Starting phenix.real_space_refine on Wed Mar 4 05:03:46 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7rhq_24466/03_2026/7rhq_24466.cif Found real_map, /net/cci-nas-00/data/ceres_data/7rhq_24466/03_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 { model { file = "/net/cci-nas-00/data/ceres_data/7rhq_24466/03_2026/7rhq_24466.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7rhq_24466/03_2026/7rhq_24466.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7rhq_24466/03_2026/7rhq_24466.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7rhq_24466/03_2026/7rhq_24466.map" } 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-5986/lib/python3.9/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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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: 2.97, per 1000 atoms: 0.28 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: 0.94 Conformation dependent library (CDL) restraints added in 625.8 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: 0.24 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: 1.68 Time building geometry restraints manager: 1.25 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: 6264 16.17 - 32.35: 341 32.35 - 48.52: 71 48.52 - 64.70: 15 64.70 - 80.87: 9 Dihedral angle restraints: 6700 sinusoidal: 2904 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 6697 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: 1.380 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: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 13.240 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 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 : 10.916 80.869 4213 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 covalent geometry : bond 0.00892 (10732) covalent geometry : angle 1.05927 (14568) SS BOND : bond 0.00374 ( 13) SS BOND : angle 1.68797 ( 26) hydrogen bonds : bond 0.31727 ( 465) hydrogen bonds : angle 10.66491 ( 1338) metal coordination : bond 0.06392 ( 3) Misc. bond : bond 0.08567 ( 2) link_BETA1-4 : bond 0.01279 ( 3) link_BETA1-4 : angle 2.62574 ( 9) link_NAG-ASN : bond 0.01262 ( 5) link_NAG-ASN : angle 5.51567 ( 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 : 0.397 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: 0.8726 (p) REVERT: C 79 ASN cc_start: 0.8670 (t0) cc_final: 0.8150 (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: 0.8260 (tp) REVERT: C 98 MET cc_start: 0.8549 (ptp) cc_final: 0.7588 (ptp) REVERT: C 102 CYS cc_start: 0.9444 (t) cc_final: 0.7957 (t) REVERT: C 160 MET cc_start: 0.8387 (tpp) cc_final: 0.8105 (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: 0.8958 (p) REVERT: G 63 TYR cc_start: 0.9170 (t80) cc_final: 0.8954 (t80) 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: 0.1166 time to fit residues: 49.5261 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 : 0.332 ------------------------------------------------------------------------------- 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: 9.9990 chunk 10 optimal weight: 0.5980 chunk 66 optimal weight: 1.9990 chunk 124 optimal weight: 10.0000 chunk 103 optimal weight: 1.9990 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: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 67 GLN G 195 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.159985 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.106002 restraints weight = 14212.196| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.104018 restraints weight = 9852.627| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.104567 restraints weight = 8519.500| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.104702 restraints weight = 7871.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.104900 restraints weight = 7615.226| |-----------------------------------------------------------------------------| r_work (final): 0.3045 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 moved from start: 0.2408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 10758 Z= 0.174 Angle : 0.728 12.212 14618 Z= 0.373 Chirality : 0.046 0.335 1676 Planarity : 0.007 0.098 1822 Dihedral : 8.395 73.274 1797 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.49 % Favored : 95.43 % Rotamer: Outliers : 2.35 % Allowed : 9.75 % 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: -3.00 (0.20), residues: 1291 helix: -1.85 (0.17), residues: 695 sheet: -2.45 (0.55), residues: 74 loop : -1.90 (0.25), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A1102 TYR 0.022 0.002 TYR A 863 PHE 0.022 0.002 PHE A 780 TRP 0.011 0.001 TRP A 389 HIS 0.009 0.001 HIS A1088 Details of bonding type rmsd covalent geometry : bond 0.00398 (10732) covalent geometry : angle 0.71097 (14568) SS BOND : bond 0.00432 ( 13) SS BOND : angle 2.58089 ( 26) hydrogen bonds : bond 0.05837 ( 465) hydrogen bonds : angle 5.21327 ( 1338) metal coordination : bond 0.00199 ( 3) Misc. bond : bond 0.00119 ( 2) link_BETA1-4 : bond 0.00463 ( 3) link_BETA1-4 : angle 1.36240 ( 9) link_NAG-ASN : bond 0.00869 ( 5) link_NAG-ASN : angle 3.50495 ( 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 272 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 246 time to evaluate : 0.426 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: symmetry clash REVERT: A 139 GLU cc_start: 0.8038 (tp30) cc_final: 0.7770 (tp30) REVERT: A 237 TYR cc_start: 0.8147 (t80) cc_final: 0.7827 (t80) REVERT: A 282 MET cc_start: 0.8956 (mmt) cc_final: 0.8656 (tpp) REVERT: A 418 ASP cc_start: 0.8341 (t70) cc_final: 0.7965 (t0) REVERT: C 79 ASN cc_start: 0.8945 (t0) cc_final: 0.8666 (t0) REVERT: C 81 ASN cc_start: 0.8651 (t0) cc_final: 0.8232 (t0) REVERT: C 97 LEU cc_start: 0.8642 (tp) cc_final: 0.8207 (tp) REVERT: C 98 MET cc_start: 0.7619 (ptp) cc_final: 0.7297 (ptp) REVERT: C 102 CYS cc_start: 0.9074 (t) cc_final: 0.7858 (t) REVERT: C 160 MET cc_start: 0.8206 (tpp) cc_final: 0.7918 (tpp) REVERT: C 176 GLU cc_start: 0.7872 (tm-30) cc_final: 0.7486 (tp30) REVERT: G 132 GLN cc_start: 0.8005 (OUTLIER) cc_final: 0.7288 (pp30) REVERT: G 238 ASN cc_start: 0.9141 (m-40) cc_final: 0.8662 (m110) outliers start: 26 outliers final: 15 residues processed: 259 average time/residue: 0.0951 time to fit residues: 35.0640 Evaluate side-chains 234 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 218 time to evaluate : 0.392 ------------------------------------------------------------------------------- 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 479 SER Chi-restraints excluded: chain A residue 530 CYS Chi-restraints excluded: chain A residue 531 LEU 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 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 139 THR 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: 4.9990 chunk 30 optimal weight: 4.9990 chunk 101 optimal weight: 20.0000 chunk 46 optimal weight: 0.9990 chunk 108 optimal weight: 5.9990 chunk 79 optimal weight: 0.7980 chunk 45 optimal weight: 7.9990 chunk 105 optimal weight: 7.9990 chunk 68 optimal weight: 0.7980 chunk 106 optimal weight: 6.9990 chunk 22 optimal weight: 8.9990 overall best weight: 2.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3791 r_free = 0.3791 target = 0.156071 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.104583 restraints weight = 14347.647| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.100311 restraints weight = 13688.556| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.101797 restraints weight = 14830.145| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.103025 restraints weight = 11099.585| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.102505 restraints weight = 9474.642| |-----------------------------------------------------------------------------| r_work (final): 0.3099 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8244 moved from start: 0.2842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.053 10758 Z= 0.288 Angle : 0.773 10.944 14618 Z= 0.388 Chirality : 0.050 0.318 1676 Planarity : 0.006 0.102 1822 Dihedral : 8.051 72.285 1796 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.04 % Favored : 93.88 % Rotamer: Outliers : 2.98 % Allowed : 12.36 % Favored : 84.66 % 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: -2.06 (0.22), residues: 1291 helix: -0.77 (0.19), residues: 704 sheet: -2.28 (0.59), residues: 68 loop : -1.97 (0.25), residues: 519 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 431 TYR 0.021 0.002 TYR A 863 PHE 0.029 0.002 PHE A 838 TRP 0.010 0.002 TRP G 49 HIS 0.015 0.002 HIS A 792 Details of bonding type rmsd covalent geometry : bond 0.00698 (10732) covalent geometry : angle 0.75931 (14568) SS BOND : bond 0.00384 ( 13) SS BOND : angle 2.53449 ( 26) hydrogen bonds : bond 0.05222 ( 465) hydrogen bonds : angle 4.96496 ( 1338) metal coordination : bond 0.00138 ( 3) Misc. bond : bond 0.00061 ( 2) link_BETA1-4 : bond 0.00505 ( 3) link_BETA1-4 : angle 1.33782 ( 9) link_NAG-ASN : bond 0.00778 ( 5) link_NAG-ASN : angle 3.27886 ( 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 260 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 227 time to evaluate : 0.355 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 418 ASP cc_start: 0.8501 (t70) cc_final: 0.8175 (t0) REVERT: C 79 ASN cc_start: 0.8970 (t0) cc_final: 0.8760 (t0) REVERT: C 97 LEU cc_start: 0.8632 (tp) cc_final: 0.8303 (tp) REVERT: C 102 CYS cc_start: 0.8820 (t) cc_final: 0.7865 (t) REVERT: G 238 ASN cc_start: 0.8910 (m-40) cc_final: 0.8526 (m110) outliers start: 33 outliers final: 23 residues processed: 244 average