Starting phenix.real_space_refine on Sun Jul 27 17:09:44 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6uox_20834/07_2025/6uox_20834.cif Found real_map, /net/cci-nas-00/data/ceres_data/6uox_20834/07_2025/6uox_20834.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.02 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6uox_20834/07_2025/6uox_20834.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6uox_20834/07_2025/6uox_20834.map" model { file = "/net/cci-nas-00/data/ceres_data/6uox_20834/07_2025/6uox_20834.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6uox_20834/07_2025/6uox_20834.cif" } resolution = 4.02 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Br 1 7.06 5 S 68 5.16 5 Cl 2 4.86 5 C 5882 2.51 5 N 1468 2.21 5 O 1717 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 9138 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 8909 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1161, 8907 Classifications: {'peptide': 1161} Incomplete info: {'truncation_to_alanine': 46} Link IDs: {'PTRANS': 62, 'TRANS': 1098} Chain breaks: 3 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 200 Unresolved non-hydrogen angles: 262 Unresolved non-hydrogen dihedrals: 180 Unresolved non-hydrogen chiralities: 14 Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 1, 'TYR:plan': 5, 'ASN:plan1': 2, 'TRP:plan': 2, 'ASP:plan': 3, 'PHE:plan': 5, 'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 124 Conformer: "B" Number of residues, atoms: 1161, 8907 Classifications: {'peptide': 1161} Incomplete info: {'truncation_to_alanine': 46} Link IDs: {'PTRANS': 62, 'TRANS': 1098} Chain breaks: 3 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 200 Unresolved non-hydrogen angles: 262 Unresolved non-hydrogen dihedrals: 180 Unresolved non-hydrogen chiralities: 14 Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 1, 'TYR:plan': 5, 'ASN:plan1': 2, 'TRP:plan': 2, 'ASP:plan': 3, 'PHE:plan': 5, 'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 124 bond proxies already assigned to first conformer: 9126 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 162 Unusual residues: {'NAG': 8, 'QDG': 1} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Time building chain proxies: 11.32, per 1000 atoms: 1.24 Number of scatterers: 9138 At special positions: 0 Unit cell: (112.86, 145.2, 114.84, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Br 1 34.99 Cl 2 17.00 S 68 16.00 O 1717 8.00 N 1468 7.00 C 5882 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=15, symmetry=0 Simple disulfide: pdb=" SG CYS A 25 " - pdb=" SG CYS A 74 " distance=2.03 Simple disulfide: pdb=" SG CYS A 31 " - pdb=" SG CYS A 42 " distance=2.03 Simple disulfide: pdb=" SG CYS A 63 " - pdb=" SG CYS A 109 " distance=2.03 Simple disulfide: pdb=" SG CYS A 75 " - pdb=" SG CYS A 113 " distance=2.03 Simple disulfide: pdb=" SG CYS A 97 " - pdb=" SG CYS A 238 " distance=2.04 Simple disulfide: pdb=" SG CYS A 100 " - pdb=" SG CYS A 160 " distance=2.03 Simple disulfide: pdb=" SG CYS A 177 " - pdb=" SG CYS A 184 " distance=2.04 Simple disulfide: pdb=" SG CYS A 227 " - pdb=" SG CYS A 243 " distance=2.03 Simple disulfide: pdb=" SG CYS A 240 " - pdb=" SG CYS A 247 " distance=2.03 Simple disulfide: pdb=" SG CYS A 468 " - pdb=" SG CYS A 479 " distance=2.03 Simple disulfide: pdb=" SG CYS A 516 " - pdb=" SG CYS A 533 " distance=2.03 Simple disulfide: pdb=" SG CYS A 909 " - pdb=" SG CYS A 914 " distance=2.03 Simple disulfide: pdb=" SG CYS A 956 " - pdb=" SG CYS A1011 " distance=2.03 Simple disulfide: pdb=" SG CYS A 957 " - pdb=" SG CYS A 979 " distance=2.03 Simple disulfide: pdb=" SG CYS A 967 " - pdb=" SG CYS A 976 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " NAG C 2 " - " MAN C 3 " BETA1-4 " NAG B 1 " - " NAG B 2 " " NAG C 1 " - " NAG C 2 " NAG-ASN " NAG A1301 " - " ASN A 452 " " NAG A1302 " - " ASN A 459 " " NAG A1305 " - " ASN A 524 " " NAG A1309 " - " ASN A 598 " " NAG A1310 " - " ASN A 916 " " NAG A1311 " - " ASN A 931 " " NAG A1312 " - " ASN A 961 " " NAG A1313 " - " ASN A 968 " " NAG B 1 " - " ASN A 478 " " NAG C 1 " - " ASN A 557 " Time building additional restraints: 2.52 Conformation dependent library (CDL) restraints added in 1.4 seconds 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2174 Finding SS restraints... Secondary structure from input PDB file: 47 helices and 12 sheets defined 51.5% alpha, 6.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.15 Creating SS restraints... Processing helix chain 'A' and resid 55 through 63 removed outlier: 3.868A pdb=" N GLU A 61 " --> pdb=" O ASP A 57 " (cutoff:3.500A) Processing helix chain 'A' and resid 76 through 87 removed outlier: 3.736A pdb=" N LEU A 80 " --> pdb=" O ASP A 76 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ASP A 85 " --> pdb=" O GLN A 81 " (cutoff:3.500A) Processing helix chain 'A' and resid 87 through 94 Processing helix chain 'A' and resid 97 through 114 removed outlier: 3.531A pdb=" N PHE A 101 " --> pdb=" O CYS A 97 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LEU A 104 " --> pdb=" O CYS A 100 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N SER A 114 " --> pdb=" O GLU A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 116 through 120 removed outlier: 3.751A pdb=" N PHE A 120 " --> pdb=" O ARG A 116 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 116 through 120' Processing helix chain 'A' and resid 150 through 161 Processing helix chain 'A' and resid 171 through 178 removed outlier: 4.107A pdb=" N LEU A 175 " --> pdb=" O LYS A 171 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N LEU A 176 " --> pdb=" O ALA A 172 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N GLY A 178 " --> pdb=" O GLY A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 185 through 195 Processing helix chain 'A' and resid 270 through 278 removed outlier: 3.579A pdb=" N ILE A 274 " --> pdb=" O VAL A 270 " (cutoff:3.500A) Processing helix chain 'A' and resid 279 through 284 Processing helix chain 'A' and resid 335 through 349 removed outlier: 3.589A pdb=" N PHE A 339 " --> pdb=" O LEU A 335 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ARG A 341 " --> pdb=" O ARG A 337 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N TRP A 342 " --> pdb=" O LEU A 338 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N PHE A 345 " --> pdb=" O ARG A 341 " (cutoff:3.500A) Processing helix chain 'A' and resid 351 through 365 removed outlier: 3.804A pdb=" N PHE A 355 " --> pdb=" O GLY A 351 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N PHE A 360 " --> pdb=" O PHE A 356 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 372 removed outlier: 3.833A pdb=" N VAL A 371 " --> pdb=" O GLY A 367 " (cutoff:3.500A) Processing helix chain 'A' and resid 386 through 393 Processing helix chain 'A' and resid 436 through 452 removed outlier: 5.235A pdb=" N GLN A 442 " --> pdb=" O GLN A 438 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N GLU A 451 " --> pdb=" O GLN A 447 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ASN A 452 " --> pdb=" O ILE A 448 " (cutoff:3.500A) Processing helix chain 'A' and resid 483 through 487 Processing helix chain 'A' and resid 508 through 516 Processing helix chain 'A' and resid 577 through 593 removed outlier: 3.659A pdb=" N TRP A 583 " --> pdb=" O ARG A 579 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N GLU A 586 " --> pdb=" O ALA A 582 " (cutoff:3.500A) Processing helix chain 'A' and resid 607 through 617 