and resid 180 through 182 removed outlier: 3.629A pdb=" N MET A 182 " --> pdb=" O LYS A 185 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 317 through 318 Processing sheet with id=AA5, first strand: chain 'A' and resid 337 through 338 removed outlier: 3.735A pdb=" N SER A 346 " --> pdb=" O VAL A 337 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 961 through 964 Processing sheet with id=AA7, first strand: chain 'C' and resid 47 through 48 removed outlier: 3.547A pdb=" N TRP C 172 " --> pdb=" O SER C 184 " (cutoff:3.500A) removed outlier: 7.156A pdb=" N ASP C 147 " --> pdb=" O THR C 125 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 77 through 78 471 hydrogen bonds defined for protein. 1338 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: 1.55 Time building geometry restraints manager: 0.84 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2531 1.33 - 1.45: 2312 1.45 - 1.58: 5789 1.58 - 1.70: 0 1.70 - 1.82: 100 Bond restraints: 10732 Sorted by residual: bond pdb=" CAY Y01 A1502 " pdb=" OAW Y01 A1502 " ideal model delta sigma weight residual 1.332 1.453 -0.121 2.00e-02 2.50e+03 3.67e+01 bond pdb=" CA THR A 133 " pdb=" C THR A 133 " ideal model delta sigma weight residual 1.523 1.474 0.048 1.41e-02 5.03e+03 1.17e+01 bond pdb=" CB VAL A 796 " pdb=" CG2 VAL A 796 " ideal model delta sigma weight residual 1.521 1.419 0.102 3.30e-02 9.18e+02 9.62e+00 bond pdb=" C1 NAG A1504 " pdb=" O5 NAG A1504 " ideal model delta sigma weight residual 1.406 1.464 -0.058 2.00e-02 2.50e+03 8.54e+00 bond pdb=" CB VAL A 159 " pdb=" CG2 VAL A 159 " ideal model delta sigma weight residual 1.521 1.435 0.086 3.30e-02 9.18e+02 6.79e+00 ... (remaining 10727 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.11: 13784 2.11 - 4.22: 671 4.22 - 6.33: 82 6.33 - 8.45: 23 8.45 - 10.56: 8 Bond angle restraints: 14568 Sorted by residual: angle pdb=" N ARG A 860 " pdb=" CA ARG A 860 " pdb=" C ARG A 860 " ideal model delta sigma weight residual 111.11 116.55 -5.44 1.20e+00 6.94e-01 2.05e+01 angle pdb=" C TYR A 791 " pdb=" N HIS A 792 " pdb=" CA HIS A 792 " ideal model delta sigma weight residual 122.19 115.89 6.30 1.41e+00 5.03e-01 2.00e+01 angle pdb=" C THR A 859 " pdb=" N ARG A 860 " pdb=" CA ARG A 860 " ideal model delta sigma weight residual 120.54 126.45 -5.91 1.35e+00 5.49e-01 1.92e+01 angle pdb=" N TYR A 802 " pdb=" CA TYR A 802 " pdb=" C TYR A 802 " ideal model delta sigma weight residual 109.81 119.26 -9.45 2.21e+00 2.05e-01 1.83e+01 angle pdb=" C ASN A 518 " pdb=" N LYS A 519 " pdb=" CA LYS A 519 " ideal model delta sigma weight residual 121.54 129.41 -7.87 1.91e+00 2.74e-01 1.70e+01 ... (remaining 14563 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.17: 5973 16.17 - 32.35: 312 32.35 - 48.52: 59 48.52 - 64.70: 9 64.70 - 80.87: 9 Dihedral angle restraints: 6362 sinusoidal: 2566 harmonic: 3796 Sorted by residual: dihedral pdb=" CA ARG A 932 " pdb=" C ARG A 932 " pdb=" N PRO A 933 " pdb=" CA PRO A 933 " ideal model delta harmonic sigma weight residual -180.00 -99.21 -80.79 0 5.00e+00 4.00e-02 2.61e+02 dihedral pdb=" CB CYS G 105 " pdb=" SG CYS G 105 " pdb=" SG CYS G 146 " pdb=" CB CYS G 146 " ideal model delta sinusoidal sigma weight residual 93.00 168.92 -75.92 1 1.00e+01 1.00e-02 7.26e+01 dihedral pdb=" CA LYS A 828 " pdb=" C LYS A 828 " pdb=" N GLN A 829 " pdb=" CA GLN A 829 " ideal model delta harmonic sigma weight residual -180.00 -149.76 -30.24 0 5.00e+00 4.00e-02 3.66e+01 ... (remaining 6359 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.087: 1473 0.087 - 0.175: 181 0.175 - 0.262: 16 0.262 - 0.350: 5 0.350 - 0.437: 1 Chirality restraints: 1676 Sorted by residual: chirality pdb=" C1 NAG E 1 " pdb=" ND2 ASN G 117 " pdb=" C2 NAG E 1 " pdb=" O5 NAG E 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.96 -0.44 2.00e-01 2.50e+01 4.78e+00 chirality pdb=" C1 NAG A1504 " pdb=" ND2 ASN A 865 " pdb=" C2 NAG A1504 " pdb=" O5 NAG A1504 " both_signs ideal model delta sigma weight residual False -2.40 -2.09 -0.31 2.00e-01 2.50e+01 2.40e+00 chirality pdb=" CB ILE A 555 " pdb=" CA ILE A 555 " pdb=" CG1 ILE A 555 " pdb=" CG2 ILE A 555 " both_signs ideal model delta sigma weight residual False 2.64 2.34 0.31 2.00e-01 2.50e+01 2.34e+00 ... (remaining 1673 not shown) Planarity restraints: 1827 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG A 932 " 0.081 5.00e-02 4.00e+02 1.24e-01 2.45e+01 pdb=" N PRO A 933 " -0.214 5.00e-02 4.00e+02 pdb=" CA PRO A 933 " 0.068 5.00e-02 4.00e+02 pdb=" CD PRO A 933 " 0.065 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB HIS A 792 " 0.032 2.00e-02 2.50e+03 2.64e-02 1.05e+01 pdb=" CG HIS A 792 " -0.054 2.00e-02 2.50e+03 pdb=" ND1 HIS A 792 " -0.003 2.00e-02 2.50e+03 pdb=" CD2 HIS A 792 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 HIS A 792 " 0.012 2.00e-02 2.50e+03 pdb=" NE2 HIS A 792 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY G 122 " -0.050 5.00e-02 4.00e+02 7.53e-02 9.07e+00 pdb=" N PRO G 123 " 0.130 5.00e-02 4.00e+02 pdb=" CA PRO G 123 " -0.038 5.00e-02 4.00e+02 pdb=" CD PRO G 123 " -0.042 5.00e-02 4.00e+02 ... (remaining 1824 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 349 2.70 - 3.25: 9931 3.25 - 3.80: 15919 3.80 - 4.35: 20475 4.35 - 4.90: 34476 Nonbonded interactions: 81150 Sorted by model distance: nonbonded pdb=" OD1 ASP C 147 " pdb="ZN ZN C 202 " model vdw 2.153 2.230 nonbonded pdb=" O SER A 484 " pdb=" NE2 GLN A 566 " model vdw 2.281 3.120 nonbonded pdb=" OH TYR A 794 " pdb=" O GLY C 29 " model vdw 2.292 3.040 nonbonded pdb=" OD2 ASP C 147 " pdb="ZN ZN C 202 " model vdw 2.317 2.230 nonbonded pdb=" O ALA A 584 " pdb=" OG SER A 587 " model vdw 2.332 3.040 ... (remaining 81145 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 Found NCS groups: ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'E' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.270 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.200 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 10.900 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.030 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:0.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8461 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 : 0.009 0.121 10758 Z= 0.395 Angle : 1.076 13.040 14618 Z= 0.577 Chirality : 0.061 0.437 1676 Planarity : 0.008 0.124 1822 Dihedral : 10.650 80.869 3875 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 3.32 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.65 % Favored : 94.27 % Rotamer: Outliers : 0.09 % Allowed : 2.35 % Favored : 97.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % Cis-general : 0.00 % Twisted Proline : 1.79 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.45 (0.16), residues: 1291 helix: -4.34 (0.08), residues: 673 sheet: -2.78 (0.55), residues: 75 loop : -2.50 (0.22), residues: 543 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 125 TYR 0.029 0.003 TYR A1002 PHE 0.050 0.003 PHE A 838 TRP 0.031 0.003 TRP A 327 HIS 0.018 0.002 HIS A 792 Details of bonding type rmsd/Z covalent geometry : bond 0.00892 / 0.38 (10732) covalent geometry : angle 1.05927 / 0.57 (14568) SS BOND : bond 0.00374 / 0.20 ( 13) SS BOND : angle 1.68797 / 0.98 ( 26) hydrogen bonds : bond 0.31727 / 20.71 ( 465) hydrogen bonds : angle 10.66491 / 7.27 ( 1338) metal coordination : bond 0.06392 / 3.20 ( 3) Misc. bond : bond 0.08567 / 4.45 ( 2) link_BETA1-4 : bond 0.01279 / 0.61 ( 3) link_BETA1-4 : angle 2.62574 / 1.19 ( 9) link_NAG-ASN : bond 0.01262 / 0.76 ( 5) link_NAG-ASN : angle 5.51567 / 3.34 ( 15) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2582 Ramachandran restraints generated. 