Starting phenix.real_space_refine on Fri Mar 15 03:41:42 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rhq_24466/03_2024/7rhq_24466.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rhq_24466/03_2024/7rhq_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 { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rhq_24466/03_2024/7rhq_24466.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rhq_24466/03_2024/7rhq_24466.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rhq_24466/03_2024/7rhq_24466.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rhq_24466/03_2024/7rhq_24466.pdb" } resolution = 3.53 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.007 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 Residue "A ARG 125": "NH1" <-> "NH2" Residue "A PHE 143": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 533": "NH1" <-> "NH2" Residue "A ARG 762": "NH1" <-> "NH2" Residue "A TYR 791": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 963": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 971": "NH1" <-> "NH2" Residue "A TYR 998": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1102": "NH1" <-> "NH2" Residue "A ARG 1103": "NH1" <-> "NH2" Residue "A ARG 1139": "NH1" <-> "NH2" Residue "C ARG 28": "NH1" <-> "NH2" Residue "C ARG 33": "NH1" <-> "NH2" Residue "C ARG 34": "NH1" <-> "NH2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/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: 6.35, per 1000 atoms: 0.60 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 - 3.50 Amino acid : False - 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: 4.08 Conformation dependent library (CDL) restraints added in 1.7 seconds 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: 1.00 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: 3.06 Time building geometry restraints manager: 4.47 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: 98.47 - 105.68: 249 105.68 - 112.88: 5752 112.88 - 120.09: 4108 120.09 - 127.29: 4349 127.29 - 134.49: 110 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 2.520 nonbonded pdb=" OH TYR A 794 " pdb=" O GLY C 29 " model vdw 2.292 2.440 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 2.440 ... (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 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: 0.600 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: 3.330 Check model and map are aligned: 0.130 Set scattering table: 0.090 Process input model: 32.130 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.530 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.190 ------------------------------------------------------------------------------- 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 10732 Z= 0.573 Angle : 1.059 10.557 14568 Z= 0.573 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.031 0.003 TRP A 327 HIS 0.018 0.002 HIS A 792 PHE 0.050 0.003 PHE A 838 TYR 0.029 0.003 TYR A1002 ARG 0.010 0.001 ARG A 125 *********************** 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 fitting. rotamer outliers: 1 poor density : 316 time to evaluate : 1.158 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 237 TYR cc_start: 0.8155 (t80) cc_final: 0.7804 (t80) REVERT: A 418 ASP cc_start: 0.8459 (t70) cc_final: 0.8048 (t0) REVERT: A 446 THR cc_start: 0.9132 (t) cc_final: 0.8897 (t) REVERT: A 512 PHE cc_start: 0.8465 (t80) cc_final: 0.8223 (t80) REVERT: A 1038 ASN cc_start: 0.8221 (t0) cc_final: 0.7687 (t0) REVERT: A 1041 THR cc_start: 0.9114 (p) cc_final: 0.8725 (p) REVERT: C 73 PHE cc_start: 0.7997 (t80) cc_final: 0.7797 (t80) REVERT: C 79 ASN cc_start: 0.8670 (t0) cc_final: 0.8149 (t0) REVERT: C 81 ASN cc_start: 0.8760 (t0) cc_final: 0.8093 (t0) REVERT: C 97 LEU cc_start: 0.8706 (tp) cc_final: 0.8260 (tp) REVERT: C 98 MET cc_start: 0.8549 (ptp) cc_final: 0.7587 (ptp) REVERT: C 102 CYS cc_start: 0.9444 (t) cc_final: 0.7955 (t) REVERT: C 160 MET cc_start: 0.8386 (tpp) cc_final: 0.8103 (tpp) REVERT: C 176 GLU cc_start: 0.7869 (tm-30) cc_final: 0.7569 (tm-30) REVERT: C 185 VAL cc_start: 0.9303 (p) cc_final: 0.9003 (p) REVERT: C 186 LYS cc_start: 0.8990 (tmtm) cc_final: 0.8717 (tptp) REVERT: G 50 GLN cc_start: 0.8774 (pt0) cc_final: 0.8555 (pt0) REVERT: G 62 SER cc_start: 0.9280 (t) cc_final: 0.8957 (p) REVERT: G 200 THR cc_start: 0.8191 (p) cc_final: 0.7756 (p) REVERT: G 237 GLU cc_start: 0.9310 (tt0) cc_final: 0.8860 (tm-30) REVERT: G 238 ASN cc_start: 0.9116 (m-40) cc_final: 0.8574 (m-40) outliers start: 1 outliers final: 1 residues processed: 317 average time/residue: 0.2701 time to fit residues: 114.3521 Evaluate side-chains 228 residues out of total 1108 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 227 time to evaluate : 1.177 ------------------------------------------------------------------------------- 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 109 optimal weight: 5.9990 chunk 98 optimal weight: 8.9990 chunk 54 optimal weight: 5.9990 chunk 33 optimal weight: 1.9990 chunk 66 optimal weight: 0.8980 chunk 52 optimal weight: 20.0000 chunk 101 optimal weight: 20.0000 chunk 39 optimal weight: 0.9990 chunk 61 optimal weight: 0.5980 chunk 75 optimal weight: 1.9990 chunk 118 optimal weight: 1.