Starting phenix.real_space_refine on Fri Feb 14 00:08:13 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6uox_20834/02_2025/6uox_20834.cif Found real_map, /net/cci-nas-00/data/ceres_data/6uox_20834/02_2025/6uox_20834.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.02 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6uox_20834/02_2025/6uox_20834.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6uox_20834/02_2025/6uox_20834.map" model { file = "/net/cci-nas-00/data/ceres_data/6uox_20834/02_2025/6uox_20834.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6uox_20834/02_2025/6uox_20834.cif" } resolution = 4.02 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= 0.001 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 Br 1 7.06 5 S 68 5.16 5 Cl 2 4.86 5 C 5882 2.51 5 N 1468 2.21 5 O 1717 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 9138 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 8909 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1161, 8907 Classifications: {'peptide': 1161} Incomplete info: {'truncation_to_alanine': 46} Link IDs: {'PTRANS': 62, 'TRANS': 1098} Chain breaks: 3 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 200 Unresolved non-hydrogen angles: 262 Unresolved non-hydrogen dihedrals: 180 Unresolved non-hydrogen chiralities: 14 Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 1, 'TYR:plan': 5, 'ASN:plan1': 2, 'TRP:plan': 2, 'ASP:plan': 3, 'PHE:plan': 5, 'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 124 Conformer: "B" Number of residues, atoms: 1161, 8907 Classifications: {'peptide': 1161} Incomplete info: {'truncation_to_alanine': 46} Link IDs: {'PTRANS': 62, 'TRANS': 1098} Chain breaks: 3 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 200 Unresolved non-hydrogen angles: 262 Unresolved non-hydrogen dihedrals: 180 Unresolved non-hydrogen chiralities: 14 Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 1, 'TYR:plan': 5, 'ASN:plan1': 2, 'TRP:plan': 2, 'ASP:plan': 3, 'PHE:plan': 5, 'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 124 bond proxies already assigned to first conformer: 9126 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: "C" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 162 Unusual residues: {'NAG': 8, 'QDG': 1} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Time building chain proxies: 10.27, per 1000 atoms: 1.12 Number of scatterers: 9138 At special positions: 0 Unit cell: (112.86, 145.2, 114.84, 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) Br 1 34.99 Cl 2 17.00 S 68 16.00 O 1717 8.00 N 1468 7.00 C 5882 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=15, symmetry=0 Simple disulfide: pdb=" SG CYS A 25 " - pdb=" SG CYS A 74 " distance=2.03 Simple disulfide: pdb=" SG CYS A 31 " - pdb=" SG CYS A 42 " distance=2.03 Simple disulfide: pdb=" SG CYS A 63 " - pdb=" SG CYS A 109 " distance=2.03 Simple disulfide: pdb=" SG CYS A 75 " - pdb=" SG CYS A 113 " distance=2.03 Simple disulfide: pdb=" SG CYS A 97 " - pdb=" SG CYS A 238 " distance=2.04 Simple disulfide: pdb=" SG CYS A 100 " - pdb=" SG CYS A 160 " distance=2.03 Simple disulfide: pdb=" SG CYS A 177 " - pdb=" SG CYS A 184 " distance=2.04 Simple disulfide: pdb=" SG CYS A 227 " - pdb=" SG CYS A 243 " distance=2.03 Simple disulfide: pdb=" SG CYS A 240 " - pdb=" SG CYS A 247 " distance=2.03 Simple disulfide: pdb=" SG CYS A 468 " - pdb=" SG CYS A 479 " distance=2.03 Simple disulfide: pdb=" SG CYS A 516 " - pdb=" SG CYS A 533 " distance=2.03 Simple disulfide: pdb=" SG CYS A 909 " - pdb=" SG CYS A 914 " distance=2.03 Simple disulfide: pdb=" SG CYS A 956 " - pdb=" SG CYS A1011 " distance=2.03 Simple disulfide: pdb=" SG CYS A 957 " - pdb=" SG CYS A 979 " distance=2.03 Simple disulfide: pdb=" SG CYS A 967 " - pdb=" SG CYS A 976 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " NAG C 2 " - " MAN C 3 " BETA1-4 " NAG B 1 " - " NAG B 2 " " NAG C 1 " - " NAG C 2 " NAG-ASN " NAG A1301 " - " ASN A 452 " " NAG A1302 " - " ASN A 459 " " NAG A1305 " - " ASN A 524 " " NAG A1309 " - " ASN A 598 " " NAG A1310 " - " ASN A 916 " " NAG A1311 " - " ASN A 931 " " NAG A1312 " - " ASN A 961 " " NAG A1313 " - " ASN A 968 " " NAG B 1 " - " ASN A 478 " " NAG C 1 " - " ASN A 557 " Time building additional restraints: 2.20 Conformation dependent library (CDL) restraints added in 1.3 seconds 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2174 Finding SS restraints... Secondary structure from input PDB file: 47 helices and 12 sheets defined 51.5% alpha, 6.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.19 Creating SS restraints... Processing helix chain 'A' and resid 55 through 63 removed outlier: 3.868A pdb=" N GLU A 61 " --> pdb=" O ASP A 57 " (cutoff:3.500A) Processing helix chain 'A' and resid 76 through 87 removed outlier: 3.736A pdb=" N LEU A 80 " --> pdb=" O ASP A 76 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ASP A 85 " --> pdb=" O GLN A 81 " (cutoff:3.500A) Processing helix chain 'A' and resid 87 through 94 Processing helix chain 'A' and resid 97 through 114 removed outlier: 3.531A pdb=" N PHE A 101 " --> pdb=" O CYS A 97 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LEU A 104 " --> pdb=" O CYS A 100 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N SER A 114 " --> pdb=" O GLU A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 116 through 120 removed outlier: 3.751A pdb=" N PHE A 120 " --> pdb=" O ARG A 116 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 116 through 120' Processing helix chain 'A' and resid 150 through 161 Processing helix chain 'A' and resid 171 through 178 removed outlier: 4.107A pdb=" N LEU A 175 " --> pdb=" O LYS A 171 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N LEU A 176 " --> pdb=" O ALA A 172 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N GLY A 178 " --> pdb=" O GLY A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 185 through 195 Processing helix chain 'A' and resid 270 through 278 removed outlier: 3.579A pdb=" N ILE A 274 " --> pdb=" O VAL A 270 " (cutoff:3.500A) Processing helix chain 'A' and resid 279 through 284 Processing helix chain 'A' and resid 335 through 349 removed outlier: 3.589A pdb=" N PHE A 339 " --> pdb=" O LEU A 335 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ARG A 341 " --> pdb=" O ARG A 337 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N TRP A 342 " --> pdb=" O LEU A 338 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N PHE A 345 " --> pdb=" O ARG A 341 " (cutoff:3.500A) Processing helix chain 'A' and resid 351 through 365 removed outlier: 3.804A pdb=" N PHE A 355 " --> pdb=" O GLY A 351 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N PHE A 360 " --> pdb=" O PHE A 356 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 372 removed