1291 Oldfield, 0 Emsley, 1291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2582 Ramachandran restraints generated. 1291 Oldfield, 0 Emsley, 1291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 316 time to evaluate : 0.362 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 237 TYR cc_start: 0.8155 (t80) cc_final: 0.7804 (t80) REVERT: A 418 ASP cc_start: 0.8459 (t70) cc_final: 0.8048 (t0) REVERT: A 446 THR cc_start: 0.9132 (t) cc_final: 0.8897 (t) REVERT: A 512 PHE cc_start: 0.8465 (t80) cc_final: 0.8223 (t80) REVERT: A 1038 ASN cc_start: 0.8221 (t0) cc_final: 0.7687 (t0) REVERT: A 1041 THR cc_start: 0.9114 (p) cc_final: 0.8725 (p) REVERT: C 73 PHE cc_start: 0.7997 (t80) cc_final: 0.7797 (t80) REVERT: C 79 ASN cc_start: 0.8670 (t0) cc_final: 0.8149 (t0) REVERT: C 81 ASN cc_start: 0.8760 (t0) cc_final: 0.8093 (t0) REVERT: C 97 LEU cc_start: 0.8706 (tp) cc_final: 0.8259 (tp) REVERT: C 98 MET cc_start: 0.8549 (ptp) cc_final: 0.7587 (ptp) REVERT: C 102 CYS cc_start: 0.9444 (t) cc_final: 0.7955 (t) REVERT: C 160 MET cc_start: 0.8387 (tpp) cc_final: 0.8103 (tpp) REVERT: C 176 GLU cc_start: 0.7869 (tm-30) cc_final: 0.7569 (tm-30) REVERT: C 185 VAL cc_start: 0.9303 (p) cc_final: 0.9003 (p) REVERT: C 186 LYS cc_start: 0.8990 (tmtm) cc_final: 0.8717 (tptp) REVERT: G 50 GLN cc_start: 0.8774 (pt0) cc_final: 0.8555 (pt0) REVERT: G 62 SER cc_start: 0.9280 (t) cc_final: 0.8957 (p) REVERT: G 200 THR cc_start: 0.8191 (p) cc_final: 0.7756 (p) REVERT: G 237 GLU cc_start: 0.9310 (tt0) cc_final: 0.8860 (tm-30) REVERT: G 238 ASN cc_start: 0.9116 (m-40) cc_final: 0.8574 (m-40) outliers start: 1 outliers final: 1 residues processed: 317 average time/residue: 0.1098 time to fit residues: 46.8772 Evaluate side-chains 228 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 227 time to evaluate : 0.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 961 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 98 optimal weight: 10.0000 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 0.5980 chunk 66 optimal weight: 1.9990 chunk 124 optimal weight: 10.0000 chunk 103 optimal weight: 0.9990 chunk 77 optimal weight: 0.6980 chunk 122 optimal weight: 7.9990 chunk 91 optimal weight: 0.8980 chunk 55 optimal weight: 0.9990 chunk 129 optimal weight: 7.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 146 GLN A 248 ASN A 326 HIS A 361 GLN A 369 HIS A 378 ASN A 398 HIS A 729 HIS A 784 GLN A 846 GLN A 940 HIS A1038 ASN A1110 HIS C 35 HIS C 100 GLN G 56 GLN G 195 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.160594 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.105322 restraints weight = 14193.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.103888 restraints weight = 11210.573| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.104931 restraints weight = 10083.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.104966 restraints weight = 8426.742| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.105206 restraints weight = 7848.088| |-----------------------------------------------------------------------------| r_work (final): 0.3102 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8446 moved from start: 0.2424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 10758 Z= 0.162 Angle : 0.720 12.267 14618 Z= 0.367 Chirality : 0.045 0.345 1676 Planarity : 0.007 0.096 1822 Dihedral : 7.150 72.941 1459 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.11 % Favored : 95.82 % Rotamer: Outliers : 2.26 % Allowed : 9.84 % Favored : 87.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % Cis-general : 0.00 % Twisted Proline : 1.79 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.07 (0.20), residues: 1291 helix: -1.94 (0.16), residues: 695 sheet: -2.47 (0.55), residues: 74 loop : -1.89 (0.25), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A1102 TYR 0.021 0.002 TYR A 863 PHE 0.021 0.002 PHE A 780 TRP 0.010 0.001 TRP A 389 HIS 0.009 0.001 HIS A1088 Details of bonding type rmsd/Z covalent geometry : bond 0.00365 / 0.16 (10732) covalent geometry : angle 0.70240 / 0.36 (14568) SS BOND : bond 0.00385 / 0.28 ( 13) SS BOND : angle 2.62863 / 1.71 ( 26) hydrogen bonds : bond 0.05805 / 3.70 ( 465) hydrogen bonds : angle 5.20331 / 3.57 ( 1338) metal coordination : bond 0.00124 / 0.06 ( 3) Misc. bond : bond 0.00025 / 0.01 ( 2) link_BETA1-4 : bond 0.00669 / 0.32 ( 3) link_BETA1-4 : angle 1.30485 / 0.61 ( 9) link_NAG-ASN : bond 0.00865 / 0.57 ( 5) link_NAG-ASN : angle 3.55348 / 2.16 ( 15) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2582 Ramachandran restraints generated. 1291 Oldfield, 0 Emsley, 1291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2582 Ramachandran restraints generated. 1291 Oldfield, 0 Emsley, 1291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 249 time to evaluate : 0.393 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 139 GLU cc_start: 0.8007 (tp30) cc_final: 0.7760 (tp30) REVERT: A 237 TYR cc_start: 0.8183 (t80) cc_final: 0.7866 (t80) REVERT: A 418 ASP cc_start: 0.8312 (t70) cc_final: 0.7940 (t0) REVERT: A 1128 MET cc_start: 0.8075 (mmm) cc_final: 0.7869 (mmm) REVERT: C 79 ASN cc_start: 0.8911 (t0) cc_final: 0.8600 (t0) REVERT: C 81 ASN cc_start: 0.8726 (t0) cc_final: 0.8240 (t0) REVERT: C 97 LEU cc_start: 0.8746 (tp) cc_final: 0.8268 (tp) REVERT: C 98 MET cc_start: 0.7623 (ptp) cc_final: 0.7290 (ptp) REVERT: C 102 CYS cc_start: 0.9143 (t) cc_final: 0.7931 (t) REVERT: C 160 MET cc_start: 0.8245 (tpp) cc_final: 0.7907 (tpp) REVERT: C 176 GLU cc_start: 0.7904 (tm-30) cc_final: 0.7446 (tp30) REVERT: G 132 GLN cc_start: 0.8090 (OUTLIER) cc_final: 0.7763 (pp30) REVERT: G 189 TYR cc_start: 0.9205 (m-80) cc_final: 0.8968 (m-80) REVERT: G 238 ASN cc_start: 0.9224 (m-40) cc_final: 0.8728 (m110) outliers start: 25 outliers final: 13 residues processed: 260 average time/residue: 0.0938 time to fit residues: 35.0511 Evaluate side-chains 234 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 220 time to evaluate : 0.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 353 MET Chi-restraints excluded: chain A residue 459 VAL Chi-restraints excluded: chain A residue 530 CYS Chi-restraints excluded: chain A residue 555 ILE Chi-restraints excluded: chain A residue 578 VAL Chi-restraints excluded: chain A residue 589 ASP Chi-restraints excluded: chain A residue 796 VAL Chi-restraints excluded: chain A residue 1060 MET Chi-restraints excluded: chain A residue 1108 LEU Chi-restraints excluded: chain A residue 1124 LEU Chi-restraints excluded: chain C residue 150 THR Chi-restraints excluded: chain C residue 183 CYS Chi-restraints excluded: chain G residue 132 GLN Chi-restraints excluded: chain G residue 232 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 98 optimal weight: 3.9990 chunk 30 optimal weight: 3.9990 chunk 101 optimal weight: 20.0000 chunk 46 optimal weight: 5.9990 chunk 108 optimal weight: 9.9990 chunk 79 optimal weight: 0.9990 chunk 45 optimal weight: 8.9990 chunk 105 optimal weight: 5.9990 chunk 68 optimal weight: 3.9990 chunk 106 optimal weight: 6.9990 chunk 22 optimal weight: 6.