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- 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 399 GLN 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 132 GLN ** G 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 moved from start: 0.2435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 10732 Z= 0.284 Angle : 0.715 11.939 14568 Z= 0.368 Chirality : 0.046 0.345 1676 Planarity : 0.007 0.099 1822 Dihedral : 8.419 72.899 1797 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.57 % Favored : 95.35 % Rotamer: Outliers : 2.62 % Allowed : 10.20 % Favored : 87.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % Cis-general : 0.00 % Twisted Proline : 1.79 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.99 (0.20), residues: 1291 helix: -1.83 (0.17), residues: 694 sheet: -2.44 (0.55), residues: 74 loop : -1.91 (0.25), residues: 523 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 389 HIS 0.009 0.001 HIS A1088 PHE 0.023 0.002 PHE A 838 TYR 0.023 0.002 TYR A 863 ARG 0.007 0.001 ARG C 72 *********************** 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 271 residues out of total 1108 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 242 time to evaluate : 1.087 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: A 139 GLU cc_start: 0.7973 (tp30) cc_final: 0.7664 (tp30) REVERT: A 237 TYR cc_start: 0.8172 (t80) cc_final: 0.7748 (t80) REVERT: A 418 ASP cc_start: 0.8421 (t70) cc_final: 0.8013 (t0) REVERT: A 1038 ASN cc_start: 0.8068 (t160) cc_final: 0.7819 (t0) REVERT: A 1128 MET cc_start: 0.8180 (mmm) cc_final: 0.7894 (mmm) REVERT: C 79 ASN cc_start: 0.8644 (t0) cc_final: 0.8301 (t0) REVERT: C 81 ASN cc_start: 0.8775 (t0) cc_final: 0.8220 (t0) REVERT: C 97 LEU cc_start: 0.8780 (tp) cc_final: 0.8296 (tp) REVERT: C 98 MET cc_start: 0.7709 (ptp) cc_final: 0.7256 (ptp) REVERT: C 102 CYS cc_start: 0.9188 (t) cc_final: 0.8002 (t) REVERT: C 176 GLU cc_start: 0.7860 (tm-30) cc_final: 0.7313 (tp30) REVERT: G 132 GLN cc_start: 0.8255 (OUTLIER) cc_final: 0.7481 (pp30) REVERT: G 189 TYR cc_start: 0.9241 (m-80) cc_final: 0.8975 (m-80) REVERT: G 238 ASN cc_start: 0.9247 (m-40) cc_final: 0.8731 (m110) outliers start: 29 outliers final: 17 residues processed: 257 average time/residue: 0.2128 time to fit residues: 78.1443 Evaluate side-chains 238 residues out of total 1108 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 220 time to evaluate : 1.038 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 353 MET Chi-restraints excluded: chain A residue 371 VAL 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 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 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 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 65 optimal weight: 0.7980 chunk 36 optimal weight: 0.7980 chunk 98 optimal weight: 0.0980 chunk 80 optimal weight: 0.5980 chunk 32 optimal weight: 0.5980 chunk 118 optimal weight: 5.9990 chunk 127 optimal weight: 0.3980 chunk 105 optimal weight: 4.9990 chunk 117 optimal weight: 0.5980 chunk 40 optimal weight: 3.9990 chunk 94 optimal weight: 0.3980 overall best weight: 0.4180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 574 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 115 ASN ** G 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 moved from start: 0.2908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 10732 Z= 0.189 Angle : 0.674 15.858 14568 Z= 0.337 Chirality : 0.044 0.322 1676 Planarity : 0.005 0.084 1822 Dihedral : 7.889 68.621 1796 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.18 % Favored : 95.74 % Rotamer: Outliers : 2.71 % Allowed : 12.82 % Favored : 84.