Starting phenix.real_space_refine on Fri Sep 11 13:16:58 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6uox_20834/09_2026/6uox_20834.cif Found real_map, /net/cci-nas-00/data/ceres_data/6uox_20834/09_2026/6uox_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 { model { file = "/net/cci-nas-00/data/ceres_data/6uox_20834/09_2026/6uox_20834.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6uox_20834/09_2026/6uox_20834.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6uox_20834/09_2026/6uox_20834.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6uox_20834/09_2026/6uox_20834.map" restraint_files = "/net/cci-nas-00/data/ceres_data/6uox_20834/09_2026/6uox_20834.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6uox_20834/09_2026/6uox_20834.cif" } resolution = 4.02 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/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: {'GLU:plan': 2, 'TYR:plan': 5, 'ASP:plan': 3, 'ARG:plan': 1, 'ASN:plan1': 2, 'GLN:plan1': 2, 'PHE:plan': 5, 'HIS:plan': 1, 'TRP:plan': 2} 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: {'GLU:plan': 2, 'TYR:plan': 5, 'ASP:plan': 3, 'ARG:plan': 1, 'ASN:plan1': 2, 'GLN:plan1': 2, 'PHE:plan': 5, 'HIS:plan': 1, 'TRP:plan': 2} 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 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 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 chiralities: 8 Time building chain proxies: 3.34, per 1000 atoms: 0.37 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: 0.76 Conformation dependent library (CDL) restraints added in 335.5 milliseconds 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: 0.31 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: 1.43 Time building geometry restraints manager: 1.01 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 - 18.06: 5133 18.06 - 36.12: 234 36.12 - 54.17: 54 54.17 - 72.23: 8 72.23 - 90.29: 4 Dihedral angle restraints: 5433 sinusoidal: 2057 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 5430 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: 0.010 Normalize map: mean=0, sd=1: 3.830 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: 0.260 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 10.110 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7793 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 9393 Z= 0.650 Angle : 1.203 13.748 12837 Z= 0.755 Chirality : 0.076 0.692 1487 Planarity : 0.005 0.081 1622 Dihedral : 11.225 78.035 3214 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -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 ARG 0.006 0.000 ARG A1227 TYR 0.015 0.002 TYR A 899 PHE 0.017 0.002 PHE A1139 TRP 0.024 0.002 TRP A1145 HIS 0.004 0.001 HIS A 897 Details of bonding type rmsd/Z covalent geometry : bond 0.01009 / 0.65 ( 9365) covalent geometry : angle 1.17884 / 0.75 (12768) SS BOND : bond 0.00482 / 0.40 ( 15) SS BOND : angle 0.94506 / 0.69 ( 30) hydrogen bonds : bond 0.21400 / 14.30 ( 350) hydrogen bonds : angle 8.22126 / 5.66 ( 1014) link_ALPHA1-3 : bond 0.00955 / 0.50 ( 1) link_ALPHA1-3 : angle 3.26971 / 1.75 ( 3) link_BETA1-4 : bond 0.01074 / 0.56 ( 2) link_BETA1-4 : angle 2.97599 / 1.24 ( 6) link_NAG-ASN : bond 0.00932 / 0.65 ( 10) link_NAG-ASN : angle 4.86756 / 3.10 ( 30) *********************** 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 : 0.308 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: 0.8782 (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: 0.8225 (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: 0.0866 time to fit residues: 26.5374 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 : 0.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 108 optimal weight: 7.9990 chunk 49 optimal weight: 2.9990 chunk 97 optimal weight: 0.4980 chunk 113 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 10.0000 chunk 33 optimal weight: 0.8980 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 5.9990 chunk 51 optimal weight: 0.9990 chunk 100 optimal weight: 4.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3603 r_free = 0.3603 target = 0.087390 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.067713 restraints weight = 30404.454| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.069211 restraints weight = 14948.853| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.070095 restraints weight = 10082.554| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.070646 restraints weight = 8740.230| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.070771 restraints weight = 7802.457| |-----------------------------------------------------------------------------| r_work (final): 0.3253 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3252 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3252 r_free = 0.3252 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3252 r_free = 0.3252 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3252 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.2149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9393 Z= 