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 399 GLN ** A 574 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1110 HIS C 115 ASN G 118 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.150598 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 87)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.098304 restraints weight = 14450.483| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.093202 restraints weight = 13595.627| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.094477 restraints weight = 14065.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.095444 restraints weight = 12025.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.095320 restraints weight = 10485.341| |-----------------------------------------------------------------------------| r_work (final): 0.2969 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8485 moved from start: 0.2960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.080 10758 Z= 0.409 Angle : 0.863 10.899 14618 Z= 0.438 Chirality : 0.054 0.309 1676 Planarity : 0.007 0.111 1822 Dihedral : 7.055 74.177 1458 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.51 % Favored : 93.42 % Rotamer: Outliers : 3.70 % Allowed : 12.09 % Favored : 84.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % Cis-general : 0.00 % Twisted Proline : 1.79 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.24 (0.22), residues: 1291 helix: -0.93 (0.19), residues: 702 sheet: -2.40 (0.59), residues: 68 loop : -2.01 (0.25), residues: 521 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG G 175 TYR 0.027 0.003 TYR A 966 PHE 0.039 0.003 PHE A 838 TRP 0.012 0.002 TRP A 841 HIS 0.020 0.002 HIS A 792 Details of bonding type rmsd/Z covalent geometry : bond 0.00995 / 0.41 (10732) covalent geometry : angle 0.85008 / 0.43 (14568) SS BOND : bond 0.00453 / 0.32 ( 13) SS BOND : angle 2.60720 / 1.76 ( 26) hydrogen bonds : bond 0.05604 / 3.54 ( 465) hydrogen bonds : angle 5.09041 / 3.45 ( 1338) metal coordination : bond 0.00223 / 0.12 ( 3) Misc. bond : bond 0.00099 / 0.05 ( 2) link_BETA1-4 : bond 0.00301 / 0.15 ( 3) link_BETA1-4 : angle 1.32040 / 0.57 ( 9) link_NAG-ASN : bond 0.00789 / 0.49 ( 5) link_NAG-ASN : angle 3.26502 / 2.01 ( 15) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2582 Ramachandran restraints generated. 1291 Oldfield, 0 Emsley, 1291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2582 Ramachandran restraints generated. 1291 Oldfield, 0 Emsley, 1291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 225 time to evaluate : 0.399 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 418 ASP cc_start: 0.8558 (t70) cc_final: 0.8194 (t0) REVERT: C 79 ASN cc_start: 0.9002 (t0) cc_final: 0.8485 (t0) REVERT: C 81 ASN cc_start: 0.8634 (t0) cc_final: 0.8372 (t0) REVERT: C 96 ARG cc_start: 0.8329 (mtp85) cc_final: 0.7466 (mtp85) REVERT: C 97 LEU cc_start: 0.8778 (tp) cc_final: 0.8386 (tp) REVERT: C 160 MET cc_start: 0.8439 (tpp) cc_final: 0.8190 (tpp) REVERT: C 176 GLU cc_start: 0.7880 (tm-30) cc_final: 0.7561 (tp30) REVERT: G 238 ASN cc_start: 0.9073 (m-40) cc_final: 0.8660 (m110) outliers start: 41 outliers final: 28 residues processed: 248 average time/residue: 0.0885 time to fit residues: 32.3806 Evaluate side-chains 243 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 215 time to evaluate : 0.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 ASP Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 249 PHE Chi-restraints excluded: chain A residue 353 MET Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 479 SER Chi-restraints excluded: chain A residue 480 LEU Chi-restraints excluded: chain A residue 530 CYS Chi-restraints excluded: chain A residue 531 LEU Chi-restraints excluded: chain A residue 538 VAL Chi-restraints excluded: chain A residue 555 ILE Chi-restraints excluded: chain A residue 578 VAL Chi-restraints excluded: chain A residue 589 ASP Chi-restraints excluded: chain A residue 796 VAL Chi-restraints excluded: chain A residue 914 THR Chi-restraints excluded: chain A residue 1060 MET Chi-restraints excluded: chain A residue 1091 LEU Chi-restraints excluded: chain A residue 1108 LEU Chi-restraints excluded: chain A residue 1122 THR Chi-restraints excluded: chain A residue 1124 LEU Chi-restraints excluded: chain A residue 1135 ASP Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 150 THR Chi-restraints excluded: chain C residue 183 CYS Chi-restraints excluded: chain G residue 62 SER Chi-restraints excluded: chain G residue 107 SER Chi-restraints excluded: chain G residue 132 GLN Chi-restraints excluded: chain G residue 232 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 106 optimal weight: 2.9990 chunk 74 optimal weight: 0.6980 chunk 66 optimal weight: 1.9990 chunk 14 optimal weight: 0.3980 chunk 48 optimal weight: 2.9990 chunk 58 optimal weight: 0.7980 chunk 72 optimal weight: 0.9990 chunk 81 optimal weight: 0.9990 chunk 113 optimal weight: 7.9990 chunk 69 optimal weight: 7.9990 chunk 114 optimal weight: 3.9990 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 248 ASN ** A 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 574 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 879 GLN A 919 ASN C 115 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.153620 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.099491 restraints weight = 14508.388| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.095342 restraints weight = 12578.780| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.095566 restraints weight = 12784.150| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.096158 restraints weight = 11842.744| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.096265 restraints weight = 10118.776| |-----------------------------------------------------------------------------| r_work (final): 0.2973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8451 moved from start: 0.3151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 10758 Z= 0.146 Angle : 0.699 12.588 14618 Z= 0.343 Chirality : 0.045 0.310 1676 Planarity : 0.005 0.092 1822 Dihedral : 6.738 71.036 1458 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.26 % Favored : 95.66 % Rotamer: Outliers : 3.25 % Allowed : 14.62 % Favored : 82.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % Cis-general : 0.00 % Twisted Proline : 1.79 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.48 (0.23), residues: 1291 helix: -0.25 (0.20), residues: 705 sheet: -2.05 (0.61), residues: 67 loop : -1.77 (0.25), residues: 519 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 178 TYR 0.020 0.002 TYR A 863 PHE 0.024 0.002 PHE A1093 TRP 0.013 0.001 TRP G 49 HIS 0.008 0.001 HIS A1088 Details of bonding type rmsd/Z covalent geometry : bond 0.00336 / 0.15 (10732) covalent geometry : angle 0.68360 / 0.34 (14568) SS BOND : bond 0.00230 / 0.15 ( 13) SS BOND : angle 2.52460 / 1.77 ( 26) hydrogen bonds : bond 0.04481 / 2.86 ( 465) hydrogen bonds : angle 4.64405 / 3.17 ( 1338) metal coordination : bond 0.00076 / 0.04 ( 3) Misc. bond : bond 0.00015 / 0.01 ( 2) link_BETA1-4 : bond 0.00487 / 0.23 ( 3) link_BETA1-4 : angle 1.12223 / 0.48 ( 9) link_NAG-ASN : bond 0.00824 / 0.51 ( 5) link_NAG-ASN : angle 3.18949 / 1.97 ( 15) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2582 Ramachandran restraints generated. 