Starting phenix.real_space_refine (version: 1.21rc1) on Sun Apr 23 07:34:02 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6w6w_21567/04_2023/6w6w_21567.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6w6w_21567/04_2023/6w6w_21567.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6w6w_21567/04_2023/6w6w_21567.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6w6w_21567/04_2023/6w6w_21567.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6w6w_21567/04_2023/6w6w_21567.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6w6w_21567/04_2023/6w6w_21567.pdb" } resolution = 3.0 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 ------------------------------------------------------------------------------- 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= 0.006 sd= 0.074 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 3445 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 1 6.06 5 P 4 5.49 5 S 57 5.16 5 C 7012 2.51 5 N 1933 2.21 5 O 1974 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 170": "NH1" <-> "NH2" Residue "A ASP 183": "OD1" <-> "OD2" Residue "A TYR 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 417": "NH1" <-> "NH2" Residue "A PHE 549": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 568": "OD1" <-> "OD2" Residue "A TYR 689": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 889": "OD1" <-> "OD2" Residue "A ASP 952": "OD1" <-> "OD2" Residue "A PHE 1023": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1203": "OE1" <-> "OE2" Residue "C ASP 36": "OD1" <-> "OD2" Residue "C ASP 58": "OD1" <-> "OD2" Residue "C GLU 118": "OE1" <-> "OE2" Residue "C GLU 143": "OE1" <-> "OE2" Residue "C GLU 218": "OE1" <-> "OE2" Residue "C GLU 230": "OE1" <-> "OE2" Residue "C ASP 285": "OD1" <-> "OD2" Residue "C PHE 287": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 299": "OD1" <-> "OD2" Residue "C GLU 341": "OE1" <-> "OE2" Residue "C GLU 362": "OE1" <-> "OE2" Residue "C PHE 368": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 10981 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 7121 Number of conformers: 1 Conformer: "" Number of residues, atoms: 905, 7121 Classifications: {'peptide': 905} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 75, 'TRANS': 829} Chain breaks: 9 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 85 Classifications: {'DNA': 4} Link IDs: {'rna3p': 3} Chain: "B" Number of atoms: 213 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 213 Classifications: {'peptide': 43} Incomplete info: {'truncation_to_alanine': 33} Link IDs: {'PTRANS': 1, 'TRANS': 41} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 112 Unresolved non-hydrogen angles: 147 Unresolved non-hydrogen dihedrals: 89 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 2, 'ASN:plan1': 1, 'TRP:plan': 1, 'HIS:plan': 2, 'GLU:plan': 3, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 59 Chain: "C" Number of atoms: 2631 Number of conformers: 1 Conformer: "" Number of residues, atoms: 323, 2631 Classifications: {'peptide': 323} Link IDs: {'PTRANS': 12, 'TRANS': 310} Chain breaks: 3 Chain: "D" Number of atoms: 930 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 930 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 6, 'TRANS': 110} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 5956 SG CYS A1043 89.942 97.205 108.219 1.00 59.44 S ATOM 5979 SG CYS A1046 89.489 94.293 111.406 1.00 63.81 S ATOM 6045 SG CYS A1055 91.655 98.287 111.217 1.00 73.01 S ATOM 6094 SG CYS A1062 93.761 95.873 109.555 1.00 82.71 S Time building chain proxies: 6.08, per 1000 atoms: 0.55 Number of scatterers: 10981 At special positions: 0 Unit cell: (143.374, 132.594, 136.906, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 1 29.99 S 57 16.00 P 4 15.00 O 1974 8.00 N 1933 7.00 C 7012 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS C 312 " - pdb=" SG CYS C 322 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.21 Conformation dependent library (CDL) restraints added in 1.6 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1301 " pdb="ZN ZN A1301 " - pdb=" SG CYS A1043 " pdb="ZN ZN A1301 " - pdb=" SG CYS A1046 " pdb="ZN ZN A1301 " - pdb=" SG CYS A1055 " pdb="ZN ZN A1301 " - pdb=" SG CYS A1062 " Number of angles added : 6 2712 Ramachandran restraints generated. 1356 Oldfield, 0 Emsley, 1356 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2622 Finding SS restraints... Secondary structure from input PDB file: 38 helices and 21 sheets defined 19.8% alpha, 27.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.91 Creating SS restraints... Processing helix chain 'A' and resid 268 through 273 removed outlier: 3.606A pdb=" N ARG A 273 " --> pdb=" O VAL A 270 " (cutoff:3.500A) Processing helix chain 'A' and resid 449 through 459 removed outlier: 3.917A pdb=" N VAL A 457 " --> pdb=" O TYR A 453 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLU A 459 " --> pdb=" O GLN A 455 " (cutoff:3.500A) Processing helix chain 'A' and resid 463 through 474 removed outlier: 3.606A pdb=" N TRP A 469 " --> pdb=" O PRO A 465 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LYS A 472 " --> pdb=" O LEU A 468 " (cutoff:3.500A) Processing helix chain 'A' and resid 487 through 492 Processing helix chain 'A' and resid 501 through 506 Processing helix chain 'A' and resid 507 through 512 Processing helix chain 'A' and resid 524 through 528 removed outlier: 3.551A pdb=" N GLU A 527 " --> pdb=" O ALA A 524 " (cutoff:3.500A) Processing helix chain 'A' and resid 