removed outlier: 3.882A pdb=" N GLU A 612 " --> pdb=" O SER A 608 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N LEU A 613 " --> pdb=" O ILE A 609 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ASN A 614 " --> pdb=" O GLU A 610 " (cutoff:3.500A) Processing helix chain 'A' and resid 618 through 620 No H-bonds generated for 'chain 'A' and resid 618 through 620' Processing helix chain 'A' and resid 621 through 638 removed outlier: 3.775A pdb=" N ILE A 626 " --> pdb=" O PHE A 622 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N SER A 627 " --> pdb=" O THR A 623 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N MET A 631 " --> pdb=" O SER A 627 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ILE A 635 " --> pdb=" O MET A 631 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N SER A 636 " --> pdb=" O PHE A 632 " (cutoff:3.500A) Processing helix chain 'A' and resid 654 through 679 removed outlier: 3.624A pdb=" N ALA A 669 " --> pdb=" O LEU A 665 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N PHE A 675 " --> pdb=" O SER A 671 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N TYR A 677 " --> pdb=" O GLY A 673 " (cutoff:3.500A) Processing helix chain 'A' and resid 685 through 711 removed outlier: 3.596A pdb=" N VAL A 689 " --> pdb=" O ILE A 685 " (cutoff:3.500A) Proline residue: A 691 - end of helix removed outlier: 3.589A pdb=" N LEU A 695 " --> pdb=" O PRO A 691 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N ASP A 700 " --> pdb=" O ALA A 696 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ASN A 701 " --> pdb=" O VAL A 697 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ILE A 702 " --> pdb=" O GLY A 698 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ILE A 704 " --> pdb=" O ASP A 700 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N GLN A 707 " --> pdb=" O PHE A 703 " (cutoff:3.500A) Processing helix chain 'A' and resid 719 through 748 Proline residue: A 733 - end of helix removed outlier: 3.993A pdb=" N LEU A 737 " --> pdb=" O PRO A 733 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N SER A 738 " --> pdb=" O SER A 734 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N GLU A 742 " --> pdb=" O SER A 738 " (cutoff:3.500A) Processing helix chain 'A' and resid 757 through 776 removed outlier: 4.170A pdb=" N LEU A 762 " --> pdb=" O HIS A 758 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N PHE A 763 " --> pdb=" O THR A 759 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N VAL A 768 " --> pdb=" O ALA A 764 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ILE A 776 " --> pdb=" O PHE A 772 " (cutoff:3.500A) Processing helix chain 'A' and resid 777 through 782 removed outlier: 3.951A pdb=" N SER A 781 " --> pdb=" O THR A 777 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LEU A 782 " --> pdb=" O CYS A 778 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 777 through 782' Processing helix chain 'A' and resid 782 through 792 Processing helix chain 'A' and resid 818 through 826 removed outlier: 3.587A pdb=" N SER A 824 " --> pdb=" O PHE A 820 " (cutoff:3.500A) Processing helix chain 'A' and resid 836 through 852 removed outlier: 3.959A pdb=" N PHE A 842 " --> pdb=" O VAL A 838 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N LEU A 846 " --> pdb=" O PHE A 842 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ALA A 851 " --> pdb=" O SER A 847 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N VAL A 852 " --> pdb=" O PHE A 848 " (cutoff:3.500A) Processing helix chain 'A' and resid 870 through 880 removed outlier: 4.191A pdb=" N ASP A 874 " --> pdb=" O SER A 870 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N SER A 880 " --> pdb=" O PHE A 876 " (cutoff:3.500A) Processing helix chain 'A' and resid 901 through 907 Processing helix chain 'A' and resid 918 through 928 removed outlier: 4.137A pdb=" N GLN A 928 " --> pdb=" O PHE A 924 " (cutoff:3.500A) Processing helix chain 'A' and resid 942 through 951 removed outlier: 3.569A pdb=" N PHE A 947 " --> pdb=" O ILE A 943 " (cutoff:3.500A) Processing helix chain 'A' and resid 952 through 955 removed outlier: 4.185A pdb=" N SER A 955 " --> pdb=" O PRO A 952 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 952 through 955' Processing helix chain 'A' and resid 993 through 1004 Proline residue: A1000 - end of helix Processing helix chain 'A' and resid 1047 through 1070 removed outlier: 3.670A pdb=" N PHE A1051 " --> pdb=" O THR A1047 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ILE A1052 " --> pdb=" O SER A1048 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LYS A1057 " --> pdb=" O ASP A1053 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLY A1070 " --> pdb=" O THR A1066 " (cutoff:3.500A) Processing helix chain 'A' and resid 1089 through 1092 Processing helix chain 'A' and resid 1093 through 1118 removed outlier: 3.670A pdb=" N ASP A1097 " --> pdb=" O THR A1093 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N THR A1098 " --> pdb=" O ILE A1094 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N ILE A1099 " --> pdb=" O ILE A1095 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N GLY A1103 " --> pdb=" O ILE A1099 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N THR A1113 " --> pdb=" O ILE A1109 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N MET A1114 " --> pdb=" O PHE A1110 " (cutoff:3.500A) Processing helix chain 'A' and resid 1120 through 1146 removed outlier: 3.669A pdb=" N ALA A1124 " --> pdb=" O GLU A1120 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ILE A1126 " --> pdb=" O TRP A1122 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N MET A1127 " --> pdb=" O SER A1123 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N LEU A1135 " --> pdb=" O ILE A1131 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ASN A1137 " --> pdb=" O MET A1133 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N TRP A1143 " --> pdb=" O PHE A1139 " (cutoff:3.500A) Processing helix chain 'A' and resid 1150 through 1164 removed outlier: 4.117A pdb=" N ASN A1156 " --> pdb=" O VAL A1152 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N SER A1160 " --> pdb=" O ASN A1156 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N CYS A1161 " --> pdb=" O LEU A1157 " (cutoff:3.500A) Processing helix chain 'A' and resid 1165 through 1177 removed outlier: 4.279A pdb=" N HIS A1170 " --> pdb=" O GLU A1166 " (cutoff:3.500A) removed outlier: 4.784A pdb=" N ILE A1171 " --> pdb=" O PHE A1167 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N ALA A1174 " --> pdb=" O HIS A1170 " (cutoff:3.500A) Processing helix chain 'A' and resid 1182 through 1194 removed outlier: 3.959A pdb=" N GLU A1188 " --> pdb=" O VAL A1184 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N GLU A1189 " --> pdb=" O GLU A1185 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ALA A1190 " --> pdb=" O ARG A1186 " (cutoff:3.500A) Processing helix chain 'A' and resid 1194 through 1201 Processing helix chain 'A' and resid 1202 through 1215 removed outlier: 3.609A pdb=" N ILE A1210 " --> pdb=" O LYS A1206 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N VAL A1211 " --> pdb=" O PHE A1207 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N VAL A1212 " --> pdb=" O GLY A1208 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LEU A1213 " --> pdb=" O GLY A1209 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N PHE A1215 " --> pdb=" O VAL A1211 " (cutoff:3.500A) Processing helix