Starting phenix.real_space_refine on Fri Sep 11 22:55:40 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6roh_4972/09_2026/6roh_4972.cif Found real_map, /net/cci-nas-00/data/ceres_data/6roh_4972/09_2026/6roh_4972.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/6roh_4972/09_2026/6roh_4972.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6roh_4972/09_2026/6roh_4972.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6roh_4972/09_2026/6roh_4972.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6roh_4972/09_2026/6roh_4972.map" model { file = "/net/cci-nas-00/data/ceres_data/6roh_4972/09_2026/6roh_4972.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6roh_4972/09_2026/6roh_4972.cif" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 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: 8 Type Number sf(0) Gaussians P 1 5.49 5 Mg 1 5.21 5 S 48 5.16 5 Be 1 3.05 5 C 7580 2.51 5 N 1917 2.21 5 O 2207 1.98 5 F 3 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 66 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 11758 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 8895 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1112, 8895 Classifications: {'peptide': 1112} Link IDs: {'PTRANS': 30, 'TRANS': 1081} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Chain: "C" Number of atoms: 2738 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 2738 Classifications: {'peptide': 337} Link IDs: {'PTRANS': 20, 'TRANS': 316} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 2, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 31 Unusual residues: {' MG': 1, 'PSF': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Time building chain proxies: 2.76, per 1000 atoms: 0.23 Number of scatterers: 11758 At special positions: 0 Unit cell: (74.313, 96.93, 173.397, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) S 48 16.00 P 1 15.00 Mg 1 11.99 F 3 9.00 O 2207 8.00 N 1917 7.00 C 7580 6.00 Be 1 4.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS C 80 " - pdb=" SG CYS C 123 " distance=2.03 Simple disulfide: pdb=" SG CYS C 176 " - pdb=" SG CYS C 190 " distance=2.05 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 BETA1-3 " BMA D 3 " - " BMA D 4 " BETA1-4 " NAG B 1 " - " NAG B 2 " " NAG D 1 " - " NAG D 2 " " NAG D 2 " - " BMA D 3 " NAG-ASN " NAG B 1 " - " ASN C 288 " " NAG C 503 " - " ASN C 216 " " NAG D 1 " - " ASN C 199 " Time building additional restraints: 1.07 Conformation dependent library (CDL) restraints added in 547.8 milliseconds 2880 Ramachandran restraints generated. 1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2740 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 12 sheets defined 41.0% alpha, 14.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.33 Creating SS restraints... Processing helix chain 'A' and resid 212 through 223 removed outlier: 3.845A pdb=" N LYS A 216 " --> pdb=" O THR A 212 " (cutoff:3.500A) Processing helix chain 'A' and resid 225 through 237 removed outlier: 3.658A pdb=" N LEU A 231 " --> pdb=" O ASN A 227 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ALA A 235 " --> pdb=" O LEU A 231 " (cutoff:3.500A) Processing helix chain 'A' and resid 248 through 270 removed outlier: 3.587A pdb=" N THR A 253 " --> pdb=" O THR A 249 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ALA A 262 " --> pdb=" O LEU A 258 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLU A 268 " --> pdb=" O LYS A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 275 removed outlier: 3.600A pdb=" N SER A 275 " --> pdb=" O LYS A 271 " (cutoff:3.500A) Processing helix chain 'A' and resid 276 through 281 removed outlier: 3.635A pdb=" N ASN A 280 " --> pdb=" O ASP A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 438 through 473 removed outlier: 3.758A pdb=" N ARG A 446 " --> pdb=" O LYS A 442 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ILE A 449 " --> pdb=" O ASN A 445 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N VAL A 454 " --> pdb=" O ALA A 450 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N VAL A 457 " --> pdb=" O THR A 453 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ASN A 466 " --> pdb=" O SER A 462 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N VAL A 467 " --> pdb=" O SER A 463 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N THR A 471 " --> pdb=" O VAL A 467 " (cutoff:3.500A) Processing helix chain 'A' and resid 488 through 502 removed outlier: 3.832A pdb=" N PHE A 492 " --> pdb=" O ALA A 488 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N THR A 497 " --> pdb=" O LYS A 493 " (cutoff:3.500A) Processing helix chain 'A' and resid 503 through 506 removed outlier: 3.517A pdb=" N VAL A 506 " --> pdb=" O SER A 503 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 503 through 506' Processing helix chain 'A' and resid 510 through 526 removed outlier: 3.508A pdb=" N LEU A 516 " --> pdb=" O VAL A 512 " (cutoff:3.500A) Processing helix chain 'A' and resid 544 through 552 removed outlier: 3.846A pdb=" N LEU A 547 " --> pdb=" O THR A 544 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N VAL A 548 " --> pdb=" O SER A 545 " (cutoff:3.500A) removed outlier: 5.246A pdb=" N GLU A 549 " --> pdb=" O SER A 546 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N GLU A 550 " --> pdb=" O LEU A 547 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LEU A 551 " --> pdb=" O VAL A 548 " (cutoff:3.500A) Processing helix chain 'A' and resid 605 through 613 Processing helix chain 'A' and resid 618 through 631 removed outlier: 4.526A pdb=" N ILE A 622 " --> pdb=" O GLU A 618 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N PHE A 626 " --> pdb=" O ILE A 622 " (cutoff:3.500A) Processing helix chain 'A' and resid 652 through 664 removed outlier: 3.510A pdb=" N VAL A 659 " --> pdb=" O GLU A 655 " (cutoff:3.500A) Processing helix chain 'A' and resid 723 through 728 Processing helix chain 'A' and resid 738 through 751 removed outlier: 3.767A pdb=" N ARG A 744 " --> pdb=" O GLU A 740 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N HIS A 745 " --> pdb=" O ALA A 741 " (cutoff:3.500A) Processing helix chain 'A' and resid 769 through 781 removed outlier: 3.747A pdb=" N SER A 774 " --> pdb=" O GLU A 770 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ILE A 775 " --> pdb=" O GLU A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 789 through 795 Processing helix chain 'A' and resid 816 through 827 Processing helix chain 'A' and resid 838 through 849 removed outlier: 3.533A pdb=" N ASN A 844 " --> pdb=" O GLU A 840 " (cutoff:3.500A) Processing helix chain 'A' and resid 865 through 881 removed outlier: 3.759A pdb=" N GLU A 870 " --> pdb=" O ARG A 866 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ALA A 879 " --> pdb=" O GLU A 875 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ASN A 881 " --> pdb=" O ILE A 877 " (cutoff:3.500A) Processing helix chain 'A' and resid 889 through 891 No H-bonds generated for 'chain 'A' and resid 889 through 891' Processing helix chain 'A' and resid 899 through 905 removed outlier: 3.546A pdb=" N PHE A 904 " --> pdb=" O LYS A 900 " (cutoff:3.500A) Processing helix chain 'A' and resid 910 through 919 removed outlier: 3.591A pdb=" N VAL A 917 " --> pdb=" O TYR A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 932 through 943 removed outlier: 3.969A pdb=" N VAL A 938 " --> pdb=" O LYS A 934 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ARG A 943 " --> pdb=" O LYS A 939 " (cutoff:3.500A) Processing helix chain 'A' and resid 955 through 958 removed outlier: 3.603A pdb=" N ASP A 958 " --> pdb=" O GLY A 955 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 955 through 958' Processing helix chain 'A' and resid 959 through 964 Processing helix chain 'A' and resid 978 through 983 removed outlier: 3.586A pdb=" N SER A 982 " --> pdb=" O GLN A 978 " (cutoff:3.500A) Processing helix chain 'A' and resid 989 through 991 No H-bonds generated for 'chain 'A' and resid 989 through 991' Processing helix chain 'A' and resid 992 through 999 Processing helix chain 'A' and resid 999 through 1019 removed outlier: 3.667A pdb=" N ILE A1008 " --> pdb=" O SER A1004 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N VAL A1010 " --> pdb=" O GLN A1006 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N SER A1015 " --> pdb=" O ALA A1011 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ASN A1019 " --> pdb=" O SER A1015 " (cutoff:3.500A) Processing helix chain 'A' and resid 1019 through 1024 removed outlier: 3.629A pdb=" N TYR A1023 " --> pdb=" O ASN A1019 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N MET A1024 " --> pdb=" O THR A1020 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1019 through 1024' Processing helix chain 'A' and resid 1024 through 1029 Processing helix chain 'A' and resid 1030 through 1032 No H-bonds generated for 'chain 'A' and resid 1030 through 1032' Processing helix chain 'A' and resid 1046 through 1052 removed outlier: 4.175A pdb=" N ASN A1050 " --> pdb=" O MET A1046 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LEU A1051 " --> pdb=" O SER A1047 " (cutoff:3.500A) Processing helix chain 'A' and resid 1055 through 1065 removed outlier: 3.533A pdb=" N PHE A1059 " --> pdb=" O VAL A1055 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLY A1062 " --> pdb=" O PRO A1058 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N ASP A1065 " --> pdb=" O ILE A1061 " (cutoff:3.500A) Processing helix chain 'A' and resid 1069 through 1076 removed outlier: 3.640A pdb=" N GLU A1074 " --> pdb=" O SER A1070 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ARG A1075 " --> pdb=" O ARG A1071 " (cutoff:3.500A) Processing helix chain 'A' and resid 1077 through 1079 No H-bonds generated for 'chain 'A' and resid 1077 through 1079' Processing helix chain 'A' and resid 1080 through 1085 removed outlier: 3.520A pdb=" N GLN A1084 " --> pdb=" O TYR A1080 " (cutoff:3.500A) Processing helix chain 'A' and resid 1094 through 1115 removed outlier: 