553 through 558 Processing helix chain 'A' and resid 568 through 573 Processing helix chain 'A' and resid 576 through 580 removed outlier: 3.973A pdb=" N SER A 579 " --> pdb=" O PRO A 576 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N TYR A 580 " --> pdb=" O GLU A 577 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 576 through 580' Processing helix chain 'A' and resid 582 through 587 Processing helix chain 'A' and resid 644 through 648 removed outlier: 3.647A pdb=" N LEU A 647 " --> pdb=" O ASP A 644 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ILE A 648 " --> pdb=" O PRO A 645 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 644 through 648' Processing helix chain 'A' and resid 671 through 675 removed outlier: 3.649A pdb=" N GLU A 674 " --> pdb=" O SER A 671 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N LEU A 675 " --> pdb=" O TRP A 672 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 671 through 675' Processing helix chain 'A' and resid 803 through 811 removed outlier: 4.021A pdb=" N ARG A 806 " --> pdb=" O SER A 803 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N TRP A 807 " --> pdb=" O SER A 804 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N PHE A 808 " --> pdb=" O VAL A 805 " (cutoff:3.500A) removed outlier: 4.765A pdb=" N GLU A 809 " --> pdb=" O ARG A 806 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N PHE A 810 " --> pdb=" O TRP A 807 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LEU A 811 " --> pdb=" O PHE A 808 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 803 through 811' Processing helix chain 'A' and resid 842 through 846 removed outlier: 3.984A pdb=" N ALA A 846 " --> pdb=" O LEU A 843 " (cutoff:3.500A) Processing helix chain 'A' and resid 883 through 887 removed outlier: 3.792A pdb=" N LEU A 887 " --> pdb=" O THR A 884 " (cutoff:3.500A) Processing helix chain 'A' and resid 951 through 955 Processing helix chain 'A' and resid 1011 through 1016 removed outlier: 3.727A pdb=" N LEU A1015 " --> pdb=" O LEU A1012 " (cutoff:3.500A) Processing helix chain 'A' and resid 1100 through 1108 Processing helix chain 'A' and resid 1140 through 1146 removed outlier: 3.515A pdb=" N THR A1144 " --> pdb=" O MET A1140 " (cutoff:3.500A) Processing helix chain 'C' and resid 13 through 17 removed outlier: 3.634A pdb=" N TRP C 17 " --> pdb=" O SER C 14 " (cutoff:3.500A) Processing helix chain 'C' and resid 20 through 25 removed outlier: 3.712A pdb=" N LEU C 24 " --> pdb=" O PRO C 21 " (cutoff:3.500A) Processing helix chain 'C' and resid 30 through 35 Processing helix chain 'C' and resid 110 through 118 removed outlier: 3.771A pdb=" N LYS C 115 " --> pdb=" O SER C 111 " (cutoff:3.500A) Processing helix chain 'C' and resid 160 through 177 removed outlier: 3.716A pdb=" N MET C 167 " --> pdb=" O GLN C 163 " (cutoff:3.500A) Proline residue: C 171 - end of helix Processing helix chain 'C' and resid 200 through 204 Processing helix chain 'C' and resid 208 through 214 removed outlier: 3.671A pdb=" N GLU C 214 " --> pdb=" O GLU C 210 " (cutoff:3.500A) Processing helix chain 'C' and resid 214 through 219 removed outlier: 4.135A pdb=" N GLU C 218 " --> pdb=" O GLU C 214 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ASN C 219 " --> pdb=" O PHE C 215 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 214 through 219' Processing helix chain 'C' and resid 226 through 230 removed outlier: 3.553A pdb=" N GLU C 230 " --> pdb=" O GLN C 226 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 226 through 230' Processing helix chain 'C' and resid 232 through 237 removed outlier: 3.629A pdb=" N SER C 237 " --> pdb=" O GLU C 233 " (cutoff:3.500A) Processing helix chain 'C' and resid 241 through 246 removed outlier: 3.854A pdb=" N HIS C 245 " --> pdb=" O PRO C 242 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N SER C 246 " --> pdb=" O VAL C 243 " (cutoff:3.500A) Processing helix chain 'C' and resid 259 through 277 removed outlier: 4.416A pdb=" N HIS C 264 " --> pdb=" O SER C 260 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N SER C 265 " --> pdb=" O LYS C 261 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N LEU C 273 " --> pdb=" O ASN C 269 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N LEU C 274 " --> pdb=" O ALA C 270 " (cutoff:3.500A) Processing helix chain 'C' and resid 300 through 305 Processing helix chain 'C' and resid 307 through 311 removed outlier: 3.693A pdb=" N GLN C 310 " --> pdb=" O ILE C 307 " (cutoff:3.500A) Processing helix chain 'C' and resid 327 through 331 removed outlier: 3.564A pdb=" N ALA C 331 " --> pdb=" O LEU C 328 " (cutoff:3.500A) Processing helix chain 'C' and resid 350 through 354 removed outlier: 4.592A pdb=" N ASP C 353 " --> pdb=" O LEU C 350 " (cutoff:3.500A) Processing helix chain 'D' and resid 11 through 17 removed outlier: 3.814A pdb=" N ALA D 17 " --> pdb=" O TRP D 13 " (cutoff:3.500A) Processing helix chain 'D' and resid 101 through 118 removed outlier: 3.893A pdb=" N ARG D 110 " --> pdb=" O GLU D 106 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N GLU D 118 " --> pdb=" O LEU D 114 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 165 through 166 Processing sheet with id=AA2, first strand: chain 'A' and resid 228 through 229 removed outlier: 3.726A pdb=" N GLY A 228 " --> pdb=" O TYR A 281 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N TYR A 281 " --> pdb=" O GLY A 228 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 245 through 249 removed outlier: 