chain 'A' and resid 1219 through 1224 Processing helix chain 'A' and resid 1226 through 1242 removed outlier: 4.152A pdb=" N LEU A1235 " --> pdb=" O ALA A1231 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N THR A1238 " --> pdb=" O LEU A1234 " (cutoff:3.500A) Processing helix chain 'A' and resid 1242 through 1249 removed outlier: 4.239A pdb=" N VAL A1246 " --> pdb=" O ILE A1242 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LEU A1247 " --> pdb=" O PHE A1243 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 28 Processing sheet with id=AA2, first strand: chain 'A' and resid 33 through 35 removed outlier: 7.200A pdb=" N LYS A 38 " --> pdb=" O ALA A 34 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 49 through 50 removed outlier: 3.512A pdb=" N LEU A 73 " --> pdb=" O LYS A 49 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 121 through 129 removed outlier: 6.487A pdb=" N GLU A 143 " --> pdb=" O THR A 124 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N THR A 126 " --> pdb=" O VAL A 141 " (cutoff:3.500A) removed outlier: 7.310A pdb=" N VAL A 141 " --> pdb=" O THR A 126 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N ASP A 128 " --> pdb=" O THR A 139 " (cutoff:3.500A) removed outlier: 5.909A pdb=" N THR A 139 " --> pdb=" O ASP A 128 " (cutoff:3.500A) removed outlier: 7.967A pdb=" N THR A 206 " --> pdb=" O LYS A 142 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N LEU A 144 " --> pdb=" O THR A 206 " (cutoff:3.500A) removed outlier: 7.560A pdb=" N VAL A 208 " --> pdb=" O LEU A 144 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N TYR A 146 " --> pdb=" O VAL A 208 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N SER A 210 " --> pdb=" O TYR A 146 " (cutoff:3.500A) removed outlier: 5.426A pdb=" N VAL A 148 " --> pdb=" O SER A 210 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 547 through 548 Processing sheet with id=AA6, first strand: chain 'A' and resid 418 through 420 Processing sheet with id=AA7, first strand: chain 'A' and resid 455 through 457 Processing sheet with id=AA8, first strand: chain 'A' and resid 499 through 500 removed outlier: 6.889A pdb=" N LYS A 499 " --> pdb=" O TYR A 506 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 1036 through 1037 Processing sheet with id=AB1, first strand: chain 'A' and resid 1036 through 1037 Processing sheet with id=AB2, first strand: chain 'A' and resid 966 through 967 removed outlier: 3.978A pdb=" N ARG A 958 " --> pdb=" O CYS A 967 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 1025 through 1027 352 hydrogen bonds defined for protein. 1014 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.51 Time building geometry restraints manager: 2.97 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.34: 2778 1.34 - 1.49: 2650 1.49 - 1.64: 3838 1.64 - 1.79: 23 1.79 - 1.94: 76 Bond restraints: 9365 Sorted by residual: bond pdb=" C17 QDG A1314 " pdb=" C49 QDG A1314 " ideal model delta sigma weight residual 1.536 1.211 0.325 2.00e-02 2.50e+03 2.64e+02 bond pdb=" C09 QDG A1314 " pdb=" O16 QDG A1314 " ideal model delta sigma weight residual 1.396 1.197 0.199 2.00e-02 2.50e+03 9.90e+01 bond pdb=" C45 QDG A1314 " pdb=" N44 QDG A1314 " ideal model delta sigma weight residual 1.283 1.445 -0.162 2.00e-02 2.50e+03 6.58e+01 bond pdb=" C17 QDG A1314 " pdb=" O16 QDG A1314 " ideal model delta sigma weight residual 1.419 1.557 -0.138 2.00e-02 2.50e+03 4.77e+01 bond pdb=" C40 QDG A1314 " pdb=" N39 QDG A1314 " ideal model delta sigma weight residual 1.453 1.333 0.120 2.00e-02 2.50e+03 3.61e+01 ... (remaining 9360 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.23: 11985 2.23 - 4.46: 720 4.46 - 6.68: 48 6.68 - 8.91: 12 8.91 - 11.14: 3 Bond angle restraints: 12768 Sorted by residual: angle pdb=" N PRO A 132 " pdb=" CA PRO A 132 " pdb=" CB PRO A 132 " ideal model delta sigma weight residual 103.25 110.45 -7.20 1.05e+00 9.07e-01 4.70e+01 angle pdb=" N PRO A 433 " pdb=" CA PRO A 433 " pdb=" C PRO A 433 " ideal model delta sigma weight residual 110.70 118.24 -7.54 1.22e+00 6.72e-01 3.82e+01 angle pdb=" N ASP A 552 " pdb=" CA ASP A 552 " pdb=" C ASP A 552 " ideal model delta sigma weight residual 110.80 121.94 -11.14 2.13e+00 2.20e-01 2.74e+01 angle pdb=" N TYR A 571 " pdb=" CA TYR A 571 " pdb=" C TYR A 571 " ideal model delta sigma weight residual 111.33 117.17 -5.84 1.21e+00 6.83e-01 2.33e+01 angle pdb=" N ILE A 962 " pdb=" CA ILE A 962 " pdb=" C ILE A 962 " ideal model delta sigma weight residual 111.90 115.78 -3.88 8.10e-01 1.52e+00 2.29e+01 ... (remaining 12763 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.32: 5458 22.32 - 44.65: 197 44.65 - 66.97: 43 66.97 - 89.29: 20 89.29 - 111.61: 13 Dihedral angle restraints: 5731 sinusoidal: 2355 harmonic: 3376 Sorted by residual: dihedral pdb=" CB CYS A 468 " pdb=" SG CYS A 468 " pdb=" SG CYS A 479 " pdb=" CB CYS A 479 " ideal model delta sinusoidal sigma weight residual -86.00 -176.29 90.29 1 1.00e+01 1.00e-02 9.65e+01 dihedral pdb=" CB CYS A 957 " pdb=" SG CYS A 957 " pdb=" SG CYS A 979 " pdb=" CB CYS A 979 " ideal model delta sinusoidal sigma weight residual 93.00 173.40 -80.40 1 1.00e+01 1.00e-02 8.00e+01 dihedral pdb=" CB CYS A 909 " pdb=" SG CYS A 909 " pdb=" SG CYS A 914 " pdb=" CB CYS A 914 " ideal model delta sinusoidal sigma weight residual 93.00 162.63 -69.63 1 1.00e+01 1.00e-02 6.26e+01 ... (remaining 5728 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.139: 1408 0.139 - 0.277: 68 0.277 - 0.415: 5 0.415 - 0.554: 4 0.554 - 0.692: 2 Chirality restraints: 1487 Sorted by residual: chirality pdb=" C1 NAG B 2 " pdb=" O4 NAG B 1 " pdb=" C2 NAG B 2 " pdb=" O5 NAG B 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.29 -0.11 2.00e-02 2.50e+03 3.05e+01 chirality pdb=" C1 NAG C 2 " pdb=" O4 NAG C 1 " pdb=" C2 NAG C 2 " pdb=" O5 NAG C 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.31 -0.09 2.00e-02 2.50e+03 2.12e+01 chirality pdb=" C1 NAG B 1 " pdb=" ND2 ASN A 478 " pdb=" C2 NAG B 1 " pdb=" O5 NAG B 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.71 -0.69 2.00e-01 2.50e+01 1.20e+01 ... (remaining 1484 not shown) Planarity restraints: 1632 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO A 253 " -0.053 5.00e-02 4.00e+02 8.06e-02 1.04e+01 pdb=" N PRO A 254 " 0.139 5.00e-02 4.00e+02 pdb=" CA PRO A 254 " -0.041 5.00e-02 4.00e+02 pdb=" CD PRO A 254 " -0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 89 " -0.040 5.00e-02 4.00e+02 6.13e-02 6.01e+00 pdb=" N PRO A 90 " 0.106 5.00e-02 4.00e+02 pdb=" CA PRO A 90 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO A 90 " -0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO A 254 " 0.032 5.00e-02 4.00e+02 4.96e-02 3.93e+00 pdb=" N PRO A 255 " -0.086 5.00e-02 4.00e+02 pdb=" CA PRO A 255 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 255 " 0.027 5.00e-02 4.00e+02 ... (remaining 1629 not shown) Histogram of nonbonded interaction distances: 2.46 - 2.95: 3640 2.95 - 3.44: 9311 3.44 - 3.92: 14119 3.92 - 4.41: 15218 4.41 - 4.90: 25057 Nonbonded interactions: 67345 Sorted by model distance: nonbonded pdb=" OG SER A 849 " pdb=" O VAL A1136 " model vdw 2.461 3.040 nonbonded pdb=" OG1 THR A 454 " pdb=" OG1 THR A 461 " model vdw 2.494 3.040 nonbonded pdb=" O ALA A1062 " pdb=" OG1 THR A1066 " model vdw 2.496 3.040 nonbonded pdb=" O TYR A 932 " pdb=" NZ LYS A1057 " model vdw 2.507 3.120 nonbonded pdb=" OG SER A 608 " pdb=" OH TYR A 871 " model vdw 2.545 3.040 ... (remaining 67340 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.950 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: 0.490 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 31.700 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7747 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.325 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 : 14.585 111.613 3512 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 0.