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % Cis-general : 0.00 % Twisted Proline : 1.79 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.76 (0.22), residues: 1291 helix: -0.62 (0.19), residues: 694 sheet: -1.90 (0.61), residues: 67 loop : -1.69 (0.25), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 246 HIS 0.004 0.001 HIS G 108 PHE 0.037 0.002 PHE C 73 TYR 0.023 0.001 TYR A 863 ARG 0.008 0.001 ARG G 175 *********************** 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 265 residues out of total 1108 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 235 time to evaluate : 1.100 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 237 TYR cc_start: 0.8249 (t80) cc_final: 0.7906 (t80) REVERT: A 418 ASP cc_start: 0.8215 (t70) cc_final: 0.7630 (t0) REVERT: A 469 LEU cc_start: 0.9149 (tt) cc_final: 0.8874 (tp) REVERT: A 588 MET cc_start: 0.8888 (mmp) cc_final: 0.8672 (mmp) REVERT: A 932 ARG cc_start: 0.8580 (mmt-90) cc_final: 0.7972 (mmp-170) REVERT: A 1038 ASN cc_start: 0.8090 (t160) cc_final: 0.7686 (t0) REVERT: A 1128 MET cc_start: 0.8207 (mmm) cc_final: 0.7926 (mmm) REVERT: C 79 ASN cc_start: 0.8645 (t0) cc_final: 0.8340 (t0) REVERT: C 81 ASN cc_start: 0.8781 (t0) cc_final: 0.8238 (t0) REVERT: C 95 ASP cc_start: 0.8127 (OUTLIER) cc_final: 0.7921 (m-30) REVERT: C 97 LEU cc_start: 0.8945 (tp) cc_final: 0.8505 (tp) REVERT: C 141 TYR cc_start: 0.8523 (m-80) cc_final: 0.8311 (m-80) REVERT: C 160 MET cc_start: 0.8258 (tpp) cc_final: 0.8036 (tpp) REVERT: C 174 TYR cc_start: 0.7989 (t80) cc_final: 0.7763 (t80) REVERT: C 176 GLU cc_start: 0.7715 (tm-30) cc_final: 0.7399 (tp30) REVERT: G 132 GLN cc_start: 0.8228 (OUTLIER) cc_final: 0.7396 (pp30) REVERT: G 238 ASN cc_start: 0.9261 (m-40) cc_final: 0.8769 (m110) outliers start: 30 outliers final: 16 residues processed: 248 average time/residue: 0.2033 time to fit residues: 73.0686 Evaluate side-chains 236 residues out of total 1108 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 218 time to evaluate : 1.143 ------------------------------------------------------------------------------- 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 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 A residue 1135 ASP Chi-restraints excluded: chain C residue 28 ARG Chi-restraints excluded: chain C residue 95 ASP 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 179 CYS 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 116 optimal weight: 0.8980 chunk 88 optimal weight: 0.9990 chunk 61 optimal weight: 0.6980 chunk 13 optimal weight: 2.9990 chunk 56 optimal weight: 2.9990 chunk 79 optimal weight: 0.1980 chunk 118 optimal weight: 4.9990 chunk 125 optimal weight: 2.9990 chunk 62 optimal weight: 0.7980 chunk 112 optimal weight: 7.9990 chunk 33 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 248 ASN ** A 574 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 846 GLN C 115 ASN G 132 GLN ** G 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8213 moved from start: 0.3204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 10732 Z= 0.188 Angle : 0.622 12.108 14568 Z= 0.307 Chirality : 0.044 0.325 1676 Planarity : 0.005 0.082 1822 Dihedral : 7.539 66.219 1796 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.26 % Favored : 95.66 % Rotamer: Outliers : 3.43 % Allowed : 14.35 % Favored : 82.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % Cis-general : 0.00 % Twisted Proline : 1.79 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.21 (0.23), residues: 1291 helix: -0.06 (0.20), residues: 701 sheet: -1.78 (0.62), residues: 67 loop : -1.63 (0.26), residues: 523 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP G 49 HIS 0.008 0.001 HIS G 108 PHE 0.023 0.001 PHE A 512 TYR 0.021 0.001 TYR A 863 ARG 0.004 0.000 ARG G 175 *********************** 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 269 residues out of total 1108 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 231 time to evaluate : 1.217 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 237 TYR cc_start: 0.8298 (t80) cc_final: 0.7946 (t80) REVERT: A 250 ASP cc_start: 0.8666 (OUTLIER) cc_final: 0.8348 (p0) REVERT: A 418 ASP cc_start: 0.8237 (t70) cc_final: 0.7635 (t0) REVERT: A 588 MET cc_start: 0.8878 (mmp) cc_final: 0.8654 (mmp) REVERT: A 932 ARG cc_start: 0.8405 (mmt-90) cc_final: 0.7491 (mmt180) REVERT: A 1038 ASN cc_start: 0.8027 (t160) cc_final: 0.7587 (t0) REVERT: A 1111 MET cc_start: 0.8579 (OUTLIER) cc_final: 0.8371 (mtt) REVERT: C 81 ASN cc_start: 0.8763 (t0) cc_final: 0.8221 (t0) REVERT: C 96 ARG cc_start: 0.8222 (mtp85) cc_final: 0.7973 (mtp85) REVERT: C 97 LEU cc_start: 0.8885 (tp) cc_final: 0.8589 (tp) REVERT: C 150 THR cc_start: 0.8766 (OUTLIER) cc_final: 0.8543 (t) REVERT: C 160 MET cc_start: 0.8346 (tpp) cc_final: 0.8139 (tpp) REVERT: C 174 TYR cc_start: 0.8118 (t80) cc_final: 0.7654 (t80) REVERT: C 176 GLU cc_start: 0.7694 (tm-30) cc_final: 0.7303 (tp30) REVERT: G 233 GLU cc_start: 0.8949 (mm-30) cc_final: 0.8628 (mm-30) REVERT: G 238 ASN cc_start: 0.9274 (m-40) cc_final: 0.8774 (m110) outliers start: 38 outliers final: 23 residues processed: 250 average time/residue: 0.2097 time to fit residues: 75.8287 Evaluate side-chains 244 residues out of total 1108 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 218 time to evaluate : 1.