outlier: 3.833A pdb=" N VAL A 371 " --> pdb=" O GLY A 367 " (cutoff:3.500A) Processing helix chain 'A' and resid 386 through 393 Processing helix chain 'A' and resid 436 through 452 removed outlier: 5.235A pdb=" N GLN A 442 " --> pdb=" O GLN A 438 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N GLU A 451 " --> pdb=" O GLN A 447 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ASN A 452 " --> pdb=" O ILE A 448 " (cutoff:3.500A) Processing helix chain 'A' and resid 483 through 487 Processing helix chain 'A' and resid 508 through 516 Processing helix chain 'A' and resid 577 through 593 removed outlier: 3.659A pdb=" N TRP A 583 " --> pdb=" O ARG A 579 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N GLU A 586 " --> pdb=" O ALA A 582 " (cutoff:3.500A) Processing helix chain 'A' and resid 607 through 617 removed outlier: 3.882A pdb=" N GLU A 612 " --> pdb=" O SER A 608 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N LEU A 613 " --> pdb=" O ILE A 609 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ASN A 614 " --> pdb=" O GLU A 610 " (cutoff:3.500A) Processing helix chain 'A' and resid 618 through 620 No H-bonds generated for 'chain 'A' and resid 618 through 620' Processing helix chain 'A' and resid 621 through 638 removed outlier: 3.775A pdb=" N ILE A 626 " --> pdb=" O PHE A 622 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N SER A 627 " --> pdb=" O THR A 623 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N MET A 631 " --> pdb=" O SER A 627 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ILE A 635 " --> pdb=" O MET A 631 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N SER A 636 " --> pdb=" O PHE A 632 " (cutoff:3.500A) Processing helix chain 'A' and resid 654 through 679 removed outlier: 3.624A pdb=" N ALA A 669 " --> pdb=" O LEU A 665 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N PHE A 675 " --> pdb=" O SER A 671 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N TYR A 677 " --> pdb=" O GLY A 673 " (cutoff:3.500A) Processing helix chain 'A' and resid 685 through 711 removed outlier: 3.596A pdb=" N VAL A 689 " --> pdb=" O ILE A 685 " (cutoff:3.500A) Proline residue: A 691 - end of helix removed outlier: 3.589A pdb=" N LEU A 695 " --> pdb=" O PRO A 691 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N ASP A 700 " --> pdb=" O ALA A 696 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ASN A 701 " --> pdb=" O VAL A 697 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ILE A 702 " --> pdb=" O GLY A 698 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ILE A 704 " --> pdb=" O ASP A 700 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N GLN A 707 " --> pdb=" O PHE A 703 " (cutoff:3.500A) Processing helix chain 'A' and resid 719 through 748 Proline residue: A 733 - end of helix removed outlier: 3.993A pdb=" N LEU A 737 " --> pdb=" O PRO A 733 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N SER A 738 " --> pdb=" O SER A 734 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N GLU A 742 " --> pdb=" O SER A 738 " (cutoff:3.500A) Processing helix chain 'A' and resid 757 through 776 removed outlier: 4.170A pdb=" N LEU A 762 " --> pdb=" O HIS A 758 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N PHE A 763 " --> pdb=" O THR A 759 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N VAL A 768 " --> pdb=" O ALA A 764 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ILE A 776 " --> pdb=" O PHE A 772 " (cutoff:3.500A) Processing helix chain 'A' and resid 777 through 782 removed outlier: 3.951A pdb=" N SER A 781 " --> pdb=" O THR A 777 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LEU A 782 " --> pdb=" O CYS A 778 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 777 through 782' Processing helix chain 'A' and resid 782 through 792 Processing helix chain 'A' and resid 818 through 826 removed outlier: 3.587A pdb=" N SER A 824 " --> pdb=" O PHE A 820 " (cutoff:3.500A) Processing helix chain 'A' and resid 836 through 852 removed outlier: 3.959A pdb=" N PHE A 842 " --> pdb=" O VAL A 838 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N LEU A 846 " --> pdb=" O PHE A 842 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ALA A 851 " --> pdb=" O SER A 847 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N VAL A 852 " --> pdb=" O PHE A 848 " (cutoff:3.500A) Processing helix chain 'A' and resid 870 through 880 removed outlier: 4.191A pdb=" N ASP A 874 " --> pdb=" O SER A 870 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N SER A 880 " --> pdb=" O PHE A 876 " (cutoff:3.500A) Processing helix chain 'A' and resid 901 through 907 Processing helix chain 'A' and resid 918 through 928 removed outlier: 4.137A pdb=" N GLN A 928 " --> pdb=" O PHE A 924 " (cutoff:3.500A) Processing helix chain 'A' and resid 942 through 951 removed outlier: 3.569A pdb=" N PHE A 947 " --> pdb=" O ILE A 943 " (cutoff:3.500A) Processing helix chain 'A' and resid 952 through 955 removed outlier: 4.185A pdb=" N SER A 955 " --> pdb=" O PRO A 952 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 952 through 955' Processing helix chain 'A' and resid 993 through 1004 Proline residue: A1000 - end of helix Processing helix chain 'A' and resid 1047 through 1070 removed outlier: 3.670A pdb=" N PHE A1051 " --> pdb=" O THR A1047 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ILE A1052 " --> pdb=" O SER A1048 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LYS A1057 " --> pdb=" O ASP A1053 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLY A1070 " --> pdb=" O THR A1066 " (cutoff:3.500A) Processing helix chain 'A' and resid 1089 through 1092 Processing helix chain 'A' and resid 1093 through 1118 removed outlier: 3.670A pdb=" N ASP A1097 " --> pdb=" O THR A1093 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N THR A1098 " --> pdb=" O ILE A1094 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N ILE A1099 " --> pdb=" O ILE A1095 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N GLY A1103 " --> pdb=" O ILE A1099 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N THR A1113 " --> pdb=" O ILE A1109 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N MET A1114 " --> pdb=" O PHE A1110 " (cutoff:3.500A) Processing helix chain 'A' and resid 1120 through 1146 removed outlier: 3.669A pdb=" N ALA A1124 " --> pdb=" O GLU A1120 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ILE A1126 " --> pdb=" O TRP A1122 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N MET A1127 " --> pdb=" O SER A1123 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N LEU A1135 " --> pdb=" O ILE A1131 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ASN A1137 " --> pdb=" O MET A1133 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N TRP A1143 " --> pdb=" O PHE A1139 " (cutoff:3.500A) Processing helix chain 'A' and resid 1150 through 1164 removed outlier: 4.117A pdb=" N ASN A1156 " --> pdb=" O VAL A1152 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N SER A1160 " --> pdb=" O ASN A1156 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N CYS A1161 " --> pdb=" O LEU A1157 " (cutoff:3.500A) Processing helix chain 'A' and resid 1165 through 1177 removed outlier: 4.279A pdb=" N HIS A1170 " --> pdb=" O GLU A1166 " (cutoff:3.500A) removed outlier: 4.784A pdb=" N ILE A1171 " --> pdb=" O PHE A1167 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N ALA A1174 " --> pdb=" O HIS A1170 " (cutoff:3.500A) Processing helix chain 'A' and resid 1182 through 1194 removed outlier: 3.959A pdb=" N GLU A1188 " --> pdb=" O VAL A1184 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N GLU A1189 " --> pdb=" O GLU A1185 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ALA A1190 " --> pdb=" O ARG A1186 " (cutoff:3.500A) Processing helix chain 'A' and resid 1194 through 1201 Processing helix chain 'A' and resid 1202 through 1215 removed outlier: 3.609A pdb=" N ILE A1210 " --> pdb=" O LYS A1206 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N VAL A1211 " --> pdb=" O PHE A1207 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N VAL A1212 " --> pdb=" O GLY A1208 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LEU A1213 " --> pdb=" O GLY A1209 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N PHE A1215 " --> pdb=" O VAL A1211 " (cutoff:3.500A) Processing helix chain 'A' and resid 1219 through 1224 Processing helix chain 'A' and resid 1226 through 1242 removed outlier: 4.152A pdb=" N LEU A1235 " --> pdb=" O ALA A1231 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N THR A1238 " --> pdb=" O LEU A1234 " (cutoff:3.500A) Processing helix chain 'A' and resid 1242 through 1249 removed outlier: 4.239A pdb=" N VAL A1246 " --> pdb=" O ILE A1242 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LEU A1247 " --> pdb=" O PHE A1243 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 28 Processing sheet with id=AA2, first strand: chain 'A' and resid 33 through 35 removed outlier: 7.200A pdb=" N LYS A 38 " --> pdb=" O ALA A 34 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 49 through 50 removed outlier: 3.512A pdb=" N LEU A 73 " --> pdb=" O LYS A 49 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 121 through 129 removed outlier: 6.487A pdb=" N GLU A 143 " --> pdb=" O THR A 124 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N THR A 126 " --> pdb=" O VAL A 141 " (cutoff:3.500A) removed outlier: 7.310A pdb=" N VAL A 141 " --> pdb=" O THR A 126 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N ASP A 128 " --> pdb=" O THR A 139 " (cutoff:3.500A) removed outlier: 5.909A pdb=" N THR A 139 " --> pdb=" O ASP A 128 " (cutoff:3.500A) removed outlier: 7.967A pdb=" N THR A 206 " --> pdb=" O LYS A 142 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N LEU A 144 " --> pdb=" O THR A 206 " (cutoff:3.500A) removed outlier: 7.560A pdb=" N VAL A 208 " --> pdb=" O LEU A 144 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N TYR A 146 " --> pdb=" O VAL A 208 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N SER A 210 " --> pdb=" O TYR A 146 " (cutoff:3.500A) removed outlier: 5.426A pdb=" N VAL A 148 " --> pdb=" O SER A 210 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 547 through 548 Processing sheet with id=AA6, first strand: chain 'A' and resid 418 through 420 Processing sheet with id=AA7, first strand: chain 'A' and resid 455 through 457 Processing sheet with id=AA8, first strand: chain 'A' and resid 499 through 500 removed outlier: 6.889A pdb=" N LYS A 499 " --> pdb=" O TYR A 506 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 1036 through 1037 Processing sheet with id=AB1, first strand: chain 'A' and resid 1036 through 1037 Processing sheet with id=AB2, first strand: chain 'A' and resid 966 through 967 removed outlier: 3.978A pdb=" N ARG A 958 " --> pdb=" O CYS A 967 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 1025 through 1027 352 hydrogen bonds defined for protein. 1014 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: 3.23 Time building geometry restraints manager: 2.58 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.34: 2778 1.34 - 1.49: 2650 1.49 - 1.64: 3838 1.64 - 1.79: 23 1.79 - 1.94: 76 Bond restraints: 9365 Sorted by residual: bond pdb=" C17 QDG A1314 " pdb=" C49 QDG A1314 " ideal model delta sigma weight residual 1.536 1.211 0.325 2.00e-02 2.50e+03 2.64e+02 bond pdb=" C09 QDG A1314 " pdb=" O16 QDG A1314 " ideal model delta sigma weight residual 1.396 1.197 0.199 2.00e-02 2.50e+03 9.90e+01 bond pdb=" C45 QDG A1314 " pdb=" N44 QDG A1314 " ideal model delta sigma weight residual 1.283 1.445 -0.162 2.00e-02 2.50e+03 6.58e+01 bond pdb=" C17 QDG A1314 " pdb=" O16 QDG A1314 " ideal model delta sigma weight residual 1.419 1.557 -0.138 2.00e-02 2.50e+03 4.77e+01 bond pdb=" C40 QDG A1314 " pdb=" N39 QDG A1314 " ideal model delta sigma weight residual 1.453 1.333 0.120 2.00e-02 2.50e+03 3.61e+01 ... (remaining 9360 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.23: 11985 2.23 - 4.46: 720 4.46 - 6.68: 48 6.68 - 8.91: 12 8.91 - 11.14: 3 Bond angle restraints: 12768 Sorted by residual: angle pdb=" N PRO A 132 " pdb=" CA PRO A 132 " pdb=" CB PRO A 132 " ideal model delta sigma weight residual 103.25 110.45 -7.20 1.05e+00 9.07e-01 4.70e+01 angle pdb=" N PRO A 433 " pdb=" CA PRO A 433 " pdb=" C PRO A 433 " ideal model delta sigma weight residual 110.70 118.24 -7.54 1.22e+00 6.72e-01 3.82e+01 angle pdb=" N ASP A 552 " pdb=" CA ASP A 552 " pdb=" C ASP A 552 " ideal model delta sigma weight residual 110.80 121.94 -11.14 2.13e+00 2.20e-01 2.74e+01 angle pdb=" N TYR A 571 " pdb=" CA TYR A 571 " pdb=" C TYR A 571 " ideal model delta sigma weight residual 111.33 117.17 -5.84 1.21e+00 6.83e-01 2.33e+01 angle pdb=" N ILE A 962 " pdb=" CA ILE A 962 " pdb=" C ILE A 962 " ideal model delta sigma weight residual 111.90 115.78 -3.88 8.10e-01 1.52e+00 2.29e+01 ... (remaining 12763 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.32: 5458 22.32 - 44.65: 197 44.65 - 66.97: 43 66.97 - 89.29: 20 89.29 - 111.61: 13 Dihedral angle restraints: 5731 sinusoidal: 2355 harmonic: 3376 Sorted by residual: dihedral pdb=" CB CYS A 468 " pdb=" SG CYS A 468 " pdb=" SG CYS A 479 " pdb=" CB CYS A 479 " ideal model delta sinusoidal sigma weight residual -86.00 -176.29 90.29 1 1.00e+01 1.00e-02 9.65e+01 dihedral pdb=" CB CYS A 957 " pdb=" SG CYS A 957 " pdb=" SG CYS A 979 " pdb=" CB CYS A 979 " ideal model delta sinusoidal sigma weight residual 93.00 173.40 -80.40 1 1.00e+01 1.00e-02 8.00e+01 dihedral pdb=" CB CYS A 909 " pdb=" SG CYS A 909 " pdb=" SG CYS A 914 " pdb=" CB CYS