time/residue: 0.0851 time to fit residues: 30.2355 Evaluate side-chains 242 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 219 time to evaluate : 0.302 ------------------------------------------------------------------------------- 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 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 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 1124 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 106 optimal weight: 5.9990 chunk 74 optimal weight: 9.9990 chunk 66 optimal weight: 7.9990 chunk 14 optimal weight: 1.9990 chunk 48 optimal weight: 0.0570 chunk 58 optimal weight: 1.9990 chunk 72 optimal weight: 1.9990 chunk 81 optimal weight: 0.7980 chunk 113 optimal weight: 10.0000 chunk 69 optimal weight: 8.9990 chunk 114 optimal weight: 6.9990 overall best weight: 1.3704 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 248 ASN ** A 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 574 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 846 GLN A 919 ASN C 115 ASN ** C 180 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.154911 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.095426 restraints weight = 14277.009| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.098038 restraints weight = 10147.904| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.098823 restraints weight = 7421.355| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.099198 restraints weight = 6739.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.099337 restraints weight = 6878.152| |-----------------------------------------------------------------------------| r_work (final): 0.2991 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 moved from start: 0.3107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 10758 Z= 0.183 Angle : 0.711 10.444 14618 Z= 0.351 Chirality : 0.046 0.319 1676 Planarity : 0.005 0.094 1822 Dihedral : 7.852 70.882 1796 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.57 % Favored : 95.35 % Rotamer: Outliers : 3.43 % Allowed : 14.62 % Favored : 81.95 % 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: -1.49 (0.23), residues: 1291 helix: -0.24 (0.20), residues: 706 sheet: -2.04 (0.61), residues: 67 loop : -1.82 (0.25), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 178 TYR 0.020 0.002 TYR A 863 PHE 0.026 0.002 PHE A1093 TRP 0.012 0.001 TRP G 49 HIS 0.009 0.001 HIS G 108 Details of bonding type rmsd covalent geometry : bond 0.00436 (10732) covalent geometry : angle 0.69658 (14568) SS BOND : bond 0.00216 ( 13) SS BOND : angle 2.35312 ( 26) hydrogen bonds : bond 0.04547 ( 465) hydrogen bonds : angle 4.69771 ( 1338) metal coordination : bond 0.00146 ( 3) Misc. bond : bond 0.00029 ( 2) link_BETA1-4 : bond 0.00485 ( 3) link_BETA1-4 : angle 1.28704 ( 9) link_NAG-ASN : bond 0.00796 ( 5) link_NAG-ASN : angle 3.21128 ( 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 260 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 222 time to evaluate : 0.351 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 418 ASP cc_start: 0.8335 (t70) cc_final: 0.8055 (t0) REVERT: A 588 MET cc_start: 0.8834 (mmp) cc_final: 0.8634 (mmp) REVERT: C 97 LEU cc_start: 0.8870 (tp) cc_final: 0.8596 (tp) REVERT: C 102 CYS cc_start: 0.8861 (t) cc_final: 0.8567 (t) REVERT: C 150 THR cc_start: 0.8842 (OUTLIER) cc_final: 0.8609 (t) REVERT: G 233 GLU cc_start: 0.8974 (mm-30) cc_final: 0.8636 (mm-30) REVERT: G 238 ASN cc_start: 0.9277 (m-40) cc_final: 0.8789 (m110) outliers start: 38 outliers final: 25 residues processed: 241 average time/residue: 0.0843 time to fit residues: 30.1149 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 : 0.391 ------------------------------------------------------------------------------- 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 371 VAL Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain A residue 444 CYS Chi-restraints excluded: chain A residue 480 LEU 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 1135 ASP Chi-restraints excluded: chain A residue 1157 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 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: 0.9980 chunk 78 optimal weight: 1.9990 chunk 39 optimal weight: 0.9980 chunk 123 optimal weight: 10.0000 chunk 112 optimal weight: 8.9990 chunk 105 optimal weight: 0.9990 chunk 3 optimal weight: 0.6980 chunk 2 optimal weight: 10.0000 chunk 15 optimal weight: 0.5980 chunk 60 optimal weight: 0.0370 chunk 63 optimal weight: 0.8980 overall best weight: 0.6458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 919 ASN A1110 HIS ** C 180 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.156641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.096885 restraints weight = 14313.302| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.099179 restraints weight = 10753.