Starting phenix.real_space_refine on Sun Jul 27 10:05:54 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6wbx_21600/07_2025/6wbx_21600.cif Found real_map, /net/cci-nas-00/data/ceres_data/6wbx_21600/07_2025/6wbx_21600.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6wbx_21600/07_2025/6wbx_21600.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6wbx_21600/07_2025/6wbx_21600.map" model { file = "/net/cci-nas-00/data/ceres_data/6wbx_21600/07_2025/6wbx_21600.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6wbx_21600/07_2025/6wbx_21600.cif" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 1.000 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: 5 Type Number sf(0) Gaussians Ca 2 9.91 5 S 18 5.16 5 C 5829 2.51 5 N 1629 2.21 5 O 1692 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 43 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 9170 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 9168 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1264, 9158 Classifications: {'peptide': 1264} Incomplete info: {'truncation_to_alanine': 68} Link IDs: {'PCIS': 1, 'PTRANS': 103, 'TRANS': 1159} Chain breaks: 9 Unresolved non-hydrogen bonds: 268 Unresolved non-hydrogen angles: 346 Unresolved non-hydrogen dihedrals: 220 Unresolved non-hydrogen chiralities: 28 Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 8, 'TYR:plan': 2, 'ASN:plan1': 1, 'TRP:plan': 2, 'HIS:plan': 3, 'PHE:plan': 2, 'GLU:plan': 5, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 153 Conformer: "B" Number of residues, atoms: 1264, 9158 Classifications: {'peptide': 1264} Incomplete info: {'truncation_to_alanine': 68} Link IDs: {'PCIS': 1, 'PTRANS': 103, 'TRANS': 1159} Chain breaks: 9 Unresolved non-hydrogen bonds: 268 Unresolved non-hydrogen angles: 346 Unresolved non-hydrogen dihedrals: 220 Unresolved non-hydrogen chiralities: 28 Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 8, 'TYR:plan': 2, 'ASN:plan1': 1, 'TRP:plan': 2, 'HIS:plan': 3, 'PHE:plan': 2, 'GLU:plan': 5, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 153 bond proxies already assigned to first conformer: 9366 Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N AHIS A 550 " occ=0.50 ... (18 atoms not shown) pdb=" NE2BHIS A 550 " occ=0.50 Time building chain proxies: 11.33, per 1000 atoms: 1.24 Number of scatterers: 9170 At special positions: 0 Unit cell: (131.502, 88.0215, 90.1425, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Ca 2 19.99 S 18 16.00 O 1692 8.00 N 1629 7.00 C 5829 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 886 " - pdb=" SG CYS A 895 " distance=2.02 Simple disulfide: pdb=" SG CYS A1104 " - pdb=" SG CYS A1139 " distance=2.03 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 Time building additional restraints: 2.49 Conformation dependent library (CDL) restraints added in 2.5 seconds 2494 Ramachandran restraints generated. 1247 Oldfield, 0 Emsley, 1247 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2308 Finding SS restraints... Secondary structure from input PDB file: 40 helices and 16 sheets defined 31.0% alpha, 14.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.14 Creating SS restraints... Processing helix chain 'A' and resid 11 through 13 No H-bonds generated for 'chain 'A' and resid 11 through 13' Processing helix chain 'A' and resid 14 through 27 removed outlier: 3.957A pdb=" N ALA A 20 " --> pdb=" O ALA A 16 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N LEU A 24 " --> pdb=" O ALA A 20 " (cutoff:3.500A) Processing helix chain 'A' and resid 40 through 45 Processing helix chain 'A' and resid 45 through 53 removed outlier: 3.604A pdb=" N ALA A 53 " --> pdb=" O PHE A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 77 through 82 removed outlier: 3.832A pdb=" N PHE A 81 " --> pdb=" O HIS A 77 " (cutoff:3.500A) Processing helix chain 'A' and resid 82 through 87 removed outlier: 3.521A pdb=" N LEU A 86 " --> pdb=" O SER A 82 " (cutoff:3.500A) Processing helix chain 'A' and resid 90 through 118 removed outlier: 3.739A pdb=" N GLN A 95 " --> pdb=" O ALA A 91 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ARG A 96 " --> pdb=" O TRP A 92 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ALA A 100 " --> pdb=" O ARG A 96 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N VAL A 104 " --> pdb=" O ALA A 100 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LEU A 110 " --> pdb=" O GLY A 106 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ARG A 112 " --> pdb=" O TRP A 108 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ALA A 114 " --> pdb=" O LEU A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 121 through 134 removed outlier: 3.839A pdb=" N ILE A 126 " --> pdb=" O ARG A 122 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N ILE A 127 " --> pdb=" O GLY A 123 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ALA A 128 " --> pdb=" O SER A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 154 Processing helix chain 'A' and resid 154 through 165 removed outlier: 3.759A pdb=" N LEU A 159 " --> pdb=" O ALA A 155 " (cutoff:3.500A) Proline residue: A 161 - end of helix Processing helix chain 'A' and resid 173 through 185 removed outlier: 4.204A pdb=" N SER A 179 " --> pdb=" O ALA A 175 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ALA A 180 " --> pdb=" O ALA A 176 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N ALA A 182 " --> pdb=" O LEU A 178 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N VAL A 183 " --> pdb=" O SER A 179 " (cutoff:3.500A) Processing helix chain 'A' and resid 190 through 198 removed outlier: 3.525A pdb=" N CYS A 198 " --> pdb=" O THR A 194 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 207 Processing helix chain 'A' and resid 211 