A 914 " ideal model delta sinusoidal sigma weight residual 93.00 162.63 -69.63 1 1.00e+01 1.00e-02 6.26e+01 ... (remaining 5728 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.139: 1408 0.139 - 0.277: 68 0.277 - 0.415: 5 0.415 - 0.554: 4 0.554 - 0.692: 2 Chirality restraints: 1487 Sorted by residual: chirality pdb=" C1 NAG B 2 " pdb=" O4 NAG B 1 " pdb=" C2 NAG B 2 " pdb=" O5 NAG B 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.29 -0.11 2.00e-02 2.50e+03 3.05e+01 chirality pdb=" C1 NAG C 2 " pdb=" O4 NAG C 1 " pdb=" C2 NAG C 2 " pdb=" O5 NAG C 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.31 -0.09 2.00e-02 2.50e+03 2.12e+01 chirality pdb=" C1 NAG B 1 " pdb=" ND2 ASN A 478 " pdb=" C2 NAG B 1 " pdb=" O5 NAG B 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.71 -0.69 2.00e-01 2.50e+01 1.20e+01 ... (remaining 1484 not shown) Planarity restraints: 1632 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO A 253 " -0.053 5.00e-02 4.00e+02 8.06e-02 1.04e+01 pdb=" N PRO A 254 " 0.139 5.00e-02 4.00e+02 pdb=" CA PRO A 254 " -0.041 5.00e-02 4.00e+02 pdb=" CD PRO A 254 " -0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 89 " -0.040 5.00e-02 4.00e+02 6.13e-02 6.01e+00 pdb=" N PRO A 90 " 0.106 5.00e-02 4.00e+02 pdb=" CA PRO A 90 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO A 90 " -0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO A 254 " 0.032 5.00e-02 4.00e+02 4.96e-02 3.93e+00 pdb=" N PRO A 255 " -0.086 5.00e-02 4.00e+02 pdb=" CA PRO A 255 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 255 " 0.027 5.00e-02 4.00e+02 ... (remaining 1629 not shown) Histogram of nonbonded interaction distances: 2.46 - 2.95: 3640 2.95 - 3.44: 9311 3.44 - 3.92: 14119 3.92 - 4.41: 15218 4.41 - 4.90: 25057 Nonbonded interactions: 67345 Sorted by model distance: nonbonded pdb=" OG SER A 849 " pdb=" O VAL A1136 " model vdw 2.461 3.040 nonbonded pdb=" OG1 THR A 454 " pdb=" OG1 THR A 461 " model vdw 2.494 3.040 nonbonded pdb=" O ALA A1062 " pdb=" OG1 THR A1066 " model vdw 2.496 3.040 nonbonded pdb=" O TYR A 932 " pdb=" NZ LYS A1057 " model vdw 2.507 3.120 nonbonded pdb=" OG SER A 608 " pdb=" OH TYR A 871 " model vdw 2.545 3.040 ... (remaining 67340 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.310 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: 0.420 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 28.120 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.070 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:2.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7747 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 : 0.010 0.325 9365 Z= 0.684 Angle : 1.179 11.140 12768 Z= 0.752 Chirality : 0.076 0.692 1487 Planarity : 0.005 0.081 1622 Dihedral : 14.585 111.613 3512 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 0.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.15 % Favored : 91.85 % Rotamer: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.23 % 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: -4.01 (0.20), residues: 1153 helix: -2.78 (0.16), residues: 549 sheet: -2.22 (0.54), residues: 90 loop : -2.48 (0.25), residues: 514 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A1145 HIS 0.004 0.001 HIS A 897 PHE 0.017 0.002 PHE A1139 TYR 0.015 0.002 TYR A 899 ARG 0.006 0.000 ARG A1227 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 217 time to evaluate : 1.497 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 ASP cc_start: 0.8849 (m-30) cc_final: 0.8550 (t0) REVERT: A 85 ASP cc_start: 0.8768 (t70) cc_final: 0.8266 (t0) REVERT: A 103 ASN cc_start: 0.9530 (m110) cc_final: 0.9082 (m110) REVERT: A 106 ASN cc_start: 0.8784 (m-40) cc_final: 0.8504 (m-40) REVERT: A 108 PHE cc_start: 0.8783 (m-80) cc_final: 0.8501 (m-80) REVERT: A 355 PHE cc_start: 0.9111 (t80) cc_final: 0.8778 (t80) REVERT: A 364 CYS cc_start: 0.8516 (m) cc_final: 0.8145 (m) REVERT: A 406 GLU cc_start: 0.8438 (mm-30) cc_final: 0.8226 (mt-10) REVERT: A 593 ASN cc_start: 0.8958 (m-40) cc_final: 0.8434 (p0) REVERT: A 634 TYR cc_start: 0.8639 (t80) cc_final: 0.8419 (t80) REVERT: A 663 ILE cc_start: 0.9179 (mt) cc_final: 0.8893 (mt) REVERT: A 689 VAL cc_start: 0.8739 (t) cc_final: 0.8266 (t) REVERT: A 730 GLU cc_start: 0.9401 (tp30) cc_final: 0.8841 (tm-30) REVERT: A 735 MET cc_start: 0.8544 (ttp) cc_final: 0.7998 (ttp) REVERT: A 834 MET cc_start: 0.7817 (mtt) cc_final: 0.7404 (mmm) REVERT: A 864 LEU cc_start: 0.8463 (mt) cc_final: 0.8200 (pp) REVERT: A 872 MET cc_start: 0.8546 (mmm) cc_final: 0.7980 (mmm) REVERT: A 922 GLN cc_start: 0.8907 (tp-100) cc_final: 0.8480 (tp-100) REVERT: A 930 ASP cc_start: 0.8554 (p0) cc_final: 0.7879 (t0) REVERT: A 933 THR cc_start: 0.8749 (t) cc_final: 0.8470 (t) REVERT: A 1122 TRP cc_start: 0.7946 (m100) cc_final: 0.7449 (m-10) REVERT: A 1150 ASN cc_start: 0.8223 (p0) cc_final: 0.7741 (p0) REVERT: A 1156 ASN cc_start: 0.8981 (t0) cc_final: 0.8777 (t0) REVERT: A 1179 MET cc_start: 0.7488 (mpp) cc_final: 0.7224 (mmm) outliers start: 0 outliers final: 0 residues processed: 217 average time/residue: 0.2139 time to fit residues: 64.6487 Evaluate side-chains 118 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 118 time to evaluate : 1.013 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 97 optimal weight: 0.4980 chunk 87 optimal weight: 7.9990 chunk 48 optimal weight: 1.9990 chunk 30 optimal weight: 8.9990 chunk 59 optimal weight: 1.9990 chunk 46 optimal weight: 0.9980 chunk 90 optimal weight: 0.7980 chunk 35 optimal weight: 9.9990 chunk 55 optimal weight: 3.9990 chunk 67 optimal weight: 2.9990 chunk 105 optimal weight: 5.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 103 ASN A 447 GLN A 988 GLN A1042 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.087647 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.066379 restraints weight = 29957.805| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.068527 restraints weight = 16110.258| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.070016 restraints weight = 10757.917| |-----------------------------------------------------------------------------| r_work (final): 0.3242 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3243 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3243 r_free = 0.3243 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3242 r_free = 0.3242 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3242 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8003 moved from start: 0.2234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9365 Z= 0.198 Angle : 0.714 8.604 12768 Z= 0.352 Chirality : 0.049 0.361 1487 Planarity : 0.005 0.078 1622 Dihedral : 13.131 90.292 1547 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.93 (0.22), residues: 1153 helix: -1.58 (0.19), residues: 