3.629A pdb=" N ASN A1100 " --> pdb=" O GLY A1096 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ILE A1107 " --> pdb=" O PHE A1103 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LEU A1114 " --> pdb=" O ILE A1110 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ILE A1115 " --> pdb=" O GLY A1111 " (cutoff:3.500A) Processing helix chain 'A' and resid 1130 through 1154 removed outlier: 3.685A pdb=" N THR A1137 " --> pdb=" O SER A1133 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N VAL A1146 " --> pdb=" O SER A1142 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU A1152 " --> pdb=" O GLY A1148 " (cutoff:3.500A) Processing helix chain 'A' and resid 1168 through 1180 Proline residue: A1177 - end of helix Processing helix chain 'A' and resid 1181 through 1187 Proline residue: A1184 - end of helix Processing helix chain 'A' and resid 1194 through 1201 Processing helix chain 'A' and resid 1202 through 1209 removed outlier: 3.957A pdb=" N TRP A1206 " --> pdb=" O SER A1202 " (cutoff:3.500A) Processing helix chain 'A' and resid 1211 through 1217 Processing helix chain 'A' and resid 1217 through 1230 Processing helix chain 'A' and resid 1253 through 1258 removed outlier: 3.968A pdb=" N GLN A1257 " --> pdb=" O VAL A1253 " (cutoff:3.500A) Processing helix chain 'A' and resid 1259 through 1263 removed outlier: 3.604A pdb=" N LYS A1262 " --> pdb=" O ALA A1259 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N VAL A1263 " --> pdb=" O ILE A1260 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1259 through 1263' Processing helix chain 'A' and resid 1280 through 1284 removed outlier: 4.253A pdb=" N GLY A1284 " --> pdb=" O GLU A1281 " (cutoff:3.500A) Processing helix chain 'C' and resid 45 through 56 Processing helix chain 'C' and resid 56 through 61 Processing helix chain 'C' and resid 63 through 68 removed outlier: 3.529A pdb=" N ALA C 67 " --> pdb=" O LEU C 63 " (cutoff:3.500A) Processing helix chain 'C' and resid 93 through 95 No H-bonds generated for 'chain 'C' and resid 93 through 95' Processing helix chain 'C' and resid 150 through 155 removed outlier: 4.358A pdb=" N GLN C 155 " --> pdb=" O ARG C 151 " (cutoff:3.500A) Processing helix chain 'C' and resid 158 through 164 Processing helix chain 'C' and resid 191 through 196 Processing helix chain 'C' and resid 226 through 231 Processing helix chain 'C' and resid 266 through 274 removed outlier: 3.749A pdb=" N VAL C 271 " --> pdb=" O GLU C 267 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N TRP C 272 " --> pdb=" O GLU C 268 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ARG C 274 " --> pdb=" O GLN C 270 " (cutoff:3.500A) Processing helix chain 'C' and resid 330 through 346 Processing helix chain 'C' and resid 349 through 356 removed outlier: 3.806A pdb=" N LYS C 353 " --> pdb=" O ILE C 349 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N LEU C 354 " --> pdb=" O PHE C 350 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N ILE C 355 " --> pdb=" O LEU C 351 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N PHE C 356 " --> pdb=" O VAL C 352 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 349 through 356' Processing sheet with id=AA1, first strand: chain 'A' and resid 183 through 186 Processing sheet with id=AA2, first strand: chain 'A' and resid 293 through 298 removed outlier: 3.929A pdb=" N ASP A 293 " --> pdb=" O SER A 288 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N SER A 288 " --> pdb=" O ASP A 293 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N GLU A 285 " --> pdb=" O ARG A 309 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 314 through 315 removed outlier: 3.763A pdb=" N GLU A 314 " --> pdb=" O LEU A 407 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N TYR A 333 " --> pdb=" O ARG A 408 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 400 through 401 removed outlier: 6.676A pdb=" N ASP A 319 " --> pdb=" O ILE A 418 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 541 through 542 removed outlier: 6.636A pdb=" N LEU A 949 " --> pdb=" O VAL A 967 " (cutoff:3.500A) removed outlier: 7.844A pdb=" N VAL A 969 " --> pdb=" O LEU A 949 " (cutoff:3.500A) removed outlier: 6.093A pdb=" N ALA A 951 " --> pdb=" O VAL A 969 " (cutoff:3.500A) removed outlier: 7.632A pdb=" N ILE A 971 " --> pdb=" O ALA A 951 " (cutoff:3.500A) removed outlier: 7.310A pdb=" N GLY A 953 " --> pdb=" O ILE A 971 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N LEU A 948 " --> pdb=" O ILE A 554 " (cutoff:3.500A) removed outlier: 7.084A pdb=" N GLU A 555 " --> pdb=" O LYS A 830 " (cutoff:3.500A) removed outlier: 7.833A pdb=" N TRP A 832 " --> pdb=" O GLU A 555 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N ILE A 557 " --> pdb=" O TRP A 832 " (cutoff:3.500A) removed outlier: 7.147A pdb=" N LEU A 834 " --> pdb=" O ILE A 557 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N SER A 559 " --> pdb=" O LEU A 834 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N ILE A 831 " --> pdb=" O VAL A 924 " (cutoff:3.500A) removed outlier: 8.403A pdb=" N CYS A 926 " --> pdb=" O ILE A 831 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N VAL A 833 " --> pdb=" O CYS A 926 " (cutoff:3.500A) removed outlier: 7.279A pdb=" N LEU A 893 " --> pdb=" O ALA A 923 " (cutoff:3.500A) removed outlier: 8.724A pdb=" N ILE A 925 " --> pdb=" O LEU A 893 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N LEU A 895 " --> pdb=" O ILE A 925 " (cutoff:3.500A) removed outlier: 7.667A pdb=" N CYS A 927 " --> pdb=" O LEU A 895 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N ILE A 897 " --> pdb=" O CYS A 927 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 580 through 583 removed outlier: 6.613A pdb=" N MET A 570 " --> pdb=" O LYS A 812 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N LYS A 812 " --> pdb=" O MET A 570 " (cutoff:3.500A) removed outlier: 5.732A pdb=" N PHE A 572 " --> pdb=" O GLU A 810 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N GLU A 810 " --> pdb=" O PHE A 572 " (cutoff:3.500A) removed outlier: 5.120A pdb=" N LEU A 803 " --> pdb=" O MET A 761 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N MET A 761 " --> pdb=" O LEU A 803 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ASN A 694 " --> pdb=" O ILE A 708 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N ARG A 710 " --> pdb=" O LEU A 692 " (cutoff:3.500A) removed outlier: 5.702A pdb=" N LEU A 692 " --> pdb=" O ARG A 710 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N SER A 676 " --> pdb=" O ARG A 672 " (cutoff:3.500A) removed outlier: 5.001A pdb=" N ARG A 672 " --> pdb=" O SER A 676 " (cutoff:3.500A) removed outlier: 7.378A pdb=" N THR A 678 " --> pdb=" O ILE A 670 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ILE A 670 " --> pdb=" O THR A 678 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 637 through 640 Processing sheet with id=AA8, first strand: chain 'C' and resid 97 through 100 Processing sheet with id=AA9, first strand: chain 'C' and resid 90 through 91 removed outlier: 3.590A pdb=" N GLU C 90 " --> pdb=" O TRP C 111 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLY C 296 " --> pdb=" O ILE C 129 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 90 through 91 removed outlier: 3.590A pdb=" N GLU C 90 " --> pdb=" O TRP C 111 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLY C 296 " --> pdb=" O ILE C 129 " (cutoff:3.500A) removed outlier: 5.429A pdb=" N ASN C 301 " --> pdb=" O VAL C 205 " (cutoff:3.500A) removed outlier: 7.406A pdb=" N VAL C 205 " --> pdb=" O ASN C 301 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 137 through 143 removed outlier: 3.507A pdb=" N ILE C 137 " --> pdb=" O ASN C 288 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N TYR C 141 " --> pdb=" O LEU C 284 " (cutoff:3.500A) removed outlier: 5.918A pdb=" N LEU C 284 " --> pdb=" O TYR C 141 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N ILE C 143 " --> pdb=" O TYR C 282 " (cutoff:3.500A) removed outlier: 5.656A pdb=" N TYR C 282 " --> pdb=" O ILE C 143 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 186 through 187 removed outlier: 6.099A pdb=" N ILE C 186 " --> pdb=" O VAL C 242 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 405 hydrogen bonds defined for protein. 1161 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: 2.41 Time building geometry restraints manager: 1.33 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3276 1.33 - 1.46: 2850 1.46 - 1.58: 5813 1.58 - 1.71: 2 1.71 - 1.83: 77 Bond restraints: 12018 Sorted by residual: bond pdb=" OD1 BFD A 560 " pdb="BE BFD A 560 " ideal model delta sigma weight residual 1.737 1.527 0.210 2.00e-02 2.50e+03 1.10e+02 bond pdb=" O2 PSF A2101 " pdb=" P PSF A2101 " ideal model delta sigma weight residual 1.637 1.701 -0.064 2.00e-02 2.50e+03 1.03e+01 bond pdb=" C1 BMA D 4 " pdb=" C2 BMA D 4 " ideal model delta sigma weight residual 1.519 1.578 -0.059 2.00e-02 2.50e+03 8.63e+00 bond pdb=" CA ASP A 189 " pdb=" CB ASP A 189 " ideal model delta sigma weight residual 1.523 1.555 -0.032 1.35e-02 5.49e+03 5.59e+00 bond pdb=" CA BFD A 560 " pdb=" C BFD A 560 " ideal model delta sigma weight residual 1.525 1.570 -0.045 2.10e-02 2.27e+03 4.52e+00 ... (remaining 12013 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.04: 15686 2.04 - 4.08: 512 4.08 - 6.13: 58 6.13 - 8.17: 18 8.17 - 10.21: 9 Bond angle restraints: 16283 Sorted by residual: angle pdb=" N ILE A1174 " pdb=" CA ILE A1174 " pdb=" C ILE A1174 " ideal model delta sigma weight residual 111.90 107.86 4.04 8.10e-01 1.52e+00 2.48e+01 angle pdb=" C ASP A 784 " pdb=" N ASN A 785 " pdb=" CA ASN A 785 " ideal model delta sigma weight residual 121.54 130.54 -9.00 1.91e+00 2.74e-01 2.22e+01 angle pdb=" C CYS C 176 " pdb=" N SER C 177 " pdb=" CA SER C 177 " ideal model delta sigma weight residual 119.78 125.42 -5.64 1.24e+00 6.50e-01 2.07e+01 angle pdb=" CA CYS C 176 " pdb=" CB CYS C 176 " pdb=" SG CYS C 176 " ideal model delta sigma weight residual 114.40 123.44 -9.04 2.30e+00 