through 229 removed outlier: 3.712A pdb=" N PHE A 217 " --> pdb=" O THR A 213 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ALA A 219 " --> pdb=" O TRP A 215 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N TRP A 220 " --> pdb=" O ARG A 216 " (cutoff:3.500A) Proline residue: A 223 - end of helix removed outlier: 3.640A pdb=" N ALA A 226 " --> pdb=" O ILE A 222 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 243 removed outlier: 3.877A pdb=" N PHE A 239 " --> pdb=" O ALA A 235 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N LYS A 241 " --> pdb=" O LEU A 237 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ILE A 242 " --> pdb=" O ILE A 238 " (cutoff:3.500A) Processing helix chain 'A' and resid 291 through 309 removed outlier: 4.060A pdb=" N ALA A 295 " --> pdb=" O ALA A 291 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N THR A 297 " --> pdb=" O VAL A 293 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N GLY A 306 " --> pdb=" O ALA A 302 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N LEU A 307 " --> pdb=" O GLY A 303 " (cutoff:3.500A) Processing helix chain 'A' and resid 314 through 331 removed outlier: 3.706A pdb=" N VAL A 319 " --> pdb=" O ARG A 315 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N ALA A 320 " --> pdb=" O GLY A 316 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N THR A 330 " --> pdb=" O LEU A 326 " (cutoff:3.500A) Processing helix chain 'A' and resid 342 through 347 Processing helix chain 'A' and resid 348 through 350 No H-bonds generated for 'chain 'A' and resid 348 through 350' Processing helix chain 'A' and resid 363 through 381 removed outlier: 3.760A pdb=" N LEU A 368 " --> pdb=" O PRO A 364 " (cutoff:3.500A) Proline residue: A 369 - end of helix removed outlier: 3.706A pdb=" N LEU A 374 " --> pdb=" O LEU A 370 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N HIS A 376 " --> pdb=" O LEU A 372 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N SER A 379 " --> pdb=" O ALA A 375 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N ARG A 380 " --> pdb=" O HIS A 376 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N ILE A 381 " --> pdb=" O ALA A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 405 No H-bonds generated for 'chain 'A' and resid 403 through 405' Processing helix chain 'A' and resid 406 through 419 removed outlier: 3.972A pdb=" N VAL A 410 " --> pdb=" O ALA A 406 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N LEU A 412 " --> pdb=" O ALA A 408 " (cutoff:3.500A) Processing helix chain 'A' and resid 443 through 448 Processing helix chain 'A' and resid 475 through 481 removed outlier: 4.199A pdb=" N ALA A 479 " --> pdb=" O GLU A 475 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N LEU A 480 " --> pdb=" O PRO A 476 " (cutoff:3.500A) Processing helix chain 'A' and resid 495 through 500 Processing helix chain 'A' and resid 502 through 512 removed outlier: 3.577A pdb=" N GLN A 506 " --> pdb=" O ILE A 502 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N LEU A 508 " --> pdb=" O SER A 504 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N PHE A 509 " --> pdb=" O VAL A 505 " (cutoff:3.500A) Processing helix chain 'A' and resid 545 through 554 removed outlier: 3.525A pdb=" N AHIS A 550 " --> pdb=" O PRO A 546 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N HIS A 551 " --> pdb=" O ILE A 547 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N THR A 552 " --> pdb=" O LEU A 548 " (cutoff:3.500A) Processing helix chain 'A' and resid 581 through 583 No H-bonds generated for 'chain 'A' and resid 581 through 583' Processing helix chain 'A' and resid 620 through 629 removed outlier: 4.544A pdb=" N ARG A 624 " --> pdb=" O GLU A 620 " (cutoff:3.500A) Processing helix chain 'A' and resid 728 through 732 removed outlier: 3.814A pdb=" N SER A 732 " --> pdb=" O PRO A 729 " (cutoff:3.500A) Processing helix chain 'A' and resid 934 through 939 removed outlier: 4.239A pdb=" N LEU A 938 " --> pdb=" O GLN A 934 " (cutoff:3.500A) Processing helix chain 'A' and resid 959 through 964 removed outlier: 3.584A pdb=" N ALA A 963 " --> pdb=" O SER A 960 " (cutoff:3.500A) Processing helix chain 'A' and resid 1094 through 1097 Processing helix chain 'A' and resid 1103 through 1107 removed outlier: 3.566A pdb=" N GLY A1107 " --> pdb=" O CYS A1104 " (cutoff:3.500A) Processing helix chain 'A' and resid 1125 through 1130 removed outlier: 4.120A pdb=" N ASP A1130 " --> pdb=" O ARG A1126 " (cutoff:3.500A) Processing helix chain 'A' and resid 1259 through 1264 Processing helix chain 'A' and resid 1268 through 1276 removed outlier: 3.547A pdb=" N ALA A1276 " --> pdb=" O LEU A1272 " (cutoff:3.500A) Processing helix chain 'A' and resid 1300 through 1308 removed outlier: 3.687A pdb=" N ALA A1304 " --> pdb=" O VAL A1300 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ALA A1305 " --> pdb=" O ALA A1301 " (cutoff:3.500A) Processing helix chain 'A' and resid 1338 through 1353 removed outlier: 3.609A pdb=" N GLY A1344 " --> pdb=" O VAL A1340 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N SER A1346 " --> pdb=" O LEU A1342 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LEU A1347 " --> pdb=" O ALA A1343 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LEU A1349 " --> pdb=" O GLY A1345 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N ALA A1350 " --> pdb=" O SER A1346 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ALA A1353 " --> pdb=" O LEU A1349 " (cutoff:3.500A) Processing helix chain 'A' and resid 1372 through 1388 removed outlier: 3.526A pdb=" N ALA A1376 " --> pdb=" O ILE A1372 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N SER A1379 " --> pdb=" O LEU A1375 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N