560 sheet: -2.29 (0.50), residues: 100 loop : -2.18 (0.26), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 583 HIS 0.003 0.001 HIS A 530 PHE 0.034 0.002 PHE A 937 TYR 0.015 0.001 TYR A1085 ARG 0.007 0.000 ARG A 958 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 153 time to evaluate : 1.025 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 106 ASN cc_start: 0.8778 (m-40) cc_final: 0.8280 (m-40) REVERT: A 110 GLU cc_start: 0.7641 (mm-30) cc_final: 0.7041 (mm-30) REVERT: A 355 PHE cc_start: 0.8818 (t80) cc_final: 0.8570 (t80) REVERT: A 586 GLU cc_start: 0.8952 (mm-30) cc_final: 0.8717 (mt-10) REVERT: A 593 ASN cc_start: 0.8663 (m-40) cc_final: 0.8390 (p0) REVERT: A 676 SER cc_start: 0.9182 (m) cc_final: 0.8906 (p) REVERT: A 730 GLU cc_start: 0.9224 (tp30) cc_final: 0.8655 (tm-30) REVERT: A 774 LEU cc_start: 0.9432 (tp) cc_final: 0.9226 (tp) REVERT: A 930 ASP cc_start: 0.8513 (p0) cc_final: 0.8247 (t0) REVERT: A 935 ILE cc_start: 0.8195 (mt) cc_final: 0.7859 (mt) REVERT: A 1150 ASN cc_start: 0.8738 (p0) cc_final: 0.8158 (p0) REVERT: A 1156 ASN cc_start: 0.8733 (t0) cc_final: 0.8508 (t0) REVERT: A 1175 PHE cc_start: 0.8314 (t80) cc_final: 0.7792 (t80) outliers start: 0 outliers final: 0 residues processed: 153 average time/residue: 0.1809 time to fit residues: 40.8549 Evaluate side-chains 105 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 105 time to evaluate : 1.014 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 85 optimal weight: 4.9990 chunk 87 optimal weight: 0.9990 chunk 75 optimal weight: 7.9990 chunk 20 optimal weight: 8.9990 chunk 26 optimal weight: 0.0170 chunk 104 optimal weight: 2.9990 chunk 11 optimal weight: 50.0000 chunk 91 optimal weight: 8.9990 chunk 36 optimal weight: 4.9990 chunk 19 optimal weight: 1.9990 chunk 111 optimal weight: 8.9990 overall best weight: 2.2026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 775 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.088194 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.067418 restraints weight = 29458.003| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.069505 restraints weight = 16233.039| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.070913 restraints weight = 10985.650| |-----------------------------------------------------------------------------| r_work (final): 0.3269 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3270 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3270 r_free = 0.3270 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3270 r_free = 0.3270 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3270 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 moved from start: 0.2660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 9365 Z= 0.234 Angle : 0.698 8.736 12768 Z= 0.341 Chirality : 0.047 0.346 1487 Planarity : 0.005 0.075 1622 Dihedral : 11.057 85.842 1547 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.54 (0.23), residues: 1153 helix: -1.13 (0.20), residues: 565 sheet: -2.65 (0.45), residues: 110 loop : -1.99 (0.27), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 583 HIS 0.013 0.002 HIS A1042 PHE 0.046 0.002 PHE A 632 TYR 0.012 0.001 TYR A1037 ARG 0.004 0.001 ARG A1227 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 138 time to evaluate : 0.959 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 ASP cc_start: 0.8806 (p0) cc_final: 0.8592 (m-30) REVERT: A 106 ASN cc_start: 0.8731 (m-40) cc_final: 0.8450 (m-40) REVERT: A 355 PHE cc_start: 0.8708 (t80) cc_final: 0.8507 (t80) REVERT: A 632 PHE cc_start: 0.7953 (m-80) cc_final: 0.7716 (m-80) REVERT: A 676 SER cc_start: 0.9300 (m) cc_final: 0.8991 (t) REVERT: A 730 GLU cc_start: 0.9031 (tp30) cc_final: 0.8668 (tm-30) REVERT: A 774 LEU cc_start: 0.9413 (tp) cc_final: 0.9197 (tp) REVERT: A 834 MET cc_start: 0.7493 (mmp) cc_final: 0.7267 (mmm) REVERT: A 935 ILE cc_start: 0.8226 (mt) cc_final: 0.8013 (mt) REVERT: A 1150 ASN cc_start: 0.8902 (p0) cc_final: 0.8278 (p0) REVERT: A 1175 PHE cc_start: 0.8477 (t80) cc_final: 0.8144 (t80) outliers start: 0 outliers final: 0 residues processed: 138 average time/residue: 0.1910 time to fit residues: 39.4433 Evaluate side-chains 101 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 101 time to evaluate : 1.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 18 optimal weight: 30.0000 chunk 74 optimal weight: 6.9990 chunk 16 optimal weight: 9.9990 chunk 105 optimal weight: 6.9990 chunk 44 optimal weight: 4.9990 chunk 9 optimal weight: 2.9990 chunk 112 optimal weight: 8.9990 chunk 60 optimal weight: 9.9990 chunk 62 optimal weight: 0.9990 chunk 43 optimal weight: 0.9980 chunk 82 optimal weight: 0.6980 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 568 ASN ** A 775 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 = 0.3628 r_free = 0.3628 target = 0.088356 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.067720 restraints weight = 29485.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.069818 restraints weight = 16156.840| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.071206 restraints weight = 10984.589| |-----------------------------------------------------------------------------| r_work (final): 0.3274 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3275 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3275 r_free = 0.3275 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3275 r_free = 0.3275 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3275 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 moved from start: 0.2939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 9365 Z= 0.224 Angle : 0.681 7.898 12768 Z= 0.334 Chirality : 0.046 0.347 1487 Planarity : 0.005 0.076 1622 Dihedral : 9.836 86.467 1547 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 0.00 % Allowed : 0.83 % Favored : 99.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -2.20 (0.23), residues: 1153 helix: -0.89 (0.21), residues: 560 sheet: -2.50 (0.49), residues: 100 loop : -1.78 (0.27), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 583 HIS 0.009 0.001 HIS A1042 PHE 0.041 0.002 PHE A 632 TYR 0.015 0.001 TYR A 875 ARG 0.005 0.000 ARG A 116 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 132 time to evaluate : 0.945 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 ASP cc_start: 0.8821 (p0) cc_final: 0.8621 (m-30) REVERT: A 106 ASN cc_start: 0.8548 (m-40) cc_final: 0.8345 (m-40) REVERT: A 355 PHE cc_start: 0.8727 (t80) cc_final: 0.8521 (t80) REVERT: A 676 SER cc_start: 0.9285 (m) cc_final: 0.9006 (p) REVERT: A 730 GLU cc_start: 0.9025 (tp30) cc_final: 0.8663 (tm-30) REVERT: A 772 PHE cc_start: 0.7461 (t80) cc_final: 0.7254 (t80) REVERT: A 945 ASP cc_start: 0.8581 (t70) cc_final: 0.8378 (t70) REVERT: A 998 PHE cc_start: 0.8753 (m-80) cc_final: 0.8458 (m-80) REVERT: A 1150 ASN cc_start: 0.8932 (p0) cc_final: 0.8316 (p0) REVERT: A 1175 PHE cc_start: 0.8453 (t80) cc_final: 0.8076 (t80) outliers start: 0 outliers final: 0 residues processed: 132 average time/residue: 0.1828 time to fit residues: 36.1534 Evaluate side-chains 100 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 100 time to evaluate : 1.