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.15 % Favored : 91.85 % Rotamer: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.23 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.01 (0.20), residues: 1153 helix: -2.78 (0.16), residues: 549 sheet: -2.22 (0.54), residues: 90 loop : -2.48 (0.25), residues: 514 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A1145 HIS 0.004 0.001 HIS A 897 PHE 0.017 0.002 PHE A1139 TYR 0.015 0.002 TYR A 899 ARG 0.006 0.000 ARG A1227 Details of bonding type rmsd link_NAG-ASN : bond 0.00932 ( 10) link_NAG-ASN : angle 4.86756 ( 30) link_BETA1-4 : bond 0.01074 ( 2) link_BETA1-4 : angle 2.97599 ( 6) link_ALPHA1-3 : bond 0.00955 ( 1) link_ALPHA1-3 : angle 3.26971 ( 3) hydrogen bonds : bond 0.21400 ( 350) hydrogen bonds : angle 8.22126 ( 1014) SS BOND : bond 0.00482 ( 15) SS BOND : angle 0.94506 ( 30) covalent geometry : bond 0.01009 ( 9365) covalent geometry : angle 1.17884 (12768) *********************** 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 : 0.934 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 ASP cc_start: 0.8849 (m-30) cc_final: 0.8550 (t0) REVERT: A 85 ASP cc_start: 0.8768 (t70) cc_final: 0.8266 (t0) REVERT: A 103 ASN cc_start: 0.9530 (m110) cc_final: 0.9082 (m110) REVERT: A 106 ASN cc_start: 0.8784 (m-40) cc_final: 0.8504 (m-40) REVERT: A 108 PHE cc_start: 0.8783 (m-80) cc_final: 0.8501 (m-80) REVERT: A 355 PHE cc_start: 0.9111 (t80) cc_final: 0.8778 (t80) REVERT: A 364 CYS cc_start: 0.8516 (m) cc_final: 0.8145 (m) REVERT: A 406 GLU cc_start: 0.8438 (mm-30) cc_final: 0.8226 (mt-10) REVERT: A 593 ASN cc_start: 0.8958 (m-40) cc_final: 0.8434 (p0) REVERT: A 634 TYR cc_start: 0.8639 (t80) cc_final: 0.8419 (t80) REVERT: A 663 ILE cc_start: 0.9179 (mt) cc_final: 0.8893 (mt) REVERT: A 689 VAL cc_start: 0.8739 (t) cc_final: 0.8266 (t) REVERT: A 730 GLU cc_start: 0.9401 (tp30) cc_final: 0.8841 (tm-30) REVERT: A 735 MET cc_start: 0.8544 (ttp) cc_final: 0.7998 (ttp) REVERT: A 834 MET cc_start: 0.7817 (mtt) cc_final: 0.7404 (mmm) REVERT: A 864 LEU cc_start: 0.8463 (mt) cc_final: 0.8200 (pp) REVERT: A 872 MET cc_start: 0.8546 (mmm) cc_final: 0.7980 (mmm) REVERT: A 922 GLN cc_start: 0.8907 (tp-100) cc_final: 0.8480 (tp-100) REVERT: A 930 ASP cc_start: 0.8554 (p0) cc_final: 0.7879 (t0) REVERT: A 933 THR cc_start: 0.8749 (t) cc_final: 0.8470 (t) REVERT: A 1122 TRP cc_start: 0.7946 (m100) cc_final: 0.7449 (m-10) REVERT: A 1150 ASN cc_start: 0.8223 (p0) cc_final: 0.7741 (p0) REVERT: A 1156 ASN cc_start: 0.8981 (t0) cc_final: 0.8777 (t0) REVERT: A 1179 MET cc_start: 0.7488 (mpp) cc_final: 0.7224 (mmm) outliers start: 0 outliers final: 0 residues processed: 217 average time/residue: 0.2080 time to fit residues: 62.6588 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 : 0.952 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 97 optimal weight: 0.4980 chunk 87 optimal weight: 7.9990 chunk 48 optimal weight: 1.9990 chunk 30 optimal weight: 8.9990 chunk 59 optimal weight: 1.9990 chunk 46 optimal weight: 0.9980 chunk 90 optimal weight: 0.7980 chunk 35 optimal weight: 9.9990 chunk 55 optimal weight: 3.9990 chunk 67 optimal weight: 2.9990 chunk 105 optimal weight: 5.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 103 ASN A 447 GLN A 988 GLN A1042 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.087647 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.066383 restraints weight = 29957.805| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.068541 restraints weight = 16117.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.070024 restraints weight = 10740.631| |-----------------------------------------------------------------------------| r_work (final): 0.3242 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3242 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3242 r_free = 0.3242 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3242 r_free = 0.3242 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3242 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8003 moved from start: 0.2234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9393 Z= 0.141 Angle : 0.738 12.232 12837 Z= 0.358 Chirality : 0.049 0.361 1487 Planarity : 0.005 0.078 1622 Dihedral : 13.131 90.292 1547 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.93 (0.22), residues: 1153 helix: -1.58 (0.19), residues: 560 sheet: -2.29 (0.50), residues: 100 loop : -2.18 (0.26), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 583 HIS 0.003 0.001 HIS A 530 PHE 0.034 0.002 PHE A 937 TYR 0.015 0.001 TYR A1085 ARG 0.007 0.000 ARG A 958 Details of bonding type rmsd link_NAG-ASN : bond 0.00489 ( 10) link_NAG-ASN : angle 3.61866 ( 30) link_BETA1-4 : bond 0.00852 ( 2) link_BETA1-4 : angle 1.93344 ( 6) link_ALPHA1-3 : bond 0.01055 ( 1) link_ALPHA1-3 : angle 2.53853 ( 3) hydrogen bonds : bond 0.04477 ( 350) hydrogen bonds : angle 5.27570 ( 1014) SS BOND : bond 0.00629 ( 15) SS BOND : angle 1.37998 ( 30) covalent geometry : bond 0.00306 ( 9365) covalent geometry : angle 0.71392 (12768) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 153 time to evaluate : 0.926 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 106 ASN cc_start: 0.8778 (m-40) cc_final: 0.8280 (m-40) REVERT: A 110 GLU cc_start: 0.7641 (mm-30) cc_final: 0.7041 (mm-30) REVERT: A 355 PHE cc_start: 0.8819 (t80) cc_final: 0.8570 (t80) REVERT: A 586 GLU cc_start: 0.8952 (mm-30) cc_final: 0.8717 (mt-10) REVERT: A 593 ASN cc_start: 0.8663 (m-40) cc_final: 0.8389 (p0) REVERT: A 676 SER cc_start: 0.9182 (m) cc_final: 0.8906 (p) REVERT: A 730 GLU cc_start: 0.9225 (tp30) cc_final: 0.8656 (tm-30) REVERT: A 774 LEU cc_start: 0.9432 (tp) cc_final: 0.9226 (tp) REVERT: A 930 ASP cc_start: 0.8513 (p0) cc_final: 0.8248 (t0) REVERT: A 935 ILE cc_start: 0.8195 (mt) cc_final: 0.7859 (mt) REVERT: A 1150 ASN cc_start: 0.8739 (p0) cc_final: 0.8158 (p0) REVERT: A 1156 ASN cc_start: 0.8731 (t0) cc_final: 0.8508 (t0) REVERT: A 1175 PHE cc_start: 0.8314 (t80) cc_final: 0.7792 (t80) outliers start: 0 outliers final: 0 residues processed: 153 average time/residue: 0.1779 time to fit residues: 40.1155 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 : 0.999 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 85 optimal weight: 5.9990 chunk 87 optimal weight: 0.6980 chunk 75 optimal weight: 8.9990 chunk 20 optimal weight: 8.9990 chunk 26 optimal weight: 9.9990 chunk 104 optimal weight: 0.8980 chunk 11 optimal weight: 50.0000 chunk 91 optimal weight: 0.7980 chunk 36 optimal weight: 4.9990 chunk 19 optimal weight: 7.9990 chunk 111 optimal weight: 8.9990 overall best weight: 2.