3.731A pdb=" N TRP A 299 " --> pdb=" O ILE A 261 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 351 through 352 Processing sheet with id=AA5, first strand: chain 'A' and resid 354 through 356 removed outlier: 3.654A pdb=" N ARG A 354 " --> pdb=" O LEU A 408 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LEU A 408 " --> pdb=" O ARG A 354 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N VAL A 406 " --> pdb=" O LEU A 356 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N GLY A 380 " --> pdb=" O LEU A 421 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 364 through 367 removed outlier: 6.654A pdb=" N LEU A 372 " --> pdb=" O LEU A 366 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 400 through 403 removed outlier: 6.707A pdb=" N CYS A 400 " --> pdb=" O GLN A 432 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 592 through 597 removed outlier: 13.580A pdb=" N SER A 629 " --> pdb=" O ALA A 686 " (cutoff:3.500A) removed outlier: 8.561A pdb=" N VAL A 688 " --> pdb=" O SER A 629 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N GLN A 640 " --> pdb=" O ALA A 636 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 592 through 597 removed outlier: 13.580A pdb=" N SER A 629 " --> pdb=" O ALA A 686 " (cutoff:3.500A) removed outlier: 8.561A pdb=" N VAL A 688 " --> pdb=" O SER A 629 " (cutoff:3.500A) removed outlier: 5.201A pdb=" N LEU A 621 " --> pdb=" O CYS A 632 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N CYS A 650 " --> pdb=" O LEU A 612 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 742 through 744 removed outlier: 7.170A pdb=" N TYR A 764 " --> pdb=" O LYS A 738 " (cutoff:3.500A) removed outlier: 5.115A pdb=" N LYS A 738 " --> pdb=" O TYR A 764 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N LEU A 766 " --> pdb=" O CYS A 736 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 728 through 738 current: chain 'A' and resid 851 through 853 Processing sheet with id=AB2, first strand: chain 'A' and resid 780 through 781 removed outlier: 5.920A pdb=" N GLY A 728 " --> pdb=" O LYS A 776 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N LEU A 766 " --> pdb=" O CYS A 736 " (cutoff:3.500A) removed outlier: 5.115A pdb=" N LYS A 738 " --> pdb=" O TYR A 764 " (cutoff:3.500A) removed outlier: 7.170A pdb=" N TYR A 764 " --> pdb=" O LYS A 738 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 760 through 769 current: chain 'A' and resid 859 through 862 Processing sheet with id=AB3, first strand: chain 'A' and resid 992 through 994 removed outlier: 8.051A pdb=" N HIS A 945 " --> pdb=" O VAL A 982 " (cutoff:3.500A) removed outlier: 8.821A pdb=" N CYS A 984 " --> pdb=" O HIS A 945 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N ASP A 947 " --> pdb=" O CYS A 984 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N LYS A 930 " --> pdb=" O ARG A 905 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N ARG A 905 " --> pdb=" O LYS A 930 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N THR A 932 " --> pdb=" O LEU A 903 " (cutoff:3.500A) removed outlier: 5.930A pdb=" N VAL A 896 " --> pdb=" O GLN A 971 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N GLN A 971 " --> pdb=" O VAL A 896 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 1024 through 1025 removed outlier: 3.591A pdb=" N ALA A1025 " --> pdb=" O PHE A1159 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 1024 through 1025 removed outlier: 3.591A pdb=" N ALA A1025 " --> pdb=" O PHE A1159 " (cutoff:3.500A) removed outlier: 6.093A pdb=" N GLU A1203 " --> pdb=" O PRO A1154 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N VAL A1156 " --> pdb=" O ILE A1201 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N ILE A1201 " --> pdb=" O VAL A1156 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N SER A1158 " --> pdb=" O LEU A1199 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N VAL A1085 " --> pdb=" O LEU A1196 " (cutoff:3.500A) removed outlier: 7.307A pdb=" N CYS A1198 " --> pdb=" O VAL A1085 " (cutoff:3.500A) removed outlier: 7.487A pdb=" N THR A1087 " --> pdb=" O CYS A1198 " (cutoff:3.500A) removed outlier: 8.624A pdb=" N SER A1200 " --> pdb=" O THR A1087 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N VAL A1086 " --> pdb=" O LEU A1075 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N ILE A1072 " --> pdb=" O LEU A1037 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N LEU A1037 " --> pdb=" O ILE A1072 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N ARG A1074 " --> pdb=" O PHE A1035 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N SER A1033 " --> pdb=" O LEU A1076 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N GLU A1078 " --> pdb=" O ILE A1031 " (cutoff:3.500A) removed outlier: 5.401A pdb=" N ILE A1031 " --> pdb=" O GLU A1078 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 1041 through 1042 Processing sheet with id=AB7, first strand: chain 'A' and resid 1175 through 1177 Processing sheet with id=AB8, first strand: chain 'A' and resid 1180 through 1181 removed outlier: 3.630A pdb=" N CYS A1181 " --> pdb=" O LEU A1184 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 38 through 39 removed outlier: 3.892A pdb=" N LYS C 38 " --> pdb=" O LEU C 48 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 57 through 65 removed outlier: 5.952A pdb=" N GLY C 76 " --> pdb=" O ILE C 64 " (cutoff:3.500A) removed outlier: 7.836A pdb=" N ARG C 145 " --> pdb=" O VAL C 83 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N