1291 Oldfield, 0 Emsley, 1291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2582 Ramachandran restraints generated. 1291 Oldfield, 0 Emsley, 1291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 219 time to evaluate : 0.317 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 418 ASP cc_start: 0.8330 (t70) cc_final: 0.8077 (t0) REVERT: A 1038 ASN cc_start: 0.7998 (t0) cc_final: 0.7790 (t0) REVERT: A 1128 MET cc_start: 0.8271 (mmm) cc_final: 0.8070 (mmm) REVERT: C 81 ASN cc_start: 0.8722 (t0) cc_final: 0.8327 (t0) REVERT: C 97 LEU cc_start: 0.8875 (tp) cc_final: 0.8570 (tp) REVERT: C 98 MET cc_start: 0.7501 (ptp) cc_final: 0.6885 (ttp) REVERT: C 150 THR cc_start: 0.8804 (OUTLIER) cc_final: 0.8595 (t) REVERT: C 160 MET cc_start: 0.8514 (tpp) cc_final: 0.8223 (tpp) REVERT: C 176 GLU cc_start: 0.7869 (tm-30) cc_final: 0.7544 (tp30) REVERT: G 233 GLU cc_start: 0.8914 (mm-30) cc_final: 0.8592 (mm-30) REVERT: G 238 ASN cc_start: 0.9245 (m-40) cc_final: 0.8773 (m110) outliers start: 36 outliers final: 20 residues processed: 237 average time/residue: 0.0781 time to fit residues: 27.4202 Evaluate side-chains 228 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 207 time to evaluate : 0.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 ASP Chi-restraints excluded: chain A residue 353 MET Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 530 CYS Chi-restraints excluded: chain A residue 555 ILE Chi-restraints excluded: chain A residue 578 VAL Chi-restraints excluded: chain A residue 796 VAL Chi-restraints excluded: chain A residue 829 GLN Chi-restraints excluded: chain A residue 914 THR Chi-restraints excluded: chain A residue 939 LEU Chi-restraints excluded: chain A residue 1060 MET Chi-restraints excluded: chain A residue 1091 LEU Chi-restraints excluded: chain A residue 1108 LEU Chi-restraints excluded: chain A residue 1124 LEU Chi-restraints excluded: chain A residue 1160 LEU Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 150 THR Chi-restraints excluded: chain C residue 183 CYS Chi-restraints excluded: chain G residue 107 SER Chi-restraints excluded: chain G residue 132 GLN Chi-restraints excluded: chain G residue 232 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 26 optimal weight: 0.0030 chunk 78 optimal weight: 2.9990 chunk 39 optimal weight: 0.6980 chunk 123 optimal weight: 6.9990 chunk 112 optimal weight: 9.9990 chunk 105 optimal weight: 0.8980 chunk 3 optimal weight: 3.9990 chunk 2 optimal weight: 0.9980 chunk 15 optimal weight: 0.5980 chunk 60 optimal weight: 0.0370 chunk 63 optimal weight: 0.9990 overall best weight: 0.4468 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 248 ASN ** A 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 566 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 574 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 846 GLN A 919 ASN A1110 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.158350 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.100279 restraints weight = 14242.338| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 66)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.102024 restraints weight = 10593.624| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.103038 restraints weight = 8844.146| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.103563 restraints weight = 7986.674| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.103563 restraints weight = 7475.860| |-----------------------------------------------------------------------------| r_work (final): 0.3075 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8422 moved from start: 0.3439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 10758 Z= 0.125 Angle : 0.649 12.927 14618 Z= 0.321 Chirality : 0.044 0.314 1676 Planarity : 0.005 0.083 1822 Dihedral : 6.432 66.971 1458 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.34 % Favored : 95.58 % Rotamer: Outliers : 3.34 % Allowed : 15.97 % Favored : 80.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % Cis-general : 0.00 % Twisted Proline : 1.79 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.99 (0.23), residues: 1291 helix: 0.18 (0.20), residues: 704 sheet: -1.85 (0.63), residues: 67 loop : -1.59 (0.26), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 204 TYR 0.021 0.001 TYR G 63 PHE 0.016 0.001 PHE A1167 TRP 0.014 0.001 TRP G 49 HIS 0.008 0.001 HIS G 108 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.12 (10732) covalent geometry : angle 0.63542 / 0.32 (14568) SS BOND : bond 0.00192 / 0.11 ( 13) SS BOND : angle 2.17238 / 1.38 ( 26) hydrogen bonds : bond 0.03968 / 2.54 ( 465) hydrogen bonds : angle 4.40159 / 3.01 ( 1338) metal coordination : bond 0.00020 / 0.01 ( 3) Misc. bond : bond 0.00022 / 0.01 ( 2) link_BETA1-4 : bond 0.00474 / 0.23 ( 3) link_BETA1-4 : angle 1.16232 / 0.50 ( 9) link_NAG-ASN : bond 0.00840 / 0.51 ( 5) link_NAG-ASN : angle 3.14086 / 1.96 ( 15) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2582 Ramachandran restraints generated. 1291 Oldfield, 0 Emsley, 1291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2582 Ramachandran restraints generated. 1291 Oldfield, 0 Emsley, 1291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 224 time to evaluate : 0.356 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 418 ASP cc_start: 0.8271 (t70) cc_final: 0.7862 (t0) REVERT: A 469 LEU cc_start: 0.9152 (tt) cc_final: 0.8842 (tp) REVERT: A 512 PHE cc_start: 0.8043 (t80) cc_final: 0.7839 (t80) REVERT: A 932 ARG cc_start: 0.8333 (mmt-90) cc_final: 0.7485 (mmt180) REVERT: A 1038 ASN cc_start: 0.8018 (t0) cc_final: 0.7747 (t0) REVERT: A 1128 MET cc_start: 0.8271 (mmm) cc_final: 0.7949 (mmm) REVERT: C 81 ASN cc_start: 0.8743 (t0) cc_final: 0.8310 (t0) REVERT: C 97 LEU cc_start: 0.8895 (tp) cc_final: 0.8635 (tp) REVERT: C 141 TYR cc_start: 0.8298 (m-80) cc_final: 0.8088 (m-80) REVERT: C 150 THR cc_start: 0.8786 (OUTLIER) cc_final: 0.8559 (t) REVERT: C 160 MET cc_start: 0.8506 (tpp) cc_final: 0.8291 (tpp) REVERT: C 176 GLU cc_start: 0.7801 (tm-30) cc_final: 0.7588 (tp30) REVERT: G 189 TYR cc_start: 0.9285 (m-80) cc_final: 0.8878 (m-80) REVERT: G 233 GLU cc_start: 0.8899 (mm-30) cc_final: 0.8600 (mm-30) REVERT: G 238 ASN cc_start: 0.9189 (m-40) cc_final: 0.8708 (m110) outliers start: 37 outliers final: 15 residues processed: 243 average time/residue: 0.0822 time to fit residues: 29.3812 Evaluate side-chains 227 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 211 time to evaluate : 0.