0.147 Angle : 0.729 12.267 12837 Z= 0.358 Chirality : 0.048 0.362 1487 Planarity : 0.005 0.078 1622 Dihedral : 6.263 83.102 1249 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.01 (0.22), residues: 1153 helix: -1.68 (0.19), residues: 560 sheet: -2.10 (0.50), residues: 105 loop : -2.22 (0.26), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 958 TYR 0.015 0.001 TYR A1085 PHE 0.031 0.002 PHE A 937 TRP 0.016 0.002 TRP A1145 HIS 0.003 0.001 HIS A 897 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.15 ( 9365) covalent geometry : angle 0.70478 / 0.35 (12768) SS BOND : bond 0.00791 / 0.72 ( 15) SS BOND : angle 1.45985 / 1.02 ( 30) hydrogen bonds : bond 0.04845 / 3.34 ( 350) hydrogen bonds : angle 5.35810 / 3.82 ( 1014) link_ALPHA1-3 : bond 0.00816 / 0.43 ( 1) link_ALPHA1-3 : angle 1.71791 / 0.94 ( 3) link_BETA1-4 : bond 0.00910 / 0.47 ( 2) link_BETA1-4 : angle 1.48620 / 0.68 ( 6) link_NAG-ASN : bond 0.00582 / 0.36 ( 10) link_NAG-ASN : angle 3.65543 / 2.22 ( 30) *********************** 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 151 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 151 time to evaluate : 0.267 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 106 ASN cc_start: 0.8739 (m-40) cc_final: 0.8234 (m-40) REVERT: A 108 PHE cc_start: 0.8482 (m-80) cc_final: 0.8275 (m-80) REVERT: A 110 GLU cc_start: 0.7663 (mm-30) cc_final: 0.7075 (mm-30) REVERT: A 355 PHE cc_start: 0.8858 (t80) cc_final: 0.8603 (t80) REVERT: A 514 LEU cc_start: 0.9127 (mt) cc_final: 0.8856 (tp) REVERT: A 586 GLU cc_start: 0.8915 (mm-30) cc_final: 0.8699 (mt-10) REVERT: A 593 ASN cc_start: 0.8625 (m-40) cc_final: 0.8375 (p0) REVERT: A 676 SER cc_start: 0.9182 (m) cc_final: 0.8851 (t) REVERT: A 730 GLU cc_start: 0.9225 (tp30) cc_final: 0.8666 (tm-30) REVERT: A 774 LEU cc_start: 0.9426 (tp) cc_final: 0.9212 (tp) REVERT: A 930 ASP cc_start: 0.8514 (p0) cc_final: 0.8261 (t0) REVERT: A 935 ILE cc_start: 0.8182 (mt) cc_final: 0.7844 (mt) REVERT: A 1150 ASN cc_start: 0.8732 (p0) cc_final: 0.8143 (p0) REVERT: A 1156 ASN cc_start: 0.8737 (t0) cc_final: 0.8330 (t0) REVERT: A 1159 MET cc_start: 0.8614 (tpp) cc_final: 0.8025 (ttp) REVERT: A 1175 PHE cc_start: 0.8358 (t80) cc_final: 0.7839 (t80) outliers start: 0 outliers final: 0 residues processed: 151 average time/residue: 0.0709 time to fit residues: 16.1288 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 : 0.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 99 optimal weight: 3.9990 chunk 36 optimal weight: 10.0000 chunk 35 optimal weight: 0.9990 chunk 13 optimal weight: 8.9990 chunk 40 optimal weight: 1.9990 chunk 14 optimal weight: 7.9990 chunk 0 optimal weight: 30.0000 chunk 25 optimal weight: 0.9980 chunk 8 optimal weight: 6.9990 chunk 73 optimal weight: 9.9990 chunk 88 optimal weight: 7.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.087267 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.066423 restraints weight = 29836.260| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.068521 restraints weight = 16376.501| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.069916 restraints weight = 11081.393| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.070829 restraints weight = 8573.822| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.071452 restraints weight = 7252.175| |-----------------------------------------------------------------------------| 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) = 0.071 | | 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) = 0.071 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3277 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8081 moved from start: 0.2617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 9393 Z= 0.192 Angle : 0.729 10.730 12837 Z= 0.359 Chirality : 0.047 0.331 1487 Planarity : 0.005 0.075 1622 Dihedral : 6.003 66.035 1249 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.64 (0.22), residues: 1153 helix: -1.28 (0.19), residues: 571 sheet: -2.64 (0.48), residues: 100 loop : -1.99 (0.27), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A1227 TYR 0.013 0.002 TYR A1037 PHE 0.044 0.002 PHE A 632 TRP 0.020 0.002 TRP A 583 HIS 0.011 0.002 HIS A1042 Details of bonding type rmsd/Z covalent geometry : bond 0.00436 / 0.19 ( 9365) covalent geometry : angle 0.70457 / 0.35 (12768) SS BOND : bond 0.00766 / 0.46 ( 15) SS BOND : angle 1.96386 / 1.41 ( 30) hydrogen bonds : bond 0.04229 / 2.83 ( 350) hydrogen bonds : angle 5.08153 / 3.64 ( 1014) link_ALPHA1-3 : bond 0.00874 / 0.46 ( 1) link_ALPHA1-3 : angle 1.56850 / 0.88 ( 3) link_BETA1-4 : bond 0.00676 / 0.34 ( 2) link_BETA1-4 : angle 1.35379 / 0.67 ( 6) link_NAG-ASN : bond 0.00365 / 0.23 ( 10) link_NAG-ASN : angle 3.41116 / 2.11 ( 30) *********************** 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 137 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 137 time to evaluate : 0.364 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 ASP cc_start: 0.8799 (p0) cc_final: 0.8593 (m-30) REVERT: A 632 PHE cc_start: 0.7939 (m-80) cc_final: 0.7694 (m-80) REVERT: A 676 SER cc_start: 0.9307 (m) cc_final: 0.8997 (t) REVERT: A 730 GLU cc_start: 0.9040 (tp30) cc_final: 0.8640 (tm-30) REVERT: A 742 GLU cc_start: 0.8085 (pp20) cc_final: 0.7849 (pp20) REVERT: A 834 MET cc_start: 0.7427 (mmp) cc_final: 0.7109 (mmt) REVERT: A 935 ILE cc_start: 0.8303 (mt) cc_final: 0.8045 (mt) REVERT: A 996 MET cc_start: 0.9134 (mtp) cc_final: 0.8914 (ttm) REVERT: A 1150 ASN cc_start: 0.8913 (p0) cc_final: 0.8301 (p0) REVERT: A 1159 MET cc_start: 0.8502 (tpp) cc_final: 0.8233 (ttp) REVERT: A 1166 GLU cc_start: 0.8141 (tp30) cc_final: 0.7735 (tp30) REVERT: A 1175 PHE cc_start: 0.8381 (t80) cc_final: 0.7787 (t80) REVERT: A 1179 MET cc_start: 0.7725 (pmm) cc_final: 0.7432 (mmm) outliers start: 0 outliers final: 0 residues processed: 137 average time/residue: 0.0750 time to fit residues: 15.8286 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 : 0.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 88 optimal weight: 0.9980 chunk 75 optimal weight: 5.9990 chunk 24 optimal weight: 10.0000 chunk 104 optimal weight: 2.9990 chunk 94 optimal weight: 0.8980 chunk 9 optimal weight: 7.9990 chunk 5 optimal weight: 5.9990 chunk 80 optimal weight: 4.9990 chunk 4 optimal weight: 0.9990 chunk 39 optimal weight: 0.9990 chunk 35 optimal weight: 0.6980 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 568 ASN A 775 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.089249 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.068365 restraints weight = 29394.826| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.070586 restraints weight = 15424.599| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.072089 restraints weight = 10181.726| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.073070 restraints weight = 7745.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 54)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.073723 restraints weight = 6483.212| |-----------------------------------------------------------------------------| r_work (final): 0.3331 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3331 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3331 r_free = 0.3331 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3331 r_free = 0.3331 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3331 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8011 moved from start: 0.2841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9393 Z= 0.117 Angle : 0.651 9.650 12837 Z= 0.318 Chirality : 0.044 0.319 1487 Planarity : 0.004 0.075 1622 Dihedral : 5.715 68.056 1249 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.26 (0.23), residues: 1153 helix: -0.90 (0.20), residues: 559 sheet: -2.42 (0.48), residues: 105 loop : -1.89 (0.27), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 116 TYR 0.010 0.001 TYR A1037 PHE 0.040 0.001 PHE A 632 TRP 0.014 0.001 TRP A 583 HIS 0.009 0.001 HIS A1042 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.12 ( 9365) covalent geometry : angle 0.63185 / 0.31 (12768) SS BOND : bond 0.00489 / 0.31 ( 15) SS BOND : angle 1.31111 / 1.02 ( 30) hydrogen bonds : bond 0.03639 / 2.48 ( 350) hydrogen bonds : angle 4.75328 / 3.40 ( 1014) link_ALPHA1-3 : bond 0.00726 / 0.38 ( 1) link_ALPHA1-3 : angle 1.49614 / 0.84 ( 3) link_BETA1-4 : bond 0.00616 / 0.31 ( 2) link_BETA1-4 : angle 1.28851 / 0.62 ( 6) link_NAG-ASN : bond 0.00503 / 0.32 ( 10) link_NAG-ASN : angle 3.05181 / 1.86 ( 30) *********************** 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 140 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 140 time to evaluate : 0.471 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 106 ASN cc_start: 0.8520 (m-40) cc_final: 0.8314 (m-40) REVERT: A 514 LEU cc_start: 0.9057 (mt) cc_final: 0.8786 (tp) REVERT: A 676 SER cc_start: 0.9293 (m) cc_final: 0.9018 (p) REVERT: A 699 VAL cc_start: 0.9031 (m) cc_final: 0.8828 (t) REVERT: A 730 GLU cc_start: 0.9003 (tp30) cc_final: 0.8647 (tm-30) REVERT: A 875 TYR cc_start: 0.8741 (t80) cc_final: 0.8318 (t80) REVERT: A 935 ILE cc_start: 0.8374 (mt) cc_final: 0.8143 (mt) REVERT: A 945 ASP cc_start: 0.8593 (t70) cc_final: 0.8385 (t70) REVERT: A 996 MET cc_start: 0.9038 (mtp) cc_final: 0.8828 (ttm) REVERT: A 998 PHE cc_start: 0.8810 (m-80) cc_final: 0.8494 (m-80) REVERT: A 1150 ASN cc_start: 0.8802 (p0) cc_final: 0.8210 (p0) REVERT: A 1175 PHE cc_start: 0.8375 (t80) cc_final: 0.7780 (t80) outliers start: 0 outliers final: 0 residues processed: 140 average time/residue: 0.0744 time to fit residues: 15.8653 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 : 0.