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 66 optimal weight: 0.6980 chunk 32 optimal weight: 4.9990 chunk 103 optimal weight: 0.9990 chunk 71 optimal weight: 4.9990 chunk 70 optimal weight: 9.9990 chunk 74 optimal weight: 5.9990 chunk 90 optimal weight: 0.8980 chunk 58 optimal weight: 9.9990 chunk 94 optimal weight: 5.9990 chunk 96 optimal weight: 6.9990 chunk 24 optimal weight: 10.0000 overall best weight: 2.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.087256 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.066617 restraints weight = 29489.078| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.068677 restraints weight = 16204.637| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.070048 restraints weight = 10995.073| |-----------------------------------------------------------------------------| r_work (final): 0.3253 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3257 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3257 r_free = 0.3257 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3257 r_free = 0.3257 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3257 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8104 moved from start: 0.3186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 9365 Z= 0.249 Angle : 0.683 9.677 12768 Z= 0.335 Chirality : 0.046 0.348 1487 Planarity : 0.005 0.073 1622 Dihedral : 8.833 86.714 1547 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.81 % Favored : 94.19 % Rotamer: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.01 (0.24), residues: 1153 helix: -0.79 (0.21), residues: 566 sheet: -2.42 (0.50), residues: 94 loop : -1.64 (0.28), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 583 HIS 0.008 0.001 HIS A1042 PHE 0.013 0.002 PHE A 692 TYR 0.023 0.001 TYR A 634 ARG 0.005 0.001 ARG A1227 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 128 time to evaluate : 0.923 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 106 ASN cc_start: 0.8573 (m-40) cc_final: 0.8357 (m-40) REVERT: A 194 PHE cc_start: 0.8917 (m-10) cc_final: 0.8693 (m-80) REVERT: A 531 ASP cc_start: 0.7917 (t0) cc_final: 0.7660 (t0) REVERT: A 632 PHE cc_start: 0.7637 (m-80) cc_final: 0.7301 (m-80) REVERT: A 676 SER cc_start: 0.9290 (m) cc_final: 0.9012 (p) REVERT: A 730 GLU cc_start: 0.9036 (tp30) cc_final: 0.8664 (tm-30) REVERT: A 834 MET cc_start: 0.7624 (mmp) cc_final: 0.6896 (mmm) REVERT: A 872 MET cc_start: 0.8088 (mmm) cc_final: 0.7399 (mmm) REVERT: A 875 TYR cc_start: 0.8987 (t80) cc_final: 0.8622 (t80) REVERT: A 945 ASP cc_start: 0.8639 (t70) cc_final: 0.8418 (t70) REVERT: A 1150 ASN cc_start: 0.8946 (p0) cc_final: 0.8320 (p0) REVERT: A 1175 PHE cc_start: 0.8447 (t80) cc_final: 0.8074 (t80) outliers start: 0 outliers final: 0 residues processed: 128 average time/residue: 0.1964 time to fit residues: 39.4042 Evaluate side-chains 97 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 97 time to evaluate : 1.099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 42 optimal weight: 0.3980 chunk 10 optimal weight: 50.0000 chunk 5 optimal weight: 9.9990 chunk 27 optimal weight: 5.9990 chunk 100 optimal weight: 4.9990 chunk 51 optimal weight: 9.9990 chunk 82 optimal weight: 1.9990 chunk 83 optimal weight: 0.8980 chunk 91 optimal weight: 6.9990 chunk 84 optimal weight: 0.0870 chunk 15 optimal weight: 9.9990 overall best weight: 1.6762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 775 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.088119 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.067531 restraints weight = 29993.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.069633 restraints weight = 16282.537| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.071078 restraints weight = 10975.060| |-----------------------------------------------------------------------------| r_work (final): 0.3276 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3277 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3277 r_free = 0.3277 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3277 r_free = 0.3277 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3277 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 moved from start: 0.3321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 9365 Z= 0.193 Angle : 0.642 9.366 12768 Z= 0.311 Chirality : 0.044 0.342 1487 Planarity : 0.004 0.074 1622 Dihedral : 8.245 89.945 1547 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.86 (0.24), residues: 1153 helix: -0.63 (0.21), residues: 568 sheet: -2.47 (0.49), residues: 99 loop : -1.56 (0.28), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 544 HIS 0.008 0.001 HIS A1042 PHE 0.028 0.001 PHE A 937 TYR 0.018 0.001 TYR A 634 ARG 0.005 0.000 ARG A1227 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 135 time to evaluate : 1.159 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 531 ASP cc_start: 0.7903 (t0) cc_final: 0.7651 (t0) REVERT: A 632 PHE cc_start: 0.7650 (m-80) cc_final: 0.7373 (m-80) REVERT: A 676 SER cc_start: 0.9301 (m) cc_final: 0.9011 (p) REVERT: A 730 GLU cc_start: 0.9023 (tp30) cc_final: 0.8670 (tm-30) REVERT: A 834 MET cc_start: 0.7594 (mmp) cc_final: 0.7232 (mmt) REVERT: A 875 TYR cc_start: 0.8939 (t80) cc_final: 0.8641 (t80) REVERT: A 907 MET cc_start: 0.8265 (mmm) cc_final: 0.8051 (mmm) REVERT: A 945 ASP cc_start: 0.8639 (t70) cc_final: 0.8408 (t70) REVERT: A 996 MET cc_start: 0.8458 (ttm) cc_final: 0.8153 (ttp) REVERT: A 1063 SER cc_start: 0.9321 (t) cc_final: 0.9019 (p) REVERT: A 1150 ASN cc_start: 0.8899 (p0) cc_final: 0.8227 (p0) REVERT: A 1175 PHE cc_start: 0.8476 (t80) cc_final: 0.8174 (t80) REVERT: A 1225 TYR cc_start: 0.8401 (m-80) cc_final: 0.8190 (m-80) REVERT: A 1228 MET cc_start: 0.8402 (mmm) cc_final: 0.8102 (mmm) outliers start: 0 outliers final: 0 residues processed: 135 average time/residue: 0.1823 time to fit residues: 36.8134 Evaluate side-chains 94 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 94 time to evaluate : 1.034 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 82 optimal weight: 0.9980 chunk 26 optimal weight: 0.7980 chunk 62 optimal weight: 3.9990 chunk 33 optimal weight: 0.5980 chunk 31 optimal weight: 1.9990 chunk 104 optimal weight: 0.0370 chunk 3 optimal weight: 2.9990 chunk 101 optimal weight: 6.9990 chunk 83 optimal weight: 0.9980 chunk 48 optimal weight: 5.9990 chunk 67 optimal weight: 3.9990 overall best