SER A1382 " --> pdb=" O ILE A1378 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N VAL A1383 " --> pdb=" O SER A1379 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ALA A1384 " --> pdb=" O VAL A1380 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N LEU A1385 " --> pdb=" O ALA A1381 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 57 through 58 Processing sheet with id=AA2, first strand: chain 'A' and resid 455 through 459 removed outlier: 5.635A pdb=" N ARG A 455 " --> pdb=" O ILE A 527 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N LEU A 457 " --> pdb=" O TYR A 529 " (cutoff:3.500A) removed outlier: 6.171A pdb=" N ALA A 594 " --> pdb=" O LYS A 561 " (cutoff:3.500A) removed outlier: 5.644A pdb=" N LYS A 561 " --> pdb=" O ALA A 594 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 577 through 579 removed outlier: 6.865A pdb=" N VAL A 578 " --> pdb=" O ARG A1061 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 1181 through 1182 removed outlier: 3.623A pdb=" N GLN A1236 " --> pdb=" O VAL A1208 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 641 through 642 removed outlier: 7.539A pdb=" N ARG A 614 " --> pdb=" O VAL A 657 " (cutoff:3.500A) removed outlier: 7.297A pdb=" N THR A 659 " --> pdb=" O ARG A 614 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N GLY A 873 " --> pdb=" O ALA A 656 " (cutoff:3.500A) removed outlier: 5.485A pdb=" N VAL A1163 " --> pdb=" O ARG A 928 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N ARG A 928 " --> pdb=" O VAL A1163 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N THR A1169 " --> pdb=" O THR A 922 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 707 through 708 Processing sheet with id=AA7, first strand: chain 'A' and resid 710 through 714 removed outlier: 7.193A pdb=" N THR A 817 " --> pdb=" O LEU A 762 " (cutoff:3.500A) removed outlier: 9.641A pdb=" N ARG A 764 " --> pdb=" O GLU A 815 " (cutoff:3.500A) removed outlier: 9.893A pdb=" N GLU A 815 " --> pdb=" O ARG A 764 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 745 through 746 removed outlier: 6.760A pdb=" N THR A 774 " --> pdb=" O THR A 838 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N LEU A 840 " --> pdb=" O THR A 772 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N THR A 772 " --> pdb=" O LEU A 840 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 843 through 844 Processing sheet with id=AB1, first strand: chain 'A' and resid 886 through 887 Processing sheet with id=AB2, first strand: chain 'A' and resid 909 through 915 Processing sheet with id=AB3, first strand: chain 'A' and resid 947 through 949 removed outlier: 6.713A pdb=" N VAL A1050 " --> pdb=" O ILE A1018 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N ILE A1018 " --> pdb=" O VAL A1050 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N VAL A1052 " --> pdb=" O VAL A1016 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N VAL A1016 " --> pdb=" O VAL A1052 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N ASP A1054 " --> pdb=" O LYS A1014 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 999 through 1002 removed outlier: 3.628A pdb=" N LEU A1002 " --> pdb=" O THR A1036 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 1099 through 1102 Processing sheet with id=AB6, first strand: chain 'A' and resid 1099 through 1102 Processing sheet with id=AB7, first strand: chain 'A' and resid 1195 through 1197 removed outlier: 3.748A pdb=" N GLY A1246 " --> pdb=" O ALA A1197 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N THR A1251 " --> pdb=" O ALA A1217 " (cutoff:3.500A) 271 hydrogen bonds defined for protein. 732 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: 5.56 Time building geometry restraints manager: 2.91 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: 2999 1.34 - 1.45: 1551 1.45 - 1.57: 4812 1.57 - 1.69: 0 1.69 - 1.81: 28 Bond restraints: 9390 Sorted by residual: bond pdb=" CB VAL A 703 " pdb=" CG2 VAL A 703 " ideal model delta sigma weight residual 1.521 1.437 0.084 3.30e-02 9.18e+02 6.52e+00 bond pdb=" CB VAL A1229 " pdb=" CG2 VAL A1229 " ideal model delta sigma weight residual 1.521 1.443 0.078 3.30e-02 9.18e+02 5.65e+00 bond pdb=" CB VAL A1009 " pdb=" CG2 VAL A1009 " ideal model delta sigma weight residual 1.521 1.445 0.076 3.30e-02 9.18e+02 5.26e+00 bond pdb=" C LYS A 993 " pdb=" N PRO A 994 " ideal model delta sigma weight residual 1.333 1.356 -0.022 1.01e-02 9.80e+03 4.79e+00 bond pdb=" CG LEU A 162 " pdb=" CD2 LEU A 162 " ideal model delta sigma weight residual 1.521 1.458 0.063 3.30e-02 9.18e+02 3.64e+00 ... (remaining 9385 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.11: 12224 2.11 - 4.22: 574 4.22 - 6.34: 88 6.34 - 8.45: 18 8.45 - 10.56: 6 Bond angle restraints: 12910 Sorted by residual: angle pdb=" N THR A 661 " pdb=" CA THR A 661 " pdb=" C THR A 661 " ideal model delta sigma weight residual 109.81 120.37 -10.56 2.21e+00 2.05e-01 2.28e+01 angle pdb=" C LEU A 362 " pdb=" N GLU A 363 " pdb=" CA GLU A 363 " ideal model delta sigma weight residual 120.51 126.61 -6.10 1.45e+00 4.76e-01 1.77e+01 angle pdb=" N PRO A1010 " pdb=" CA PRO A1010 " pdb=" C PRO A1010 " ideal model delta sigma weight residual 112.47 104.76 7.71 2.06e+00 2.36e-01 1.40e+01 angle pdb=" C VAL A 615 " pdb=" N ALA A 616 " pdb=" CA ALA A 616 " ideal model delta sigma weight residual 122.65 116.88 5.77 1.60e+00 3.91e-01 1.30e+01 angle pdb=" N LEU A 724 " pdb=" CA LEU A 724 " pdb=" C LEU A 724 " ideal model delta sigma weight residual 109.81 117.66 -7.85 2.21e+00 2.05e-01 1.26e+01 ... (remaining 12905 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.54: 5069 17.54 - 35.07: 401 35.07 - 52.60: 77 52.60 - 70.14: 7 70.14 - 87.67: 6 Dihedral angle restraints: 5560 