1.89e-01 1.55e+01 angle pdb=" C PRO A 240 " pdb=" N HIS A 241 " pdb=" CA HIS A 241 " ideal model delta sigma weight residual 123.47 129.36 -5.89 1.53e+00 4.27e-01 1.48e+01 ... (remaining 16278 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.98: 6278 15.98 - 31.96: 677 31.96 - 47.95: 125 47.95 - 63.93: 25 63.93 - 79.91: 7 Dihedral angle restraints: 7112 sinusoidal: 2864 harmonic: 4248 Sorted by residual: dihedral pdb=" CA LEU A1114 " pdb=" C LEU A1114 " pdb=" N ILE A1115 " pdb=" CA ILE A1115 " ideal model delta harmonic sigma weight residual 180.00 152.62 27.38 0 5.00e+00 4.00e-02 3.00e+01 dihedral pdb=" CA THR C 320 " pdb=" C THR C 320 " pdb=" N THR C 321 " pdb=" CA THR C 321 " ideal model delta harmonic sigma weight residual 180.00 155.22 24.78 0 5.00e+00 4.00e-02 2.46e+01 dihedral pdb=" CA LEU A 490 " pdb=" C LEU A 490 " pdb=" N PHE A 491 " pdb=" CA PHE A 491 " ideal model delta harmonic sigma weight residual 180.00 158.20 21.80 0 5.00e+00 4.00e-02 1.90e+01 ... (remaining 7109 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 1427 0.059 - 0.118: 351 0.118 - 0.177: 63 0.177 - 0.236: 13 0.236 - 0.295: 1 Chirality restraints: 1855 Sorted by residual: chirality pdb=" C5 BMA D 4 " pdb=" C4 BMA D 4 " pdb=" C6 BMA D 4 " pdb=" O5 BMA D 4 " both_signs ideal model delta sigma weight residual False -2.27 -2.57 0.29 2.00e-01 2.50e+01 2.17e+00 chirality pdb=" C5 BMA D 3 " pdb=" C4 BMA D 3 " pdb=" C6 BMA D 3 " pdb=" O5 BMA D 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.51 0.23 2.00e-01 2.50e+01 1.36e+00 chirality pdb=" CG LEU A 480 " pdb=" CB LEU A 480 " pdb=" CD1 LEU A 480 " pdb=" CD2 LEU A 480 " both_signs ideal model delta sigma weight residual False -2.59 -2.36 -0.23 2.00e-01 2.50e+01 1.31e+00 ... (remaining 1852 not shown) Planarity restraints: 2042 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP C 111 " 0.026 2.00e-02 2.50e+03 2.60e-02 1.68e+01 pdb=" CG TRP C 111 " -0.071 2.00e-02 2.50e+03 pdb=" CD1 TRP C 111 " 0.031 2.00e-02 2.50e+03 pdb=" CD2 TRP C 111 " 0.003 2.00e-02 2.50e+03 pdb=" NE1 TRP C 111 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP C 111 " 0.003 2.00e-02 2.50e+03 pdb=" CE3 TRP C 111 " 0.009 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 111 " 0.004 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 111 " 0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP C 111 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO A1057 " 0.049 5.00e-02 4.00e+02 7.29e-02 8.51e+00 pdb=" N PRO A1058 " -0.126 5.00e-02 4.00e+02 pdb=" CA PRO A1058 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO A1058 " 0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA MET A 977 " 0.013 2.00e-02 2.50e+03 2.71e-02 7.37e+00 pdb=" C MET A 977 " -0.047 2.00e-02 2.50e+03 pdb=" O MET A 977 " 0.018 2.00e-02 2.50e+03 pdb=" N GLN A 978 " 0.016 2.00e-02 2.50e+03 ... (remaining 2039 not shown) Histogram of nonbonded interaction distances: 1.71 - 2.35: 20 2.35 - 2.99: 5542 2.99 - 3.62: 16798 3.62 - 4.26: 28335 4.26 - 4.90: 46220 Nonbonded interactions: 96915 Sorted by model distance: nonbonded pdb=" F2 BFD A 560 " pdb="MG MG A2102 " model vdw 1.709 2.120 nonbonded pdb="MG MG A2102 " pdb=" O HOH A2201 " model vdw 1.742 2.170 nonbonded pdb="MG MG A2102 " pdb=" O HOH A2202 " model vdw 1.906 2.170 nonbonded pdb=" O THR A 562 " pdb=" O HOH A2201 " model vdw 1.909 3.040 nonbonded pdb=" O THR A 562 " pdb="MG MG A2102 " model vdw 2.042 2.170 ... (remaining 96910 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.470 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: 0.200 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 12.400 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.010 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7865 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 : 0.006 0.210 12027 Z= 0.282 Angle : 0.901 10.208 16308 Z= 0.504 Chirality : 0.055 0.295 1855 Planarity : 0.006 0.073 2039 Dihedral : 13.561 79.911 4366 Min Nonbonded Distance : 1.709 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 0.23 % Allowed : 5.71 % Favored : 94.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.73 (0.17), residues: 1440 helix: -4.68 (0.08), residues: 565 sheet: -1.21 (0.33), residues: 234 loop : -2.22 (0.20), residues: 641 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 755 TYR 0.018 0.002 TYR C 141 PHE 0.028 0.002 PHE A1094 TRP 0.071 0.002 TRP C 111 HIS 0.010 0.001 HIS A 634 Details of bonding type rmsd/Z covalent geometry : bond 0.00626 / 0.28 (12018) covalent geometry : angle 0.89285 / 0.50 (16283) SS BOND : bond 0.01207 / 0.86 ( 2) SS BOND : angle 1.31670 / 0.79 ( 4) hydrogen bonds : bond 0.29641 / 19.01 ( 393) hydrogen bonds : angle 9.95180 / 6.96 ( 1161) link_BETA1-3 : bond 0.00377 / 0.25 ( 1) link_BETA1-3 : angle 2.63258 / 1.58 ( 3) link_BETA1-4 : bond 0.00720 / 0.42 ( 3) link_BETA1-4 : angle 1.79778 / 1.10 ( 9) link_NAG-ASN : bond 0.00573 / 0.39 ( 3) link_NAG-ASN : angle 4.74640 / 3.25 ( 9) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2880 Ramachandran restraints generated. 1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2880 Ramachandran restraints generated. 1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 223 time to evaluate : 0.464 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 204 SER cc_start: 0.7218 (p) cc_final: 0.6901 (p) REVERT: A 263 MET cc_start: 0.6907 (mtt) cc_final: 0.6519 (mmp) REVERT: A 291 HIS cc_start: 0.6491 (t70) cc_final: 0.6291 (t70) REVERT: A 335 GLU cc_start: 0.7569 (tt0) cc_final: 0.7328 (tt0) REVERT: A 356 LYS cc_start: 0.7472 (mmtm) cc_final: 0.7268 (mtpt) REVERT: A 400 MET cc_start: 0.7561 (ttt) cc_final: 0.7156 (tpt) REVERT: A 469 MET cc_start: 0.8151 (ttm) cc_final: 0.7885 (mtp) REVERT: A 520 TYR cc_start: 0.6702 (t80) cc_final: 0.6416 (t80) REVERT: A 535 LYS cc_start: 0.8221 (tttm) cc_final: 0.7594 (ttmm) REVERT: A 540 THR cc_start: 0.8625 (t) cc_final: 0.8351 (m) REVERT: A 571 GLU cc_start: 0.7089 (tt0) cc_final: 0.6641 (mt-10) REVERT: A 604 LYS cc_start: 0.7763 (mtpp) cc_final: 0.7562 (mtpp) REVERT: A 724 ASP cc_start: 0.8116 (p0) cc_final: 0.7845 (p0) REVERT: A 838 ARG cc_start: 0.7376 (mtm-85) cc_final: 0.7162 (mtt90) REVERT: A 856 MET cc_start: 0.8409 (ttt) cc_final: 0.8168 (ttm) REVERT: A 871 ARG cc_start: 0.7778 (mtt180) cc_final: 0.7532 (mtp180) REVERT: A 881 ASN cc_start: 0.7158 (t0) cc_final: 0.6082 (p0) REVERT: A 1156 GLN cc_start: 0.8369 (tt0) cc_final: 0.7814 (tt0) REVERT: A 1269 MET cc_start: 0.7130 (mmm) cc_final: 0.6799 (mmp) REVERT: A 1285 GLN cc_start: 0.7973 (pm20) cc_final: 0.7503 (pm20) REVERT: A 1296 GLN cc_start: 0.7576 (tt0) cc_final: 0.7130 (tt0) REVERT: C 114 THR cc_start: 0.8176 (m) cc_final: 0.7802 (m) REVERT: C 124 GLU cc_start: 0.8035 (mt-10) cc_final: 0.7616 (mt-10) REVERT: C 135 LYS cc_start: 0.8146 (mttt) cc_final: 0.7495 (ttpp) REVERT: C 197 MET cc_start: 0.8891 (ttt) cc_final: 0.8654 (ttt) REVERT: C 229 HIS cc_start: 0.7194 (m90) cc_final: 0.6638 (m-70) REVERT: C 250 LYS cc_start: 0.8486 (ttmm) cc_final: 0.8164 (tttt) REVERT: C 295 LYS cc_start: 0.8156 (ttpt) cc_final: 0.7598 (tptt) outliers start: 3 outliers final: 1 residues processed: 225 average time/residue: 0.5870 time to fit residues: 143.0232 Evaluate side-chains 131 residues out of total 1279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 130 time to evaluate : 0.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 877 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 0.6980 chunk 130 optimal weight: 0.8980 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 0.9980 chunk 77 optimal weight: 0.7980 chunk 122 optimal weight: 0.6980 chunk 91 optimal weight: 0.7980 chunk 55 optimal weight: 6.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 227 ASN A 422 HIS A 580 HIS A 649 GLN A 694 ASN A 736 ASN A 839 GLN A 862 ASN A 891 ASN A1019 ASN A1038 GLN A1050 ASN C 30 GLN C 37 GLN C 121 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.154962 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.122266 restraints weight = 13626.554| |-----------------------------------------------------------------------------| r_work (start): 0.3450 rms_B_bonded: 2.08 r_work: 0.3214 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3083 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3083 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8368 moved from start: 0.1549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 12027 Z= 0.144 Angle : 0.621 9.258 16308 Z= 0.327 Chirality : 0.044 0.163 1855 Planarity : 0.005 0.047 2039 Dihedral : 5.951 42.900 1580 Min Nonbonded Distance : 1.838 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 2.19 % Allowed : 12.67 % Favored : 85.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.33 (0.19), residues: 1440 helix: -3.01 (0.15), residues: 585 sheet: -0.95 (0.33), residues: 230 loop : -1.68 (0.22), residues: 625 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 230 TYR 0.011 0.001 TYR C 188 PHE 0.021 0.001 PHE A1094 TRP 0.023 0.001 TRP C 111 HIS 0.006 0.001 HIS A 634 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.14 (12018) covalent geometry : angle 0.61381 / 0.33 (16283) SS BOND : bond 0.00754 / 0.54 ( 2) SS BOND : angle 0.89386 / 0.51 ( 4) hydrogen bonds : bond 0.05252 / 3.35 ( 393) hydrogen bonds : angle 5.28840 / 3.67 ( 1161) link_BETA1-3 : bond 0.00841 / 0.56 ( 1) link_BETA1-3 : angle 2.55000 / 1.56 ( 3) link_BETA1-4 : bond 0.00638 / 0.36 ( 3) link_BETA1-4 : angle 1.73055 / 1.13 ( 9) link_NAG-ASN : bond 0.00328 / 0.20 ( 3) link_NAG-ASN : angle 3.25127 / 2.33 ( 9) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2880 Ramachandran restraints generated. 1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2880 Ramachandran restraints generated. 