ASN C 85 " --> pdb=" O ARG C 145 " (cutoff:3.500A) removed outlier: 5.467A pdb=" N ILE C 147 " --> pdb=" O ARG C 139 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N ARG C 139 " --> pdb=" O ILE C 147 " (cutoff:3.500A) removed outlier: 5.511A pdb=" N ALA C 149 " --> pdb=" O SER C 137 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N SER C 137 " --> pdb=" O ALA C 149 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N THR C 131 " --> pdb=" O VAL C 155 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 223 through 225 Processing sheet with id=AC3, first strand: chain 'D' and resid 25 through 26 removed outlier: 6.280A pdb=" N ILE D 74 " --> pdb=" O LEU D 94 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N LEU D 94 " --> pdb=" O ILE D 74 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N LEU D 76 " --> pdb=" O ARG D 92 " (cutoff:3.500A) removed outlier: 9.418A pdb=" N VAL D 89 " --> pdb=" O GLN D 54 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N LEU D 56 " --> pdb=" O VAL D 89 " (cutoff:3.500A) removed outlier: 7.122A pdb=" N ALA D 91 " --> pdb=" O LEU D 56 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N CYS D 58 " --> pdb=" O ALA D 91 " (cutoff:3.500A) removed outlier: 8.444A pdb=" N VAL D 93 " --> pdb=" O CYS D 58 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N THR D 43 " --> pdb=" O LEU D 34 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N LEU D 34 " --> pdb=" O THR D 43 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N MET D 45 " --> pdb=" O LEU D 32 " (cutoff:3.500A) removed outlier: 5.583A pdb=" N LEU D 32 " --> pdb=" O MET D 45 " (cutoff:3.500A) removed outlier: 8.678A pdb=" N GLN D 47 " --> pdb=" O GLY D 30 " (cutoff:3.500A) removed outlier: 9.971A pdb=" N GLY D 30 " --> pdb=" O GLN D 47 " (cutoff:3.500A) 279 hydrogen bonds defined for protein. 711 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: 4.26 Time building geometry restraints manager: 4.52 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3519 1.34 - 1.46: 2384 1.46 - 1.58: 5263 1.58 - 1.70: 7 1.70 - 1.82: 73 Bond restraints: 11246 Sorted by residual: bond pdb=" C VAL A 265 " pdb=" N PRO A 266 " ideal model delta sigma weight residual 1.334 1.389 -0.055 2.34e-02 1.83e+03 5.55e+00 bond pdb=" C VAL A1113 " pdb=" N PRO A1114 " ideal model delta sigma weight residual 1.334 1.385 -0.051 2.34e-02 1.83e+03 4.74e+00 bond pdb=" C GLU A1136 " pdb=" N PRO A1137 " ideal model delta sigma weight residual 1.334 1.384 -0.050 2.34e-02 1.83e+03 4.55e+00 bond pdb=" CA VAL B 20 " pdb=" CB VAL B 20 " ideal model delta sigma weight residual 1.550 1.532 0.018 1.03e-02 9.43e+03 3.07e+00 bond pdb=" C GLU D 63 " pdb=" N PRO D 64 " ideal model delta sigma weight residual 1.334 1.374 -0.040 2.34e-02 1.83e+03 2.90e+00 ... (remaining 11241 not shown) Histogram of bond angle deviations from ideal: 95.41 - 103.16: 116 103.16 - 110.91: 4092 110.91 - 118.66: 4882 118.66 - 126.41: 5943 126.41 - 134.16: 259 Bond angle restraints: 15292 Sorted by residual: angle pdb=" N PRO B 35 " pdb=" CA PRO B 35 " pdb=" CB PRO B 35 " ideal model delta sigma weight residual 103.25 113.53 -10.28 1.05e+00 9.07e-01 9.58e+01 angle pdb=" C CYS B 34 " pdb=" N PRO B 35 " pdb=" CA PRO B 35 " ideal model delta sigma weight residual 119.84 127.79 -7.95 1.25e+00 6.40e-01 4.04e+01 angle pdb=" C ASN A1090 " pdb=" N HIS A1091 " pdb=" CA HIS A1091 " ideal model delta sigma weight residual 121.54 131.39 -9.85 1.91e+00 2.74e-01 2.66e+01 angle pdb=" N CYS A 482 " pdb=" CA CYS A 482 " pdb=" C CYS A 482 " ideal model delta sigma weight residual 109.81 121.07 -11.26 2.21e+00 2.05e-01 2.59e+01 angle pdb=" C GLU A 941 " pdb=" N PHE A 942 " pdb=" CA PHE A 942 " ideal model delta sigma weight residual 121.80 133.83 -12.03 2.44e+00 1.68e-01 2.43e+01 ... (remaining 15287 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.68: 5970 16.68 - 33.37: 627 33.37 - 50.05: 152 50.05 - 66.74: 20 66.74 - 83.42: 16 Dihedral angle restraints: 6785 sinusoidal: 2752 harmonic: 4033 Sorted by residual: dihedral pdb=" CA PRO B 35 " pdb=" C PRO B 35 " pdb=" N ARG B 36 " pdb=" CA ARG B 36 " ideal model delta harmonic sigma weight residual 180.00 132.63 47.37 0 5.00e+00 4.00e-02 8.98e+01 dihedral pdb=" CA CYS A 535 " pdb=" C CYS A 535 " pdb=" N PRO A 536 " pdb=" CA PRO A 536 " ideal model delta harmonic sigma weight residual 180.00 -142.56 -37.44 0 5.00e+00 4.00e-02 5.61e+01 dihedral pdb=" CA LEU A 236 " pdb=" C LEU A 236 " pdb=" N VAL A 237 " pdb=" CA VAL A 237 " ideal model delta harmonic sigma weight residual 180.00 150.73 29.27 0 5.00e+00 4.00e-02 3.43e+01 ... (remaining 6782 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 1318 0.058 - 0.115: 328 0.115 - 0.173: 75 0.173 - 0.231: 7 0.231 - 0.288: 5 Chirality restraints: 1733 Sorted by residual: chirality pdb=" CB ILE A1005 " pdb=" CA ILE A1005 " pdb=" CG1 ILE A1005 " pdb=" CG2 ILE A1005 " both_signs ideal model delta sigma weight residual False 2.64 2.36 0.29 2.00e-01 2.50e+01 2.08e+00 chirality pdb=" CB ILE C 244 " pdb=" CA ILE C 244 " pdb=" CG1 ILE C 244 " pdb=" CG2 ILE C 244 " both_signs ideal model delta sigma weight residual False 2.64 2.91 -0.27 2.00e-01 2.50e+01 1.80e+00 chirality pdb=" CA CYS A 482 " pdb=" N CYS A 482 " pdb=" C CYS A 482 " pdb=" CB CYS A 482 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.27 2.00e-01 2.50e+01 1.76e+00 ... (remaining 1730 not shown) Planarity restraints: 1942 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER A 496 " -0.062 5.00e-02 