sinusoidal: 1984 harmonic: 3576 Sorted by residual: dihedral pdb=" CA PRO A 355 " pdb=" C PRO A 355 " pdb=" N LEU A 356 " pdb=" CA LEU A 356 " ideal model delta harmonic sigma weight residual 180.00 150.28 29.72 0 5.00e+00 4.00e-02 3.53e+01 dihedral pdb=" CA PRO A 866 " pdb=" C PRO A 866 " pdb=" N ALA A 867 " pdb=" CA ALA A 867 " ideal model delta harmonic sigma weight residual -180.00 -153.58 -26.42 0 5.00e+00 4.00e-02 2.79e+01 dihedral pdb=" CA PRO A 588 " pdb=" C PRO A 588 " pdb=" N ALA A 589 " pdb=" CA ALA A 589 " ideal model delta harmonic sigma weight residual 180.00 -157.30 -22.70 0 5.00e+00 4.00e-02 2.06e+01 ... (remaining 5557 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.083: 1289 0.083 - 0.165: 229 0.165 - 0.248: 14 0.248 - 0.331: 3 0.331 - 0.414: 2 Chirality restraints: 1537 Sorted by residual: chirality pdb=" CB VAL A 405 " pdb=" CA VAL A 405 " pdb=" CG1 VAL A 405 " pdb=" CG2 VAL A 405 " both_signs ideal model delta sigma weight residual False -2.63 -2.22 -0.41 2.00e-01 2.50e+01 4.28e+00 chirality pdb=" CA THR A 661 " pdb=" N THR A 661 " pdb=" C THR A 661 " pdb=" CB THR A 661 " both_signs ideal model delta sigma weight residual False 2.53 2.19 0.33 2.00e-01 2.50e+01 2.78e+00 chirality pdb=" CB ILE A 491 " pdb=" CA ILE A 491 " pdb=" CG1 ILE A 491 " pdb=" CG2 ILE A 491 " both_signs ideal model delta sigma weight residual False 2.64 2.35 0.29 2.00e-01 2.50e+01 2.16e+00 ... (remaining 1534 not shown) Planarity restraints: 1681 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A 61 " 0.053 5.00e-02 4.00e+02 7.96e-02 1.01e+01 pdb=" N PRO A 62 " -0.138 5.00e-02 4.00e+02 pdb=" CA PRO A 62 " 0.041 5.00e-02 4.00e+02 pdb=" CD PRO A 62 " 0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE A 222 " 0.051 5.00e-02 4.00e+02 7.66e-02 9.38e+00 pdb=" N PRO A 223 " -0.132 5.00e-02 4.00e+02 pdb=" CA PRO A 223 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO A 223 " 0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER A 35 " 0.045 5.00e-02 4.00e+02 6.84e-02 7.49e+00 pdb=" N PRO A 36 " -0.118 5.00e-02 4.00e+02 pdb=" CA PRO A 36 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO A 36 " 0.038 5.00e-02 4.00e+02 ... (remaining 1678 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 1121 2.73 - 3.27: 8173 3.27 - 3.82: 14406 3.82 - 4.36: 16921 4.36 - 4.90: 30591 Nonbonded interactions: 71212 Sorted by model distance: nonbonded pdb=" O ALA A 962 " pdb="CA CA A2002 " model vdw 2.190 2.510 nonbonded pdb=" O THR A 970 " pdb="CA CA A2002 " model vdw 2.243 2.510 nonbonded pdb=" OG SER A 715 " pdb=" OE1 GLN A 756 " model vdw 2.268 3.040 nonbonded pdb=" O ASP A 967 " pdb="CA CA A2002 " model vdw 2.281 2.510 nonbonded pdb=" O GLY A 617 " pdb=" OG1 THR A 661 " model vdw 2.283 3.040 ... (remaining 71207 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 8.430 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: 0.370 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 36.570 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.080 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:3.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8405 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 : 0.012 0.084 9392 Z= 0.493 Angle : 1.069 10.559 12914 Z= 0.578 Chirality : 0.063 0.414 1537 Planarity : 0.010 0.080 1681 Dihedral : 13.487 87.672 3246 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.88 % Favored : 92.04 % Rotamer: Outliers : 0.11 % Allowed : 7.91 % Favored : 91.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.96 % 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: -5.51 (0.17), residues: 1247 helix: -5.01 (0.08), residues: 363 sheet: -2.68 (0.32), residues: 208 loop : -3.23 (0.18), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.003 TRP A 221 HIS 0.010 0.002 HIS A 675 PHE 0.028 0.003 PHE A 433 TYR 0.018 0.003 TYR A1258 ARG 0.011 0.001 ARG A1219 Details of bonding type rmsd hydrogen bonds : bond 0.31484 ( 267) hydrogen bonds : angle 11.60990 ( 732) SS BOND : bond 0.00546 ( 2) SS BOND : angle 0.70394 ( 4) covalent geometry : bond 0.01172 ( 9390) covalent geometry : angle 1.06909 (12910) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2494 Ramachandran restraints generated. 1247 Oldfield, 0 Emsley, 1247 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2494 Ramachandran restraints generated. 1247 Oldfield, 0 Emsley, 1247 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 88 time to evaluate : 1.329 Fit side-chains REVERT: A 673 ASP cc_start: 0.7801 (p0) cc_final: 0.7579 (p0) REVERT: A 1099 LYS cc_start: 0.9021 (ttpt) cc_final: 0.8681 (tttp) REVERT: A 1119 MET cc_start: 0.8999 (mtt) cc_final: 0.8666 (mtt) outliers start: 1 outliers final: 1 residues processed: 89 average time/residue: 0.4211 time to fit residues: 51.0464 Evaluate side-chains 59 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 58 time to evaluate : 2.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1036 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 106 optimal weight: 4.9990 chunk 95 optimal weight: 5.9990 chunk 52 optimal weight: 0.8980 chunk 32 optimal weight: 4.9990 chunk 64 optimal weight: 0.8980 chunk 51 optimal weight: 1.9990 chunk 98 optimal weight: 6.9990 chunk 38 optimal weight: 0.9990 chunk 60 optimal weight: 1.9990 chunk 73 optimal weight: 0.6980 chunk 114 optimal weight: 0.7980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 346 GLN A 551 HIS A 675 HIS A1151 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.115925 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.088967 restraints weight = 38485.237| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.091262 restraints weight = 15754.519| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.094086 restraints weight = 8563.391| |-----------------------------------------------------------------------------| r_work (final): 0.3048 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3050 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3050 r_free = 0.3050 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3050 r_free = 0.3050 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3050 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8052 moved from start: 0.1306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9392 Z= 0.140 Angle : 0.646 11.548 12914 Z= 0.323 Chirality : 0.044 0.176 1537 Planarity : 0.007 0.066 1681 Dihedral : 5.508 19.517 1340 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 1.21 % Allowed : 10.88 % Favored : 87.