1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 148 time to evaluate : 0.469 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 263 MET cc_start: 0.7729 (mtt) cc_final: 0.7176 (mmp) REVERT: A 342 GLU cc_start: 0.8188 (mt-10) cc_final: 0.7907 (mt-10) REVERT: A 356 LYS cc_start: 0.7569 (mmtm) cc_final: 0.7205 (mtmt) REVERT: A 364 LYS cc_start: 0.8269 (pttm) cc_final: 0.7793 (ptmm) REVERT: A 385 THR cc_start: 0.8269 (m) cc_final: 0.8016 (t) REVERT: A 401 ILE cc_start: 0.8429 (OUTLIER) cc_final: 0.7855 (mt) REVERT: A 469 MET cc_start: 0.8400 (ttm) cc_final: 0.8183 (ttt) REVERT: A 490 LEU cc_start: 0.6235 (pp) cc_final: 0.5877 (mp) REVERT: A 535 LYS cc_start: 0.8462 (tttm) cc_final: 0.7868 (ttmm) REVERT: A 571 GLU cc_start: 0.8201 (tt0) cc_final: 0.7721 (mt-10) REVERT: A 838 ARG cc_start: 0.7996 (mtm-85) cc_final: 0.7357 (mmt-90) REVERT: A 871 ARG cc_start: 0.8245 (mtt180) cc_final: 0.8042 (mtt180) REVERT: A 1155 ASN cc_start: 0.7332 (m-40) cc_final: 0.6988 (m110) REVERT: A 1156 GLN cc_start: 0.8550 (tt0) cc_final: 0.8039 (tt0) REVERT: A 1296 GLN cc_start: 0.7782 (tt0) cc_final: 0.7310 (tt0) REVERT: C 47 PRO cc_start: 0.6917 (Cg_exo) cc_final: 0.6667 (Cg_endo) REVERT: C 135 LYS cc_start: 0.8482 (mttt) cc_final: 0.7811 (ttpp) REVERT: C 197 MET cc_start: 0.9195 (ttt) cc_final: 0.8992 (ttt) REVERT: C 229 HIS cc_start: 0.7608 (m90) cc_final: 0.7183 (m-70) REVERT: C 295 LYS cc_start: 0.8506 (ttpt) cc_final: 0.7888 (tptt) outliers start: 28 outliers final: 10 residues processed: 168 average time/residue: 0.4977 time to fit residues: 91.9026 Evaluate side-chains 134 residues out of total 1279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 123 time to evaluate : 0.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 288 SER Chi-restraints excluded: chain A residue 401 ILE Chi-restraints excluded: chain A residue 643 ASP Chi-restraints excluded: chain A residue 804 ILE Chi-restraints excluded: chain A residue 867 ASP Chi-restraints excluded: chain A residue 880 LEU Chi-restraints excluded: chain A residue 920 LEU Chi-restraints excluded: chain A residue 959 VAL Chi-restraints excluded: chain A residue 1069 SER Chi-restraints excluded: chain A residue 1115 ILE Chi-restraints excluded: chain C residue 285 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 25 optimal weight: 6.9990 chunk 98 optimal weight: 1.9990 chunk 76 optimal weight: 4.9990 chunk 15 optimal weight: 3.9990 chunk 69 optimal weight: 0.7980 chunk 58 optimal weight: 0.9990 chunk 36 optimal weight: 0.9980 chunk 97 optimal weight: 0.7980 chunk 44 optimal weight: 0.6980 chunk 82 optimal weight: 0.9990 chunk 56 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 291 HIS A 736 ASN A 839 GLN A 862 ASN C 37 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.153859 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.119353 restraints weight = 13601.282| |-----------------------------------------------------------------------------| r_work (start): 0.3416 rms_B_bonded: 2.07 r_work: 0.3188 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3055 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3055 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8400 moved from start: 0.1930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 12027 Z= 0.140 Angle : 0.576 7.585 16308 Z= 0.299 Chirality : 0.044 0.158 1855 Planarity : 0.004 0.041 2039 Dihedral : 5.516 38.143 1578 Min Nonbonded Distance : 1.891 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 2.81 % Allowed : 15.32 % Favored : 81.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.41 (0.20), residues: 1440 helix: -1.98 (0.19), residues: 586 sheet: -0.79 (0.33), residues: 230 loop : -1.35 (0.23), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 230 TYR 0.011 0.001 TYR A 667 PHE 0.021 0.001 PHE A1094 TRP 0.020 0.001 TRP C 111 HIS 0.006 0.001 HIS A 634 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.14 (12018) covalent geometry : angle 0.57025 / 0.30 (16283) SS BOND : bond 0.00642 / 0.46 ( 2) SS BOND : angle 0.91137 / 0.52 ( 4) hydrogen bonds : bond 0.04217 / 2.66 ( 393) hydrogen bonds : angle 4.73277 / 3.28 ( 1161) link_BETA1-3 : bond 0.00661 / 0.44 ( 1) link_BETA1-3 : angle 2.15586 / 1.26 ( 3) link_BETA1-4 : bond 0.00370 / 0.20 ( 3) link_BETA1-4 : angle 1.53731 / 0.99 ( 9) link_NAG-ASN : bond 0.00274 / 0.18 ( 3) link_NAG-ASN : angle 3.07156 / 2.26 ( 9) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2880 Ramachandran restraints generated. 1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2880 Ramachandran restraints generated. 1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 138 time to evaluate : 0.435 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 208 TYR cc_start: 0.7569 (OUTLIER) cc_final: 0.5763 (p90) REVERT: A 263 MET cc_start: 0.7810 (mtt) cc_final: 0.7230 (mmp) REVERT: A 342 GLU cc_start: 0.8231 (mt-10) cc_final: 0.8028 (mt-10) REVERT: A 364 LYS cc_start: 0.8352 (pttm) cc_final: 0.7878 (ptmm) REVERT: A 385 THR cc_start: 0.8329 (m) cc_final: 0.8063 (t) REVERT: A 391 ARG cc_start: 0.7588 (mtp85) cc_final: 0.7342 (mtp85) REVERT: A 400 MET cc_start: 0.8539 (tpt) cc_final: 0.7873 (tpt) REVERT: A 401 ILE cc_start: 0.8512 (OUTLIER) cc_final: 0.7972 (mt) REVERT: A 469 MET cc_start: 0.8406 (ttm) cc_final: 0.8184 (ttt) REVERT: A 490 LEU cc_start: 0.6234 (pp) cc_final: 0.5916 (mp) REVERT: A 535 LYS cc_start: 0.8502 (tttm) cc_final: 0.7920 (ttmm) REVERT: A 549 GLU cc_start: 0.8595 (OUTLIER) cc_final: 0.8034 (pp20) REVERT: A 571 GLU cc_start: 0.8237 (tt0) cc_final: 0.7755 (mt-10) REVERT: A 610 LYS cc_start: 0.8053 (mttm) cc_final: 0.7672 (mmtp) REVERT: A 689 GLU cc_start: 0.8361 (OUTLIER) cc_final: 0.7907 (tm-30) REVERT: A 697 GLU cc_start: 0.7895 (OUTLIER) cc_final: 0.7565 (mm-30) REVERT: A 838 ARG cc_start: 0.8054 (mtm-85) cc_final: 0.7374 (mmt-90) REVERT: A 871 ARG cc_start: 0.8242 (mtt180) cc_final: 0.8042 (mtt180) REVERT: A 1155 ASN cc_start: 0.7329 (m-40) cc_final: 0.7069 (m110) REVERT: A 1296 GLN cc_start: 0.7799 (tt0) cc_final: 0.7323 (tt0) REVERT: C 47 PRO cc_start: 0.6888 (Cg_exo) cc_final: 0.6664 (Cg_endo) REVERT: C 114 THR cc_start: 0.8198 (m) cc_final: 0.7922 (m) REVERT: C 135 LYS cc_start: 0.8525 (mttt) cc_final: 0.7873 (ttpp) REVERT: C 229 HIS cc_start: 0.7584 (m90) cc_final: 0.7152 (m-70) REVERT: C 295 LYS cc_start: 0.8538 (ttpt) cc_final: 0.7922 (tptt) outliers start: 36 outliers final: 17 residues processed: 168 average time/residue: 0.5001 time to fit residues: 92.1306 Evaluate side-chains 141 residues out of total 1279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 119 time to evaluate : 0.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 208 TYR Chi-restraints excluded: chain A residue 288 SER Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 401 ILE Chi-restraints excluded: chain A residue 408 ARG Chi-restraints excluded: chain A residue 480 LEU Chi-restraints excluded: chain A residue 549 GLU Chi-restraints excluded: chain A residue 584 ASP Chi-restraints excluded: chain A residue 620 SER Chi-restraints excluded: chain A residue 622 ILE Chi-restraints excluded: chain A residue 689 GLU Chi-restraints excluded: chain A residue 695 ILE Chi-restraints excluded: chain A residue 697 GLU Chi-restraints excluded: chain A residue 701 THR Chi-restraints excluded: chain A residue 880 LEU Chi-restraints excluded: chain A residue 920 LEU Chi-restraints excluded: chain A residue 959 VAL Chi-restraints excluded: chain A residue 1069 SER Chi-restraints excluded: chain A residue 1093 ILE Chi-restraints excluded: chain A residue 1115 ILE Chi-restraints excluded: chain C residue 222 ILE Chi-restraints excluded: chain C residue 285 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 96 optimal weight: 0.5980 chunk 72 optimal weight: 3.9990 chunk 95 optimal weight: 1.9990 chunk 41 optimal weight: 7.9990 chunk 38 optimal weight: 0.9980 chunk 97 optimal weight: 2.9990 chunk 58 optimal weight: 1.9990 chunk 13 optimal weight: 0.9990 chunk 45 optimal weight: 5.9990 chunk 70 optimal weight: 9.9990 chunk 108 optimal weight: 0.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 291 HIS A 374 GLN A 649 GLN A 736 ASN A1254 GLN C 25 ASN C 37 GLN C 148 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.152953 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.118490 restraints weight = 13609.064| |-----------------------------------------------------------------------------| r_work (start): 0.3402 rms_B_bonded: 2.10 r_work: 0.3170 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3037 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3037 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8408 moved from start: 0.2157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 12027 Z= 0.163 Angle : 0.599 10.887 16308 Z= 0.305 Chirality : 0.045 0.159 1855 Planarity : 0.004 0.041 2039 Dihedral : 5.421 42.737 1578 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 3.05 % Allowed : 16.26 % Favored : 80.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.97 (0.21), residues: 1440 helix: -1.51 (0.20), residues: 590 sheet: -0.64 (0.33), residues: 230 loop : -1.17 (0.23), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1273 TYR 0.012 0.001 TYR C 141 PHE 0.021 0.002 PHE A1094 TRP 0.021 0.001 TRP C 111 HIS 0.008 0.001 HIS A 634 Details of bonding type rmsd/Z covalent geometry : bond 0.00389 / 0.16 (12018) covalent geometry : angle 0.59208 / 0.30 (16283) SS BOND : bond 0.00680 / 0.49 ( 2) SS BOND : angle 1.05773 / 0.60 ( 4) hydrogen bonds : bond 0.04029 / 2.54 ( 393) hydrogen bonds : angle 4.55739 / 3.16 ( 1161) link_BETA1-3 : bond 0.00689 / 0.46 ( 1) link_BETA1-3 : angle 2.01340 / 1.15 ( 3) link_BETA1-4 : bond 0.00294 / 0.18 ( 3) link_BETA1-4 : angle 1.60239 / 1.05 ( 9) link_NAG-ASN : bond 0.00369 / 0.25 ( 3) link_NAG-ASN : angle 3.27169 / 2.44 ( 9) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2880 Ramachandran restraints generated. 1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2880 Ramachandran restraints generated. 