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.100082 restraints weight = 7827.173| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.100017 restraints weight = 7207.511| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.100143 restraints weight = 7333.204| |-----------------------------------------------------------------------------| r_work (final): 0.2998 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8229 moved from start: 0.3382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 10758 Z= 0.132 Angle : 0.653 11.748 14618 Z= 0.322 Chirality : 0.045 0.321 1676 Planarity : 0.005 0.085 1822 Dihedral : 7.549 67.746 1796 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.57 % Favored : 95.35 % Rotamer: Outliers : 3.43 % Allowed : 15.43 % Favored : 81.14 % 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: -0.94 (0.23), residues: 1291 helix: 0.21 (0.20), residues: 699 sheet: -1.79 (0.63), residues: 67 loop : -1.54 (0.26), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 204 TYR 0.019 0.001 TYR A 863 PHE 0.017 0.001 PHE A1167 TRP 0.014 0.001 TRP G 49 HIS 0.007 0.001 HIS A1088 Details of bonding type rmsd covalent geometry : bond 0.00302 (10732) covalent geometry : angle 0.63876 (14568) SS BOND : bond 0.00257 ( 13) SS BOND : angle 2.11073 ( 26) hydrogen bonds : bond 0.04039 ( 465) hydrogen bonds : angle 4.46940 ( 1338) metal coordination : bond 0.00044 ( 3) Misc. bond : bond 0.00025 ( 2) link_BETA1-4 : bond 0.00518 ( 3) link_BETA1-4 : angle 1.24418 ( 9) link_NAG-ASN : bond 0.00828 ( 5) link_NAG-ASN : angle 3.19323 ( 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: 38 poor density : 223 time to evaluate : 0.386 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 418 ASP cc_start: 0.8295 (t70) cc_final: 0.7839 (t0) REVERT: A 588 MET cc_start: 0.8853 (mmp) cc_final: 0.8569 (mmp) REVERT: A 1051 LEU cc_start: 0.8975 (mt) cc_final: 0.8668 (mp) REVERT: C 97 LEU cc_start: 0.8872 (tp) cc_final: 0.8512 (tp) REVERT: C 98 MET cc_start: 0.7347 (ptp) cc_final: 0.6992 (ttm) REVERT: C 102 CYS cc_start: 0.8739 (t) cc_final: 0.8485 (t) REVERT: C 150 THR cc_start: 0.8851 (OUTLIER) cc_final: 0.8621 (t) REVERT: C 174 TYR cc_start: 0.8047 (t80) cc_final: 0.7452 (t80) REVERT: G 132 GLN cc_start: 0.8219 (OUTLIER) cc_final: 0.7992 (pp30) REVERT: G 233 GLU cc_start: 0.8961 (mm-30) cc_final: 0.8567 (mm-30) REVERT: G 238 ASN cc_start: 0.9258 (m-40) cc_final: 0.8775 (m110) outliers start: 38 outliers final: 19 residues processed: 241 average time/residue: 0.0797 time to fit residues: 28.4714 Evaluate side-chains 231 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 210 time to evaluate : 0.272 ------------------------------------------------------------------------------- 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 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 531 LEU 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 A residue 1108 LEU Chi-restraints excluded: chain A residue 1157 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 132 GLN 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: 0.9990 chunk 112 optimal weight: 10.0000 chunk 52 optimal weight: 8.9990 chunk 69 optimal weight: 3.9990 chunk 33 optimal weight: 1.9990 chunk 41 optimal weight: 0.7980 chunk 125 optimal weight: 7.9990 chunk 23 optimal weight: 4.9990 chunk 21 optimal weight: 0.7980 chunk 70 optimal weight: 3.9990 chunk 88 optimal weight: 0.0870 overall best weight: 0.9362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 248 ASN ** A 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 566 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 115 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.156774 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.100485 restraints weight = 14302.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.099251 restraints weight = 10535.456| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.099809 restraints weight = 9084.588| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.099810 restraints weight = 8159.563| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.100077 restraints weight = 7954.183| |-----------------------------------------------------------------------------| r_work (final): 0.2992 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8243 moved from start: 0.3549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 10758 Z= 0.152 Angle : 0.698 17.639 14618 Z= 0.341 Chirality : 0.045 0.321 1676 Planarity : 0.005 0.085 1822 Dihedral : 7.424 66.661 1796 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.65 % Favored : 95.27 % Rotamer: Outliers : 3.52 % Allowed : 16.61 % Favored : 79.87 % 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: -0.65 (0.23), residues: 1291 helix: 0.43 (0.20), residues: 705 sheet: -1.75 (0.63), residues: 67 loop : -1.39 (0.26), residues: 519 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 144 TYR 0.021 0.001 TYR G 63 PHE 0.014 0.001 PHE A 780 TRP 0.012 0.001 TRP G 49 HIS 0.005 0.001 HIS G 108 Details of bonding type rmsd covalent geometry : bond 0.00361 (10732) covalent geometry : angle 0.68352 (14568) SS BOND : bond 0.00266 ( 13) SS BOND : angle 2.45917 ( 26) hydrogen bonds : bond 0.04055 ( 465) hydrogen bonds : angle 4.46326 ( 1338) metal coordination : bond 0.00042 ( 3) Misc. bond : bond 0.00029 ( 2) link_BETA1-4 : bond 0.00601 ( 3) link_BETA1-4 : angle 1.28453 ( 9) link_NAG-ASN : bond 0.00803 ( 5) link_NAG-ASN : angle 3.14522 ( 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 257 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 218 time to evaluate : 0.362 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 418 ASP cc_start: 0.8292 (t70) cc_final: 0.7828 (t0) REVERT: A 588 MET cc_start: 0.8872 (mmp) cc_final: 0.8634 (mmp) REVERT: A 1052 MET cc_start: 0.8612 (ttm) cc_final: 0.8237 (ttm) REVERT: C 97 LEU cc_start: 0.8882 (tp) cc_final: 0.8622 (tp) REVERT: C 98 MET cc_start: 0.7387 (ptp) cc_final: 0.7182 (ttp) REVERT: C 150 THR cc_start: 0.8830 (OUTLIER) cc_final: 0.8600 (t) REVERT: G 192 LYS cc_start: 0.8359 (mmmt) cc_final: 0.8121 (tppt) REVERT: G 238 ASN cc_start: 0.9224 (m-40) cc_final: 0.8754 (m110) outliers start: 39 outliers final: 29 residues processed: 235 average time/residue: 0.0829 time to fit residues: 28.6244 Evaluate side-chains 239 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 209 time to evaluate : 0.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 ASP Chi-restraints excluded: chain A residue 151 THR Chi-restraints excluded: chain A residue 249 PHE Chi-restraints excluded: chain A residue 252 LEU 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 572 VAL 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 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 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 76 LEU Chi-restraints excluded: chain G residue 132 GLN 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: 0.6980 chunk 116 optimal weight: 0.8980 chunk 70 optimal weight: 2.9990 chunk 34 optimal weight: 0.7980 chunk 38 optimal weight: 6.9990 chunk 108 optimal weight: 9.9990 chunk 113 optimal weight: 6.9990 chunk 31 optimal weight: 2.9990 chunk 129 optimal weight: 2.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 248 ASN ** A 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.155916 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.097831 restraints weight = 14097.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.099542 restraints weight = 9641.091| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.099939 restraints weight = 7747.914| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.100643 restraints weight = 6958.594| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.101001 restraints weight = 6820.128| |-----------------------------------------------------------------------------| r_work (final): 0.3001 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8224 moved from start: 0.3671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 10758 Z= 0.155 Angle : 0.707 19.508 14618 Z= 0.343 Chirality : 0.046 0.351 1676 Planarity : 0.005 0.084 1822 Dihedral : 7.273 66.433 1796 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.73 % Favored : 95.20 % Rotamer: Outliers : 3.79 % Allowed : 17.33 % Favored : 78.88 % 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: -0.51 (0.24), residues: 1291 helix: 0.59 (0.20), residues: 706 sheet: -1.68 (0.64), residues: 67 loop : -1.42 (0.26), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 431 TYR 0.022 0.001 TYR G 68 PHE 0.017 0.001 PHE A1167 TRP 0.012 0.001 TRP G 49 HIS 0.006 0.001 HIS A1088 Details of bonding type rmsd covalent geometry : bond 0.00369 (10732) covalent geometry : angle 0.69316 (14568) SS BOND : bond 0.00224 ( 13) SS BOND : angle 2.42123 ( 26) hydrogen bonds : bond 0.04039 ( 465) hydrogen bonds : angle 4.41507 ( 1338) metal coordination : bond 0.00023 ( 3) Misc. bond : bond 0.00037 ( 2) link_BETA1-4 : bond 0.00520 ( 3) link_BETA1-4 : angle 1.29312 ( 9) link_NAG-ASN : bond 0.00804 ( 5) link_NAG-ASN : angle 3.10869 ( 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 261 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 219 time to evaluate : 0.374 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 418 ASP cc_start: 0.8304 (t70) cc_final: 0.7826 (t0) REVERT: A 588 MET cc_start: 0.8862 (mmp) cc_final: 0.8611 (mmp) REVERT: A 932 ARG cc_start: 0.8317 (OUTLIER) cc_final: 0.7755 (mmp-170) REVERT: A 1052 MET cc_start: 0.8617 (ttm) cc_final: 0.8292 (ttm) REVERT: C 97 LEU cc_start: 0.8835 (tp) cc_final: 0.8542 (tp) REVERT: C 150 THR cc_start: 0.8829 (OUTLIER) cc_final: 0.8602 (t) REVERT: G 192 LYS cc_start: 0.8315 (mmmt) cc_final: 0.8100 (tppt) REVERT: G 233 GLU cc_start: 0.9024 (mm-30) cc_final: 0.8600 (mm-30) REVERT: G 236 LYS cc_start: 0.8948 (mmtt) cc_final: 0.8561 (mmtt) REVERT: G 238 ASN cc_start: 0.9155 (m-40) cc_final: 0.8628 (m110) outliers start: 42 outliers final: 29 residues processed: 235 average time/residue: 0.0867 time to fit residues: 29.5638 Evaluate side-chains 246 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 215 time to evaluate : 0.