4.00e+02 9.29e-02 1.38e+01 pdb=" N PRO A 497 " 0.161 5.00e-02 4.00e+02 pdb=" CA PRO A 497 " -0.048 5.00e-02 4.00e+02 pdb=" CD PRO A 497 " -0.051 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C CYS A 482 " -0.049 5.00e-02 4.00e+02 7.44e-02 8.85e+00 pdb=" N PRO A 483 " 0.129 5.00e-02 4.00e+02 pdb=" CA PRO A 483 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO A 483 " -0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA A 508 " -0.049 5.00e-02 4.00e+02 7.28e-02 8.49e+00 pdb=" N PRO A 509 " 0.126 5.00e-02 4.00e+02 pdb=" CA PRO A 509 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO A 509 " -0.041 5.00e-02 4.00e+02 ... (remaining 1939 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 3100 2.82 - 3.34: 8606 3.34 - 3.86: 16764 3.86 - 4.38: 19469 4.38 - 4.90: 34277 Nonbonded interactions: 82216 Sorted by model distance: nonbonded pdb=" OG SER A 970 " pdb=" O THR A 990 " model vdw 2.303 2.440 nonbonded pdb=" O GLY A1080 " pdb=" OH TYR C 178 " model vdw 2.309 2.440 nonbonded pdb=" OG1 THR A 363 " pdb=" O LEU A 375 " model vdw 2.319 2.440 nonbonded pdb=" OG SER A1148 " pdb=" OG SER A1150 " model vdw 2.355 2.440 nonbonded pdb=" OD1 ASN A 225 " pdb=" OG1 THR A 284 " model vdw 2.361 2.440 ... (remaining 82211 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== 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: 3.510 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.070 Construct map_model_manager: 0.010 Extract box with map and model: 14.020 Check model and map are aligned: 0.160 Set scattering table: 0.100 Process input model: 32.640 Find NCS groups from input model: 0.320 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 63.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8134 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 0.063 11246 Z= 0.376 Angle : 0.993 16.704 15292 Z= 0.531 Chirality : 0.055 0.288 1733 Planarity : 0.008 0.093 1942 Dihedral : 14.870 83.419 4160 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 2.69 Ramachandran Plot: Outliers : 0.29 % Allowed : 12.09 % Favored : 87.61 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.08 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.09 (0.18), residues: 1356 helix: -5.07 (0.09), residues: 269 sheet: -2.15 (0.26), residues: 375 loop : -3.42 (0.19), residues: 712 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2712 Ramachandran restraints generated. 1356 Oldfield, 0 Emsley, 1356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2712 Ramachandran restraints generated. 1356 Oldfield, 0 Emsley, 1356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 159 time to evaluate : 1.209 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 159 average time/residue: 1.3577 time to fit residues: 231.5701 Evaluate side-chains 108 residues out of total 1224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 108 time to evaluate : 1.173 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.7159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 115 optimal weight: 7.9990 chunk 103 optimal weight: 0.2980 chunk 57 optimal weight: 7.9990 chunk 35 optimal weight: 0.6980 chunk 70 optimal weight: 0.5980 chunk 55 optimal weight: 1.9990 chunk 107 optimal weight: 0.8980 chunk 41 optimal weight: 0.6980 chunk 65 optimal weight: 2.9990 chunk 79 optimal weight: 0.7980 chunk 124 optimal weight: 10.0000 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 156 HIS A 178 HIS A 407 HIS A 432 GLN ** A 442 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 523 ASN A 585 GLN A 587 ASN A 638 HIS A 682 GLN A 691 GLN A 971 GLN A1030 HIS A1120 GLN C 117 GLN C 148 HIS C 226 GLN C 245 HIS C 282 GLN C 289 ASN D 53 HIS D 66 HIS Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 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 11246 Z= 0.211 Angle : 0.680 9.950 15292 Z= 0.344 Chirality : 0.044 0.166 1733 Planarity : 0.006 0.059 1942 Dihedral : 7.929 64.842 1535 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.15 % Allowed : 10.47 % Favored : 89.38 % Rotamer Outliers : 1.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.15 (0.20), residues: 1356 helix: -3.96 (0.20), residues: 266 sheet: -1.71 (0.27), residues: 366 loop : -2.88 (0.20), residues: 724 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2712 Ramachandran restraints generated. 1356 Oldfield, 0 Emsley, 1356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2712 Ramachandran restraints generated. 1356 Oldfield, 0 Emsley, 1356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 117 time to evaluate : 1.216 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 19 outliers final: 7 residues processed: 126 average time/residue: 1.3408 time to fit residues: 182.0126 Evaluate side-chains 109 residues out of total 1224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 102 time to evaluate : 1.268 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 3 residues processed: 4 average time/residue: 0.5609 time to fit residues: 4.3632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 69 optimal weight: 0.9980 chunk 38 optimal weight: 0.7980 chunk 103 optimal weight: 0.0570 chunk 84 optimal weight: 0.0170 chunk 34 optimal weight: 0.6980 chunk 124 optimal weight: 0.8980 chunk 134 optimal weight: 1.9990 chunk 110 optimal weight: 20.0000 chunk 123 optimal weight: 2.9990 chunk 42 optimal weight: 0.9990 chunk 99 optimal weight: 1.9990 overall best weight: 0.4936 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 442 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 289 ASN D 66 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 moved from start: 0.1924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.041 11246 Z= 0.186 Angle : 0.646 11.636 15292 Z= 0.318 Chirality : 0.044 0.201 1733 Planarity : 0.005 0.056 1942 Dihedral : 7.587 64.329 1535 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.15 % Allowed : 10.25 % Favored : 89.60 % Rotamer Outliers : 1.