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 ASP Chi-restraints excluded: chain A residue 250 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 571 VAL Chi-restraints excluded: chain A residue 572 VAL 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 1111 MET Chi-restraints excluded: chain A residue 1124 LEU Chi-restraints excluded: chain A residue 1135 ASP Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 150 THR Chi-restraints excluded: chain C residue 183 CYS Chi-restraints excluded: chain G residue 107 SER 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 104 optimal weight: 5.9990 chunk 71 optimal weight: 0.9980 chunk 1 optimal weight: 6.9990 chunk 93 optimal weight: 4.9990 chunk 51 optimal weight: 6.9990 chunk 107 optimal weight: 20.0000 chunk 86 optimal weight: 2.9990 chunk 0 optimal weight: 9.9990 chunk 64 optimal weight: 0.9990 chunk 112 optimal weight: 9.9990 chunk 31 optimal weight: 2.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 248 ASN ** A 574 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 108 HIS ** G 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8307 moved from start: 0.3276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.061 10732 Z= 0.454 Angle : 0.750 17.115 14568 Z= 0.376 Chirality : 0.050 0.319 1676 Planarity : 0.006 0.097 1822 Dihedral : 7.696 69.492 1796 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 10.35 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.50 % Favored : 94.42 % Rotamer: Outliers : 4.06 % Allowed : 15.43 % Favored : 80.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % Cis-general : 0.00 % Twisted Proline : 1.79 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.11 (0.23), residues: 1291 helix: 0.08 (0.20), residues: 709 sheet: -2.04 (0.60), residues: 68 loop : -1.65 (0.26), residues: 514 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 841 HIS 0.011 0.002 HIS A 792 PHE 0.028 0.002 PHE A1093 TYR 0.023 0.002 TYR A 966 ARG 0.003 0.000 ARG A 864 *********************** 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 264 residues out of total 1108 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 219 time to evaluate : 1.148 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 418 ASP cc_start: 0.8458 (t70) cc_final: 0.7848 (t0) REVERT: A 1038 ASN cc_start: 0.7973 (t160) cc_final: 0.7578 (t0) REVERT: A 1128 MET cc_start: 0.8274 (mmm) cc_final: 0.7990 (mmm) REVERT: C 81 ASN cc_start: 0.8805 (t0) cc_final: 0.8248 (t0) REVERT: C 91 ASN cc_start: 0.9102 (m-40) cc_final: 0.8898 (m-40) REVERT: C 97 LEU cc_start: 0.8895 (tp) cc_final: 0.8625 (tp) REVERT: C 160 MET cc_start: 0.8462 (tpp) cc_final: 0.8201 (tpp) REVERT: C 176 GLU cc_start: 0.7745 (tm-30) cc_final: 0.7373 (tp30) REVERT: G 189 TYR cc_start: 0.9357 (m-80) cc_final: 0.8900 (m-80) REVERT: G 192 LYS cc_start: 0.8694 (mmmt) cc_final: 0.8486 (mmmt) REVERT: G 233 GLU cc_start: 0.8980 (mm-30) cc_final: 0.8635 (mm-30) REVERT: G 238 ASN cc_start: 0.9281 (m-40) cc_final: 0.8795 (m110) outliers start: 45 outliers final: 31 residues processed: 237 average time/residue: 0.2012 time to fit residues: 69.3094 Evaluate side-chains 238 residues out of total 1108 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 207 time to evaluate : 1.217 ------------------------------------------------------------------------------- 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 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 572 VAL 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 1040 TRP Chi-restraints excluded: chain A residue 1051 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 1117 ASP Chi-restraints excluded: chain A residue 1124 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 76 LEU Chi-restraints excluded: chain G residue 107 SER 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 42 optimal weight: 0.0020 chunk 113 optimal weight: 40.0000 chunk 24 optimal weight: 0.3980 chunk 73 optimal weight: 0.5980 chunk 31 optimal weight: 0.9990 chunk 125 optimal weight: 10.0000 chunk 104 optimal weight: 6.9990 chunk 58 optimal weight: 0.6980 chunk 10 optimal weight: 0.5980 chunk 41 optimal weight: 6.9990 chunk 66 optimal weight: 0.5980 overall best weight: 0.4388 ------------------------------------------------------------------------------- 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** G 108 HIS G 195 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8227 moved from start: 0.3531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 10732 Z= 0.178 Angle : 0.666 18.689 14568 Z= 0.324 Chirality : 0.045 0.321 1676 Planarity : 0.005 0.083 1822 Dihedral : 7.462 66.979 1796 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 10.30 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.11 % Favored : 95.82 % Rotamer: Outliers : 3.25 % Allowed : 17.24 % Favored : 79.