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 572 VAL Chi-restraints excluded: chain A residue 578 VAL Chi-restraints excluded: chain A residue 581 ILE 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 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 122 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 232 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 30 optimal weight: 5.9990 chunk 53 optimal weight: 0.3980 chunk 34 optimal weight: 0.9980 chunk 26 optimal weight: 0.0040 chunk 31 optimal weight: 0.6980 chunk 100 optimal weight: 0.1980 chunk 79 optimal weight: 0.9980 chunk 127 optimal weight: 8.9990 chunk 15 optimal weight: 0.5980 chunk 91 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 overall best weight: 0.3792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 248 ASN A 351 GLN A 566 GLN A 784 GLN ** A1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 115 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.159381 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.100640 restraints weight = 14028.807| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.102625 restraints weight = 10064.532| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.103549 restraints weight = 8072.131| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.103896 restraints weight = 6799.103| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.104051 restraints weight = 6863.795| |-----------------------------------------------------------------------------| r_work (final): 0.3064 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 moved from start: 0.3881 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= 0.127 Angle : 0.702 17.244 14618 Z= 0.339 Chirality : 0.045 0.320 1676 Planarity : 0.005 0.079 1822 Dihedral : 7.024 64.584 1796 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.95 % Favored : 95.97 % Rotamer: Outliers : 3.07 % Allowed : 18.32 % Favored : 78.61 % 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: -0.34 (0.24), residues: 1291 helix: 0.73 (0.20), residues: 706 sheet: -1.65 (0.64), residues: 68 loop : -1.33 (0.27), residues: 517 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 61 TYR 0.026 0.001 TYR G 68 PHE 0.013 0.001 PHE A 780 TRP 0.013 0.001 TRP G 49 HIS 0.009 0.001 HIS G 108 Details of bonding type rmsd covalent geometry : bond 0.00288 (10732) covalent geometry : angle 0.68763 (14568) SS BOND : bond 0.00266 ( 13) SS BOND : angle 2.37862 ( 26) hydrogen bonds : bond 0.03816 ( 465) hydrogen bonds : angle 4.37758 ( 1338) metal coordination : bond 0.00032 ( 3) Misc. bond : bond 0.00037 ( 2) link_BETA1-4 : bond 0.00398 ( 3) link_BETA1-4 : angle 1.30184 ( 9) link_NAG-ASN : bond 0.00799 ( 5) link_NAG-ASN : angle 3.09960 ( 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 257 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 223 time to evaluate : 0.355 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 308 ASP cc_start: 0.7748 (t0) cc_final: 0.7413 (p0) REVERT: A 418 ASP cc_start: 0.8261 (t70) cc_final: 0.7735 (t0) REVERT: A 469 LEU cc_start: 0.9116 (tt) cc_final: 0.8902 (tp) REVERT: A 588 MET cc_start: 0.8845 (mmp) cc_final: 0.8635 (mmp) REVERT: A 777 GLU cc_start: 0.8113 (pm20) cc_final: 0.7746 (mp0) REVERT: A 1052 MET cc_start: 0.8546 (ttm) cc_final: 0.8215 (ttm) REVERT: C 97 LEU cc_start: 0.8816 (tp) cc_final: 0.8535 (tp) REVERT: G 192 LYS cc_start: 0.8354 (mmmt) cc_final: 0.8097 (tppt) REVERT: G 238 ASN cc_start: 0.9120 (m-40) cc_final: 0.8690 (m110) outliers start: 34 outliers final: 20 residues processed: 238 average time/residue: 0.0860 time to fit residues: 30.0580 Evaluate side-chains 234 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 214 time to evaluate : 0.352 ------------------------------------------------------------------------------- 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 353 MET Chi-restraints excluded: chain A residue 444 CYS Chi-restraints excluded: chain A residue 550 PHE Chi-restraints excluded: chain A residue 578 VAL Chi-restraints excluded: chain A residue 796 VAL Chi-restraints excluded: chain A residue 851 HIS 