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.57 (0.21), residues: 1356 helix: -3.14 (0.26), residues: 267 sheet: -1.50 (0.28), residues: 356 loop : -2.55 (0.21), residues: 733 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2712 Ramachandran restraints generated. 1356 Oldfield, 0 Emsley, 1356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2712 Ramachandran restraints generated. 1356 Oldfield, 0 Emsley, 1356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 116 time to evaluate : 1.308 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 20 outliers final: 9 residues processed: 126 average time/residue: 1.3236 time to fit residues: 179.9276 Evaluate side-chains 114 residues out of total 1224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 105 time to evaluate : 1.295 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 3 residues processed: 6 average time/residue: 0.5545 time to fit residues: 5.6226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 123 optimal weight: 0.0970 chunk 93 optimal weight: 9.9990 chunk 64 optimal weight: 1.9990 chunk 13 optimal weight: 0.6980 chunk 59 optimal weight: 3.9990 chunk 83 optimal weight: 2.9990 chunk 125 optimal weight: 9.9990 chunk 132 optimal weight: 0.4980 chunk 65 optimal weight: 1.9990 chunk 118 optimal weight: 0.9990 chunk 35 optimal weight: 0.4980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1020 GLN ** C 148 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 289 ASN D 66 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8085 moved from start: 0.2164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 11246 Z= 0.188 Angle : 0.627 12.276 15292 Z= 0.309 Chirality : 0.043 0.215 1733 Planarity : 0.004 0.054 1942 Dihedral : 7.404 64.286 1535 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.07 % Allowed : 10.62 % Favored : 89.31 % Rotamer Outliers : 2.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.21 (0.22), residues: 1356 helix: -2.67 (0.29), residues: 265 sheet: -1.28 (0.28), residues: 354 loop : -2.39 (0.21), residues: 737 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2712 Ramachandran restraints generated. 1356 Oldfield, 0 Emsley, 1356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2712 Ramachandran restraints generated. 1356 Oldfield, 0 Emsley, 1356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 116 time to evaluate : 1.336 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 31 outliers final: 14 residues processed: 133 average time/residue: 1.3003 time to fit residues: 187.1328 Evaluate side-chains 115 residues out of total 1224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 101 time to evaluate : 1.302 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 6 residues processed: 8 average time/residue: 0.5138 time to fit residues: 6.6468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 110 optimal weight: 0.3980 chunk 75 optimal weight: 1.9990 chunk 1 optimal weight: 3.9990 chunk 98 optimal weight: 2.9990 chunk 54 optimal weight: 0.0670 chunk 113 optimal weight: 5.9990 chunk 91 optimal weight: 10.0000 chunk 0 optimal weight: 3.9990 chunk 67 optimal weight: 0.6980 chunk 118 optimal weight: 4.9990 chunk 33 optimal weight: 2.9990 overall best weight: 1.2322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 432 GLN A 442 HIS A1189 HIS ** C 148 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 289 ASN D 66 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8138 moved from start: 0.2241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.043 11246 Z= 0.299 Angle : 0.678 12.412 15292 Z= 0.337 Chirality : 0.045 0.209 1733 Planarity : 0.005 0.054 1942 Dihedral : 7.585 64.102 1535 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.07 % Allowed : 11.28 % Favored : 88.64 % Rotamer Outliers : 2.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.08 (0.22), residues: 1356 helix: -2.45 (0.30), residues: 259 sheet: -1.23 (0.28), residues: 376 loop : -2.35 (0.22), residues: 721 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2712 Ramachandran restraints generated. 1356 Oldfield, 0 Emsley, 1356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2712 Ramachandran restraints generated. 1356 Oldfield, 0 Emsley, 1356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 112 time to evaluate : 1.314 Fit side-chains revert: symmetry clash outliers start: 29 outliers final: 18 residues processed: 130 average time/residue: 1.2373 time to fit residues: 175.0803 Evaluate side-chains 123 residues out of total 1224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 105 time to evaluate : 1.356 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 12 residues processed: 6 average time/residue: 0.9696 time to fit residues: 8.2335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 44 optimal weight: 0.6980 chunk 119 optimal weight: 8.9990 chunk 26 optimal weight: 0.6980 chunk 77 optimal weight: 7.9990 chunk 32 optimal weight: 0.9980 chunk 132 optimal weight: 0.6980 chunk 110 optimal weight: 5.9990 chunk 61 optimal weight: 0.0570 chunk 11 optimal weight: 5.9990 chunk 43 optimal weight: 2.9990 chunk 69 optimal weight: 1.9990 overall best weight: 0.6298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 268 GLN A 737 HIS ** C 148 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 289 ASN D 66 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 moved from start: 0.2393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 11246 Z= 0.200 Angle : 0.645 13.049 15292 Z= 0.317 Chirality : 0.044 0.205 1733 Planarity : 0.004 0.054 1942 Dihedral : 7.408 63.566 1535 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.07 % Allowed : 10.47 % Favored : 89.45 % Rotamer Outliers : 3.