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.96 % 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: -4.44 (0.19), residues: 1247 helix: -3.81 (0.16), residues: 378 sheet: -2.03 (0.35), residues: 207 loop : -2.72 (0.20), residues: 662 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 205 HIS 0.004 0.001 HIS A 675 PHE 0.011 0.001 PHE A 246 TYR 0.010 0.001 TYR A 593 ARG 0.005 0.000 ARG A 523 Details of bonding type rmsd hydrogen bonds : bond 0.04642 ( 267) hydrogen bonds : angle 6.42180 ( 732) SS BOND : bond 0.00200 ( 2) SS BOND : angle 0.29439 ( 4) covalent geometry : bond 0.00323 ( 9390) covalent geometry : angle 0.64580 (12910) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2494 Ramachandran restraints generated. 1247 Oldfield, 0 Emsley, 1247 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2494 Ramachandran restraints generated. 1247 Oldfield, 0 Emsley, 1247 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 67 time to evaluate : 0.896 Fit side-chains REVERT: A 648 GLN cc_start: 0.8555 (tp-100) cc_final: 0.8123 (tt0) REVERT: A 1119 MET cc_start: 0.9032 (mtt) cc_final: 0.8647 (mtt) outliers start: 11 outliers final: 6 residues processed: 75 average time/residue: 0.3882 time to fit residues: 41.2903 Evaluate side-chains 61 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 55 time to evaluate : 1.632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 SER Chi-restraints excluded: chain A residue 954 ILE Chi-restraints excluded: chain A residue 1036 THR Chi-restraints excluded: chain A residue 1078 ILE Chi-restraints excluded: chain A residue 1141 THR Chi-restraints excluded: chain A residue 1150 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 30 optimal weight: 2.9990 chunk 25 optimal weight: 7.9990 chunk 66 optimal weight: 5.9990 chunk 36 optimal weight: 0.5980 chunk 84 optimal weight: 0.9980 chunk 51 optimal weight: 0.8980 chunk 26 optimal weight: 8.9990 chunk 94 optimal weight: 5.9990 chunk 59 optimal weight: 0.8980 chunk 23 optimal weight: 0.9980 chunk 31 optimal weight: 10.0000 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.118012 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.091760 restraints weight = 26912.934| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.094169 restraints weight = 13261.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.095139 restraints weight = 8061.376| |-----------------------------------------------------------------------------| r_work (final): 0.3059 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3061 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3061 r_free = 0.3061 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3061 r_free = 0.3061 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3061 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8023 moved from start: 0.1694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9392 Z= 0.132 Angle : 0.587 8.975 12914 Z= 0.288 Chirality : 0.043 0.147 1537 Planarity : 0.006 0.058 1681 Dihedral : 4.826 22.563 1340 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer: Outliers : 1.10 % Allowed : 11.76 % Favored : 87.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.96 % 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: -3.51 (0.21), residues: 1247 helix: -2.65 (0.21), residues: 378 sheet: -1.83 (0.35), residues: 205 loop : -2.28 (0.22), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 205 HIS 0.002 0.000 HIS A 551 PHE 0.010 0.001 PHE A 464 TYR 0.012 0.001 TYR A 593 ARG 0.006 0.000 ARG A 523 Details of bonding type rmsd hydrogen bonds : bond 0.03566 ( 267) hydrogen bonds : angle 5.50046 ( 732) SS BOND : bond 0.00158 ( 2) SS BOND : angle 0.75617 ( 4) covalent geometry : bond 0.00314 ( 9390) covalent geometry : angle 0.58669 (12910) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2494 Ramachandran restraints generated. 1247 Oldfield, 0 Emsley, 1247 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2494 Ramachandran restraints generated. 1247 Oldfield, 0 Emsley, 1247 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 72 time to evaluate : 0.936 Fit side-chains REVERT: A 73 TYR cc_start: 0.9109 (m-80) cc_final: 0.8803 (m-80) REVERT: A 421 LEU cc_start: 0.8117 (mp) cc_final: 0.7708 (tp) REVERT: A 648 GLN cc_start: 0.8529 (tp-100) cc_final: 0.8137 (tt0) REVERT: A 1099 LYS cc_start: 0.9044 (tttt) cc_final: 0.8588 (tttp) REVERT: A 1119 MET cc_start: 0.9007 (mtt) cc_final: 0.8592 (mtt) outliers start: 10 outliers final: 9 residues processed: 79 average time/residue: 0.2154 time to fit residues: 24.6788 Evaluate side-chains 72 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 63 time to evaluate : 0.906 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 SER Chi-restraints excluded: chain A residue 750 LEU Chi-restraints excluded: chain A residue 913 LEU Chi-restraints excluded: chain A residue 954 ILE Chi-restraints excluded: chain A residue 1036 THR Chi-restraints excluded: chain A residue 1077 VAL Chi-restraints excluded: chain