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 775 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.087668 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.066888 restraints weight = 29569.332| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.068893 restraints weight = 16364.206| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.070293 restraints weight = 11177.460| |-----------------------------------------------------------------------------| r_work (final): 0.3255 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3254 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3254 r_free = 0.3254 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3254 r_free = 0.3254 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3254 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8098 moved from start: 0.2648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 9393 Z= 0.181 Angle : 0.739 10.518 12837 Z= 0.356 Chirality : 0.047 0.350 1487 Planarity : 0.005 0.075 1622 Dihedral : 11.254 83.854 1547 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.72 % Favored : 94.28 % Rotamer: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.60 (0.23), residues: 1153 helix: -1.17 (0.20), residues: 565 sheet: -2.73 (0.45), residues: 110 loop : -2.00 (0.27), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 583 HIS 0.012 0.002 HIS A1042 PHE 0.045 0.002 PHE A 632 TYR 0.013 0.002 TYR A1037 ARG 0.005 0.001 ARG A 411 Details of bonding type rmsd link_NAG-ASN : bond 0.00396 ( 10) link_NAG-ASN : angle 3.39035 ( 30) link_BETA1-4 : bond 0.00739 ( 2) link_BETA1-4 : angle 2.22726 ( 6) link_ALPHA1-3 : bond 0.01613 ( 1) link_ALPHA1-3 : angle 2.77592 ( 3) hydrogen bonds : bond 0.04114 ( 350) hydrogen bonds : angle 5.01245 ( 1014) SS BOND : bond 0.00520 ( 15) SS BOND : angle 1.81144 ( 30) covalent geometry : bond 0.00410 ( 9365) covalent geometry : angle 0.71385 (12768) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 138 time to evaluate : 0.956 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 ASP cc_start: 0.8799 (p0) cc_final: 0.8589 (m-30) REVERT: A 106 ASN cc_start: 0.8764 (m-40) cc_final: 0.8461 (m-40) REVERT: A 355 PHE cc_start: 0.8699 (t80) cc_final: 0.8498 (t80) REVERT: A 632 PHE cc_start: 0.7942 (m-80) cc_final: 0.7724 (m-80) REVERT: A 676 SER cc_start: 0.9311 (m) cc_final: 0.8989 (t) REVERT: A 730 GLU cc_start: 0.9029 (tp30) cc_final: 0.8630 (tm-30) REVERT: A 774 LEU cc_start: 0.9421 (tp) cc_final: 0.9194 (tp) REVERT: A 834 MET cc_start: 0.7516 (mmp) cc_final: 0.7275 (mmm) REVERT: A 872 MET cc_start: 0.8077 (mmm) cc_final: 0.7870 (mmm) REVERT: A 935 ILE cc_start: 0.8243 (mt) cc_final: 0.8021 (mt) REVERT: A 996 MET cc_start: 0.9099 (mtp) cc_final: 0.8896 (ttm) REVERT: A 1150 ASN cc_start: 0.8939 (p0) cc_final: 0.8322 (p0) REVERT: A 1159 MET cc_start: 0.8471 (tpp) cc_final: 0.8176 (ttp) REVERT: A 1166 GLU cc_start: 0.8087 (tp30) cc_final: 0.7674 (tp30) REVERT: A 1175 PHE cc_start: 0.8463 (t80) cc_final: 0.8140 (t80) outliers start: 0 outliers final: 0 residues processed: 138 average time/residue: 0.1727 time to fit residues: 35.6755 Evaluate side-chains 98 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 98 time to evaluate : 0.934 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 18 optimal weight: 20.0000 chunk 74 optimal weight: 6.9990 chunk 16 optimal weight: 10.0000 chunk 105 optimal weight: 5.9990 chunk 44 optimal weight: 7.9990 chunk 9 optimal weight: 8.9990 chunk 112 optimal weight: 8.9990 chunk 60 optimal weight: 9.9990 chunk 62 optimal weight: 1.9990 chunk 43 optimal weight: 6.9990 chunk 82 optimal weight: 0.7980 overall best weight: 4.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 775 GLN ** 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 = 0.3564 r_free = 0.3564 target = 0.084741 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.063791 restraints weight = 29905.690| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.065752 restraints weight = 16313.602| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.067103 restraints weight = 11101.496| |-----------------------------------------------------------------------------| r_work (final): 0.3190 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3193 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3193 r_free = 0.3193 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3193 r_free = 0.3193 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3193 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 moved from start: 0.3131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 9393 Z= 0.269 Angle : 0.807 9.729 12837 Z= 0.395 Chirality : 0.050 0.362 1487 Planarity : 0.005 0.075 1622 Dihedral : 10.047 80.512 1547 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.94 % Favored : 93.06 % Rotamer: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.45 (0.23), residues: 1153 helix: -1.11 (0.20), residues: 572 sheet: -2.81 (0.47), residues: 95 loop : -1.88 (0.28), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 583 HIS 0.012 0.002 HIS A1042 PHE 0.043 0.002 PHE A 632 TYR 0.014 0.002 TYR A1037 ARG 0.008 0.001 ARG A 116 Details of bonding type rmsd link_NAG-ASN : bond 0.00283 ( 10) link_NAG-ASN : angle 3.33082 ( 30) link_BETA1-4 : bond 0.00860 ( 2) link_BETA1-4 : angle 2.53438 ( 6) link_ALPHA1-3 : bond 0.01896 ( 1) link_ALPHA1-3 : angle 2.60332 ( 3) hydrogen bonds : bond 0.04274 ( 350) hydrogen bonds : angle 5.17438 ( 1014) SS BOND : bond 0.00400 ( 15) SS BOND : angle 1.54078 ( 30) covalent geometry : bond 0.00607 ( 9365) covalent geometry : angle 0.78603 (12768) *********************** 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 122 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 122 time to evaluate : 1.060 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 676 SER cc_start: 0.9298 (m) cc_final: 0.9003 (p) REVERT: A 730 GLU cc_start: 0.9192 (tp30) cc_final: 0.8616 (tm-30) REVERT: A 872 MET cc_start: 0.8217 (mmm) cc_final: 0.7693 (mmm) REVERT: A 996 MET cc_start: 0.9226 (mtp) cc_final: 0.8892 (ttm) REVERT: A 1150 ASN cc_start: 0.9017 (p0) cc_final: 0.8371 (p0) REVERT: A 1166 GLU cc_start: 0.8231 (tp30) cc_final: 0.7868 (tp30) outliers start: 0 outliers final: 0 residues processed: 122 average time/residue: 0.1848 time to fit residues: 33.6718 Evaluate side-chains 87 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 87 time to evaluate : 1.012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 66 optimal weight: 8.9990 chunk 32 optimal weight: 0.9990 chunk 103 optimal weight: 0.9990 chunk 71 optimal weight: 5.9990 chunk 70 optimal weight: 0.9990 chunk 74 optimal weight: 2.9990 chunk 90 optimal weight: 2.9990 chunk 58 optimal weight: 10.0000 chunk 94 optimal weight: 1.9990 chunk 96 optimal weight: 0.8980 chunk 24 optimal weight: 10.0000 overall best weight: 1.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 568 ASN ** A 775 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1239 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.088074 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.067305 restraints weight = 29442.