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.85 (0.22), residues: 1356 helix: -2.21 (0.32), residues: 259 sheet: -1.14 (0.28), residues: 365 loop : -2.19 (0.22), residues: 732 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2712 Ramachandran restraints generated. 1356 Oldfield, 0 Emsley, 1356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2712 Ramachandran restraints generated. 1356 Oldfield, 0 Emsley, 1356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 114 time to evaluate : 1.339 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 36 outliers final: 18 residues processed: 137 average time/residue: 1.2380 time to fit residues: 184.1269 Evaluate side-chains 127 residues out of total 1224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 109 time to evaluate : 1.199 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 11 residues processed: 7 average time/residue: 0.3640 time to fit residues: 5.1217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 127 optimal weight: 1.9990 chunk 14 optimal weight: 0.0270 chunk 75 optimal weight: 1.9990 chunk 96 optimal weight: 2.9990 chunk 74 optimal weight: 2.9990 chunk 111 optimal weight: 10.0000 chunk 132 optimal weight: 0.8980 chunk 82 optimal weight: 0.3980 chunk 80 optimal weight: 3.9990 chunk 60 optimal weight: 2.9990 chunk 81 optimal weight: 0.9980 overall best weight: 0.8640 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 268 GLN A 432 GLN A 737 HIS ** C 148 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 289 ASN D 66 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8115 moved from start: 0.2444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.045 11246 Z= 0.239 Angle : 0.660 13.120 15292 Z= 0.325 Chirality : 0.044 0.212 1733 Planarity : 0.004 0.054 1942 Dihedral : 7.418 63.756 1535 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.15 % Allowed : 11.06 % Favored : 88.79 % Rotamer Outliers : 2.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.77 (0.23), residues: 1356 helix: -2.10 (0.32), residues: 259 sheet: -1.10 (0.28), residues: 365 loop : -2.13 (0.22), residues: 732 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2712 Ramachandran restraints generated. 1356 Oldfield, 0 Emsley, 1356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2712 Ramachandran restraints generated. 1356 Oldfield, 0 Emsley, 1356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 113 time to evaluate : 1.303 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 30 outliers final: 20 residues processed: 132 average time/residue: 1.1944 time to fit residues: 171.5924 Evaluate side-chains 127 residues out of total 1224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 107 time to evaluate : 1.399 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 13 residues processed: 8 average time/residue: 0.5346 time to fit residues: 6.8310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 52 optimal weight: 1.9990 chunk 78 optimal weight: 0.9990 chunk 39 optimal weight: 2.9990 chunk 25 optimal weight: 0.9990 chunk 83 optimal weight: 3.9990 chunk 89 optimal weight: 0.3980 chunk 65 optimal weight: 0.6980 chunk 12 optimal weight: 6.9990 chunk 103 optimal weight: 0.7980 chunk 120 optimal weight: 0.8980 chunk 126 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 737 HIS A1017 GLN ** C 148 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 289 ASN D 68 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 moved from start: 0.2556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.056 11246 Z= 0.220 Angle : 0.662 13.393 15292 Z= 0.324 Chirality : 0.044 0.215 1733 Planarity : 0.004 0.054 1942 Dihedral : 7.377 63.446 1535 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.15 % Allowed : 10.32 % Favored : 89.53 % Rotamer Outliers : 2.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.67 (0.23), residues: 1356 helix: -1.94 (0.32), residues: 260 sheet: -1.08 (0.28), residues: 365 loop : -2.08 (0.23), residues: 731 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2712 Ramachandran restraints generated. 1356 Oldfield, 0 Emsley, 1356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2712 Ramachandran restraints generated. 