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 ASP Chi-restraints excluded: chain A residue 252 LEU Chi-restraints excluded: chain A residue 353 MET Chi-restraints excluded: chain A residue 444 CYS Chi-restraints excluded: chain A residue 530 CYS Chi-restraints excluded: chain A residue 578 VAL Chi-restraints excluded: chain A residue 796 VAL Chi-restraints excluded: chain A residue 1040 TRP Chi-restraints excluded: chain A residue 1060 MET Chi-restraints excluded: chain A residue 1091 LEU Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 150 THR Chi-restraints excluded: chain C residue 183 CYS Chi-restraints excluded: chain G residue 200 THR Chi-restraints excluded: chain G residue 232 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 122 optimal weight: 7.9990 chunk 112 optimal weight: 9.9990 chunk 52 optimal weight: 8.9990 chunk 69 optimal weight: 1.9990 chunk 33 optimal weight: 0.9990 chunk 41 optimal weight: 2.9990 chunk 125 optimal weight: 20.0000 chunk 23 optimal weight: 3.9990 chunk 21 optimal weight: 0.8980 chunk 70 optimal weight: 1.9990 chunk 88 optimal weight: 0.5980 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 248 ASN ** A 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 115 ASN ** G 108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.156722 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 95)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.104468 restraints weight = 14377.259| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.100092 restraints weight = 13833.044| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.101435 restraints weight = 14475.333| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.102726 restraints weight = 11970.145| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.102129 restraints weight = 10316.929| |-----------------------------------------------------------------------------| r_work (final): 0.3090 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8416 moved from start: 0.3536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 10758 Z= 0.175 Angle : 0.687 13.219 14618 Z= 0.340 Chirality : 0.046 0.314 1676 Planarity : 0.005 0.087 1822 Dihedral : 6.391 67.097 1458 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.57 % Favored : 95.35 % Rotamer: Outliers : 3.52 % Allowed : 17.78 % Favored : 78.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % Cis-general : 0.00 % Twisted Proline : 1.79 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.79 (0.23), residues: 1291 helix: 0.36 (0.20), residues: 711 sheet: -1.84 (0.63), residues: 67 loop : -1.56 (0.26), residues: 513 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 144 TYR 0.020 0.002 TYR G 68 PHE 0.015 0.002 PHE A 838 TRP 0.012 0.001 TRP G 49 HIS 0.011 0.001 HIS G 108 Details of bonding type rmsd/Z covalent geometry : bond 0.00422 / 0.17 (10732) covalent geometry : angle 0.67490 / 0.34 (14568) SS BOND : bond 0.00428 / 0.34 ( 13) SS BOND : angle 2.12425 / 1.30 ( 26) hydrogen bonds : bond 0.04086 / 2.61 ( 465) hydrogen bonds : angle 4.42419 / 3.01 ( 1338) metal coordination : bond 0.00061 / 0.03 ( 3) Misc. bond : bond 0.00034 / 0.02 ( 2) link_BETA1-4 : bond 0.00441 / 0.21 ( 3) link_BETA1-4 : angle 1.12707 / 0.49 ( 9) link_NAG-ASN : bond 0.00800 / 0.49 ( 5) link_NAG-ASN : angle 3.08591 / 1.93 ( 15) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2582 Ramachandran restraints generated. 1291 Oldfield, 0 Emsley, 1291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2582 Ramachandran restraints generated. 1291 Oldfield, 0 Emsley, 1291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 217 time to evaluate : 0.399 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 418 ASP cc_start: 0.8348 (t70) cc_final: 0.7912 (t0) REVERT: A 512 PHE cc_start: 0.7843 (t80) cc_final: 0.7553 (t80) REVERT: A 1038 ASN cc_start: 0.8045 (t0) cc_final: 0.7752 (t0) REVERT: A 1052 MET cc_start: 0.8621 (ttm) cc_final: 0.8115 (ttm) REVERT: C 81 ASN cc_start: 0.8602 (t0) cc_final: 0.8215 (t0) REVERT: C 97 LEU cc_start: 0.8717 (tp) cc_final: 0.8442 (tp) REVERT: G 189 TYR cc_start: 0.9009 (m-80) cc_final: 0.8783 (m-80) REVERT: G 238 ASN cc_start: 0.9010 (m-40) cc_final: 0.8582 (m110) outliers start: 39 outliers final: 26 residues processed: 235 average time/residue: 0.0941 time to fit residues: 32.3378 Evaluate side-chains 235 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 209 time to evaluate : 0.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 ASP Chi-restraints excluded: chain A residue 249 PHE Chi-restraints excluded: chain A residue 252 LEU Chi-restraints excluded: chain A residue 309 VAL Chi-restraints excluded: chain A residue 353 MET Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain A residue 444 CYS Chi-restraints excluded: chain A residue 530 CYS Chi-restraints excluded: chain A residue 550 PHE Chi-restraints excluded: chain A residue 555 ILE Chi-restraints excluded: chain A residue 578 VAL Chi-restraints excluded: chain A residue 796 VAL Chi-restraints excluded: chain A residue 829 GLN Chi-restraints excluded: chain A residue 879 GLN Chi-restraints excluded: chain A residue 1040 TRP Chi-restraints excluded: chain A residue 1060 MET Chi-restraints excluded: chain A residue 1091 LEU Chi-restraints excluded: chain A residue 1135 ASP Chi-restraints excluded: chain A residue 1157 LEU Chi-restraints excluded: chain A residue 1160 LEU Chi-restraints excluded: chain C residue 66 ILE Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 183 CYS Chi-restraints excluded: chain G residue 76 LEU Chi-restraints excluded: chain G residue 232 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 80 optimal weight: 1.9990 chunk 87 optimal weight: 0.5980 chunk 39 optimal weight: 0.9980 chunk 116 optimal weight: 0.9990 chunk 70 optimal weight: 1.9990 chunk 34 optimal weight: 0.5980 chunk 38 optimal weight: 0.9990 chunk 108 optimal weight: 8.9990 chunk 113 optimal weight: 8.9990 chunk 31 optimal weight: 1.9990 chunk 129 optimal weight: 5.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 248 ASN ** A 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1038 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 180 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.158375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 91)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.103758 restraints weight = 14114.340| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.103070 restraints weight = 10676.142| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.103027 restraints weight = 8949.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.103116 restraints weight = 8779.826| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.103192 restraints weight = 8554.402| |-----------------------------------------------------------------------------| r_work (final): 0.2991 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8443 moved from start: 0.3698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 10758 Z= 0.143 Angle : 0.687 13.592 14618 Z= 0.334 Chirality : 0.045 0.314 1676 Planarity : 0.005 0.083 1822 Dihedral : 6.318 66.337 1458 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.26 % Favored : 95.66 % Rotamer: Outliers : 3.61 % Allowed : 17.96 % Favored : 78.