weight: 0.6858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.089595 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.069029 restraints weight = 30202.468| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.071233 restraints weight = 16199.439| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.072700 restraints weight = 10808.951| |-----------------------------------------------------------------------------| r_work (final): 0.3307 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3305 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3305 r_free = 0.3305 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3305 r_free = 0.3305 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3305 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8040 moved from start: 0.3478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9365 Z= 0.161 Angle : 0.638 11.654 12768 Z= 0.308 Chirality : 0.044 0.356 1487 Planarity : 0.004 0.072 1622 Dihedral : 8.095 84.734 1547 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 0.00 % Allowed : 0.31 % Favored : 99.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.76 (0.24), residues: 1153 helix: -0.57 (0.21), residues: 569 sheet: -2.30 (0.50), residues: 99 loop : -1.51 (0.28), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A1145 HIS 0.007 0.001 HIS A1042 PHE 0.017 0.001 PHE A 194 TYR 0.014 0.001 TYR A 634 ARG 0.004 0.000 ARG A1227 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 131 time to evaluate : 1.037 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 110 GLU cc_start: 0.7269 (mm-30) cc_final: 0.7009 (mm-30) REVERT: A 531 ASP cc_start: 0.7871 (t0) cc_final: 0.7660 (t0) REVERT: A 632 PHE cc_start: 0.7603 (m-80) cc_final: 0.7253 (m-80) REVERT: A 676 SER cc_start: 0.9282 (m) cc_final: 0.9021 (p) REVERT: A 730 GLU cc_start: 0.8944 (tp30) cc_final: 0.8633 (tm-30) REVERT: A 834 MET cc_start: 0.7536 (mmp) cc_final: 0.7184 (mmt) REVERT: A 872 MET cc_start: 0.7929 (mmm) cc_final: 0.7602 (mmm) REVERT: A 945 ASP cc_start: 0.8625 (t70) cc_final: 0.8379 (t70) REVERT: A 996 MET cc_start: 0.8391 (ttm) cc_final: 0.8067 (ttp) REVERT: A 1063 SER cc_start: 0.9272 (t) cc_final: 0.8973 (p) REVERT: A 1150 ASN cc_start: 0.8829 (p0) cc_final: 0.8187 (p0) REVERT: A 1175 PHE cc_start: 0.8504 (t80) cc_final: 0.8180 (t80) outliers start: 0 outliers final: 0 residues processed: 131 average time/residue: 0.1868 time to fit residues: 36.4649 Evaluate side-chains 97 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 97 time to evaluate : 0.957 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 49 optimal weight: 0.9980 chunk 10 optimal weight: 30.0000 chunk 56 optimal weight: 0.6980 chunk 81 optimal weight: 7.9990 chunk 58 optimal weight: 0.9980 chunk 112 optimal weight: 10.0000 chunk 94 optimal weight: 1.9990 chunk 37 optimal weight: 0.9990 chunk 9 optimal weight: 10.0000 chunk 46 optimal weight: 0.0170 chunk 89 optimal weight: 6.9990 overall best weight: 0.7420 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.089739 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.069235 restraints weight = 30667.158| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.071416 restraints weight = 16218.990| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.072929 restraints weight = 10737.088| |-----------------------------------------------------------------------------| r_work (final): 0.3313 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3311 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3311 r_free = 0.3311 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3311 r_free = 0.3311 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3311 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8025 moved from start: 0.3691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 9365 Z= 0.153 Angle : 0.615 10.179 12768 Z= 0.298 Chirality : 0.043 0.323 1487 Planarity : 0.004 0.072 1622 Dihedral : 7.536 84.640 1547 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 0.00 % Allowed : 1.03 % Favored : 98.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.51 (0.24), residues: 1153 helix: -0.30 (0.22), residues: 560 sheet: -2.00 (0.53), residues: 95 loop : -1.52 (0.28), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 544 HIS 0.008 0.001 HIS A1042 PHE 0.015 0.001 PHE A 339 TYR 0.014 0.001 TYR A 634 ARG 0.007 0.000 ARG A1186 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 129 time to evaluate : 1.074 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 110 GLU cc_start: 0.7110 (mm-30) cc_final: 0.6832 (mm-30) REVERT: A 531 ASP cc_start: 0.7819 (t0) cc_final: 0.7606 (t0) REVERT: A 635 ILE cc_start: 0.9048 (mm) cc_final: 0.8802 (tp) REVERT: A 676 SER cc_start: 0.9268 (m) cc_final: 0.9013 (p) REVERT: A 730 GLU cc_start: 0.8931 (tp30) cc_final: 0.8637 (tm-30) REVERT: A 872 MET cc_start: 0.7909 (mmm) cc_final: 0.7579 (mmm) REVERT: A 1063 SER cc_start: 0.9268 (t) cc_final: 0.8960 (p) REVERT: A 1150 ASN cc_start: 0.8751 (p0) cc_final: 0.7831 (p0) REVERT: A 1159 MET cc_start: 0.8259 (ttm) cc_final: 0.8006 (ttp) REVERT: A 1175 PHE cc_start: 0.8513 (t80) cc_final: 0.8221 (t80) outliers start: 0 outliers final: 0 residues processed: 129 average time/residue: 0.1798 time to fit residues: 34.4268 Evaluate side-chains 102 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 102 time to evaluate : 0.970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 110 optimal weight: 8.9990 chunk 55 optimal weight: 1.9990 chunk 83 optimal weight: 0.9990 chunk 23 optimal weight: 10.0000 chunk 51 optimal weight: 7.9990 chunk 34 optimal weight: 7.9990 chunk 65 optimal weight: 1.9990 chunk 15 optimal weight: 20.0000 chunk 44 optimal weight: 10.0000 chunk 33 optimal weight: 0.9990 chunk 77 optimal weight: 3.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 897 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.088429 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.067690 restraints weight = 29668.499| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.069791 restraints weight = 16116.636| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.071154 restraints weight = 10865.552| |-----------------------------------------------------------------------------| r_work (final): 0.3276 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3275 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3275 r_free = 0.3275 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3275 r_free = 0.3275 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3275 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8073 moved from start: 0.3812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 9365 Z= 0.207 Angle : 0.640 10.335 12768 Z= 0.312 Chirality : 0.045 0.326 1487 Planarity : 0.004 0.071 1622 Dihedral : 7.488 88.407 1547 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.55 % Favored : 94.45 % Rotamer: Outliers : 0.00 % Allowed : 0.62 % Favored : 99.