1356 Oldfield, 0 Emsley, 1356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 111 time to evaluate : 1.175 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 28 outliers final: 18 residues processed: 128 average time/residue: 1.1464 time to fit residues: 160.1272 Evaluate side-chains 123 residues out of total 1224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 105 time to evaluate : 1.267 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 13 residues processed: 5 average time/residue: 0.6041 time to fit residues: 5.3549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 115 optimal weight: 6.9990 chunk 123 optimal weight: 0.9980 chunk 126 optimal weight: 0.6980 chunk 74 optimal weight: 3.9990 chunk 53 optimal weight: 8.9990 chunk 96 optimal weight: 1.9990 chunk 37 optimal weight: 0.7980 chunk 111 optimal weight: 0.0070 chunk 116 optimal weight: 4.9990 chunk 122 optimal weight: 9.9990 chunk 80 optimal weight: 1.9990 overall best weight: 0.9000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 432 GLN A 737 HIS ** C 148 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 289 ASN D 68 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8116 moved from start: 0.2593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.044 11246 Z= 0.247 Angle : 0.682 13.838 15292 Z= 0.334 Chirality : 0.045 0.208 1733 Planarity : 0.004 0.054 1942 Dihedral : 7.412 63.593 1535 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.15 % Allowed : 11.14 % Favored : 88.72 % Rotamer Outliers : 1.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.66 (0.23), residues: 1356 helix: -1.81 (0.32), residues: 265 sheet: -1.09 (0.28), residues: 383 loop : -2.13 (0.23), residues: 708 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2712 Ramachandran restraints generated. 1356 Oldfield, 0 Emsley, 1356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2712 Ramachandran restraints generated. 1356 Oldfield, 0 Emsley, 1356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 116 time to evaluate : 1.209 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 19 outliers final: 17 residues processed: 130 average time/residue: 1.1387 time to fit residues: 161.3895 Evaluate side-chains 128 residues out of total 1224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 111 time to evaluate : 1.272 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 13 residues processed: 5 average time/residue: 0.4796 time to fit residues: 4.6575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 130 optimal weight: 4.9990 chunk 79 optimal weight: 2.9990 chunk 61 optimal weight: 0.9990 chunk 90 optimal weight: 10.0000 chunk 136 optimal weight: 0.8980 chunk 125 optimal weight: 2.9990 chunk 108 optimal weight: 0.9990 chunk 11 optimal weight: 2.9990 chunk 83 optimal weight: 0.0770 chunk 66 optimal weight: 0.5980 chunk 86 optimal weight: 0.7980 overall best weight: 0.6740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 432 GLN A 737 HIS ** C 148 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 289 ASN D 68 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 moved from start: 0.2679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 11246 Z= 0.217 Angle : 0.682 14.177 15292 Z= 0.332 Chirality : 0.044 0.246 1733 Planarity : 0.004 0.055 1942 Dihedral : 7.346 63.549 1535 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.22 % Allowed : 10.18 % Favored : 89.60 % Rotamer Outliers : 1.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.57 (0.23), residues: 1356 helix: -1.71 (0.33), residues: 265 sheet: -1.06 (0.28), residues: 372 loop : -2.05 (0.23), residues: 719 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2712 Ramachandran restraints generated. 1356 Oldfield, 0 Emsley, 1356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2712 Ramachandran restraints generated. 1356 Oldfield, 0 Emsley, 1356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 1224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 110 time to evaluate : 1.328 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 15 outliers final: 13 residues processed: 125 average time/residue: 1.2399 time to fit residues: 168.9828 Evaluate side-chains 120 residues out of total 1224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 107 time to evaluate : 1.306 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 13 residues processed: 1 average time/residue: 0.2918 time to fit residues: 2.2079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 115 optimal weight: 9.9990 chunk 33 optimal weight: 1.9990 chunk 100 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 chunk 30 optimal weight: 3.9990 chunk 108 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 chunk 111 optimal weight: 10.0000 chunk 13 optimal weight: 1.9990 chunk 20 optimal weight: 0.8980 chunk 95 optimal weight: 0.7980 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 178 HIS A 432 GLN ** C 148 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 269 ASN C 289 ASN D 68 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.134119 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.093388 restraints weight = 15174.216| |-----------------------------------------------------------------------------| r_work (start): 0.3048 rms_B_bonded: 2.23 r_work: 0.2932 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2795 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.2795 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8459 moved from start: 0.2635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.051 11246 Z= 0.361 Angle : 0.738 14.372 15292 Z= 0.365 Chirality : 0.048 0.230 1733 Planarity : 0.005 0.055 1942 Dihedral : 7.640 63.896 1535 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.29 % Allowed : 11.80 % Favored : 87.91 % Rotamer Outliers : 1.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.68 (0.23), residues: 1356 helix: -1.77 (0.33), residues: 260 sheet: -1.14 (0.28), residues: 383 loop : -2.15 (0.23), residues: 713 =============================================================================== Job complete usr+sys time: 3932.42 seconds wall clock time: 70 minutes 33.21 seconds (4233.21 seconds total)