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % Cis-general : 0.00 % Twisted Proline : 1.79 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.61 (0.24), residues: 1291 helix: 0.52 (0.20), residues: 711 sheet: -1.76 (0.63), residues: 68 loop : -1.49 (0.26), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 28 TYR 0.023 0.001 TYR G 68 PHE 0.016 0.001 PHE A1167 TRP 0.012 0.001 TRP G 49 HIS 0.009 0.001 HIS G 108 Details of bonding type rmsd/Z covalent geometry : bond 0.00339 / 0.14 (10732) covalent geometry : angle 0.67396 / 0.33 (14568) SS BOND : bond 0.00180 / 0.08 ( 13) SS BOND : angle 2.21809 / 1.27 ( 26) hydrogen bonds : bond 0.03878 / 2.48 ( 465) hydrogen bonds : angle 4.34216 / 2.95 ( 1338) metal coordination : bond 0.00121 / 0.06 ( 3) Misc. bond : bond 0.00026 / 0.01 ( 2) link_BETA1-4 : bond 0.00383 / 0.19 ( 3) link_BETA1-4 : angle 1.14694 / 0.49 ( 9) link_NAG-ASN : bond 0.00817 / 0.50 ( 5) link_NAG-ASN : angle 3.06903 / 1.92 ( 15) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2582 Ramachandran restraints generated. 1291 Oldfield, 0 Emsley, 1291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2582 Ramachandran restraints generated. 1291 Oldfield, 0 Emsley, 1291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 216 time to evaluate : 0.401 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 418 ASP cc_start: 0.8319 (t70) cc_final: 0.7849 (t0) REVERT: A 447 MET cc_start: 0.8632 (OUTLIER) cc_final: 0.7864 (ttp) REVERT: A 512 PHE cc_start: 0.8089 (t80) cc_final: 0.7790 (t80) REVERT: A 932 ARG cc_start: 0.8308 (OUTLIER) cc_final: 0.7795 (mmp-170) REVERT: A 1038 ASN cc_start: 0.8074 (t0) cc_final: 0.7721 (t0) REVERT: A 1052 MET cc_start: 0.8664 (ttm) cc_final: 0.8238 (ttm) REVERT: A 1128 MET cc_start: 0.8249 (mmm) cc_final: 0.7969 (mmm) REVERT: C 81 ASN cc_start: 0.8772 (t0) cc_final: 0.8281 (t0) REVERT: C 97 LEU cc_start: 0.8859 (tp) cc_final: 0.8616 (tp) REVERT: C 186 LYS cc_start: 0.9272 (tptp) cc_final: 0.8756 (tptt) REVERT: G 189 TYR cc_start: 0.9170 (m-80) cc_final: 0.8855 (m-80) REVERT: G 233 GLU cc_start: 0.8871 (mm-30) cc_final: 0.8480 (mm-30) REVERT: G 237 GLU cc_start: 0.8981 (tt0) cc_final: 0.8548 (tm-30) REVERT: G 238 ASN cc_start: 0.9059 (m-40) cc_final: 0.8525 (m-40) outliers start: 40 outliers final: 30 residues processed: 233 average time/residue: 0.0920 time to fit residues: 31.6407 Evaluate side-chains 244 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 212 time to evaluate : 0.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 ARG Chi-restraints excluded: chain A residue 131 ASP Chi-restraints excluded: chain A residue 200 ILE Chi-restraints excluded: chain A residue 249 PHE Chi-restraints excluded: chain A residue 252 LEU Chi-restraints excluded: chain A residue 309 VAL Chi-restraints excluded: chain A residue 353 MET Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain A residue 444 CYS Chi-restraints excluded: chain A residue 447 MET Chi-restraints excluded: chain A residue 480 LEU Chi-restraints excluded: chain A residue 530 CYS Chi-restraints excluded: chain A residue 550 PHE Chi-restraints excluded: chain A residue 578 VAL Chi-restraints excluded: chain A residue 586 LEU Chi-restraints excluded: chain A residue 796 VAL Chi-restraints excluded: chain A residue 829 GLN Chi-restraints excluded: chain A residue 879 GLN Chi-restraints excluded: chain A residue 914 THR Chi-restraints excluded: chain A residue 932 ARG Chi-restraints excluded: chain A residue 1040 TRP Chi-restraints excluded: chain A residue 1060 MET Chi-restraints excluded: chain A residue 1091 LEU Chi-restraints excluded: chain A residue 1108 LEU Chi-restraints excluded: chain A residue 1135 ASP Chi-restraints excluded: chain A residue 1157 LEU Chi-restraints excluded: chain A residue 1160 LEU Chi-restraints excluded: chain C residue 66 ILE Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 183 CYS Chi-restraints excluded: chain G residue 232 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 30 optimal weight: 0.6980 chunk 53 optimal weight: 0.0980 chunk 34 optimal weight: 0.9990 chunk 26 optimal weight: 3.9990 chunk 31 optimal weight: 0.6980 chunk 100 optimal weight: 10.0000 chunk 79 optimal weight: 0.7980 chunk 127 optimal weight: 7.9990 chunk 15 optimal weight: 0.6980 chunk 91 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 248 ASN ** A 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 566 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 784 GLN ** A1038 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.159318 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.105451 restraints weight = 14099.037| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.102339 restraints weight = 12069.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.102647 restraints weight = 11273.036| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.103233 restraints weight = 10387.406| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.103390 restraints weight = 9339.268| |-----------------------------------------------------------------------------| r_work (final): 0.3049 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8427 moved from start: 0.3854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 10758 Z= 0.129 Angle : 0.699 13.850 14618 Z= 0.336 Chirality : 0.045 0.316 1676 Planarity : 0.005 0.080 1822 Dihedral : 6.177 64.995 1458 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.87 % Favored : 96.05 % Rotamer: Outliers : 2.80 % Allowed : 19.40 % Favored : 77.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % Cis-general : 0.00 % Twisted Proline : 1.79 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.40 (0.24), residues: 1291 helix: 0.66 (0.20), residues: 713 sheet: -1.57 (0.65), residues: 66 loop : -1.37 (0.27), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 175 TYR 0.026 0.001 TYR G 68 PHE 0.036 0.001 PHE A1112 TRP 0.014 0.001 TRP G 49 HIS 0.005 0.001 HIS A1088 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.13 (10732) covalent geometry : angle 0.68601 / 0.33 (14568) SS BOND : bond 0.00201 / 0.12 ( 13) SS BOND : angle 2.21284 / 1.28 ( 26) hydrogen bonds : bond 0.03734 / 2.39 ( 465) hydrogen bonds : angle 4.30702 / 2.93 ( 1338) metal coordination : bond 0.00095 / 0.05 ( 3) Misc. bond : bond 0.00027 / 0.01 ( 2) link_BETA1-4 : bond 0.00349 / 0.17 ( 3) link_BETA1-4 : angle 1.16857 / 0.50 ( 9) link_NAG-ASN : bond 0.00824 / 0.50 ( 5) link_NAG-ASN : angle 3.03728 / 1.90 ( 15) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2582 Ramachandran restraints generated. 1291 Oldfield, 0 Emsley, 1291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2582 Ramachandran restraints generated. 1291 Oldfield, 0 Emsley, 1291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 223 time to evaluate : 0.406 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 418 ASP cc_start: 0.8304 (t70) cc_final: 0.7815 (t0) REVERT: A 447 MET cc_start: 0.8592 (OUTLIER) cc_final: 0.7841 (ttp) REVERT: A 512 PHE cc_start: 0.8049 (t80) cc_final: 0.7738 (t80) REVERT: A 1038 ASN cc_start: 0.8129 (t0) cc_final: 0.7788 (t0) REVERT: A 1052 MET cc_start: 0.8622 (ttm) cc_final: 0.8157 (ttm) REVERT: A 1111 MET cc_start: 0.8620 (ttm) cc_final: 0.8265 (mtm) REVERT: C 81 ASN cc_start: 0.8743 (t0) cc_final: 0.8238 (t0) REVERT: C 97 LEU cc_start: 0.8863 (tp) cc_final: 0.8584 (tp) REVERT: C 186 LYS cc_start: 0.9297 (tptp) cc_final: 0.9087 (tptp) REVERT: G 132 GLN cc_start: 0.7494 (mm-40) cc_final: 0.7256 (mm110) REVERT: G 237 GLU cc_start: 0.8955 (tt0) cc_final: 0.8529 (tm-30) REVERT: G 238 ASN cc_start: 0.9022 (m-40) cc_final: 0.8512 (m-40) outliers start: 31 outliers final: 21 residues processed: 238 average time/residue: 0.0959 time to fit residues: 33.2245 Evaluate side-chains 227 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 205 time to evaluate : 0.