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.47 (0.25), residues: 1153 helix: -0.31 (0.22), residues: 570 sheet: -2.08 (0.52), residues: 94 loop : -1.44 (0.28), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 544 HIS 0.008 0.001 HIS A1042 PHE 0.023 0.002 PHE A 937 TYR 0.012 0.001 TYR A 102 ARG 0.004 0.000 ARG A1227 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 125 time to evaluate : 1.093 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 110 GLU cc_start: 0.7146 (mm-30) cc_final: 0.6859 (mm-30) REVERT: A 194 PHE cc_start: 0.9006 (m-10) cc_final: 0.8796 (m-80) REVERT: A 531 ASP cc_start: 0.7899 (t0) cc_final: 0.7684 (t0) REVERT: A 635 ILE cc_start: 0.9080 (mm) cc_final: 0.8839 (tp) REVERT: A 676 SER cc_start: 0.9293 (m) cc_final: 0.9058 (p) REVERT: A 730 GLU cc_start: 0.8930 (tp30) cc_final: 0.8627 (tm-30) REVERT: A 834 MET cc_start: 0.7249 (mmm) cc_final: 0.6921 (mmm) REVERT: A 872 MET cc_start: 0.7995 (mmm) cc_final: 0.7646 (mmm) REVERT: A 875 TYR cc_start: 0.8903 (t80) cc_final: 0.8604 (t80) REVERT: A 996 MET cc_start: 0.8405 (ttm) cc_final: 0.8182 (ttp) REVERT: A 1063 SER cc_start: 0.9290 (t) cc_final: 0.8999 (p) REVERT: A 1150 ASN cc_start: 0.8923 (p0) cc_final: 0.8062 (p0) REVERT: A 1175 PHE cc_start: 0.8548 (t80) cc_final: 0.8272 (t80) outliers start: 0 outliers final: 0 residues processed: 125 average time/residue: 0.1902 time to fit residues: 35.8406 Evaluate side-chains 97 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 97 time to evaluate : 0.977 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 29 optimal weight: 9.9990 chunk 114 optimal weight: 5.9990 chunk 100 optimal weight: 4.9990 chunk 28 optimal weight: 8.9990 chunk 99 optimal weight: 0.7980 chunk 67 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 13 optimal weight: 9.9990 chunk 55 optimal weight: 10.0000 chunk 85 optimal weight: 0.6980 chunk 34 optimal weight: 4.9990 overall best weight: 2.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 897 HIS A1239 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.087835 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.067004 restraints weight = 30350.961| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.069104 restraints weight = 16498.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.070480 restraints weight = 11134.145| |-----------------------------------------------------------------------------| r_work (final): 0.3260 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3259 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3259 r_free = 0.3259 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3259 r_free = 0.3259 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3259 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.3897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 9365 Z= 0.225 Angle : 0.664 11.247 12768 Z= 0.322 Chirality : 0.045 0.327 1487 Planarity : 0.004 0.072 1622 Dihedral : 7.514 88.874 1547 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.07 % Favored : 93.93 % Rotamer: Outliers : 0.00 % Allowed : 0.41 % Favored : 99.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.41 (0.24), residues: 1153 helix: -0.23 (0.22), residues: 562 sheet: -1.82 (0.55), residues: 84 loop : -1.50 (0.28), residues: 507 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 544 HIS 0.009 0.001 HIS A1042 PHE 0.022 0.001 PHE A 937 TYR 0.014 0.001 TYR A 634 ARG 0.008 0.001 ARG A 78 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 119 time to evaluate : 1.046 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 110 GLU cc_start: 0.7143 (mm-30) cc_final: 0.6849 (mm-30) REVERT: A 194 PHE cc_start: 0.9017 (m-10) cc_final: 0.8804 (m-80) REVERT: A 531 ASP cc_start: 0.7950 (t0) cc_final: 0.7725 (t0) REVERT: A 632 PHE cc_start: 0.7561 (m-80) cc_final: 0.7304 (m-80) REVERT: A 676 SER cc_start: 0.9312 (m) cc_final: 0.9077 (p) REVERT: A 730 GLU cc_start: 0.8948 (tp30) cc_final: 0.8629 (tm-30) REVERT: A 834 MET cc_start: 0.7241 (mmm) cc_final: 0.6891 (mmm) REVERT: A 872 MET cc_start: 0.7999 (mmm) cc_final: 0.7645 (mmm) REVERT: A 875 TYR cc_start: 0.8928 (t80) cc_final: 0.8676 (t80) REVERT: A 1063 SER cc_start: 0.9282 (t) cc_final: 0.8986 (p) REVERT: A 1138 MET cc_start: 0.9014 (tpp) cc_final: 0.8754 (ttm) REVERT: A 1150 ASN cc_start: 0.8912 (p0) cc_final: 0.8152 (p0) REVERT: A 1175 PHE cc_start: 0.8588 (t80) cc_final: 0.8272 (t80) outliers start: 0 outliers final: 0 residues processed: 119 average time/residue: 0.1726 time to fit residues: 31.3423 Evaluate side-chains 95 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 95 time to evaluate : 1.079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 99 optimal weight: 0.0470 chunk 18 optimal weight: 30.0000 chunk 69 optimal weight: 0.9990 chunk 83 optimal weight: 4.9990 chunk 49 optimal weight: 0.9980 chunk 30 optimal weight: 9.9990 chunk 92 optimal weight: 4.9990 chunk 104 optimal weight: 0.9980 chunk 0 optimal weight: 30.0000 chunk 3 optimal weight: 9.9990 chunk 82 optimal weight: 0.9990 overall best weight: 0.8082 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.089279 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.068601 restraints weight = 29878.603| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.070820 restraints weight = 15898.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.072266 restraints weight = 10527.265| |-----------------------------------------------------------------------------| r_work (final): 0.3299 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3301 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3301 r_free = 0.3301 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3301 r_free = 0.3301 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3301 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8037 moved from start: 0.3971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 9365 Z= 0.154 Angle : 0.626 11.982 12768 Z= 0.301 Chirality : 0.043 0.318 1487 Planarity : 0.004 0.071 1622 Dihedral : 7.101 89.184 1547 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.55 % Favored : 94.45 % Rotamer: Outliers : 0.00 % Allowed : 0.21 % Favored : 99.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.34 (0.24), residues: 1153 helix: -0.14 (0.22), residues: 557 sheet: -1.60 (0.56), residues: 85 loop : -1.54 (0.27), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 544 HIS 0.007 0.001 HIS A1042 PHE 0.021 0.001 PHE A 937 TYR 0.014 0.001 TYR A 102 ARG 0.006 0.000 ARG A 78 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3462.33 seconds wall clock time: 62 minutes 59.41 seconds (3779.41 seconds total)