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.069414 restraints weight = 16136.860| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.070839 restraints weight = 10900.449| |-----------------------------------------------------------------------------| r_work (final): 0.3268 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3268 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3268 r_free = 0.3268 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3268 r_free = 0.3268 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3268 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8085 moved from start: 0.3203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9393 Z= 0.131 Angle : 0.691 11.064 12837 Z= 0.329 Chirality : 0.046 0.357 1487 Planarity : 0.005 0.073 1622 Dihedral : 9.328 81.938 1547 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.13 (0.24), residues: 1153 helix: -0.84 (0.21), residues: 573 sheet: -2.45 (0.49), residues: 94 loop : -1.77 (0.28), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 544 HIS 0.010 0.001 HIS A1042 PHE 0.027 0.002 PHE A 937 TYR 0.012 0.001 TYR A 875 ARG 0.005 0.000 ARG A1227 Details of bonding type rmsd link_NAG-ASN : bond 0.00497 ( 10) link_NAG-ASN : angle 3.03394 ( 30) link_BETA1-4 : bond 0.00866 ( 2) link_BETA1-4 : angle 2.54615 ( 6) link_ALPHA1-3 : bond 0.02233 ( 1) link_ALPHA1-3 : angle 2.35181 ( 3) hydrogen bonds : bond 0.03544 ( 350) hydrogen bonds : angle 4.79608 ( 1014) SS BOND : bond 0.00434 ( 15) SS BOND : angle 1.35065 ( 30) covalent geometry : bond 0.00291 ( 9365) covalent geometry : angle 0.67033 (12768) *********************** 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 135 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 135 time to evaluate : 2.349 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 106 ASN cc_start: 0.8642 (m-40) cc_final: 0.8356 (m-40) REVERT: A 531 ASP cc_start: 0.7915 (t0) cc_final: 0.7666 (t0) REVERT: A 632 PHE cc_start: 0.7757 (m-80) cc_final: 0.7349 (m-80) REVERT: A 676 SER cc_start: 0.9297 (m) cc_final: 0.9012 (p) REVERT: A 730 GLU cc_start: 0.8999 (tp30) cc_final: 0.8631 (tm-30) REVERT: A 872 MET cc_start: 0.7866 (mmm) cc_final: 0.7153 (mmm) REVERT: A 945 ASP cc_start: 0.8602 (t70) cc_final: 0.8375 (t70) REVERT: A 996 MET cc_start: 0.9138 (mtp) cc_final: 0.8864 (ttm) REVERT: A 1150 ASN cc_start: 0.8912 (p0) cc_final: 0.8274 (p0) REVERT: A 1175 PHE cc_start: 0.8392 (t80) cc_final: 0.7746 (t80) outliers start: 0 outliers final: 0 residues processed: 135 average time/residue: 0.3023 time to fit residues: 62.4300 Evaluate side-chains 100 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 100 time to evaluate : 1.793 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 42 optimal weight: 0.7980 chunk 10 optimal weight: 6.9990 chunk 5 optimal weight: 6.9990 chunk 27 optimal weight: 9.9990 chunk 100 optimal weight: 6.9990 chunk 51 optimal weight: 6.9990 chunk 82 optimal weight: 0.3980 chunk 83 optimal weight: 3.9990 chunk 91 optimal weight: 3.9990 chunk 84 optimal weight: 3.9990 chunk 15 optimal weight: 10.0000 overall best weight: 2.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.086438 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.065647 restraints weight = 30457.679| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.067714 restraints weight = 16609.240| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.069103 restraints weight = 11237.312| |-----------------------------------------------------------------------------| r_work (final): 0.3234 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3231 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3231 r_free = 0.3231 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3231 r_free = 0.3231 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3231 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8131 moved from start: 0.3407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 9393 Z= 0.173 Angle : 0.698 9.011 12837 Z= 0.336 Chirality : 0.046 0.352 1487 Planarity : 0.005 0.074 1622 Dihedral : 8.704 84.463 1547 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.90 % Favored : 94.10 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.91 (0.24), residues: 1153 helix: -0.67 (0.21), residues: 567 sheet: -2.54 (0.49), residues: 94 loop : -1.59 (0.28), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 583 HIS 0.010 0.002 HIS A1042 PHE 0.013 0.002 PHE A 632 TYR 0.024 0.002 TYR A 875 ARG 0.007 0.001 ARG A1227 Details of bonding type rmsd link_NAG-ASN : bond 0.00369 ( 10) link_NAG-ASN : angle 2.93209 ( 30) link_BETA1-4 : bond 0.00936 ( 2) link_BETA1-4 : angle 2.67646 ( 6) link_ALPHA1-3 : bond 0.02316 ( 1) link_ALPHA1-3 : angle 2.00708 ( 3) hydrogen bonds : bond 0.03596 ( 350) hydrogen bonds : angle 4.80942 ( 1014) SS BOND : bond 0.00383 ( 15) SS BOND : angle 1.36402 ( 30) covalent geometry : bond 0.00397 ( 9365) covalent geometry : angle 0.67859 (12768) *********************** 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 129 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 129 time to evaluate : 0.923 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 110 GLU cc_start: 0.7376 (mm-30) cc_final: 0.7114 (mm-30) REVERT: A 531 ASP cc_start: 0.8012 (t0) cc_final: 0.7751 (t0) REVERT: A 632 PHE cc_start: 0.7612 (m-80) cc_final: 0.7403 (m-80) REVERT: A 676 SER cc_start: 0.9309 (m) cc_final: 0.9009 (p) REVERT: A 720 LEU cc_start: 0.8809 (pt) cc_final: 0.8453 (tp) REVERT: A 730 GLU cc_start: 0.9052 (tp30) cc_final: 0.8682 (tm-30) REVERT: A 772 PHE cc_start: 0.7494 (t80) cc_final: 0.7292 (t80) REVERT: A 834 MET cc_start: 0.7782 (mmt) cc_final: 0.7479 (mmm) REVERT: A 872 MET cc_start: 0.7914 (mmm) cc_final: 0.7225 (mmm) REVERT: A 907 MET cc_start: 0.8357 (mmm) cc_final: 0.8122 (mmm) REVERT: A 945 ASP cc_start: 0.8661 (t70) cc_final: 0.8429 (t70) REVERT: A 996 MET cc_start: 0.9149 (mtp) cc_final: 0.8825 (ttm) REVERT: A 1150 ASN cc_start: 0.8944 (p0) cc_final: 0.8038 (p0) REVERT: A 1175 PHE cc_start: 0.8458 (t80) cc_final: 0.8039 (t80) outliers start: 0 outliers final: 0 residues processed: 129 average time/residue: 0.1825 time to fit residues: 36.3315 Evaluate side-chains 94 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 94 time to evaluate : 0.939 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 82 optimal weight: 0.5980 chunk 26 optimal weight: 20.0000 chunk 62 optimal weight: 0.9990 chunk 33 optimal weight: 0.2980 chunk 31 optimal weight: 6.9990 chunk 104 optimal weight: 0.9990 chunk 3 optimal weight: 2.9990 chunk 101 optimal weight: 0.8980 chunk 83 optimal weight: 2.9990 chunk 48 optimal weight: 6.9990 chunk 67 optimal weight: 0.5980 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 775 GLN A1239 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.088980 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.068397 restraints weight = 30457.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.070638 restraints weight = 16204.257| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.072142 restraints weight = 10735.531| |-----------------------------------------------------------------------------| r_work (final): 0.3296 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3296 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3296 r_free = 0.3296 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 = 0.3296 r_free = 0.3296 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3296 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8047 moved from start: 0.3504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 9393 Z= 0.115 Angle : 0.646 10.000 12837 Z= 0.311 Chirality : 0.044 0.331 1487 Planarity : 0.004 0.073 1622 Dihedral : 8.095 89.927 1547 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 0.00 % Allowed : 1.24 % Favored : 98.