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 25 optimal weight: 5.9990 chunk 44 optimal weight: 6.9990 chunk 58 optimal weight: 10.0000 chunk 20 optimal weight: 20.0000 chunk 26 optimal weight: 20.0000 chunk 103 optimal weight: 0.9990 chunk 106 optimal weight: 0.9990 chunk 82 optimal weight: 3.9990 chunk 107 optimal weight: 5.9990 chunk 79 optimal weight: 2.9990 chunk 60 optimal weight: 0.6980 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.088306 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.067615 restraints weight = 29632.704| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.069681 restraints weight = 16222.495| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.071093 restraints weight = 10974.400| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.071955 restraints weight = 8469.159| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.072583 restraints weight = 7207.772| |-----------------------------------------------------------------------------| r_work (final): 0.3310 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3310 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3310 r_free = 0.3310 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 = 0.3310 r_free = 0.3310 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3310 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8044 moved from start: 0.3058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 9393 Z= 0.142 Angle : 0.656 10.082 12837 Z= 0.319 Chirality : 0.045 0.321 1487 Planarity : 0.005 0.074 1622 Dihedral : 5.605 64.580 1249 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.02 (0.24), residues: 1153 helix: -0.72 (0.21), residues: 560 sheet: -2.39 (0.50), residues: 99 loop : -1.72 (0.27), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1227 TYR 0.024 0.001 TYR A 192 PHE 0.025 0.002 PHE A 937 TRP 0.013 0.002 TRP A1145 HIS 0.010 0.001 HIS A1042 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.14 ( 9365) covalent geometry : angle 0.63798 / 0.31 (12768) SS BOND : bond 0.00383 / 0.26 ( 15) SS BOND : angle 1.26008 / 0.97 ( 30) hydrogen bonds : bond 0.03488 / 2.35 ( 350) hydrogen bonds : angle 4.72512 / 3.38 ( 1014) link_ALPHA1-3 : bond 0.00584 / 0.31 ( 1) link_ALPHA1-3 : angle 1.39273 / 0.78 ( 3) link_BETA1-4 : bond 0.00637 / 0.32 ( 2) link_BETA1-4 : angle 1.28877 / 0.65 ( 6) link_NAG-ASN : bond 0.00398 / 0.25 ( 10) link_NAG-ASN : angle 2.94170 / 1.80 ( 30) *********************** 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 134 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 134 time to evaluate : 0.367 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 632 PHE cc_start: 0.7711 (m-80) cc_final: 0.7253 (m-80) REVERT: A 676 SER cc_start: 0.9269 (m) cc_final: 0.9006 (p) REVERT: A 692 PHE cc_start: 0.8314 (t80) cc_final: 0.8082 (t80) REVERT: A 730 GLU cc_start: 0.8945 (tp30) cc_final: 0.8618 (tm-30) REVERT: A 875 TYR cc_start: 0.8761 (t80) cc_final: 0.8256 (t80) REVERT: A 945 ASP cc_start: 0.8609 (t70) cc_final: 0.8376 (t70) REVERT: A 996 MET cc_start: 0.9047 (mtp) cc_final: 0.8801 (ttm) REVERT: A 998 PHE cc_start: 0.8698 (m-80) cc_final: 0.8409 (m-10) REVERT: A 1063 SER cc_start: 0.9339 (t) cc_final: 0.8994 (p) REVERT: A 1150 ASN cc_start: 0.8844 (p0) cc_final: 0.7976 (p0) REVERT: A 1175 PHE cc_start: 0.8467 (t80) cc_final: 0.8095 (t80) outliers start: 0 outliers final: 0 residues processed: 134 average time/residue: 0.0776 time to fit residues: 16.4040 Evaluate side-chains 104 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 104 time to evaluate : 0.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 13 optimal weight: 10.0000 chunk 114 optimal weight: 4.9990 chunk 115 optimal weight: 6.9990 chunk 40 optimal weight: 0.0470 chunk 71 optimal weight: 0.9990 chunk 59 optimal weight: 7.9990 chunk 17 optimal weight: 20.0000 chunk 31 optimal weight: 5.9990 chunk 33 optimal weight: 0.1980 chunk 103 optimal weight: 2.9990 chunk 65 optimal weight: 7.9990 overall best weight: 1.8484 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 775 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.088160 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.067478 restraints weight = 29961.298| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.069574 restraints weight = 16185.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.070997 restraints weight = 10907.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.071957 restraints weight = 8405.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.072502 restraints weight = 7065.522| |-----------------------------------------------------------------------------| r_work (final): 0.3310 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3310 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3310 r_free = 0.3310 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 = 0.3310 r_free = 0.3310 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3310 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8046 moved from start: 0.3198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 9393 Z= 0.136 Angle : 0.641 9.255 12837 Z= 0.313 Chirality : 0.044 0.322 1487 Planarity : 0.004 0.074 1622 Dihedral : 5.498 60.846 1249 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 6.03 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.86 (0.24), residues: 1153 helix: -0.63 (0.21), residues: 567 sheet: -2.21 (0.52), residues: 94 loop : -1.63 (0.28), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1227 