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 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: 0.9990 chunk 13 optimal weight: 2.9990 chunk 97 optimal weight: 0.0870 chunk 81 optimal weight: 1.9990 chunk 71 optimal weight: 0.9990 chunk 55 optimal weight: 1.9990 chunk 96 optimal weight: 0.5980 chunk 84 optimal weight: 3.9990 chunk 66 optimal weight: 2.9990 chunk 110 optimal weight: 5.9990 chunk 34 optimal weight: 0.8980 overall best weight: 0.7162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 248 ASN A 374 HIS A1155 ASN C 91 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.156097 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.097655 restraints weight = 14117.134| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.098439 restraints weight = 9876.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.099433 restraints weight = 7998.662| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.099593 restraints weight = 6877.214| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.099702 restraints weight = 6860.380| |-----------------------------------------------------------------------------| r_work (final): 0.3036 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.3969 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= 0.139 Angle : 0.733 18.280 14618 Z= 0.353 Chirality : 0.046 0.344 1676 Planarity : 0.005 0.082 1822 Dihedral : 6.897 64.289 1796 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.03 % Favored : 95.89 % Rotamer: Outliers : 2.62 % Allowed : 19.04 % Favored : 78.34 % 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: -0.21 (0.24), residues: 1291 helix: 0.84 (0.20), residues: 706 sheet: -1.63 (0.64), residues: 68 loop : -1.26 (0.27), residues: 517 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 204 TYR 0.022 0.001 TYR G 68 PHE 0.031 0.002 PHE A1112 TRP 0.014 0.001 TRP G 49 HIS 0.005 0.001 HIS A1088 Details of bonding type rmsd covalent geometry : bond 0.00326 (10732) covalent geometry : angle 0.72067 (14568) SS BOND : bond 0.00204 ( 13) SS BOND : angle 2.23708 ( 26) hydrogen bonds : bond 0.03831 ( 465) hydrogen bonds : angle 4.34056 ( 1338) metal coordination : bond 0.00033 ( 3) Misc. bond : bond 0.00038 ( 2) link_BETA1-4 : bond 0.00509 ( 3) link_BETA1-4 : angle 1.30757 ( 9) link_NAG-ASN : bond 0.00780 ( 5) link_NAG-ASN : angle 3.06026 ( 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 251 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 222 time to evaluate : 0.383 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 308 ASP cc_start: 0.7682 (t0) cc_final: 0.7366 (p0) REVERT: A 418 ASP cc_start: 0.8289 (t70) cc_final: 0.7748 (t0) REVERT: A 777 GLU cc_start: 0.8124 (pm20) cc_final: 0.7792 (mp0) REVERT: A 1052 MET cc_start: 0.8631 (ttm) cc_final: 0.8254 (ttm) REVERT: A 1111 MET cc_start: 0.8659 (ttm) cc_final: 0.8364 (mtm) REVERT: A 1163 LEU cc_start: 0.9247 (mt) cc_final: 0.9015 (mp) REVERT: C 97 LEU cc_start: 0.8778 (tp) cc_final: 0.8506 (tp) REVERT: G 233 GLU cc_start: 0.8823 (mm-30) cc_final: 0.8617 (mm-30) REVERT: G 238 ASN cc_start: 0.9048 (m-40) cc_final: 0.8596 (m110) outliers start: 29 outliers final: 24 residues processed: 235 average time/residue: 0.0910 time to fit residues: 31.3781 Evaluate side-chains 237 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 213 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 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 353 MET Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain A residue 444 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 851 HIS 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 Chi-restraints excluded: chain G residue 232 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 45 optimal weight: 6.9990 chunk 39 optimal weight: 0.9990 chunk 65 optimal weight: 1.9990 chunk 9 optimal weight: 0.4980 chunk 119 optimal weight: 0.3980 chunk 113 optimal weight: 1.9990 chunk 6 optimal weight: 0.1980 chunk 50 optimal weight: 0.9980 chunk 2 optimal weight: 0.6980 chunk 109 optimal weight: 3.9990 chunk 78 optimal weight: 0.7980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 248 ASN A 827 ASN A 940 HIS A1155 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.159000 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.100074 restraints weight = 14022.609| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.102094 restraints weight = 10467.661| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.102563 restraints weight = 7873.