1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 127 time to evaluate : 0.450 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 208 TYR cc_start: 0.7727 (OUTLIER) cc_final: 0.5499 (p90) REVERT: A 263 MET cc_start: 0.7754 (mtt) cc_final: 0.7154 (mmp) REVERT: A 342 GLU cc_start: 0.8265 (mt-10) cc_final: 0.8021 (mt-10) REVERT: A 351 ARG cc_start: 0.7992 (OUTLIER) cc_final: 0.7665 (mmm160) REVERT: A 364 LYS cc_start: 0.8389 (pttm) cc_final: 0.7909 (ptmm) REVERT: A 385 THR cc_start: 0.8364 (m) cc_final: 0.8104 (t) REVERT: A 391 ARG cc_start: 0.7586 (mtp85) cc_final: 0.7335 (mtp85) REVERT: A 401 ILE cc_start: 0.8502 (OUTLIER) cc_final: 0.8021 (mt) REVERT: A 469 MET cc_start: 0.8406 (ttm) cc_final: 0.8176 (ttt) REVERT: A 490 LEU cc_start: 0.6146 (pp) cc_final: 0.5854 (mp) REVERT: A 535 LYS cc_start: 0.8526 (tttm) cc_final: 0.7958 (ttmm) REVERT: A 549 GLU cc_start: 0.8655 (OUTLIER) cc_final: 0.8165 (pp20) REVERT: A 571 GLU cc_start: 0.8223 (tt0) cc_final: 0.7738 (mt-10) REVERT: A 689 GLU cc_start: 0.8367 (OUTLIER) cc_final: 0.7965 (tm-30) REVERT: A 697 GLU cc_start: 0.7839 (OUTLIER) cc_final: 0.7534 (mm-30) REVERT: A 838 ARG cc_start: 0.8069 (mtm-85) cc_final: 0.7396 (mmt-90) REVERT: A 1094 PHE cc_start: 0.8348 (OUTLIER) cc_final: 0.7628 (t80) REVERT: A 1190 ARG cc_start: 0.8624 (OUTLIER) cc_final: 0.7939 (mtm180) REVERT: A 1296 GLN cc_start: 0.7891 (tt0) cc_final: 0.7417 (tt0) REVERT: C 47 PRO cc_start: 0.6798 (Cg_exo) cc_final: 0.6566 (Cg_endo) REVERT: C 113 LEU cc_start: 0.8786 (OUTLIER) cc_final: 0.8547 (tt) REVERT: C 135 LYS cc_start: 0.8560 (mttt) cc_final: 0.7836 (ttpp) REVERT: C 229 HIS cc_start: 0.7590 (m90) cc_final: 0.7134 (m-70) REVERT: C 295 LYS cc_start: 0.8504 (ttpt) cc_final: 0.7915 (tptt) outliers start: 39 outliers final: 16 residues processed: 158 average time/residue: 0.5573 time to fit residues: 96.3036 Evaluate side-chains 137 residues out of total 1279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 112 time to evaluate : 0.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 202 HIS Chi-restraints excluded: chain A residue 204 SER Chi-restraints excluded: chain A residue 208 TYR Chi-restraints excluded: chain A residue 288 SER Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 351 ARG Chi-restraints excluded: chain A residue 401 ILE Chi-restraints excluded: chain A residue 408 ARG Chi-restraints excluded: chain A residue 480 LEU Chi-restraints excluded: chain A residue 549 GLU Chi-restraints excluded: chain A residue 577 ILE Chi-restraints excluded: chain A residue 584 ASP Chi-restraints excluded: chain A residue 620 SER Chi-restraints excluded: chain A residue 689 GLU Chi-restraints excluded: chain A residue 695 ILE Chi-restraints excluded: chain A residue 697 GLU Chi-restraints excluded: chain A residue 701 THR Chi-restraints excluded: chain A residue 880 LEU Chi-restraints excluded: chain A residue 1069 SER Chi-restraints excluded: chain A residue 1094 PHE Chi-restraints excluded: chain A residue 1115 ILE Chi-restraints excluded: chain A residue 1190 ARG Chi-restraints excluded: chain C residue 113 LEU Chi-restraints excluded: chain C residue 222 ILE Chi-restraints excluded: chain C residue 285 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 77 optimal weight: 3.9990 chunk 50 optimal weight: 2.9990 chunk 60 optimal weight: 3.9990 chunk 15 optimal weight: 0.9980 chunk 37 optimal weight: 1.9990 chunk 36 optimal weight: 0.8980 chunk 106 optimal weight: 7.9990 chunk 29 optimal weight: 0.8980 chunk 46 optimal weight: 3.9990 chunk 117 optimal weight: 3.9990 chunk 90 optimal weight: 4.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 291 HIS A 649 GLN A 736 ASN A 839 GLN A 862 ASN ** C 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.151126 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.116609 restraints weight = 13553.894| |-----------------------------------------------------------------------------| r_work (start): 0.3377 rms_B_bonded: 2.06 r_work: 0.3141 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3008 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3008 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8441 moved from start: 0.2360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 12027 Z= 0.211 Angle : 0.633 8.779 16308 Z= 0.323 Chirality : 0.046 0.180 1855 Planarity : 0.004 0.042 2039 Dihedral : 5.517 44.491 1578 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 3.83 % Allowed : 16.65 % Favored : 79.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.75 (0.21), residues: 1440 helix: -1.33 (0.20), residues: 592 sheet: -0.46 (0.34), residues: 220 loop : -1.06 (0.24), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 871 TYR 0.013 0.002 TYR C 153 PHE 0.023 0.002 PHE A1094 TRP 0.021 0.002 TRP C 111 HIS 0.009 0.001 HIS A 634 Details of bonding type rmsd/Z covalent geometry : bond 0.00507 / 0.21 (12018) covalent geometry : angle 0.62544 / 0.32 (16283) SS BOND : bond 0.00741 / 0.53 ( 2) SS BOND : angle 1.24444 / 0.68 ( 4) hydrogen bonds : bond 0.04334 / 2.74 ( 393) hydrogen bonds : angle 4.62079 / 3.20 ( 1161) link_BETA1-3 : bond 0.00743 / 0.50 ( 1) link_BETA1-3 : angle 2.22889 / 1.26 ( 3) link_BETA1-4 : bond 0.00361 / 0.25 ( 3) link_BETA1-4 : angle 1.75640 / 1.20 ( 9) link_NAG-ASN : bond 0.00615 / 0.41 ( 3) link_NAG-ASN : angle 3.61935 / 2.75 ( 9) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2880 Ramachandran restraints generated. 1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2880 Ramachandran restraints generated. 1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 124 time to evaluate : 0.527 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 208 TYR cc_start: 0.7983 (OUTLIER) cc_final: 0.5433 (p90) REVERT: A 263 MET cc_start: 0.7791 (mtt) cc_final: 0.7492 (mtp) REVERT: A 351 ARG cc_start: 0.8001 (OUTLIER) cc_final: 0.7665 (mmm160) REVERT: A 385 THR cc_start: 0.8398 (m) cc_final: 0.8137 (t) REVERT: A 391 ARG cc_start: 0.7564 (mtp85) cc_final: 0.7344 (mtp85) REVERT: A 401 ILE cc_start: 0.8496 (OUTLIER) cc_final: 0.8051 (mt) REVERT: A 469 MET cc_start: 0.8455 (ttm) cc_final: 0.8210 (ttt) REVERT: A 535 LYS cc_start: 0.8504 (tttm) cc_final: 0.7894 (ttmm) REVERT: A 571 GLU cc_start: 0.8253 (tt0) cc_final: 0.7790 (mt-10) REVERT: A 606 ASP cc_start: 0.7750 (p0) cc_final: 0.7543 (p0) REVERT: A 610 LYS cc_start: 0.7965 (mttm) cc_final: 0.7547 (mmtp) REVERT: A 689 GLU cc_start: 0.8403 (OUTLIER) cc_final: 0.7345 (tm-30) REVERT: A 697 GLU cc_start: 0.7823 (OUTLIER) cc_final: 0.7532 (mm-30) REVERT: A 748 ASP cc_start: 0.8281 (m-30) cc_final: 0.7951 (t0) REVERT: A 838 ARG cc_start: 0.8159 (mtm-85) cc_final: 0.7457 (mmt180) REVERT: A 871 ARG cc_start: 0.7889 (mtt180) cc_final: 0.7686 (mtt180) REVERT: A 944 LYS cc_start: 0.8704 (OUTLIER) cc_final: 0.8450 (mptt) REVERT: A 1094 PHE cc_start: 0.8382 (OUTLIER) cc_final: 0.7748 (t80) REVERT: A 1190 ARG cc_start: 0.8869 (OUTLIER) cc_final: 0.8125 (mtm180) REVERT: A 1296 GLN cc_start: 0.7936 (tt0) cc_final: 0.7465 (tt0) REVERT: C 47 PRO cc_start: 0.6692 (Cg_exo) cc_final: 0.6463 (Cg_endo) REVERT: C 135 LYS cc_start: 0.8612 (mttt) cc_final: 0.7851 (ttpp) REVERT: C 174 THR cc_start: 0.8731 (t) cc_final: 0.8510 (t) REVERT: C 229 HIS cc_start: 0.7633 (m90) cc_final: 0.7223 (m-70) REVERT: C 295 LYS cc_start: 0.8514 (ttpt) cc_final: 0.7945 (tptt) outliers start: 49 outliers final: 21 residues processed: 164 average time/residue: 0.5317 time to fit residues: 95.9597 Evaluate side-chains 147 residues out of total 1279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 118 time to evaluate : 0.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 208 TYR Chi-restraints excluded: chain A residue 288 SER Chi-restraints excluded: chain A residue 301 ASP Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 321 ILE Chi-restraints excluded: chain A residue 351 ARG Chi-restraints excluded: chain A residue 401 ILE Chi-restraints excluded: chain A residue 408 ARG Chi-restraints excluded: chain A residue 417 VAL Chi-restraints excluded: chain A residue 480 LEU Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 577 ILE Chi-restraints excluded: chain A residue 584 ASP Chi-restraints excluded: chain A residue 620 SER Chi-restraints excluded: chain A residue 622 ILE Chi-restraints excluded: chain A residue 689 GLU Chi-restraints excluded: chain A residue 695 ILE Chi-restraints excluded: chain A residue 697 GLU Chi-restraints excluded: chain A residue 701 THR Chi-restraints excluded: chain A residue 880 LEU Chi-restraints excluded: chain A residue 920 LEU Chi-restraints excluded: chain A residue 944 LYS Chi-restraints excluded: chain A residue 1094 PHE Chi-restraints excluded: chain A residue 1115 ILE Chi-restraints excluded: chain A residue 1153 VAL Chi-restraints excluded: chain A residue 1190 ARG Chi-restraints excluded: chain C residue 105 VAL Chi-restraints excluded: chain C residue 222 ILE Chi-restraints excluded: chain C residue 285 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 67 optimal weight: 3.9990 chunk 15 optimal weight: 1.9990 chunk 89 optimal weight: 2.9990 chunk 0 optimal weight: 5.9990 chunk 136 optimal weight: 1.9990 chunk 119 optimal weight: 0.2980 chunk 126 optimal weight: 2.9990 chunk 113 optimal weight: 0.9980 chunk 38 optimal weight: 0.9980 chunk 46 optimal weight: 4.9990 chunk 17 optimal weight: 5.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 291 HIS ** A 649 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 736 ASN A 839 GLN A 862 ASN C 25 ASN ** C 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.151761 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.117765 restraints weight = 13582.263| |-----------------------------------------------------------------------------| r_work (start): 0.3392 rms_B_bonded: 2.08 r_work: 0.3146 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3012 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3012 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8440 moved from start: 0.2441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 12027 Z= 0.178 Angle : 0.601 8.738 16308 Z= 0.306 Chirality : 0.045 0.159 1855 Planarity : 0.004 0.043 2039 Dihedral : 5.406 45.011 1578 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 3.21 % Allowed : 17.51 % Favored : 79.