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.75 (0.24), residues: 1153 helix: -0.52 (0.21), residues: 569 sheet: -2.37 (0.49), residues: 99 loop : -1.56 (0.28), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 544 HIS 0.008 0.001 HIS A1042 PHE 0.024 0.001 PHE A 937 TYR 0.021 0.001 TYR A 875 ARG 0.003 0.000 ARG A1227 Details of bonding type rmsd link_NAG-ASN : bond 0.00563 ( 10) link_NAG-ASN : angle 2.66989 ( 30) link_BETA1-4 : bond 0.01020 ( 2) link_BETA1-4 : angle 2.54658 ( 6) link_ALPHA1-3 : bond 0.02416 ( 1) link_ALPHA1-3 : angle 1.55325 ( 3) hydrogen bonds : bond 0.03262 ( 350) hydrogen bonds : angle 4.58166 ( 1014) SS BOND : bond 0.00389 ( 15) SS BOND : angle 1.21915 ( 30) covalent geometry : bond 0.00249 ( 9365) covalent geometry : angle 0.62938 (12768) *********************** 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 139 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 139 time to evaluate : 1.065 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 110 GLU cc_start: 0.7346 (mm-30) cc_final: 0.7065 (mm-30) REVERT: A 531 ASP cc_start: 0.7951 (t0) cc_final: 0.7724 (t0) REVERT: A 632 PHE cc_start: 0.7618 (m-80) cc_final: 0.7315 (m-80) REVERT: A 676 SER cc_start: 0.9290 (m) cc_final: 0.9007 (p) REVERT: A 730 GLU cc_start: 0.9007 (tp30) cc_final: 0.8653 (tm-30) REVERT: A 872 MET cc_start: 0.7759 (mmm) cc_final: 0.7419 (mmm) REVERT: A 945 ASP cc_start: 0.8662 (t70) cc_final: 0.8406 (t70) REVERT: A 996 MET cc_start: 0.9063 (mtp) cc_final: 0.8773 (ttm) REVERT: A 1063 SER cc_start: 0.9295 (t) cc_final: 0.8979 (p) REVERT: A 1150 ASN cc_start: 0.8821 (p0) cc_final: 0.7936 (p0) REVERT: A 1166 GLU cc_start: 0.8204 (tp30) cc_final: 0.7905 (tp30) REVERT: A 1175 PHE cc_start: 0.8416 (t80) cc_final: 0.7985 (t80) outliers start: 0 outliers final: 0 residues processed: 139 average time/residue: 0.1817 time to fit residues: 37.4438 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 : 0.979 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 49 optimal weight: 1.9990 chunk 10 optimal weight: 50.0000 chunk 56 optimal weight: 0.8980 chunk 81 optimal weight: 5.9990 chunk 58 optimal weight: 3.9990 chunk 112 optimal weight: 10.0000 chunk 94 optimal weight: 0.7980 chunk 37 optimal weight: 2.9990 chunk 9 optimal weight: 9.9990 chunk 46 optimal weight: 5.9990 chunk 89 optimal weight: 0.0040 overall best weight: 1.3396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3631 r_free = 0.3631 target = 0.088559 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.067774 restraints weight = 30486.611| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.069934 restraints weight = 16275.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.071365 restraints weight = 10876.085| |-----------------------------------------------------------------------------| r_work (final): 0.3280 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3280 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3280 r_free = 0.3280 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 = 0.3280 r_free = 0.3280 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3280 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 moved from start: 0.3650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 9393 Z= 0.127 Angle : 0.659 11.549 12837 Z= 0.318 Chirality : 0.044 0.330 1487 Planarity : 0.004 0.072 1622 Dihedral : 7.785 86.274 1547 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 0.00 % Allowed : 0.62 % Favored : 99.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.60 (0.24), residues: 1153 helix: -0.39 (0.21), residues: 571 sheet: -2.35 (0.50), residues: 99 loop : -1.46 (0.28), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 544 HIS 0.009 0.001 HIS A1042 PHE 0.013 0.001 PHE A 769 TYR 0.030 0.001 TYR A 192 ARG 0.005 0.000 ARG A1227 Details of bonding type rmsd link_NAG-ASN : bond 0.00467 ( 10) link_NAG-ASN : angle 2.59841 ( 30) link_BETA1-4 : bond 0.00958 ( 2) link_BETA1-4 : angle 2.42564 ( 6) link_ALPHA1-3 : bond 0.01954 ( 1) link_ALPHA1-3 : angle 1.26249 ( 3) hydrogen bonds : bond 0.03301 ( 350) hydrogen bonds : angle 4.66454 ( 1014) SS BOND : bond 0.00309 ( 15) SS BOND : angle 1.32583 ( 30) covalent geometry : bond 0.00288 ( 9365) covalent geometry : angle 0.64294 (12768) *********************** 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 131 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 131 time to evaluate : 1.008 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 110 GLU cc_start: 0.7218 (mm-30) cc_final: 0.6912 (mm-30) REVERT: A 194 PHE cc_start: 0.8967 (m-10) cc_final: 0.8747 (m-80) REVERT: A 531 ASP cc_start: 0.7949 (t0) cc_final: 0.7736 (t0) REVERT: A 632 PHE cc_start: 0.7593 (m-80) cc_final: 0.7311 (m-80) REVERT: A 676 SER cc_start: 0.9295 (m) cc_final: 0.9033 (p) REVERT: A 730 GLU cc_start: 0.8971 (tp30) cc_final: 0.8626 (tm-30) REVERT: A 872 MET cc_start: 0.7758 (mmm) cc_final: 0.7438 (mmt) REVERT: A 945 ASP cc_start: 0.8647 (t70) cc_final: 0.8395 (t70) REVERT: A 996 MET cc_start: 0.9100 (mtp) cc_final: 0.8724 (ttm) REVERT: A 1063 SER cc_start: 0.9294 (t) cc_final: 0.9000 (p) REVERT: A 1150 ASN cc_start: 0.8917 (p0) cc_final: 0.8025 (p0) REVERT: A 1166 GLU cc_start: 0.8063 (tp30) cc_final: 0.7779 (tp30) REVERT: A 1175 PHE cc_start: 0.8478 (t80) cc_final: 0.8086 (t80) outliers start: 0 outliers final: 0 residues processed: 131 average time/residue: 0.2594 time to fit residues: 52.9955 Evaluate side-chains 95 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 95 time to evaluate : 1.601 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 110 optimal weight: 10.0000 chunk 55 optimal weight: 10.0000 chunk 83 optimal weight: 4.9990 chunk 23 optimal weight: 20.0000 chunk 51 optimal weight: 7.9990 chunk 34 optimal weight: 5.9990 chunk 65 optimal weight: 0.9980 chunk 15 optimal weight: 10.0000 chunk 44 optimal weight: 4.9990 chunk 33 optimal weight: 0.2980 chunk 77 optimal weight: 9.9990 overall best weight: 3.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1239 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.085685 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.064863 restraints weight = 29949.997| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.066829 restraints weight = 16616.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.068163 restraints weight = 11346.207| |-----------------------------------------------------------------------------| r_work (final): 0.3215 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3215 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3215 r_free = 0.3215 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3215 r_free = 0.3215 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3215 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8151 moved from start: 0.3812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 9393 Z= 0.207 Angle : 0.718 10.522 12837 Z= 0.353 Chirality : 0.047 0.338 1487 Planarity : 0.005 0.072 1622 Dihedral : 7.886 84.664 1547 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.46 % Favored : 92.54 % Rotamer: Outliers : 0.00 % Allowed : 0.41 % Favored : 99.