TYR 0.014 0.001 TYR A 192 PHE 0.024 0.002 PHE A 108 TRP 0.012 0.001 TRP A1145 HIS 0.009 0.001 HIS A1042 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.14 ( 9365) covalent geometry : angle 0.62512 / 0.31 (12768) SS BOND : bond 0.00320 / 0.21 ( 15) SS BOND : angle 1.16376 / 0.89 ( 30) hydrogen bonds : bond 0.03406 / 2.28 ( 350) hydrogen bonds : angle 4.61002 / 3.28 ( 1014) link_ALPHA1-3 : bond 0.00791 / 0.42 ( 1) link_ALPHA1-3 : angle 1.48190 / 0.83 ( 3) link_BETA1-4 : bond 0.00630 / 0.32 ( 2) link_BETA1-4 : angle 1.28991 / 0.65 ( 6) link_NAG-ASN : bond 0.00400 / 0.25 ( 10) link_NAG-ASN : angle 2.77074 / 1.69 ( 30) *********************** 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 136 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 136 time to evaluate : 0.364 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 106 ASN cc_start: 0.8608 (m-40) cc_final: 0.8294 (m-40) REVERT: A 514 LEU cc_start: 0.9051 (mt) cc_final: 0.8774 (tp) REVERT: A 531 ASP cc_start: 0.7881 (t0) cc_final: 0.7626 (t0) REVERT: A 632 PHE cc_start: 0.7603 (m-80) cc_final: 0.7296 (m-80) REVERT: A 676 SER cc_start: 0.9276 (m) cc_final: 0.9012 (p) REVERT: A 730 GLU cc_start: 0.8962 (tp30) cc_final: 0.8623 (tm-30) REVERT: A 735 MET cc_start: 0.8035 (ttp) cc_final: 0.7598 (ttm) REVERT: A 772 PHE cc_start: 0.7527 (t80) cc_final: 0.7274 (t80) REVERT: A 875 TYR cc_start: 0.8768 (t80) cc_final: 0.8318 (t80) REVERT: A 945 ASP cc_start: 0.8638 (t70) cc_final: 0.8392 (t70) REVERT: A 996 MET cc_start: 0.9026 (mtp) cc_final: 0.8756 (ttm) REVERT: A 998 PHE cc_start: 0.8669 (m-80) cc_final: 0.8385 (m-10) REVERT: A 1063 SER cc_start: 0.9317 (t) cc_final: 0.8986 (p) REVERT: A 1150 ASN cc_start: 0.8863 (p0) cc_final: 0.8211 (p0) REVERT: A 1175 PHE cc_start: 0.8490 (t80) cc_final: 0.8124 (t80) outliers start: 0 outliers final: 0 residues processed: 136 average time/residue: 0.0798 time to fit residues: 16.4700 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 : 0.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 40 optimal weight: 3.9990 chunk 5 optimal weight: 10.0000 chunk 58 optimal weight: 2.9990 chunk 72 optimal weight: 2.9990 chunk 32 optimal weight: 4.9990 chunk 93 optimal weight: 2.9990 chunk 20 optimal weight: 20.0000 chunk 29 optimal weight: 0.8980 chunk 115 optimal weight: 0.8980 chunk 30 optimal weight: 2.9990 chunk 60 optimal weight: 0.7980 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.088357 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.067770 restraints weight = 30567.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.069950 restraints weight = 16288.115| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.071414 restraints weight = 10874.977| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.072370 restraints weight = 8317.564| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.072934 restraints weight = 7000.349| |-----------------------------------------------------------------------------| r_work (final): 0.3313 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3314 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3314 r_free = 0.3314 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 = 0.3314 r_free = 0.3314 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3314 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8038 moved from start: 0.3345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 9393 Z= 0.133 Angle : 0.652 8.843 12837 Z= 0.314 Chirality : 0.045 0.324 1487 Planarity : 0.004 0.073 1622 Dihedral : 5.538 73.541 1249 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 0.00 % Allowed : 0.52 % Favored : 99.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.78 (0.24), residues: 1153 helix: -0.56 (0.21), residues: 570 sheet: -2.16 (0.52), residues: 94 loop : -1.61 (0.28), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1227 TYR 0.013 0.001 TYR A 192 PHE 0.027 0.001 PHE A 937 TRP 0.016 0.001 TRP A 544 HIS 0.009 0.001 HIS A1042 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.13 ( 9365) covalent geometry : angle 0.63730 / 0.31 (12768) SS BOND : bond 0.00343 / 0.20 ( 15) SS BOND : angle 1.16333 / 0.89 ( 30) hydrogen bonds : bond 0.03345 / 2.27 ( 350) hydrogen bonds : angle 4.66110 / 3.36 ( 1014) link_ALPHA1-3 : bond 0.00721 / 0.38 ( 1) link_ALPHA1-3 : angle 1.46581 / 0.82 ( 3) link_BETA1-4 : bond 0.00640 / 0.33 ( 2) link_BETA1-4 : angle 1.27912 / 0.65 ( 6) link_NAG-ASN : bond 0.00401 / 0.25 ( 10) link_NAG-ASN : angle 2.66425 / 1.62 ( 30) *********************** 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 134 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 134 time to evaluate : 0.358 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 110 GLU cc_start: 0.7245 (mm-30) cc_final: 0.6986 (mm-30) REVERT: A 514 LEU cc_start: 0.9081 (mt) cc_final: 0.8795 (tp) REVERT: A 531 ASP cc_start: 0.7945 (t0) cc_final: 0.7697 (t0) REVERT: A 632 PHE cc_start: 0.7691 (m-80) cc_final: 0.7466 (m-80) REVERT: A 676 SER cc_start: 0.9269 (m) cc_final: 0.8991 (p) REVERT: A 730 GLU cc_start: 0.8988 (tp30) cc_final: 0.8637 (tm-30) REVERT: A 875 TYR cc_start: 0.8805 (t80) cc_final: 0.8349 (t80) REVERT: A 907 MET cc_start: 0.8215 (mmm) cc_final: 0.7973 (mmm) REVERT: A 945 ASP cc_start: 0.8661 (t70) cc_final: 0.8410 (t70) REVERT: A 996 MET cc_start: 0.8968 (mtp) cc_final: 0.8687 (ttm) REVERT: A 1063 SER cc_start: 0.9342 (t) cc_final: 0.9012 (p) REVERT: A 1150 ASN cc_start: 0.8846 (p0) cc_final: 0.7972 (p0) REVERT: A 1166 GLU cc_start: 0.8171 (tp30) cc_final: 0.7892 (tp30) REVERT: A 1175 PHE cc_start: 0.8464 (t80) cc_final: 0.8097 (t80) outliers start: 0 outliers final: 0 residues processed: 134 average time/residue: 0.0754 time to fit residues: 15.5704 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 : 0.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 30 optimal weight: 6.9990 chunk 111 optimal weight: 2.9990 chunk 99 optimal weight: 3.9990 chunk 57 optimal weight: 1.9990 chunk 47 optimal weight: 0.5980 chunk 91 optimal weight: 1.9990 chunk 24 optimal weight: 9.9990 chunk 92 optimal weight: 7.9990 chunk 100 optimal weight: 4.9990 chunk 108 optimal weight: 5.9990 chunk 16 optimal weight: 2.9990 overall best weight: 2.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.087755 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.066957 restraints weight = 30207.169| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.069112 restraints weight = 16316.377| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.070552 restraints weight = 10880.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.071404 restraints weight = 8336.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 47)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.072070 restraints weight = 7069.506| |-----------------------------------------------------------------------------| r_work (final): 0.3302 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3301 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3301 r_free = 0.3301 target_work(ls_wunit_k1) = 0.071 | | 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) = 0.071 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3301 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 moved from start: 0.3475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9393 Z= 0.148 Angle : 0.657 11.757 12837 Z= 0.321 Chirality : 0.045 0.324 1487 Planarity : 0.004 0.073 1622 Dihedral : 5.438 74.375 1249 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.55 % Favored : 94.45 % Rotamer: Outliers : 0.00 % Allowed : 0.52 % Favored : 99.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.73 (0.24), residues: 1153 helix: -0.52 (0.21), residues: 571 sheet: -2.18 (0.52), residues: 94 loop : -1.57 (0.28), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1227 TYR 0.012 0.001 TYR A 102 PHE 0.016 0.001 PHE A1243 TRP 0.011 0.001 TRP A 544 HIS 0.010 0.001 HIS A1042 Details of bonding type rmsd/Z covalent geometry : bond 0.00340 / 0.15 ( 9365) covalent geometry : angle 0.64289 / 0.32 (12768) SS BOND : bond 0.00309 / 0.20 ( 15) SS BOND : angle 1.22639 / 0.93 ( 30) hydrogen bonds : bond 0.03431 / 2.32 ( 350) hydrogen bonds : angle 4.73917 / 3.43 ( 1014) link_ALPHA1-3 : bond 0.00680 / 0.36 ( 1) link_ALPHA1-3 : angle 1.44121 / 0.81 ( 3) link_BETA1-4 : bond 0.00653 / 0.33 ( 2) link_BETA1-4 : angle 1.30966 / 0.67 ( 6) link_NAG-ASN : bond 0.00351 / 0.22 ( 10) link_NAG-ASN : angle 2.58873 / 1.58 ( 30) *********************** 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 : 0.350 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 110 GLU cc_start: 0.7173 (mm-30) cc_final: 0.6900 (mm-30) REVERT: A 514 LEU cc_start: 0.9057 (mt) cc_final: 0.8775 (tp) REVERT: A 531 ASP cc_start: 0.7947 (t0) cc_final: 0.7725 (t0) REVERT: A 632 PHE cc_start: 0.7651 (m-80) cc_final: 0.7341 (m-80) REVERT: A 676 SER cc_start: 0.9296 (m) cc_final: 0.9036 (p) REVERT: A 730 GLU cc_start: 0.8963 (tp30) cc_final: 0.8621 (tm-30) REVERT: A 875 TYR cc_start: 0.8799 (t80) cc_final: 0.8308 (t80) REVERT: A 945 ASP cc_start: 0.8664 (t70) cc_final: 0.8412 (t70) REVERT: A 996 MET cc_start: 0.8996 (mtp) cc_final: 0.8696 (ttm) REVERT: A 1063 SER cc_start: 0.9309 (t) cc_final: 0.8992 (p) REVERT: A 1150 ASN cc_start: 0.8901 (p0) cc_final: 0.8028 (p0) REVERT: A 1166 GLU cc_start: 0.8131 (tp30) cc_final: 0.7777 (tp30) REVERT: A 1175 PHE cc_start: 0.8543 (t80) cc_final: 0.8182 (t80) outliers start: 0 outliers final: 0 residues processed: 129 average time/residue: 0.0721 time to fit residues: 14.2740 Evaluate side-chains 96 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 96 time to evaluate : 0.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 16 optimal weight: 0.9990 chunk 64 optimal weight: 3.9990 chunk 26 optimal weight: 0.3980 chunk 92 optimal weight: 7.9990 chunk 74 optimal weight: 4.9990 chunk 97 optimal weight: 10.0000 chunk 77 optimal weight: 4.9990 chunk 36 optimal weight: 0.6980 chunk 113 optimal weight: 4.9990 chunk 115 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 overall best weight: 1.