A residue 1078 ILE Chi-restraints excluded: chain A residue 1141 THR Chi-restraints excluded: chain A residue 1150 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 107 optimal weight: 3.9990 chunk 104 optimal weight: 0.6980 chunk 60 optimal weight: 5.9990 chunk 16 optimal weight: 3.9990 chunk 123 optimal weight: 30.0000 chunk 80 optimal weight: 0.9990 chunk 17 optimal weight: 0.7980 chunk 120 optimal weight: 0.0060 chunk 65 optimal weight: 6.9990 chunk 73 optimal weight: 0.8980 chunk 88 optimal weight: 2.9990 overall best weight: 0.6798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 69 GLN A 534 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.113311 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2905 r_free = 0.2905 target = 0.087369 restraints weight = 43073.106| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.089989 restraints weight = 20070.367| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.090160 restraints weight = 14919.606| |-----------------------------------------------------------------------------| r_work (final): 0.2903 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2981 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2981 r_free = 0.2981 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2981 r_free = 0.2981 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2981 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 moved from start: 0.1926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9392 Z= 0.111 Angle : 0.555 8.279 12914 Z= 0.269 Chirality : 0.043 0.143 1537 Planarity : 0.005 0.053 1681 Dihedral : 4.507 23.031 1340 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 1.65 % Allowed : 12.75 % Favored : 85.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.96 % 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: -2.98 (0.22), residues: 1247 helix: -2.01 (0.23), residues: 386 sheet: -1.70 (0.35), residues: 213 loop : -2.02 (0.23), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 205 HIS 0.002 0.000 HIS A 551 PHE 0.010 0.001 PHE A 347 TYR 0.011 0.001 TYR A 593 ARG 0.004 0.000 ARG A 523 Details of bonding type rmsd hydrogen bonds : bond 0.03085 ( 267) hydrogen bonds : angle 5.11457 ( 732) SS BOND : bond 0.00126 ( 2) SS BOND : angle 0.85198 ( 4) covalent geometry : bond 0.00267 ( 9390) covalent geometry : angle 0.55476 (12910) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2494 Ramachandran restraints generated. 1247 Oldfield, 0 Emsley, 1247 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2494 Ramachandran restraints generated. 1247 Oldfield, 0 Emsley, 1247 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 68 time to evaluate : 0.996 Fit side-chains REVERT: A 73 TYR cc_start: 0.9044 (m-80) cc_final: 0.8785 (m-80) REVERT: A 421 LEU cc_start: 0.8118 (mp) cc_final: 0.7738 (tp) REVERT: A 648 GLN cc_start: 0.8368 (tp-100) cc_final: 0.8091 (tt0) REVERT: A 1099 LYS cc_start: 0.8947 (tttt) cc_final: 0.8669 (tttm) REVERT: A 1119 MET cc_start: 0.8991 (mtt) cc_final: 0.8609 (mtt) outliers start: 15 outliers final: 12 residues processed: 78 average time/residue: 0.2231 time to fit residues: 25.0814 Evaluate side-chains 71 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 59 time to evaluate : 0.940 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 SER Chi-restraints excluded: chain A residue 610 ASP Chi-restraints excluded: chain A residue 750 LEU Chi-restraints excluded: chain A residue 913 LEU Chi-restraints excluded: chain A residue 954 ILE Chi-restraints excluded: chain A residue 1036 THR Chi-restraints excluded: chain A residue 1077 VAL Chi-restraints excluded: chain A residue 1078 ILE Chi-restraints excluded: chain A residue 1141 THR Chi-restraints excluded: chain A residue 1150 ILE Chi-restraints excluded: chain A residue 1227 THR Chi-restraints excluded: chain A residue 1248 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 48 optimal weight: 0.9980 chunk 8 optimal weight: 1.9990 chunk 16 optimal weight: 3.9990 chunk 110 optimal weight: 1.9990 chunk 33 optimal weight: 5.9990 chunk 87 optimal weight: 0.7980 chunk 53 optimal weight: 0.7980 chunk 49 optimal weight: 0.7980 chunk 75 optimal weight: 4.9990 chunk 114 optimal weight: 0.6980 chunk 101 optimal weight: 5.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1092 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.113177 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2906 r_free = 0.2906 target = 0.087271 restraints weight = 40781.173| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2932 r_free = 0.2932 target = 0.089602 restraints weight = 20082.202| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2936 r_free = 0.2936 target = 0.090007 restraints weight = 14480.360| |-----------------------------------------------------------------------------| r_work (final): 0.2903 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2909 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2909 r_free = 0.2909 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2909 r_free = 0.2909 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2909 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 moved from start: 0.2015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9392 Z= 0.122 Angle : 0.565 7.784 12914 Z= 0.272 Chirality : 0.043 0.213 1537 Planarity : 0.005 0.053 1681 Dihedral : 4.388 22.860 1340 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 1.87 % Allowed : 13.85 % Favored : 84.