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.58 (0.21), residues: 1440 helix: -1.16 (0.21), residues: 592 sheet: -0.41 (0.34), residues: 220 loop : -0.99 (0.24), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG A 981 TYR 0.012 0.001 TYR C 141 PHE 0.022 0.002 PHE A1094 TRP 0.015 0.001 TRP C 111 HIS 0.008 0.001 HIS A 634 Details of bonding type rmsd/Z covalent geometry : bond 0.00426 / 0.18 (12018) covalent geometry : angle 0.59444 / 0.31 (16283) SS BOND : bond 0.00665 / 0.47 ( 2) SS BOND : angle 1.15504 / 0.64 ( 4) hydrogen bonds : bond 0.03975 / 2.51 ( 393) hydrogen bonds : angle 4.53079 / 3.13 ( 1161) link_BETA1-3 : bond 0.00713 / 0.48 ( 1) link_BETA1-3 : angle 2.04241 / 1.17 ( 3) link_BETA1-4 : bond 0.00298 / 0.19 ( 3) link_BETA1-4 : angle 1.59020 / 1.05 ( 9) link_NAG-ASN : bond 0.00439 / 0.29 ( 3) link_NAG-ASN : angle 3.20910 / 2.40 ( 9) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2880 Ramachandran restraints generated. 1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2880 Ramachandran restraints generated. 1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 123 time to evaluate : 0.355 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 208 TYR cc_start: 0.7929 (OUTLIER) cc_final: 0.5356 (p90) REVERT: A 263 MET cc_start: 0.7736 (mtt) cc_final: 0.7455 (mtp) REVERT: A 351 ARG cc_start: 0.7971 (OUTLIER) cc_final: 0.7637 (mmm160) REVERT: A 385 THR cc_start: 0.8381 (m) cc_final: 0.8093 (t) REVERT: A 401 ILE cc_start: 0.8466 (OUTLIER) cc_final: 0.8056 (mt) REVERT: A 469 MET cc_start: 0.8455 (ttm) cc_final: 0.8210 (ttt) REVERT: A 535 LYS cc_start: 0.8500 (tttm) cc_final: 0.7927 (ttmm) REVERT: A 549 GLU cc_start: 0.8592 (OUTLIER) cc_final: 0.8287 (pp20) REVERT: A 571 GLU cc_start: 0.8265 (tt0) cc_final: 0.7808 (mt-10) REVERT: A 577 ILE cc_start: 0.7583 (OUTLIER) cc_final: 0.7007 (tp) REVERT: A 606 ASP cc_start: 0.7734 (p0) cc_final: 0.7518 (p0) REVERT: A 610 LYS cc_start: 0.7987 (mttm) cc_final: 0.7568 (mmtp) REVERT: A 689 GLU cc_start: 0.8397 (OUTLIER) cc_final: 0.7964 (tm-30) REVERT: A 697 GLU cc_start: 0.7833 (OUTLIER) cc_final: 0.7543 (mm-30) REVERT: A 838 ARG cc_start: 0.8167 (mtm-85) cc_final: 0.7440 (mmt-90) REVERT: A 855 ASP cc_start: 0.7150 (m-30) cc_final: 0.6713 (m-30) REVERT: A 871 ARG cc_start: 0.7744 (mtt180) cc_final: 0.7472 (mtt180) REVERT: A 1094 PHE cc_start: 0.8332 (OUTLIER) cc_final: 0.7574 (t80) REVERT: A 1190 ARG cc_start: 0.8807 (OUTLIER) cc_final: 0.8094 (mtm180) REVERT: A 1296 GLN cc_start: 0.7923 (tt0) cc_final: 0.7470 (tt0) REVERT: C 47 PRO cc_start: 0.6665 (Cg_exo) cc_final: 0.6435 (Cg_endo) REVERT: C 135 LYS cc_start: 0.8592 (mttt) cc_final: 0.7840 (ttpp) REVERT: C 174 THR cc_start: 0.8626 (t) cc_final: 0.8405 (t) REVERT: C 229 HIS cc_start: 0.7664 (m90) cc_final: 0.7258 (m-70) REVERT: C 295 LYS cc_start: 0.8505 (ttpt) cc_final: 0.7936 (tptt) outliers start: 41 outliers final: 20 residues processed: 154 average time/residue: 0.5426 time to fit residues: 91.4878 Evaluate side-chains 147 residues out of total 1279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 118 time to evaluate : 0.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 208 TYR Chi-restraints excluded: chain A residue 288 SER Chi-restraints excluded: chain A residue 301 ASP Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 351 ARG Chi-restraints excluded: chain A residue 401 ILE Chi-restraints excluded: chain A residue 408 ARG Chi-restraints excluded: chain A residue 438 THR Chi-restraints excluded: chain A residue 480 LEU Chi-restraints excluded: chain A residue 549 GLU Chi-restraints excluded: chain A residue 577 ILE Chi-restraints excluded: chain A residue 584 ASP Chi-restraints excluded: chain A residue 620 SER Chi-restraints excluded: chain A residue 622 ILE Chi-restraints excluded: chain A residue 689 GLU Chi-restraints excluded: chain A residue 695 ILE Chi-restraints excluded: chain A residue 697 GLU Chi-restraints excluded: chain A residue 701 THR Chi-restraints excluded: chain A residue 777 ASN Chi-restraints excluded: chain A residue 804 ILE Chi-restraints excluded: chain A residue 880 LEU Chi-restraints excluded: chain A residue 920 LEU Chi-restraints excluded: chain A residue 1094 PHE Chi-restraints excluded: chain A residue 1115 ILE Chi-restraints excluded: chain A residue 1153 VAL Chi-restraints excluded: chain A residue 1190 ARG Chi-restraints excluded: chain C residue 218 THR Chi-restraints excluded: chain C residue 222 ILE Chi-restraints excluded: chain C residue 285 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 80 optimal weight: 2.9990 chunk 128 optimal weight: 0.7980 chunk 19 optimal weight: 0.2980 chunk 129 optimal weight: 3.9990 chunk 55 optimal weight: 0.9980 chunk 74 optimal weight: 0.9980 chunk 29 optimal weight: 0.7980 chunk 117 optimal weight: 5.9990 chunk 41 optimal weight: 10.0000 chunk 2 optimal weight: 5.9990 chunk 48 optimal weight: 5.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 291 HIS A 736 ASN A1258 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.153369 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.119211 restraints weight = 13555.499| |-----------------------------------------------------------------------------| r_work (start): 0.3412 rms_B_bonded: 2.05 r_work: 0.3172 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3038 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3038 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8413 moved from start: 0.2550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 12027 Z= 0.129 Angle : 0.566 8.746 16308 Z= 0.286 Chirality : 0.043 0.157 1855 Planarity : 0.003 0.042 2039 Dihedral : 5.184 47.060 1578 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 3.05 % Allowed : 18.37 % Favored : 78.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.37 (0.22), residues: 1440 helix: -0.94 (0.21), residues: 594 sheet: -0.35 (0.34), residues: 218 loop : -0.90 (0.24), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 981 TYR 0.012 0.001 TYR C 141 PHE 0.021 0.001 PHE A1094 TRP 0.012 0.001 TRP C 111 HIS 0.005 0.001 HIS A 634 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.13 (12018) covalent geometry : angle 0.56131 / 0.29 (16283) SS BOND : bond 0.00540 / 0.39 ( 2) SS BOND : angle 0.92300 / 0.53 ( 4) hydrogen bonds : bond 0.03487 / 2.19 ( 393) hydrogen bonds : angle 4.36591 / 3.03 ( 1161) link_BETA1-3 : bond 0.00731 / 0.49 ( 1) link_BETA1-3 : angle 1.73042 / 1.03 ( 3) link_BETA1-4 : bond 0.00324 / 0.18 ( 3) link_BETA1-4 : angle 1.40801 / 0.88 ( 9) link_NAG-ASN : bond 0.00256 / 0.17 ( 3) link_NAG-ASN : angle 2.81608 / 2.08 ( 9) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2880 Ramachandran restraints generated. 1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2880 Ramachandran restraints generated. 1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 130 time to evaluate : 0.500 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 208 TYR cc_start: 0.7749 (OUTLIER) cc_final: 0.5210 (p90) REVERT: A 263 MET cc_start: 0.7648 (mtt) cc_final: 0.7377 (mtp) REVERT: A 385 THR cc_start: 0.8369 (m) cc_final: 0.8100 (t) REVERT: A 401 ILE cc_start: 0.8342 (OUTLIER) cc_final: 0.7930 (mt) REVERT: A 469 MET cc_start: 0.8446 (ttm) cc_final: 0.8196 (ttt) REVERT: A 535 LYS cc_start: 0.8416 (tttm) cc_final: 0.7938 (ttmm) REVERT: A 571 GLU cc_start: 0.8179 (tt0) cc_final: 0.7842 (mt-10) REVERT: A 577 ILE cc_start: 0.7586 (OUTLIER) cc_final: 0.7014 (tp) REVERT: A 697 GLU cc_start: 0.7795 (OUTLIER) cc_final: 0.7516 (mm-30) REVERT: A 726 VAL cc_start: 0.8556 (t) cc_final: 0.8224 (m) REVERT: A 812 LYS cc_start: 0.8870 (mmmm) cc_final: 0.8500 (mptp) REVERT: A 838 ARG cc_start: 0.8131 (mtm-85) cc_final: 0.7393 (mmt-90) REVERT: A 855 ASP cc_start: 0.7063 (m-30) cc_final: 0.6630 (m-30) REVERT: A 871 ARG cc_start: 0.7801 (mtt180) cc_final: 0.7527 (mtt180) REVERT: A 1094 PHE cc_start: 0.8332 (OUTLIER) cc_final: 0.7465 (t80) REVERT: A 1190 ARG cc_start: 0.8797 (OUTLIER) cc_final: 0.8094 (mtm180) REVERT: A 1296 GLN cc_start: 0.7920 (tt0) cc_final: 0.7447 (tt0) REVERT: A 1304 LEU cc_start: 0.6920 (OUTLIER) cc_final: 0.6489 (tt) REVERT: C 47 PRO cc_start: 0.6597 (Cg_exo) cc_final: 0.6362 (Cg_endo) REVERT: C 135 LYS cc_start: 0.8630 (mttt) cc_final: 0.7858 (ttpp) REVERT: C 174 THR cc_start: 0.8514 (t) cc_final: 0.8285 (t) REVERT: C 229 HIS cc_start: 0.7631 (m90) cc_final: 0.7200 (m-70) REVERT: C 295 LYS cc_start: 0.8506 (ttpt) cc_final: 0.7879 (tptt) outliers start: 39 outliers final: 21 residues processed: 160 average time/residue: 0.5025 time to fit residues: 88.2760 Evaluate side-chains 148 residues out of total 1279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 120 time to evaluate : 0.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 208 TYR Chi-restraints excluded: chain A residue 288 SER Chi-restraints excluded: chain A residue 301 ASP Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 401 ILE Chi-restraints excluded: chain A residue 408 ARG Chi-restraints excluded: chain A residue 480 LEU Chi-restraints excluded: chain A residue 577 ILE Chi-restraints excluded: chain A residue 620 SER Chi-restraints excluded: chain A residue 629 LEU Chi-restraints excluded: chain A residue 695 ILE Chi-restraints excluded: chain A residue 697 GLU Chi-restraints excluded: chain A residue 701 THR Chi-restraints excluded: chain A residue 736 ASN Chi-restraints excluded: chain A residue 877 ILE Chi-restraints excluded: chain A residue 880 LEU Chi-restraints excluded: chain A residue 920 LEU Chi-restraints excluded: chain A residue 959 VAL Chi-restraints excluded: chain A residue 1093 ILE Chi-restraints excluded: chain A residue 1094 PHE Chi-restraints excluded: chain A residue 1115 ILE Chi-restraints excluded: chain A residue 1153 VAL Chi-restraints excluded: chain A residue 1190 ARG Chi-restraints excluded: chain A residue 1304 LEU Chi-restraints excluded: chain C residue 105 VAL Chi-restraints excluded: chain C residue 218 THR Chi-restraints excluded: chain C residue 222 ILE Chi-restraints excluded: chain C residue 285 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 29 optimal weight: 0.7980 chunk 26 optimal weight: 0.9990 chunk 36 optimal weight: 0.7980 chunk 121 optimal weight: 4.9990 chunk 65 optimal weight: 0.0470 chunk 58 optimal weight: 0.9980 chunk 107 optimal weight: 2.9990 chunk 117 optimal weight: 1.9990 chunk 94 optimal weight: 0.7980 chunk 67 optimal weight: 0.9980 chunk 7 optimal weight: 0.8980 overall best weight: 0.6678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 291 HIS A 736 ASN C 25 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.153924 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.119676 restraints weight = 13498.409| |-----------------------------------------------------------------------------| r_work (start): 0.3418 rms_B_bonded: 2.05 r_work: 0.3183 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3050 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3050 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8405 moved from start: 0.2583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 12027 Z= 0.120 Angle : 0.558 9.504 16308 Z= 0.282 Chirality : 0.043 0.158 1855 Planarity : 0.003 0.041 2039 Dihedral : 5.112 48.034 1578 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 3.13 % Allowed : 18.69 % Favored : 78.