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % Cis-general : 0.00 % Twisted Proline : 1.79 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.59 (0.24), residues: 1291 helix: 0.50 (0.20), residues: 705 sheet: -1.76 (0.63), residues: 67 loop : -1.39 (0.27), residues: 519 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP G 49 HIS 0.005 0.001 HIS G 108 PHE 0.026 0.001 PHE A1093 TYR 0.021 0.001 TYR A 863 ARG 0.005 0.000 ARG G 175 *********************** 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 fitting. rotamer outliers: 36 poor density : 221 time to evaluate : 1.144 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 250 ASP cc_start: 0.8676 (OUTLIER) cc_final: 0.8316 (p0) REVERT: A 418 ASP cc_start: 0.8264 (t70) cc_final: 0.7694 (t0) REVERT: A 932 ARG cc_start: 0.8344 (OUTLIER) cc_final: 0.7342 (mmp80) REVERT: A 1038 ASN cc_start: 0.7914 (t160) cc_final: 0.7518 (t0) REVERT: A 1052 MET cc_start: 0.8571 (ttm) cc_final: 0.8282 (ttm) REVERT: A 1128 MET cc_start: 0.8247 (mmm) cc_final: 0.7908 (mmm) REVERT: C 81 ASN cc_start: 0.8814 (t0) cc_final: 0.8248 (t0) REVERT: C 91 ASN cc_start: 0.9074 (m-40) cc_final: 0.8865 (m-40) REVERT: C 97 LEU cc_start: 0.8905 (tp) cc_final: 0.8593 (tp) REVERT: C 150 THR cc_start: 0.8781 (OUTLIER) cc_final: 0.8554 (t) REVERT: C 160 MET cc_start: 0.8486 (tpp) cc_final: 0.8218 (tpp) REVERT: C 174 TYR cc_start: 0.8027 (t80) cc_final: 0.7455 (t80) REVERT: C 176 GLU cc_start: 0.7684 (tm-30) cc_final: 0.7218 (tp30) REVERT: G 132 GLN cc_start: 0.8263 (pp30) cc_final: 0.7926 (pp30) REVERT: G 189 TYR cc_start: 0.9326 (m-80) cc_final: 0.8938 (m-80) REVERT: G 192 LYS cc_start: 0.8578 (mmmt) cc_final: 0.8317 (tppt) REVERT: G 238 ASN cc_start: 0.9260 (m-40) cc_final: 0.8772 (m110) outliers start: 36 outliers final: 20 residues processed: 236 average time/residue: 0.1922 time to fit residues: 66.3710 Evaluate side-chains 235 residues out of total 1108 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 212 time to evaluate : 1.060 ------------------------------------------------------------------------------- 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 250 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 531 LEU Chi-restraints excluded: chain A residue 540 LEU Chi-restraints excluded: chain A residue 578 VAL Chi-restraints excluded: chain A residue 796 VAL 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 1157 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 121 optimal weight: 4.9990 chunk 14 optimal weight: 0.9990 chunk 71 optimal weight: 0.8980 chunk 91 optimal weight: 3.9990 chunk 105 optimal weight: 2.9990 chunk 70 optimal weight: 0.7980 chunk 125 optimal weight: 6.9990 chunk 78 optimal weight: 2.9990 chunk 76 optimal weight: 0.9990 chunk 57 optimal weight: 2.9990 chunk 77 optimal weight: 0.6980 overall best weight: 0.8784 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** G 108 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 moved from start: 0.3647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 10732 Z= 0.215 Angle : 0.692 19.404 14568 Z= 0.339 Chirality : 0.046 0.340 1676 Planarity : 0.005 0.083 1822 Dihedral : 7.349 65.839 1796 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 10.25 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.65 % Favored : 95.27 % Rotamer: Outliers : 3.07 % Allowed : 18.86 % Favored : 78.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % Cis-general : 0.00 % Twisted Proline : 1.79 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.38 (0.24), residues: 1291 helix: 0.69 (0.21), residues: 705 sheet: -1.67 (0.64), residues: 67 loop : -1.33 (0.27), residues: 519 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP G 49 HIS 0.006 0.001 HIS G 108 PHE 0.027 0.001 PHE A1093 TYR 0.023 0.001 TYR G 68 ARG 0.002 0.000 ARG A 864 *********************** 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 257 residues out of total 1108 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 223 time to evaluate : 1.184 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 250 ASP cc_start: 0.8712 (OUTLIER) cc_final: 0.8364 (p0) REVERT: A 418 ASP cc_start: 0.8283 (t70) cc_final: 