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.96 % 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: -2.63 (0.22), residues: 1247 helix: -1.54 (0.25), residues: 386 sheet: -1.61 (0.35), residues: 213 loop : -1.88 (0.23), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 205 HIS 0.002 0.000 HIS A 551 PHE 0.010 0.001 PHE A 347 TYR 0.011 0.001 TYR A 593 ARG 0.003 0.000 ARG A 212 Details of bonding type rmsd hydrogen bonds : bond 0.02993 ( 267) hydrogen bonds : angle 5.03726 ( 732) SS BOND : bond 0.00148 ( 2) SS BOND : angle 0.50672 ( 4) covalent geometry : bond 0.00295 ( 9390) covalent geometry : angle 0.56528 (12910) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2494 Ramachandran restraints generated. 1247 Oldfield, 0 Emsley, 1247 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2494 Ramachandran restraints generated. 1247 Oldfield, 0 Emsley, 1247 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 60 time to evaluate : 0.861 Fit side-chains REVERT: A 73 TYR cc_start: 0.9076 (m-80) cc_final: 0.8811 (m-80) REVERT: A 304 MET cc_start: 0.8318 (mmm) cc_final: 0.7922 (tmm) REVERT: A 421 LEU cc_start: 0.8168 (mp) cc_final: 0.7836 (tp) REVERT: A 1061 ARG cc_start: 0.7084 (mmm160) cc_final: 0.6614 (tpt90) REVERT: A 1099 LYS cc_start: 0.8953 (tttt) cc_final: 0.8663 (tttm) REVERT: A 1119 MET cc_start: 0.9032 (mtt) cc_final: 0.8652 (mtt) outliers start: 17 outliers final: 13 residues processed: 72 average time/residue: 0.2273 time to fit residues: 23.4710 Evaluate side-chains 69 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 56 time to evaluate : 0.917 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 SER Chi-restraints excluded: chain A residue 610 ASP Chi-restraints excluded: chain A residue 711 THR Chi-restraints excluded: chain A residue 750 LEU Chi-restraints excluded: chain A residue 913 LEU Chi-restraints excluded: chain A residue 954 ILE Chi-restraints excluded: chain A residue 1036 THR Chi-restraints excluded: chain A residue 1077 VAL Chi-restraints excluded: chain A residue 1078 ILE Chi-restraints excluded: chain A residue 1141 THR Chi-restraints excluded: chain A residue 1150 ILE Chi-restraints excluded: chain A residue 1227 THR Chi-restraints excluded: chain A residue 1248 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 103 optimal weight: 3.9990 chunk 112 optimal weight: 0.7980 chunk 82 optimal weight: 0.9990 chunk 76 optimal weight: 3.9990 chunk 53 optimal weight: 0.6980 chunk 125 optimal weight: 20.0000 chunk 57 optimal weight: 2.9990 chunk 8 optimal weight: 0.9980 chunk 111 optimal weight: 2.9990 chunk 43 optimal weight: 0.9980 chunk 10 optimal weight: 0.6980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1092 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.113265 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2909 r_free = 0.2909 target = 0.087538 restraints weight = 32892.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2931 r_free = 0.2931 target = 0.089391 restraints weight = 14836.848| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2940 r_free = 0.2940 target = 0.090126 restraints weight = 10900.701| |-----------------------------------------------------------------------------| r_work (final): 0.2908 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2911 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2911 r_free = 0.2911 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2911 r_free = 0.2911 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2911 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 moved from start: 0.2137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9392 Z= 0.122 Angle : 0.558 7.779 12914 Z= 0.268 Chirality : 0.043 0.165 1537 Planarity : 0.005 0.055 1681 Dihedral : 4.281 22.393 1340 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 1.87 % Allowed : 14.84 % Favored : 83.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.96 % 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: -2.31 (0.23), residues: 1247 helix: -1.15 (0.26), residues: 386 sheet: -1.49 (0.35), residues: 206 loop : -1.74 (0.23), residues: 655 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 205 HIS 0.002 0.000 HIS A 551 PHE 0.010 0.001 PHE A 347 TYR 0.011 0.001 TYR A 593 ARG 0.004 0.000 ARG A 523 Details of bonding type rmsd hydrogen bonds : bond 0.02910 ( 267) hydrogen bonds : angle 4.93029 ( 732) SS BOND : bond 0.00176 ( 2) SS BOND : angle 0.46423 ( 4) covalent geometry : bond 0.00296 ( 9390) covalent geometry : angle 0.55775 (12910) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2494 Ramachandran restraints generated. 1247 Oldfield, 0 Emsley, 1247 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2494 Ramachandran restraints generated. 1247 Oldfield, 0 Emsley, 1247 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 60 time to evaluate : 1.040 Fit side-chains REVERT: A 73 TYR cc_start: 0.9053 (m-80) cc_final: 0.8819 (m-80) REVERT: A 304 MET cc_start: 0.8316 (mmm) cc_final: 0.7923 (tmm) REVERT: A 421 LEU cc_start: 0.8168 (mp) cc_final: 0.7867 (tp) REVERT: A 1119 MET cc_start: 0.9014 (mtt) cc_final: 0.8636 (mtt) outliers start: 17 outliers final: 13 residues processed: 71 average time/residue: 0.2343 time to fit residues: 24.0259 Evaluate side-chains 68 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 55 time to evaluate : 0.901 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 SER Chi-restraints excluded: chain A residue 610 ASP Chi-restraints excluded: chain A residue 711 THR Chi-restraints excluded: chain A residue 750 LEU Chi-restraints excluded: chain A residue 913 LEU Chi-restraints excluded: chain A residue 954 ILE Chi-restraints excluded: chain A residue 1036 THR Chi-restraints excluded: chain A residue 1077 VAL Chi-restraints excluded: chain A residue 1078 ILE Chi-restraints excluded: chain A residue 1141 THR Chi-restraints excluded: chain A residue 1150 ILE Chi-restraints excluded: chain A residue 1227 THR Chi-restraints excluded: chain A residue 1248 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 63 optimal weight: 0.7980 chunk 50 optimal weight: 3.9990 chunk 49 optimal weight: 0.6980 chunk 116 optimal weight: 0.8980 chunk 93 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 chunk 112 optimal weight: 0.8980 chunk 22 optimal weight: 0.0370 chunk 18 optimal weight: 0.9980 chunk 51 optimal weight: 0.1980 chunk 70 optimal weight: 2.9990 overall best weight: 0.5258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 77 HIS A1092 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.115019 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2918 r_free = 0.2918 target = 0.088298 restraints weight = 40239.