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.24 (0.22), residues: 1440 helix: -0.81 (0.21), residues: 593 sheet: -0.35 (0.34), residues: 218 loop : -0.82 (0.24), residues: 629 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 981 TYR 0.012 0.001 TYR C 141 PHE 0.023 0.001 PHE A 491 TRP 0.011 0.001 TRP C 111 HIS 0.005 0.001 HIS A 634 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.12 (12018) covalent geometry : angle 0.55318 / 0.28 (16283) SS BOND : bond 0.00549 / 0.39 ( 2) SS BOND : angle 0.87666 / 0.51 ( 4) hydrogen bonds : bond 0.03352 / 2.10 ( 393) hydrogen bonds : angle 4.32704 / 3.01 ( 1161) link_BETA1-3 : bond 0.00707 / 0.47 ( 1) link_BETA1-3 : angle 1.68463 / 1.00 ( 3) link_BETA1-4 : bond 0.00343 / 0.20 ( 3) link_BETA1-4 : angle 1.41124 / 0.90 ( 9) link_NAG-ASN : bond 0.00249 / 0.17 ( 3) link_NAG-ASN : angle 2.72956 / 2.02 ( 9) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2880 Ramachandran restraints generated. 1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2880 Ramachandran restraints generated. 1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 122 time to evaluate : 0.417 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 208 TYR cc_start: 0.7758 (OUTLIER) cc_final: 0.5231 (p90) REVERT: A 263 MET cc_start: 0.7735 (mtt) cc_final: 0.7437 (mtp) REVERT: A 385 THR cc_start: 0.8383 (m) cc_final: 0.8115 (t) REVERT: A 391 ARG cc_start: 0.7230 (OUTLIER) cc_final: 0.6793 (mtp85) REVERT: A 401 ILE cc_start: 0.8325 (OUTLIER) cc_final: 0.7878 (mt) REVERT: A 469 MET cc_start: 0.8443 (ttm) cc_final: 0.8191 (ttt) REVERT: A 535 LYS cc_start: 0.8420 (tttm) cc_final: 0.7933 (ttmm) REVERT: A 571 GLU cc_start: 0.8193 (tt0) cc_final: 0.7756 (mt-10) REVERT: A 577 ILE cc_start: 0.7565 (OUTLIER) cc_final: 0.6998 (tp) REVERT: A 610 LYS cc_start: 0.7979 (mttm) cc_final: 0.7564 (mmtp) REVERT: A 697 GLU cc_start: 0.7805 (OUTLIER) cc_final: 0.7555 (mm-30) REVERT: A 736 ASN cc_start: 0.7192 (OUTLIER) cc_final: 0.6952 (p0) REVERT: A 838 ARG cc_start: 0.8125 (mtm-85) cc_final: 0.7397 (mmt-90) REVERT: A 855 ASP cc_start: 0.7038 (m-30) cc_final: 0.6607 (m-30) REVERT: A 871 ARG cc_start: 0.7810 (mtt180) cc_final: 0.7531 (mtt180) REVERT: A 1094 PHE cc_start: 0.8323 (OUTLIER) cc_final: 0.7459 (t80) REVERT: A 1190 ARG cc_start: 0.8800 (OUTLIER) cc_final: 0.8092 (mtm180) REVERT: A 1296 GLN cc_start: 0.7925 (tt0) cc_final: 0.7453 (tt0) REVERT: A 1304 LEU cc_start: 0.6986 (OUTLIER) cc_final: 0.6560 (tt) REVERT: C 47 PRO cc_start: 0.6600 (Cg_exo) cc_final: 0.6374 (Cg_endo) REVERT: C 135 LYS cc_start: 0.8562 (mttt) cc_final: 0.7777 (ttpp) REVERT: C 174 THR cc_start: 0.8514 (t) cc_final: 0.8273 (t) REVERT: C 229 HIS cc_start: 0.7618 (m90) cc_final: 0.7192 (m-70) REVERT: C 250 LYS cc_start: 0.8909 (ttmm) cc_final: 0.8602 (tttt) REVERT: C 295 LYS cc_start: 0.8497 (ttpt) cc_final: 0.7882 (tptt) outliers start: 40 outliers final: 21 residues processed: 155 average time/residue: 0.5122 time to fit residues: 87.3491 Evaluate side-chains 149 residues out of total 1279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 119 time to evaluate : 0.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 208 TYR Chi-restraints excluded: chain A residue 288 SER Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 391 ARG Chi-restraints excluded: chain A residue 401 ILE Chi-restraints excluded: chain A residue 408 ARG Chi-restraints excluded: chain A residue 438 THR Chi-restraints excluded: chain A residue 480 LEU Chi-restraints excluded: chain A residue 505 LEU Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 577 ILE Chi-restraints excluded: chain A residue 620 SER Chi-restraints excluded: chain A residue 622 ILE Chi-restraints excluded: chain A residue 629 LEU Chi-restraints excluded: chain A residue 695 ILE Chi-restraints excluded: chain A residue 697 GLU Chi-restraints excluded: chain A residue 701 THR Chi-restraints excluded: chain A residue 736 ASN Chi-restraints excluded: chain A residue 877 ILE Chi-restraints excluded: chain A residue 880 LEU Chi-restraints excluded: chain A residue 959 VAL Chi-restraints excluded: chain A residue 1094 PHE Chi-restraints excluded: chain A residue 1115 ILE Chi-restraints excluded: chain A residue 1153 VAL Chi-restraints excluded: chain A residue 1190 ARG Chi-restraints excluded: chain A residue 1304 LEU Chi-restraints excluded: chain C residue 105 VAL Chi-restraints excluded: chain C residue 218 THR Chi-restraints excluded: chain C residue 222 ILE Chi-restraints excluded: chain C residue 285 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 121 optimal weight: 4.9990 chunk 13 optimal weight: 0.3980 chunk 85 optimal weight: 0.9990 chunk 29 optimal weight: 2.9990 chunk 115 optimal weight: 1.9990 chunk 118 optimal weight: 1.9990 chunk 112 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 6.9990 chunk 91 optimal weight: 3.9990 overall best weight: 1.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 241 HIS A 246 ASN A 291 HIS A 736 ASN C 299 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.152231 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.118363 restraints weight = 13363.334| |-----------------------------------------------------------------------------| r_work (start): 0.3396 rms_B_bonded: 2.03 r_work: 0.3166 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3032 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3032 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8407 moved from start: 0.2622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 12027 Z= 0.200 Angle : 0.618 9.181 16308 Z= 0.313 Chirality : 0.046 0.158 1855 Planarity : 0.004 0.043 2039 Dihedral : 5.295 47.443 1578 Min Nonbonded Distance : 1.880 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 3.21 % Allowed : 18.92 % Favored : 77.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.31 (0.22), residues: 1440 helix: -0.89 (0.21), residues: 593 sheet: -0.39 (0.34), residues: 220 loop : -0.84 (0.24), residues: 627 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 981 TYR 0.014 0.001 TYR C 153 PHE 0.022 0.002 PHE A1094 TRP 0.016 0.002 TRP C 111 HIS 0.009 0.001 HIS A 634 Details of bonding type rmsd/Z covalent geometry : bond 0.00483 / 0.20 (12018) covalent geometry : angle 0.61182 / 0.31 (16283) SS BOND : bond 0.00721 / 0.52 ( 2) SS BOND : angle 1.17859 / 0.65 ( 4) hydrogen bonds : bond 0.03949 / 2.50 ( 393) hydrogen bonds : angle 4.41966 / 3.07 ( 1161) link_BETA1-3 : bond 0.00654 / 0.44 ( 1) link_BETA1-3 : angle 1.96047 / 1.11 ( 3) link_BETA1-4 : bond 0.00373 / 0.26 ( 3) link_BETA1-4 : angle 1.63338 / 1.09 ( 9) link_NAG-ASN : bond 0.00560 / 0.37 ( 3) link_NAG-ASN : angle 3.32556 / 2.50 ( 9) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2880 Ramachandran restraints generated. 1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2880 Ramachandran restraints generated. 1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 122 time to evaluate : 0.400 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 208 TYR cc_start: 0.8082 (OUTLIER) cc_final: 0.5400 (p90) REVERT: A 263 MET cc_start: 0.7790 (mtt) cc_final: 0.7502 (mtp) REVERT: A 385 THR cc_start: 0.8325 (m) cc_final: 0.8045 (t) REVERT: A 391 ARG cc_start: 0.7163 (OUTLIER) cc_final: 0.6747 (mtp85) REVERT: A 401 ILE cc_start: 0.8284 (OUTLIER) cc_final: 0.7778 (mt) REVERT: A 453 THR cc_start: 0.7856 (OUTLIER) cc_final: 0.7495 (p) REVERT: A 469 MET cc_start: 0.8423 (ttm) cc_final: 0.8167 (ttt) REVERT: A 535 LYS cc_start: 0.8358 (tttm) cc_final: 0.7833 (ttmm) REVERT: A 571 GLU cc_start: 0.8059 (tt0) cc_final: 0.7631 (mt-10) REVERT: A 610 LYS cc_start: 0.8008 (mttm) cc_final: 0.7623 (mmtp) REVERT: A 697 GLU cc_start: 0.7776 (OUTLIER) cc_final: 0.7508 (mm-30) REVERT: A 736 ASN cc_start: 0.7267 (OUTLIER) cc_final: 0.7057 (p0) REVERT: A 838 ARG cc_start: 0.8008 (mtm-85) cc_final: 0.7365 (mmt-90) REVERT: A 855 ASP cc_start: 0.7029 (m-30) cc_final: 0.6618 (m-30) REVERT: A 871 ARG cc_start: 0.7785 (mtt180) cc_final: 0.7473 (mtt180) REVERT: A 977 MET cc_start: 0.6908 (ttm) cc_final: 0.6690 (ttm) REVERT: A 1094 PHE cc_start: 0.8427 (OUTLIER) cc_final: 0.7731 (t80) REVERT: A 1190 ARG cc_start: 0.8885 (OUTLIER) cc_final: 0.8139 (mtm180) REVERT: A 1296 GLN cc_start: 0.7951 (tt0) cc_final: 0.7479 (tt0) REVERT: A 1304 LEU cc_start: 0.6925 (OUTLIER) cc_final: 0.6497 (tt) REVERT: C 47 PRO cc_start: 0.6588 (Cg_exo) cc_final: 0.6354 (Cg_endo) REVERT: C 135 LYS cc_start: 0.8539 (mttt) cc_final: 0.7776 (ttpp) REVERT: C 174 THR cc_start: 0.8687 (t) cc_final: 0.8462 (t) REVERT: C 229 HIS cc_start: 0.7649 (m90) cc_final: 0.7241 (m-70) REVERT: C 295 LYS cc_start: 0.8483 (ttpt) cc_final: 0.7846 (tptt) REVERT: C 299 GLN cc_start: 0.8756 (tt0) cc_final: 0.8484 (tt0) outliers start: 41 outliers final: 23 residues processed: 157 average time/residue: 0.5122 time to fit residues: 88.8477 Evaluate side-chains 153 residues out of total 1279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 121 time to evaluate : 0.