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 897 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.089020 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.068320 restraints weight = 30027.872| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.070497 restraints weight = 16080.378| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.071939 restraints weight = 10731.662| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.072883 restraints weight = 8246.726| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.073443 restraints weight = 6929.655| |-----------------------------------------------------------------------------| r_work (final): 0.3327 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3327 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3327 r_free = 0.3327 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3327 r_free = 0.3327 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3327 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8025 moved from start: 0.3591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 9393 Z= 0.118 Angle : 0.634 10.871 12837 Z= 0.309 Chirality : 0.044 0.320 1487 Planarity : 0.004 0.072 1622 Dihedral : 5.357 67.904 1249 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 0.00 % Allowed : 0.52 % Favored : 99.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.59 (0.24), residues: 1153 helix: -0.39 (0.21), residues: 571 sheet: -2.01 (0.53), residues: 94 loop : -1.56 (0.28), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1227 TYR 0.013 0.001 TYR A1229 PHE 0.028 0.001 PHE A 998 TRP 0.015 0.001 TRP A 544 HIS 0.008 0.001 HIS A1042 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.12 ( 9365) covalent geometry : angle 0.62140 / 0.31 (12768) SS BOND : bond 0.00305 / 0.19 ( 15) SS BOND : angle 1.10364 / 0.83 ( 30) hydrogen bonds : bond 0.03248 / 2.20 ( 350) hydrogen bonds : angle 4.67044 / 3.39 ( 1014) link_ALPHA1-3 : bond 0.00702 / 0.37 ( 1) link_ALPHA1-3 : angle 1.44053 / 0.81 ( 3) link_BETA1-4 : bond 0.00567 / 0.29 ( 2) link_BETA1-4 : angle 1.24219 / 0.63 ( 6) link_NAG-ASN : bond 0.00444 / 0.28 ( 10) link_NAG-ASN : angle 2.46846 / 1.48 ( 30) *********************** 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 134 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 134 time to evaluate : 0.360 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 110 GLU cc_start: 0.7140 (mm-30) cc_final: 0.6857 (mm-30) REVERT: A 514 LEU cc_start: 0.9054 (mt) cc_final: 0.8783 (tp) REVERT: A 531 ASP cc_start: 0.7900 (t0) cc_final: 0.7695 (t0) REVERT: A 632 PHE cc_start: 0.7618 (m-80) cc_final: 0.7318 (m-80) REVERT: A 676 SER cc_start: 0.9305 (m) cc_final: 0.9068 (p) REVERT: A 720 LEU cc_start: 0.8755 (pt) cc_final: 0.8398 (tp) REVERT: A 730 GLU cc_start: 0.8918 (tp30) cc_final: 0.8608 (tm-30) REVERT: A 875 TYR cc_start: 0.8728 (t80) cc_final: 0.8297 (t80) REVERT: A 945 ASP cc_start: 0.8668 (t70) cc_final: 0.8394 (t70) REVERT: A 996 MET cc_start: 0.9000 (mtp) cc_final: 0.8736 (ttm) REVERT: A 1063 SER cc_start: 0.9263 (t) cc_final: 0.8975 (p) REVERT: A 1150 ASN cc_start: 0.8858 (p0) cc_final: 0.8015 (p0) REVERT: A 1166 GLU cc_start: 0.8032 (tp30) cc_final: 0.7619 (tp30) REVERT: A 1175 PHE cc_start: 0.8493 (t80) cc_final: 0.8108 (t80) outliers start: 0 outliers final: 0 residues processed: 134 average time/residue: 0.0745 time to fit residues: 15.3028 Evaluate side-chains 99 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 99 time to evaluate : 0.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 106 optimal weight: 2.9990 chunk 36 optimal weight: 0.0980 chunk 57 optimal weight: 4.9990 chunk 14 optimal weight: 10.0000 chunk 27 optimal weight: 8.9990 chunk 51 optimal weight: 7.9990 chunk 35 optimal weight: 10.0000 chunk 56 optimal weight: 5.9990 chunk 103 optimal weight: 1.9990 chunk 65 optimal weight: 0.9980 chunk 63 optimal weight: 3.9990 overall best weight: 2.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A1239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.087794 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.066993 restraints weight = 30021.921| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.069124 restraints weight = 16228.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.070550 restraints weight = 10819.492| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.071479 restraints weight = 8342.466| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.072017 restraints weight = 7031.328| |-----------------------------------------------------------------------------| r_work (final): 0.3298 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3297 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3297 r_free = 0.3297 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3297 r_free = 0.3297 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3297 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 moved from start: 0.3712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 9393 Z= 0.144 Angle : 0.660 11.535 12837 Z= 0.322 Chirality : 0.045 0.321 1487 Planarity : 0.004 0.072 1622 Dihedral : 5.391 83.946 1249 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.81 % Favored : 94.19 % Rotamer: Outliers : 0.00 % Allowed : 0.10 % Favored : 99.