0.7692 (t0) REVERT: A 932 ARG cc_start: 0.8295 (OUTLIER) cc_final: 0.7308 (mmp80) REVERT: A 1038 ASN cc_start: 0.7906 (t160) cc_final: 0.7506 (t0) REVERT: A 1052 MET cc_start: 0.8654 (ttm) cc_final: 0.8326 (ttm) REVERT: C 81 ASN cc_start: 0.8804 (t0) cc_final: 0.8228 (t0) REVERT: C 97 LEU cc_start: 0.8973 (tp) cc_final: 0.8735 (tp) REVERT: C 150 THR cc_start: 0.8744 (OUTLIER) cc_final: 0.8523 (t) REVERT: C 160 MET cc_start: 0.8492 (tpp) cc_final: 0.8224 (tpp) REVERT: C 176 GLU cc_start: 0.7640 (tm-30) cc_final: 0.7355 (tp30) REVERT: G 132 GLN cc_start: 0.8211 (pp30) cc_final: 0.7929 (pp30) REVERT: G 140 LYS cc_start: 0.8809 (mttm) cc_final: 0.8589 (mttt) REVERT: G 173 CYS cc_start: 0.5897 (p) cc_final: 0.5666 (p) REVERT: G 192 LYS cc_start: 0.8543 (mmmt) cc_final: 0.8279 (tppt) REVERT: G 197 LEU cc_start: 0.8006 (tt) cc_final: 0.7762 (tt) REVERT: G 233 GLU cc_start: 0.8944 (mm-30) cc_final: 0.8513 (mm-30) REVERT: G 238 ASN cc_start: 0.9196 (m-40) cc_final: 0.8701 (m110) outliers start: 34 outliers final: 25 residues processed: 238 average time/residue: 0.2067 time to fit residues: 71.2554 Evaluate side-chains 244 residues out of total 1108 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 216 time to evaluate : 1.115 ------------------------------------------------------------------------------- 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 250 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 540 LEU 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 914 THR Chi-restraints excluded: chain A residue 932 ARG Chi-restraints excluded: chain A residue 1040 TRP Chi-restraints excluded: chain A residue 1051 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 1157 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 50 optimal weight: 0.9980 chunk 74 optimal weight: 0.8980 chunk 37 optimal weight: 4.9990 chunk 24 optimal weight: 3.9990 chunk 79 optimal weight: 0.7980 chunk 85 optimal weight: 0.8980 chunk 61 optimal weight: 0.8980 chunk 11 optimal weight: 2.9990 chunk 98 optimal weight: 0.8980 chunk 113 optimal weight: 9.9990 chunk 120 optimal weight: 2.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 248 ASN ** A 566 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 846 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 moved from start: 0.3763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 10732 Z= 0.215 Angle : 0.686 19.385 14568 Z= 0.335 Chirality : 0.045 0.320 1676 Planarity : 0.005 0.082 1822 Dihedral : 7.295 65.585 1796 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 10.59 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.42 % Favored : 95.51 % Rotamer: Outliers : 3.70 % Allowed : 18.59 % Favored : 77.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % Cis-general : 0.00 % Twisted Proline : 1.79 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.29 (0.24), residues: 1291 helix: 0.76 (0.21), residues: 706 sheet: -1.61 (0.65), residues: 67 loop : -1.30 (0.27), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP G 49 HIS 0.004 0.001 HIS G 108 PHE 0.034 0.002 PHE A1112 TYR 0.025 0.001 TYR G 68 ARG 0.002 0.000 ARG C 144 *********************** 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 258 residues out of total 1108 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 217 time to evaluate : 1.245 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 250 ASP cc_start: 0.8707 (OUTLIER) cc_final: 0.8360 (p0) REVERT: A 418 ASP cc_start: 0.8279 (t70) cc_final: 0.7675 (t0) REVERT: A 932 ARG cc_start: 0.8241 (OUTLIER) cc_final: 0.7998 (tpp-160) REVERT: A 1038 ASN cc_start: 0.7884 (t160) cc_final: 0.7515 (t0) REVERT: A 1052 MET cc_start: 0.8634 (ttm) cc_final: 0.8325 (ttm) REVERT: C 81 ASN cc_start: 0.8815 (t0) cc_final: 0.8223 (t0) REVERT: C 97 LEU cc_start: 0.9007 (tp) cc_final: 0.8735 (tp) REVERT: C 150 THR cc_start: 0.8658 (OUTLIER) cc_final: 0.8440 (t) REVERT: C 160 MET cc_start: 0.8517 (tpp) cc_final: 0.8248 (tpp) REVERT: C 176 GLU cc_start: 0.7646 (tm-30) cc_final: 0.7371 (tp30) REVERT: G 192 LYS cc_start: 0.8490 (mmmt) cc_final: 0.8228 (tppt) REVERT: G 197 LEU cc_start: 0.7985 (tt) cc_final: 0.7767 (tt) REVERT: G 233 GLU cc_start: 0.8960 (mm-30) cc_final: 0.8564 (mm-30) REVERT: G 237 GLU cc_start: 0.9087 (tt0) cc_final: 0.8604 (tm-30) REVERT: G 238 ASN cc_start: 0.9153 (m-40) cc_final: 0.8698 (m-40) outliers start: 41 outliers final: 29 residues processed: 234 average time/residue: 0.2096 time to fit residues: 70.3812 Evaluate side-chains 246 residues out of total 1108 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 214 time to evaluate : 1.178 ------------------------------------------------------------------------------- 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 250 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 540 LEU 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 932 ARG Chi-restraints excluded: chain A residue 1040 TRP Chi-restraints excluded: chain A residue 1051 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 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 232 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 109 optimal weight: 6.9990 chunk 116 optimal weight: 0.8980 chunk 120 optimal weight: 5.9990 chunk 70 optimal weight: 2.9990 chunk 50 optimal weight: 0.9990 chunk 91 optimal weight: 2.9990 chunk 35 optimal weight: 0.2980 chunk 105 optimal weight: 1.9990 chunk 110 optimal weight: 4.9990 chunk 76 optimal weight: 0.0970 chunk 123 optimal weight: 0.8980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 566 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 846 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8220 moved from start: 0.3870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 10732 Z= 0.191 Angle : 0.689 19.977 14568 Z= 0.336 Chirality : 0.045 0.320 1676 Planarity : 0.005 0.080 1822 Dihedral : 7.155 64.759 1796 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.11 % Favored : 95.82 % Rotamer: Outliers : 2.98 % Allowed : 19.49 % Favored : 77.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % Cis-general : 0.00 % Twisted Proline : 1.79 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.08 (0.24), residues: 1291 helix: 0.94 (0.21), residues: 699 sheet: -1.56 (0.65), residues: 67 loop : -1.17 (0.27), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP G 49 HIS 0.005 0.001 HIS G 108 PHE 0.031 0.001 PHE A1112 TYR 0.023 0.001 TYR G 68 ARG 0.002 0.000 ARG C 28 *********************** 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 252 residues out of total 1108 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 219 time to evaluate : 0.918 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 250 ASP cc_start: 0.8675 (OUTLIER) cc_final: 0.8323 (p0) REVERT: A 375 MET cc_start: 0.7281 (ptt) cc_final: 0.7031 (ptt) REVERT: A 418 ASP cc_start: 0.8272 (t70) cc_final: 0.7631 (t0) REVERT: A 1038 ASN cc_start: 0.7901 (t160) cc_final: 0.7549 (t0) REVERT: A 1052 MET cc_start: 0.8631 (ttm) cc_final: 0.8337 (ttm) REVERT: A 1111 MET cc_start: 0.8399 (mtt) cc_final: 0.8142 (mtt) REVERT: A 1163 LEU cc_start: 0.9254 (mt) cc_final: 0.9004 (mp) REVERT: C 81 ASN cc_start: 0.8758 (t0) cc_final: 0.8070 (t0) REVERT: C 97 LEU cc_start: 0.9006 (tp) cc_final: 0.8741 (tp) REVERT: C 160 MET cc_start: 0.8553 (tpp) cc_final: 0.8257 (tpp) REVERT: C 176 GLU cc_start: 0.7636 (tm-30) cc_final: 0.7373 (tp30) REVERT: G 173 CYS cc_start: 0.6166 (p) cc_final: 0.5721 (p) REVERT: G 192 LYS cc_start: 0.8471 (mmmt) cc_final: 0.8249 (tppt) REVERT: G 238 ASN cc_start: 0.9095 (m-40) cc_final: 0.8582 (m110) outliers start: 33 outliers final: 26 residues processed: 230 average time/residue: 0.2158 time to fit residues: 71.5689 Evaluate side-chains 238 residues out of total 1108 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 211 time to evaluate : 1.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 ARG Chi-restraints excluded: chain A residue 151 THR Chi-restraints excluded: chain A residue 200 ILE Chi-restraints excluded: chain A residue 250 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 466 LEU Chi-restraints excluded: chain A residue 469 LEU Chi-restraints excluded: chain A residue 530 CYS Chi-restraints excluded: chain A residue 531 LEU Chi-restraints excluded: chain A residue 540 LEU 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 829 GLN Chi-restraints excluded: chain A residue 914 THR Chi-restraints excluded: chain A residue 1040 TRP Chi-restraints excluded: chain A residue 1051 LEU Chi-restraints excluded: chain A residue 1060 MET Chi-restraints excluded: chain A residue 1108 LEU Chi-restraints excluded: chain A residue 1157 LEU 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 75 optimal weight: 20.0000 chunk 58 optimal weight: 0.8980 chunk 85 optimal weight: 1.9990 chunk 129 optimal weight: 1.9990 chunk 119 optimal weight: 0.8980 chunk 103 optimal weight: 0.1980 chunk 10 optimal weight: 0.5980 chunk 79 optimal weight: 0.8980 chunk 63 optimal weight: 1.9990 chunk 81 optimal weight: 0.9980 chunk 109 optimal weight: 8.