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.56 (0.24), residues: 1153 helix: -0.36 (0.21), residues: 566 sheet: -2.20 (0.51), residues: 84 loop : -1.51 (0.28), residues: 503 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 381 HIS 0.011 0.002 HIS A1042 PHE 0.027 0.002 PHE A1139 TYR 0.022 0.002 TYR A 192 ARG 0.008 0.001 ARG A 78 Details of bonding type rmsd link_NAG-ASN : bond 0.00355 ( 10) link_NAG-ASN : angle 2.74834 ( 30) link_BETA1-4 : bond 0.00916 ( 2) link_BETA1-4 : angle 2.50580 ( 6) link_ALPHA1-3 : bond 0.01668 ( 1) link_ALPHA1-3 : angle 1.12615 ( 3) hydrogen bonds : bond 0.03771 ( 350) hydrogen bonds : angle 4.88810 ( 1014) SS BOND : bond 0.00331 ( 15) SS BOND : angle 1.32956 ( 30) covalent geometry : bond 0.00472 ( 9365) covalent geometry : angle 0.70175 (12768) *********************** 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 120 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 120 time to evaluate : 0.947 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 110 GLU cc_start: 0.7251 (mm-30) cc_final: 0.6926 (mm-30) REVERT: A 194 PHE cc_start: 0.8965 (m-10) cc_final: 0.8764 (m-80) REVERT: A 531 ASP cc_start: 0.8094 (t0) cc_final: 0.7844 (t0) REVERT: A 632 PHE cc_start: 0.7607 (m-80) cc_final: 0.7325 (m-80) REVERT: A 676 SER cc_start: 0.9353 (m) cc_final: 0.9077 (p) REVERT: A 720 LEU cc_start: 0.8803 (pt) cc_final: 0.8423 (tp) REVERT: A 730 GLU cc_start: 0.9034 (tp30) cc_final: 0.8619 (tm-30) REVERT: A 872 MET cc_start: 0.7942 (mmm) cc_final: 0.7506 (mmm) REVERT: A 996 MET cc_start: 0.9216 (mtp) cc_final: 0.8773 (ttm) REVERT: A 1055 LEU cc_start: 0.9130 (tp) cc_final: 0.8899 (tp) REVERT: A 1150 ASN cc_start: 0.9007 (p0) cc_final: 0.8127 (p0) REVERT: A 1166 GLU cc_start: 0.8176 (tp30) cc_final: 0.7930 (tp30) REVERT: A 1175 PHE cc_start: 0.8546 (t80) cc_final: 0.8212 (t80) outliers start: 0 outliers final: 0 residues processed: 120 average time/residue: 0.2683 time to fit residues: 49.1376 Evaluate side-chains 91 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 91 time to evaluate : 1.042 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 29 optimal weight: 0.5980 chunk 114 optimal weight: 0.9980 chunk 100 optimal weight: 1.9990 chunk 28 optimal weight: 7.9990 chunk 99 optimal weight: 0.7980 chunk 67 optimal weight: 0.0370 chunk 32 optimal weight: 3.9990 chunk 13 optimal weight: 10.0000 chunk 55 optimal weight: 10.0000 chunk 85 optimal weight: 0.9990 chunk 34 optimal weight: 6.9990 overall best weight: 0.6860 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1156 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.088998 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.068403 restraints weight = 29850.088| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.070598 restraints weight = 15924.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.072067 restraints weight = 10547.175| |-----------------------------------------------------------------------------| r_work (final): 0.3294 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3294 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3294 r_free = 0.3294 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 = 0.3294 r_free = 0.3294 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3294 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8053 moved from start: 0.3895 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= 0.116 Angle : 0.662 12.644 12837 Z= 0.321 Chirality : 0.044 0.324 1487 Planarity : 0.004 0.072 1622 Dihedral : 7.421 82.582 1547 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 0.00 % Allowed : 0.21 % Favored : 99.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.44 (0.25), residues: 1153 helix: -0.28 (0.22), residues: 562 sheet: -1.89 (0.55), residues: 84 loop : -1.49 (0.28), residues: 507 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 544 HIS 0.008 0.001 HIS A1042 PHE 0.013 0.001 PHE A 399 TYR 0.023 0.001 TYR A 192 ARG 0.007 0.000 ARG A 78 Details of bonding type rmsd link_NAG-ASN : bond 0.00541 ( 10) link_NAG-ASN : angle 2.51969 ( 30) link_BETA1-4 : bond 0.01036 ( 2) link_BETA1-4 : angle 2.26163 ( 6) link_ALPHA1-3 : bond 0.01451 ( 1) link_ALPHA1-3 : angle 0.98948 ( 3) hydrogen bonds : bond 0.03284 ( 350) hydrogen bonds : angle 4.72673 ( 1014) SS BOND : bond 0.00305 ( 15) SS BOND : angle 1.24206 ( 30) covalent geometry : bond 0.00253 ( 9365) covalent geometry : angle 0.64757 (12768) ********************** 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 124 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 124 time to evaluate : 0.945 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 110 GLU cc_start: 0.7176 (mm-30) cc_final: 0.6857 (mm-30) REVERT: A 194 PHE cc_start: 0.8982 (m-10) cc_final: 0.8778 (m-80) REVERT: A 531 ASP cc_start: 0.7944 (t0) cc_final: 0.7716 (t0) REVERT: A 632 PHE cc_start: 0.7532 (m-80) cc_final: 0.7281 (m-80) REVERT: A 676 SER cc_start: 0.9322 (m) cc_final: 0.9072 (p) REVERT: A 730 GLU cc_start: 0.8960 (tp30) cc_final: 0.8607 (tm-30) REVERT: A 872 MET cc_start: 0.7692 (mmm) cc_final: 0.7401 (mmt) REVERT: A 907 MET cc_start: 0.8471 (mmm) cc_final: 0.8091 (mmm) REVERT: A 945 ASP cc_start: 0.8683 (t70) cc_final: 0.8432 (t70) REVERT: A 996 MET cc_start: 0.9107 (mtp) cc_final: 0.8692 (ttm) REVERT: A 1001 MET cc_start: 0.8622 (pmm) cc_final: 0.8339 (pmm) REVERT: A 1063 SER cc_start: 0.9252 (t) cc_final: 0.8962 (p) REVERT: A 1150 ASN cc_start: 0.8880 (p0) cc_final: 0.7985 (p0) REVERT: A 1159 MET cc_start: 0.8405 (ttm) cc_final: 0.8059 (ttp) REVERT: A 1166 GLU cc_start: 0.7971 (tp30) cc_final: 0.7605 (tp30) REVERT: A 1175 PHE cc_start: 0.8507 (t80) cc_final: 0.8158 (t80) outliers start: 0 outliers final: 0 residues processed: 124 average time/residue: 0.1692 time to fit residues: 31.8178 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 : 0.898 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 99 optimal weight: 0.0870 chunk 18 optimal weight: 30.0000 chunk 69 optimal weight: 4.9990 chunk 83 optimal weight: 6.9990 chunk 49 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 92 optimal weight: 9.9990 chunk 104 optimal weight: 4.9990 chunk 0 optimal weight: 30.0000 chunk 3 optimal weight: 8.9990 chunk 82 optimal weight: 0.5980 overall best weight: 1.9364 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3615 r_free = 0.3615 target = 0.087730 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.067122 restraints weight = 30269.616| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.069180 restraints weight = 16446.057| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.070626 restraints weight = 11111.207| |-----------------------------------------------------------------------------| r_work (final): 0.3262 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3262 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3262 r_free = 0.3262 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3262 r_free = 0.3262 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3262 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8094 moved from start: 0.3964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 9393 Z= 0.144 Angle : 0.671 11.312 12837 Z= 0.325 Chirality : 0.045 0.326 1487 Planarity : 0.004 0.071 1622 Dihedral : 7.624 87.625 1547 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.90 % Favored : 94.10 % Rotamer: Outliers : 0.00 % Allowed : 0.21 % Favored : 99.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.42 (0.25), residues: 1153 helix: -0.28 (0.22), residues: 569 sheet: -1.90 (0.55), residues: 84 loop : -1.45 (0.28), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 544 HIS 0.009 0.001 HIS A1042 PHE 0.030 0.001 PHE A 937 TYR 0.022 0.001 TYR A 192 ARG 0.007 0.000 ARG A 78 Details of bonding type rmsd link_NAG-ASN : bond 0.00404 ( 10) link_NAG-ASN : angle 2.48724 ( 30) link_BETA1-4 : bond 0.00907 ( 2) link_BETA1-4 : angle 2.19164 ( 6) link_ALPHA1-3 : bond 0.01263 ( 1) link_ALPHA1-3 : angle 0.98366 ( 3) hydrogen bonds : bond 0.03219 ( 350) hydrogen bonds : angle 4.73766 ( 1014) SS BOND : bond 0.00310 ( 15) SS BOND : angle 1.28351 ( 30) covalent geometry : bond 0.00330 ( 9365) covalent geometry : angle 0.65701 (12768) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3864.86 seconds wall clock time: 69 minutes 15.42 seconds (4155.42 seconds total)