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.50 (0.24), residues: 1153 helix: -0.32 (0.22), residues: 573 sheet: -1.95 (0.53), residues: 91 loop : -1.52 (0.28), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1227 TYR 0.013 0.001 TYR A 102 PHE 0.017 0.001 PHE A1139 TRP 0.011 0.002 TRP A 544 HIS 0.009 0.001 HIS A1042 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.14 ( 9365) covalent geometry : angle 0.64830 / 0.32 (12768) SS BOND : bond 0.00338 / 0.21 ( 15) SS BOND : angle 1.11110 / 0.84 ( 30) hydrogen bonds : bond 0.03343 / 2.24 ( 350) hydrogen bonds : angle 4.70576 / 3.42 ( 1014) link_ALPHA1-3 : bond 0.00794 / 0.42 ( 1) link_ALPHA1-3 : angle 1.47644 / 0.83 ( 3) link_BETA1-4 : bond 0.00566 / 0.29 ( 2) link_BETA1-4 : angle 1.23563 / 0.63 ( 6) link_NAG-ASN : bond 0.00346 / 0.22 ( 10) link_NAG-ASN : angle 2.44259 / 1.48 ( 30) ********************** 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 : 0.386 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 110 GLU cc_start: 0.7161 (mm-30) cc_final: 0.6864 (mm-30) REVERT: A 514 LEU cc_start: 0.9055 (mt) cc_final: 0.8772 (tp) REVERT: A 531 ASP cc_start: 0.7937 (t0) cc_final: 0.7702 (t0) REVERT: A 632 PHE cc_start: 0.7632 (m-80) cc_final: 0.7322 (m-80) REVERT: A 676 SER cc_start: 0.9340 (m) cc_final: 0.9087 (p) REVERT: A 720 LEU cc_start: 0.8758 (pt) cc_final: 0.8407 (tp) REVERT: A 730 GLU cc_start: 0.8946 (tp30) cc_final: 0.8596 (tm-30) REVERT: A 875 TYR cc_start: 0.8766 (t80) cc_final: 0.8305 (t80) REVERT: A 996 MET cc_start: 0.9076 (mtp) cc_final: 0.8720 (ttm) REVERT: A 1063 SER cc_start: 0.9309 (t) cc_final: 0.8999 (p) REVERT: A 1150 ASN cc_start: 0.8913 (p0) cc_final: 0.8046 (p0) REVERT: A 1166 GLU cc_start: 0.8123 (tp30) cc_final: 0.7774 (tp30) REVERT: A 1175 PHE cc_start: 0.8539 (t80) cc_final: 0.8218 (t80) REVERT: A 1232 MET cc_start: 0.7946 (ttp) cc_final: 0.7721 (ttp) outliers start: 0 outliers final: 0 residues processed: 119 average time/residue: 0.0798 time to fit residues: 14.5109 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 : 0.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 108 optimal weight: 7.9990 chunk 54 optimal weight: 2.9990 chunk 34 optimal weight: 4.9990 chunk 17 optimal weight: 1.9990 chunk 110 optimal weight: 6.9990 chunk 89 optimal weight: 7.9990 chunk 67 optimal weight: 5.9990 chunk 49 optimal weight: 0.9990 chunk 40 optimal weight: 0.9980 chunk 33 optimal weight: 4.9990 chunk 101 optimal weight: 4.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1156 ASN A1239 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.087087 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.066336 restraints weight = 30175.344| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.068381 restraints weight = 16357.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.069805 restraints weight = 11042.161| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.070760 restraints weight = 8500.709| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.071383 restraints weight = 7160.401| |-----------------------------------------------------------------------------| r_work (final): 0.3285 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3285 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3285 r_free = 0.3285 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3285 r_free = 0.3285 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3285 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 moved from start: 0.3841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 9393 Z= 0.159 Angle : 0.672 11.142 12837 Z= 0.327 Chirality : 0.045 0.325 1487 Planarity : 0.004 0.072 1622 Dihedral : 5.506 87.916 1249 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.16 % Favored : 93.84 % 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 : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.44 (0.25), residues: 1153 helix: -0.23 (0.22), residues: 565 sheet: -1.84 (0.55), residues: 84 loop : -1.56 (0.28), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A1227 TYR 0.014 0.001 TYR A 102 PHE 0.027 0.002 PHE A 937 TRP 0.017 0.002 TRP A 544 HIS 0.008 0.001 HIS A1042 Details of bonding type rmsd/Z covalent geometry : bond 0.00365 / 0.16 ( 9365) covalent geometry : angle 0.66011 / 0.32 (12768) SS BOND : bond 0.00330 / 0.21 ( 15) SS BOND : angle 1.14099 / 0.88 ( 30) hydrogen bonds : bond 0.03402 / 2.28 ( 350) hydrogen bonds : angle 4.75916 / 3.45 ( 1014) link_ALPHA1-3 : bond 0.00660 / 0.35 ( 1) link_ALPHA1-3 : angle 1.40191 / 0.79 ( 3) link_BETA1-4 : bond 0.00638 / 0.33 ( 2) link_BETA1-4 : angle 1.25368 / 0.64 ( 6) link_NAG-ASN : bond 0.00319 / 0.20 ( 10) link_NAG-ASN : angle 2.45825 / 1.50 ( 30) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1908.43 seconds wall clock time: 33 minutes 32.03 seconds (2012.03 seconds total)