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 208 TYR Chi-restraints excluded: chain A residue 288 SER Chi-restraints excluded: chain A residue 301 ASP Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 391 ARG Chi-restraints excluded: chain A residue 401 ILE Chi-restraints excluded: chain A residue 408 ARG Chi-restraints excluded: chain A residue 417 VAL Chi-restraints excluded: chain A residue 438 THR Chi-restraints excluded: chain A residue 453 THR Chi-restraints excluded: chain A residue 480 LEU Chi-restraints excluded: chain A residue 505 LEU Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 577 ILE Chi-restraints excluded: chain A residue 620 SER Chi-restraints excluded: chain A residue 622 ILE Chi-restraints excluded: chain A residue 629 LEU Chi-restraints excluded: chain A residue 695 ILE Chi-restraints excluded: chain A residue 697 GLU Chi-restraints excluded: chain A residue 701 THR Chi-restraints excluded: chain A residue 736 ASN Chi-restraints excluded: chain A residue 877 ILE Chi-restraints excluded: chain A residue 880 LEU Chi-restraints excluded: chain A residue 959 VAL Chi-restraints excluded: chain A residue 1094 PHE Chi-restraints excluded: chain A residue 1153 VAL Chi-restraints excluded: chain A residue 1190 ARG Chi-restraints excluded: chain A residue 1304 LEU Chi-restraints excluded: chain C residue 105 VAL Chi-restraints excluded: chain C residue 218 THR Chi-restraints excluded: chain C residue 222 ILE Chi-restraints excluded: chain C residue 285 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 27 optimal weight: 0.8980 chunk 4 optimal weight: 0.5980 chunk 79 optimal weight: 5.9990 chunk 58 optimal weight: 0.9990 chunk 3 optimal weight: 0.5980 chunk 105 optimal weight: 0.9990 chunk 61 optimal weight: 5.9990 chunk 2 optimal weight: 0.0040 chunk 108 optimal weight: 0.8980 chunk 67 optimal weight: 3.9990 chunk 132 optimal weight: 3.9990 overall best weight: 0.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 246 ASN A 291 HIS A 736 ASN C 25 ASN ** C 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.154295 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.120169 restraints weight = 13454.282| |-----------------------------------------------------------------------------| r_work (start): 0.3424 rms_B_bonded: 2.04 r_work: 0.3202 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3070 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3070 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8370 moved from start: 0.2662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 12027 Z= 0.117 Angle : 0.566 8.935 16308 Z= 0.287 Chirality : 0.043 0.156 1855 Planarity : 0.004 0.049 2039 Dihedral : 5.134 48.913 1578 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 2.89 % Allowed : 19.23 % Favored : 77.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.09 (0.22), residues: 1440 helix: -0.69 (0.22), residues: 592 sheet: -0.12 (0.35), residues: 208 loop : -0.80 (0.24), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 943 TYR 0.012 0.001 TYR C 141 PHE 0.021 0.001 PHE A1094 TRP 0.010 0.001 TRP C 111 HIS 0.005 0.001 HIS A 634 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.12 (12018) covalent geometry : angle 0.56161 / 0.29 (16283) SS BOND : bond 0.00601 / 0.43 ( 2) SS BOND : angle 0.90579 / 0.53 ( 4) hydrogen bonds : bond 0.03336 / 2.09 ( 393) hydrogen bonds : angle 4.30725 / 3.00 ( 1161) link_BETA1-3 : bond 0.00788 / 0.53 ( 1) link_BETA1-3 : angle 1.75585 / 1.04 ( 3) link_BETA1-4 : bond 0.00340 / 0.20 ( 3) link_BETA1-4 : angle 1.40349 / 0.89 ( 9) link_NAG-ASN : bond 0.00249 / 0.17 ( 3) link_NAG-ASN : angle 2.67313 / 1.97 ( 9) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2880 Ramachandran restraints generated. 1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2880 Ramachandran restraints generated. 1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 131 time to evaluate : 0.445 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 208 TYR cc_start: 0.7787 (OUTLIER) cc_final: 0.5292 (p90) REVERT: A 263 MET cc_start: 0.7747 (mtt) cc_final: 0.7472 (mtp) REVERT: A 385 THR cc_start: 0.8310 (m) cc_final: 0.8033 (t) REVERT: A 391 ARG cc_start: 0.7223 (OUTLIER) cc_final: 0.6799 (mtp85) REVERT: A 401 ILE cc_start: 0.8172 (OUTLIER) cc_final: 0.7681 (mt) REVERT: A 453 THR cc_start: 0.7866 (OUTLIER) cc_final: 0.7524 (p) REVERT: A 469 MET cc_start: 0.8403 (ttm) cc_final: 0.8147 (ttt) REVERT: A 535 LYS cc_start: 0.8385 (tttm) cc_final: 0.7874 (ttmm) REVERT: A 571 GLU cc_start: 0.8042 (tt0) cc_final: 0.7609 (mt-10) REVERT: A 577 ILE cc_start: 0.7554 (OUTLIER) cc_final: 0.6965 (tp) REVERT: A 610 LYS cc_start: 0.7951 (mttm) cc_final: 0.7563 (mmtp) REVERT: A 689 GLU cc_start: 0.8297 (OUTLIER) cc_final: 0.7778 (tm-30) REVERT: A 697 GLU cc_start: 0.7761 (OUTLIER) cc_final: 0.7494 (mm-30) REVERT: A 838 ARG cc_start: 0.8034 (mtm-85) cc_final: 0.7325 (mmt-90) REVERT: A 855 ASP cc_start: 0.6959 (m-30) cc_final: 0.6577 (m-30) REVERT: A 871 ARG cc_start: 0.7763 (mtt180) cc_final: 0.7474 (mtt180) REVERT: A 1065 ASP cc_start: 0.7597 (t0) cc_final: 0.7397 (t0) REVERT: A 1094 PHE cc_start: 0.8338 (OUTLIER) cc_final: 0.7405 (t80) REVERT: A 1190 ARG cc_start: 0.8848 (OUTLIER) cc_final: 0.8110 (mtm180) REVERT: A 1296 GLN cc_start: 0.7923 (tt0) cc_final: 0.7442 (tt0) REVERT: A 1304 LEU cc_start: 0.6959 (OUTLIER) cc_final: 0.6536 (tt) REVERT: C 47 PRO cc_start: 0.6572 (Cg_exo) cc_final: 0.6345 (Cg_endo) REVERT: C 135 LYS cc_start: 0.8505 (mttt) cc_final: 0.7742 (ttpp) REVERT: C 174 THR cc_start: 0.8479 (t) cc_final: 0.8250 (t) REVERT: C 229 HIS cc_start: 0.7614 (m90) cc_final: 0.7188 (m-70) REVERT: C 295 LYS cc_start: 0.8504 (ttpt) cc_final: 0.7845 (tptt) REVERT: C 299 GLN cc_start: 0.8751 (tt0) cc_final: 0.8528 (tt0) outliers start: 37 outliers final: 22 residues processed: 162 average time/residue: 0.4994 time to fit residues: 89.3434 Evaluate side-chains 157 residues out of total 1279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 125 time to evaluate : 0.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 208 TYR Chi-restraints excluded: chain A residue 288 SER Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 391 ARG Chi-restraints excluded: chain A residue 401 ILE Chi-restraints excluded: chain A residue 408 ARG Chi-restraints excluded: chain A residue 417 VAL Chi-restraints excluded: chain A residue 438 THR Chi-restraints excluded: chain A residue 453 THR Chi-restraints excluded: chain A residue 480 LEU Chi-restraints excluded: chain A residue 505 LEU Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 577 ILE Chi-restraints excluded: chain A residue 620 SER Chi-restraints excluded: chain A residue 629 LEU Chi-restraints excluded: chain A residue 689 GLU Chi-restraints excluded: chain A residue 695 ILE Chi-restraints excluded: chain A residue 697 GLU Chi-restraints excluded: chain A residue 701 THR Chi-restraints excluded: chain A residue 736 ASN Chi-restraints excluded: chain A residue 880 LEU Chi-restraints excluded: chain A residue 959 VAL Chi-restraints excluded: chain A residue 1094 PHE Chi-restraints excluded: chain A residue 1153 VAL Chi-restraints excluded: chain A residue 1190 ARG Chi-restraints excluded: chain A residue 1304 LEU Chi-restraints excluded: chain C residue 105 VAL Chi-restraints excluded: chain C residue 218 THR Chi-restraints excluded: chain C residue 222 ILE Chi-restraints excluded: chain C residue 240 ASP Chi-restraints excluded: chain C residue 285 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 86 optimal weight: 2.9990 chunk 34 optimal weight: 0.0670 chunk 101 optimal weight: 0.6980 chunk 30 optimal weight: 2.9990 chunk 18 optimal weight: 0.2980 chunk 3 optimal weight: 0.8980 chunk 79 optimal weight: 0.7980 chunk 84 optimal weight: 0.7980 chunk 78 optimal weight: 0.0980 chunk 98 optimal weight: 1.9990 chunk 73 optimal weight: 3.9990 overall best weight: 0.3918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 241 HIS A 246 ASN A 291 HIS A 736 ASN A1000 HIS ** C 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.155509 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.120747 restraints weight = 13538.116| |-----------------------------------------------------------------------------| r_work (start): 0.3431 rms_B_bonded: 2.08 r_work: 0.3212 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3079 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3079 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8358 moved from start: 0.2717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 12027 Z= 0.101 Angle : 0.546 8.879 16308 Z= 0.276 Chirality : 0.043 0.158 1855 Planarity : 0.003 0.046 2039 Dihedral : 4.989 50.810 1578 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 2.58 % Allowed : 19.62 % Favored : 77.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.96 (0.22), residues: 1440 helix: -0.56 (0.22), residues: 590 sheet: -0.07 (0.35), residues: 206 loop : -0.74 (0.24), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 943 TYR 0.012 0.001 TYR C 140 PHE 0.026 0.001 PHE A 491 TRP 0.010 0.001 TRP A1134 HIS 0.004 0.001 HIS A 634 Details of bonding type rmsd/Z covalent geometry : bond 0.00235 / 0.10 (12018) covalent geometry : angle 0.54214 / 0.28 (16283) SS BOND : bond 0.00547 / 0.39 ( 2) SS BOND : angle 0.78704 / 0.48 ( 4) hydrogen bonds : bond 0.03082 / 1.93 ( 393) hydrogen bonds : angle 4.23434 / 2.95 ( 1161) link_BETA1-3 : bond 0.00697 / 0.46 ( 1) link_BETA1-3 : angle 1.57351 / 0.97 ( 3) link_BETA1-4 : bond 0.00394 / 0.23 ( 3) link_BETA1-4 : angle 1.31376 / 0.81 ( 9) link_NAG-ASN : bond 0.00263 / 0.17 ( 3) link_NAG-ASN : angle 2.41054 / 1.75 ( 9) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4298.92 seconds wall clock time: 74 minutes 9.57 seconds (4449.57 seconds total)