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 ARG Chi-restraints excluded: chain A residue 131 ASP Chi-restraints excluded: chain A residue 151 THR Chi-restraints excluded: chain A residue 200 ILE Chi-restraints excluded: chain A residue 249 PHE Chi-restraints excluded: chain A residue 252 LEU Chi-restraints excluded: chain A residue 309 VAL Chi-restraints excluded: chain A residue 353 MET Chi-restraints excluded: chain A residue 447 MET Chi-restraints excluded: chain A residue 550 PHE Chi-restraints excluded: chain A residue 578 VAL Chi-restraints excluded: chain A residue 586 LEU Chi-restraints excluded: chain A residue 796 VAL Chi-restraints excluded: chain A residue 879 GLN Chi-restraints excluded: chain A residue 1040 TRP Chi-restraints excluded: chain A residue 1060 MET Chi-restraints excluded: chain A residue 1091 LEU Chi-restraints excluded: chain A residue 1135 ASP Chi-restraints excluded: chain C residue 66 ILE Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 183 CYS Chi-restraints excluded: chain G residue 232 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 74 optimal weight: 1.9990 chunk 13 optimal weight: 2.9990 chunk 97 optimal weight: 0.0000 chunk 81 optimal weight: 1.9990 chunk 71 optimal weight: 0.5980 chunk 55 optimal weight: 2.9990 chunk 96 optimal weight: 1.9990 chunk 84 optimal weight: 0.0670 chunk 66 optimal weight: 0.9990 chunk 110 optimal weight: 1.9990 chunk 34 optimal weight: 0.0000 overall best weight: 0.3328 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 248 ASN A 351 GLN A 374 HIS A 566 GLN ** A1038 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 91 ASN C 115 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.160087 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 83)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.106539 restraints weight = 14077.952| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.103093 restraints weight = 12081.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.103775 restraints weight = 12274.564| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.104476 restraints weight = 10479.650| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.104732 restraints weight = 9232.229| |-----------------------------------------------------------------------------| r_work (final): 0.3125 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8392 moved from start: 0.4041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 10758 Z= 0.128 Angle : 0.739 18.370 14618 Z= 0.351 Chirality : 0.045 0.318 1676 Planarity : 0.005 0.079 1822 Dihedral : 6.147 64.068 1458 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.18 % Favored : 95.74 % Rotamer: Outliers : 2.44 % Allowed : 20.04 % Favored : 77.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % Cis-general : 0.00 % Twisted Proline : 1.79 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.22 (0.24), residues: 1291 helix: 0.81 (0.20), residues: 709 sheet: -1.59 (0.64), residues: 68 loop : -1.25 (0.27), residues: 514 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG G 178 TYR 0.028 0.001 TYR G 68 PHE 0.030 0.001 PHE A1112 TRP 0.015 0.001 TRP G 49 HIS 0.006 0.001 HIS G 108 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.13 (10732) covalent geometry : angle 0.72664 / 0.35 (14568) SS BOND : bond 0.00207 / 0.14 ( 13) SS BOND : angle 2.30276 / 1.30 ( 26) hydrogen bonds : bond 0.03761 / 2.41 ( 465) hydrogen bonds : angle 4.33797 / 2.94 ( 1338) metal coordination : bond 0.00100 / 0.05 ( 3) Misc. bond : bond 0.00024 / 0.01 ( 2) link_BETA1-4 : bond 0.00553 / 0.27 ( 3) link_BETA1-4 : angle 1.16615 / 0.50 ( 9) link_NAG-ASN : bond 0.00824 / 0.50 ( 5) link_NAG-ASN : angle 3.02616 / 1.90 ( 15) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2582 Ramachandran restraints generated. 1291 Oldfield, 0 Emsley, 1291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2582 Ramachandran restraints generated. 1291 Oldfield, 0 Emsley, 1291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 211 time to evaluate : 0.349 Fit side-chains revert: symmetry clash REVERT: A 418 ASP cc_start: 0.8285 (t70) cc_final: 0.7792 (t0) REVERT: A 447 MET cc_start: 0.8505 (OUTLIER) cc_final: 0.7829 (ttp) REVERT: A 469 LEU cc_start: 0.9056 (tt) cc_final: 0.8805 (tp) REVERT: A 480 LEU cc_start: 0.8208 (tt) cc_final: 0.7502 (mt) REVERT: A 512 PHE cc_start: 0.8025 (t80) cc_final: 0.7726 (t80) REVERT: A 777 GLU cc_start: 0.8019 (pm20) cc_final: 0.7759 (mp0) REVERT: A 1038 ASN cc_start: 0.8157 (t0) cc_final: 0.7812 (t0) REVERT: A 1052 MET cc_start: 0.8635 (ttm) cc_final: 0.8186 (ttm) REVERT: A 1111 MET cc_start: 0.8514 (ttm) cc_final: 0.8102 (mtm) REVERT: C 97 LEU cc_start: 0.8805 (tp) cc_final: 0.8411 (tp) REVERT: C 186 LYS cc_start: 0.9291 (tptp) cc_final: 0.8823 (tptt) REVERT: G 233 GLU cc_start: 0.8762 (mm-30) cc_final: 0.8136 (mm-30) REVERT: G 238 ASN cc_start: 0.8951 (m-40) cc_final: 0.8544 (m110) outliers start: 27 outliers final: 22 residues processed: 224 average time/residue: 0.0827 time to fit residues: 27.4597 Evaluate side-chains 228 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 205 time to evaluate : 0.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 ARG Chi-restraints excluded: chain A residue 131 ASP Chi-restraints excluded: chain A residue 151 THR Chi-restraints excluded: chain A residue 200 ILE Chi-restraints excluded: chain A residue 249 PHE Chi-restraints excluded: chain A residue 252 LEU Chi-restraints excluded: chain A residue 309 VAL Chi-restraints excluded: chain A residue 353 MET Chi-restraints excluded: chain A residue 447 MET Chi-restraints excluded: chain A residue 550 PHE Chi-restraints excluded: chain A residue 578 VAL Chi-restraints excluded: chain A residue 586 LEU Chi-restraints excluded: chain A residue 796 VAL Chi-restraints excluded: chain A residue 914 THR Chi-restraints excluded: chain A residue 1040 TRP Chi-restraints excluded: chain A residue 1060 MET Chi-restraints excluded: chain A residue 1091 LEU Chi-restraints excluded: chain A residue 1108 LEU Chi-restraints excluded: chain A residue 1135 ASP Chi-restraints excluded: chain C residue 33 ARG Chi-restraints excluded: chain C residue 66 ILE Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 183 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 45 optimal weight: 7.9990 chunk 39 optimal weight: 0.4980 chunk 65 optimal weight: 0.7980 chunk 9 optimal weight: 0.7980 chunk 119 optimal weight: 6.9990 chunk 113 optimal weight: 10.0000 chunk 6 optimal weight: 0.0030 chunk 50 optimal weight: 0.9980 chunk 2 optimal weight: 10.0000 chunk 109 optimal weight: 6.9990 chunk 78 optimal weight: 1.9990 overall best weight: 0.6190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 248 ASN ** A1038 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 108 HIS G 132 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.156270 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 84)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.101277 restraints weight = 14125.348| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.098902 restraints weight = 12371.181| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.099106 restraints weight = 11640.321| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.099731 restraints weight = 11013.137| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.100092 restraints weight = 9475.081| |-----------------------------------------------------------------------------| r_work (final): 0.3039 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8394 moved from start: 0.4095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 10758 Z= 0.135 Angle : 0.729 17.609 14618 Z= 0.347 Chirality : 0.046 0.338 1676 Planarity : 0.005 0.081 1822 Dihedral : 6.081 63.891 1458 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.34 % Favored : 95.58 % Rotamer: Outliers : 2.35 % Allowed : 20.31 % Favored : 77.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % Cis-general : 0.00 % Twisted Proline : 1.79 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.20 (0.24), residues: 1291 helix: 0.83 (0.20), residues: 712 sheet: -1.57 (0.64), residues: 68 loop : -1.27 (0.28), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 178 TYR 0.025 0.001 TYR G 68 PHE 0.030 0.001 PHE A1112 TRP 0.014 0.001 TRP G 49 HIS 0.005 0.001 HIS A1088 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.13 (10732) covalent geometry : angle 0.72215 / 0.35 (14568) SS BOND : bond 0.00214 / 0.13 ( 13) SS BOND : angle 1.07890 / 0.82 ( 26) hydrogen bonds : bond 0.03716 / 2.38 ( 465) hydrogen bonds : angle 4.31952 / 2.93 ( 1338) metal coordination : bond 0.00092 / 0.05 ( 3) Misc. bond : bond 0.00027 / 0.01 ( 2) link_BETA1-4 : bond 0.00540 / 0.26 ( 3) link_BETA1-4 : angle 1.20537 / 0.52 ( 9) link_NAG-ASN : bond 0.00810 / 0.49 ( 5) link_NAG-ASN : angle 3.00707 / 1.88 ( 15) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2582 Ramachandran restraints generated. 1291 Oldfield, 0 Emsley, 1291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2582 Ramachandran restraints generated. 1291 Oldfield, 0 Emsley, 1291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 204 time to evaluate : 0.383 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 375 MET cc_start: 0.8063 (ptt) cc_final: 0.7827 (ptt) REVERT: A 418 ASP cc_start: 0.8315 (t70) cc_final: 0.7819 (t0) REVERT: A 447 MET cc_start: 0.8548 (OUTLIER) cc_final: 0.7875 (ttp) REVERT: A 469 LEU cc_start: 0.9060 (tt) cc_final: 0.8831 (tp) REVERT: A 480 LEU cc_start: 0.8252 (tt) cc_final: 0.7554 (mt) REVERT: A 512 PHE cc_start: 0.8037 (t80) cc_final: 0.7735 (t80) REVERT: A 777 GLU cc_start: 0.7989 (pm20) cc_final: 0.7743 (mp0) REVERT: A 1038 ASN cc_start: 0.8177 (t0) cc_final: 0.7807 (t0) REVERT: A 1052 MET cc_start: 0.8663 (ttm) cc_final: 0.8194 (ttm) REVERT: C 81 ASN cc_start: 0.8623 (t0) cc_final: 0.8333 (t0) REVERT: G 238 ASN cc_start: 0.8968 (m-40) cc_final: 0.8571 (m110) outliers start: 26 outliers final: 21 residues processed: 214 average time/residue: 0.0762 time to fit residues: 24.5709 Evaluate side-chains 223 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 201 time to evaluate : 0.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 ARG Chi-restraints excluded: chain A residue 151 THR Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 200 ILE Chi-restraints excluded: chain A residue 249 PHE Chi-restraints excluded: chain A residue 252 LEU Chi-restraints excluded: chain A residue 309 VAL Chi-restraints excluded: chain A residue 353 MET Chi-restraints excluded: chain A residue 447 MET Chi-restraints excluded: chain A residue 550 PHE Chi-restraints excluded: chain A residue 578 VAL Chi-restraints excluded: chain A residue 586 LEU Chi-restraints excluded: chain A residue 796 VAL Chi-restraints excluded: chain A residue 914 THR Chi-restraints excluded: chain A residue 1040 TRP Chi-restraints excluded: chain A residue 1060 MET Chi-restraints excluded: chain A residue 1091 LEU Chi-restraints excluded: chain A residue 1108 LEU Chi-restraints excluded: chain A residue 1135 ASP Chi-restraints excluded: chain C residue 66 ILE Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 183 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 26 optimal weight: 0.0770 chunk 129 optimal weight: 3.9990 chunk 14 optimal weight: 0.7980 chunk 89 optimal weight: 0.8980 chunk 70 optimal weight: 0.0010 chunk 0 optimal weight: 10.0000 chunk 71 optimal weight: 0.6980 chunk 29 optimal weight: 1.9990 chunk 115 optimal weight: 2.9990 chunk 78 optimal weight: 1.9990 chunk 68 optimal weight: 0.4980 overall best weight: 0.4144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 248 ASN A 827 ASN ** A1038 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 91 ASN C 115 ASN G 195 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.156390 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 90)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.100441 restraints weight = 14250.093| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.099093 restraints weight = 11270.794| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.099548 restraints weight = 9111.653| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.099773 restraints weight = 8645.310| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.099822 restraints weight = 8474.593| |-----------------------------------------------------------------------------| r_work (final): 0.3013 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8419 moved from start: 0.4199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 10758 Z= 0.132 Angle : 0.752 16.767 14618 Z= 0.356 Chirality : 0.046 0.324 1676 Planarity : 0.005 0.079 1822 Dihedral : 6.079 63.619 1458 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.18 % Favored : 95.74 % Rotamer: Outliers : 2.53 % Allowed : 20.31 % Favored : 77.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % Cis-general : 0.00 % Twisted Proline : 1.79 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.14 (0.24), residues: 1291 helix: 0.90 (0.20), residues: 713 sheet: -1.55 (0.64), residues: 68 loop : -1.29 (0.27), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 178 TYR 0.024 0.001 TYR G 68 PHE 0.030 0.001 PHE A1112 TRP 0.014 0.001 TRP G 49 HIS 0.008 0.001 HIS G 108 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.13 (10732) covalent geometry : angle 0.74536 / 0.35 (14568) SS BOND : bond 0.00242 / 0.15 ( 13) SS BOND : angle 0.98988 / 0.76 ( 26) hydrogen bonds : bond 0.03774 / 2.43 ( 465) hydrogen bonds : angle 4.34925 / 2.94 ( 1338) metal coordination : bond 0.00113 / 0.06 ( 3) Misc. bond : bond 0.00027 / 0.01 ( 2) link_BETA1-4 : bond 0.00399 / 0.20 ( 3) link_BETA1-4 : angle 1.18637 / 0.51 ( 9) link_NAG-ASN : bond 0.00816 / 0.49 ( 5) link_NAG-ASN : angle 2.99553 / 1.88 ( 15) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1938.43 seconds wall clock time: 34 minutes 9.65 seconds (2049.65 seconds total)