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.102793 restraints weight = 7143.842| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.102928 restraints weight = 7276.906| |-----------------------------------------------------------------------------| r_work (final): 0.3008 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 moved from start: 0.4117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 10758 Z= 0.135 Angle : 0.761 16.574 14618 Z= 0.360 Chirality : 0.046 0.338 1676 Planarity : 0.005 0.080 1822 Dihedral : 6.819 64.064 1796 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.11 % Favored : 95.82 % Rotamer: Outliers : 2.08 % Allowed : 19.86 % Favored : 78.07 % 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: -0.11 (0.24), residues: 1291 helix: 0.92 (0.20), residues: 703 sheet: -1.58 (0.64), residues: 68 loop : -1.20 (0.27), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG G 178 TYR 0.023 0.001 TYR G 63 PHE 0.030 0.001 PHE A1112 TRP 0.015 0.001 TRP G 49 HIS 0.010 0.001 HIS G 108 Details of bonding type rmsd covalent geometry : bond 0.00313 (10732) covalent geometry : angle 0.75071 (14568) SS BOND : bond 0.00256 ( 13) SS BOND : angle 1.85955 ( 26) hydrogen bonds : bond 0.03770 ( 465) hydrogen bonds : angle 4.40910 ( 1338) metal coordination : bond 0.00038 ( 3) Misc. bond : bond 0.00037 ( 2) link_BETA1-4 : bond 0.00492 ( 3) link_BETA1-4 : angle 1.27466 ( 9) link_NAG-ASN : bond 0.00781 ( 5) link_NAG-ASN : angle 3.05478 ( 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 239 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 216 time to evaluate : 0.290 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 308 ASP cc_start: 0.7678 (t0) cc_final: 0.7368 (p0) REVERT: A 418 ASP cc_start: 0.8249 (t70) cc_final: 0.7734 (t0) REVERT: A 480 LEU cc_start: 0.8211 (tt) cc_final: 0.7487 (mt) REVERT: A 777 GLU cc_start: 0.8024 (pm20) cc_final: 0.7732 (mp0) REVERT: A 1052 MET cc_start: 0.8628 (ttm) cc_final: 0.8244 (ttm) REVERT: A 1111 MET cc_start: 0.8532 (ttm) cc_final: 0.8095 (mtt) REVERT: C 97 LEU cc_start: 0.8838 (tp) cc_final: 0.8385 (tp) REVERT: G 238 ASN cc_start: 0.9055 (m-40) cc_final: 0.8504 (m-40) outliers start: 23 outliers final: 18 residues processed: 225 average time/residue: 0.0821 time to fit residues: 27.0275 Evaluate side-chains 222 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 204 time to evaluate : 0.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 ARG 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 353 MET Chi-restraints excluded: chain A residue 440 LEU 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 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: 0.2980 chunk 129 optimal weight: 5.9990 chunk 14 optimal weight: 0.6980 chunk 89 optimal weight: 7.9990 chunk 70 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 71 optimal weight: 0.9990 chunk 29 optimal weight: 2.9990 chunk 115 optimal weight: 0.4980 chunk 78 optimal weight: 0.9990 chunk 68 optimal weight: 3.9990 overall best weight: 0.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 248 ASN A 374 HIS A 940 HIS A1155 ASN C 91 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.159171 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.100144 restraints weight = 14215.234| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.102208 restraints weight = 10263.923| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.103146 restraints weight = 8172.323| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.103287 restraints weight = 6920.616| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.103740 restraints weight = 6980.759| |-----------------------------------------------------------------------------| r_work (final): 0.3044 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 moved from start: 0.4217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 10758 Z= 0.144 Angle : 0.766 16.696 14618 Z= 0.362 Chirality : 0.046 0.317 1676 Planarity : 0.005 0.081 1822 Dihedral : 6.773 64.041 1796 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.18 % Favored : 95.74 % Rotamer: Outliers : 2.08 % Allowed : 20.22 % Favored : 77.71 % 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: -0.12 (0.24), residues: 1291 helix: 0.91 (0.20), residues: 707 sheet: -1.59 (0.64), residues: 68 loop : -1.22 (0.28), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1102 TYR 0.020 0.001 TYR G 68 PHE 0.029 0.002 PHE A1112 TRP 0.014 0.001 TRP G 49 HIS 0.012 0.001 HIS G 108 Details of bonding type rmsd covalent geometry : bond 0.00340 (10732) covalent geometry : angle 0.75816 (14568) SS BOND : bond 0.00234 ( 13) SS BOND : angle 1.52598 ( 26) hydrogen bonds : bond 0.03812 ( 465) hydrogen bonds : angle 4.41101 ( 1338) metal coordination : bond 0.00032 ( 3) Misc. bond : bond 0.00037 ( 2) link_BETA1-4 : bond 0.00538 ( 3) link_BETA1-4 : angle 1.29708 ( 9) link_NAG-ASN : bond 0.00776 ( 5) link_NAG-ASN : angle 3.03042 ( 15) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1915.50 seconds wall clock time: 33 minutes 37.43 seconds (2017.43 seconds total)