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 566 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 moved from start: 0.3991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 10732 Z= 0.203 Angle : 0.716 18.512 14568 Z= 0.343 Chirality : 0.045 0.319 1676 Planarity : 0.005 0.081 1822 Dihedral : 7.049 64.461 1796 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 10.44 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.34 % Favored : 95.58 % Rotamer: Outliers : 3.07 % Allowed : 19.40 % Favored : 77.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % Cis-general : 0.00 % Twisted Proline : 1.79 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.04 (0.24), residues: 1291 helix: 0.97 (0.21), residues: 703 sheet: -1.55 (0.64), residues: 67 loop : -1.16 (0.27), residues: 521 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP G 49 HIS 0.005 0.001 HIS G 108 PHE 0.030 0.002 PHE A1112 TYR 0.022 0.001 TYR G 68 ARG 0.007 0.000 ARG A 431 ********************** 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 249 residues out of total 1108 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 215 time to evaluate : 1.061 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 250 ASP cc_start: 0.8675 (OUTLIER) cc_final: 0.8326 (p0) REVERT: A 418 ASP cc_start: 0.8261 (t70) cc_final: 0.7621 (t0) REVERT: A 431 ARG cc_start: 0.8277 (mtm-85) cc_final: 0.7797 (mtp85) REVERT: A 480 LEU cc_start: 0.8232 (tt) cc_final: 0.7466 (mt) REVERT: A 1038 ASN cc_start: 0.7885 (t160) cc_final: 0.7534 (t0) REVERT: A 1052 MET cc_start: 0.8679 (ttm) cc_final: 0.8390 (ttm) REVERT: A 1111 MET cc_start: 0.8318 (mtt) cc_final: 0.8053 (mtt) REVERT: A 1128 MET cc_start: 0.8097 (mmm) cc_final: 0.7624 (tmm) REVERT: C 81 ASN cc_start: 0.8727 (t0) cc_final: 0.8042 (t0) REVERT: C 97 LEU cc_start: 0.9014 (tp) cc_final: 0.8667 (tp) REVERT: C 160 MET cc_start: 0.8559 (tpp) cc_final: 0.8269 (tpp) REVERT: G 173 CYS cc_start: 0.6190 (p) cc_final: 0.5743 (p) REVERT: G 197 LEU cc_start: 0.8030 (tt) cc_final: 0.7763 (tt) REVERT: G 233 GLU cc_start: 0.8930 (mm-30) cc_final: 0.8273 (mm-30) REVERT: G 238 ASN cc_start: 0.9158 (m-40) cc_final: 0.8597 (m110) outliers start: 34 outliers final: 24 residues processed: 226 average time/residue: 0.2033 time to fit residues: 67.2883 Evaluate side-chains 233 residues out of total 1108 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 208 time to evaluate : 1.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 ARG Chi-restraints excluded: chain A residue 151 THR Chi-restraints excluded: chain A residue 200 ILE Chi-restraints excluded: chain A residue 249 PHE Chi-restraints excluded: chain A residue 250 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 469 LEU Chi-restraints excluded: chain A residue 530 CYS Chi-restraints excluded: chain A residue 531 LEU Chi-restraints excluded: chain A residue 540 LEU 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 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 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 31 optimal weight: 2.9990 chunk 95 optimal weight: 0.4980 chunk 15 optimal weight: 0.9990 chunk 28 optimal weight: 0.8980 chunk 103 optimal weight: 0.0980 chunk 43 optimal weight: 0.8980 chunk 106 optimal weight: 3.9990 chunk 13 optimal weight: 0.6980 chunk 19 optimal weight: 2.9990 chunk 90 optimal weight: 6.9990 chunk 5 optimal weight: 1.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 566 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 827 ASN C 100 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.160485 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.106901 restraints weight = 14013.904| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.107945 restraints weight = 10458.957| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.107565 restraints weight = 8369.448| |-----------------------------------------------------------------------------| r_work (final): 0.3139 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 moved from start: 0.4074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 10732 Z= 0.199 Angle : 0.728 18.612 14568 Z= 0.344 Chirality : 0.045 0.319 1676 Planarity : 0.005 0.081 1822 Dihedral : 6.974 64.125 1796 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 10.16 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.49 % Favored : 95.43 % Rotamer: Outliers : 2.71 % Allowed : 19.58 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.02 (0.24), residues: 1291 helix: 0.99 (0.21), residues: 705 sheet: -1.54 (0.65), residues: 67 loop : -1.10 (0.27), residues: 519 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP G 49 HIS 0.005 0.001 HIS G 108 PHE 0.030 0.001 PHE A1112 TYR 0.022 0.001 TYR G 63 ARG 0.006 0.000 ARG A 431 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2290.35 seconds wall clock time: 41 minutes 58.81 seconds (2518.81 seconds total)