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.092132 restraints weight = 18281.633| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.092181 restraints weight = 11515.724| |-----------------------------------------------------------------------------| r_work (final): 0.2926 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2926 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2926 r_free = 0.2926 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2926 r_free = 0.2926 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2926 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 moved from start: 0.2299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 9392 Z= 0.098 Angle : 0.538 7.418 12914 Z= 0.258 Chirality : 0.043 0.239 1537 Planarity : 0.005 0.051 1681 Dihedral : 4.130 22.246 1340 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 1.87 % Allowed : 15.49 % Favored : 82.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.96 % 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: -2.08 (0.23), residues: 1247 helix: -0.87 (0.26), residues: 390 sheet: -1.33 (0.35), residues: 213 loop : -1.69 (0.24), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 205 HIS 0.002 0.000 HIS A 551 PHE 0.011 0.001 PHE A 347 TYR 0.011 0.001 TYR A 593 ARG 0.003 0.000 ARG A 523 Details of bonding type rmsd hydrogen bonds : bond 0.02713 ( 267) hydrogen bonds : angle 4.82331 ( 732) SS BOND : bond 0.00134 ( 2) SS BOND : angle 0.44521 ( 4) covalent geometry : bond 0.00237 ( 9390) covalent geometry : angle 0.53844 (12910) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2494 Ramachandran restraints generated. 1247 Oldfield, 0 Emsley, 1247 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2494 Ramachandran restraints generated. 1247 Oldfield, 0 Emsley, 1247 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 55 time to evaluate : 1.018 Fit side-chains REVERT: A 73 TYR cc_start: 0.9033 (m-80) cc_final: 0.8787 (m-80) REVERT: A 421 LEU cc_start: 0.8168 (mp) cc_final: 0.7882 (tp) REVERT: A 937 ASP cc_start: 0.7735 (OUTLIER) cc_final: 0.7015 (m-30) REVERT: A 1099 LYS cc_start: 0.8806 (tttm) cc_final: 0.8569 (tptm) REVERT: A 1119 MET cc_start: 0.8954 (mtt) cc_final: 0.8575 (mtt) outliers start: 17 outliers final: 13 residues processed: 67 average time/residue: 0.2336 time to fit residues: 22.4847 Evaluate side-chains 65 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 51 time to evaluate : 0.977 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 SER Chi-restraints excluded: chain A residue 610 ASP Chi-restraints excluded: chain A residue 750 LEU Chi-restraints excluded: chain A residue 761 ASP Chi-restraints excluded: chain A residue 913 LEU Chi-restraints excluded: chain A residue 937 ASP Chi-restraints excluded: chain A residue 954 ILE Chi-restraints excluded: chain A residue 1007 THR Chi-restraints excluded: chain A residue 1036 THR Chi-restraints excluded: chain A residue 1077 VAL Chi-restraints excluded: chain A residue 1078 ILE Chi-restraints excluded: chain A residue 1141 THR Chi-restraints excluded: chain A residue 1150 ILE Chi-restraints excluded: chain A residue 1227 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 79 optimal weight: 1.9990 chunk 51 optimal weight: 0.9990 chunk 2 optimal weight: 0.7980 chunk 122 optimal weight: 0.0370 chunk 73 optimal weight: 0.2980 chunk 101 optimal weight: 0.1980 chunk 36 optimal weight: 0.6980 chunk 21 optimal weight: 2.9990 chunk 112 optimal weight: 3.9990 chunk 47 optimal weight: 0.8980 chunk 93 optimal weight: 0.9980 overall best weight: 0.4058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.114961 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2928 r_free = 0.2928 target = 0.088607 restraints weight = 32039.079| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.091364 restraints weight = 15018.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.091721 restraints weight = 10708.408| |-----------------------------------------------------------------------------| r_work (final): 0.2949 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2959 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2959 r_free = 0.2959 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2959 r_free = 0.2959 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2959 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 moved from start: 0.2456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 9392 Z= 0.091 Angle : 0.529 7.261 12914 Z= 0.253 Chirality : 0.042 0.186 1537 Planarity : 0.005 0.050 1681 Dihedral : 3.989 22.046 1340 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 1.87 % Allowed : 15.49 % Favored : 82.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.96 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.90 (0.23), residues: 1247 helix: -0.65 (0.26), residues: 397 sheet: -1.25 (0.35), residues: 213 loop : -1.62 (0.24), residues: 637 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 205 HIS 0.001 0.000 HIS A 551 PHE 0.011 0.001 PHE A 347 TYR 0.011 0.001 TYR A 593 ARG 0.004 0.000 ARG A 169 Details of bonding type rmsd hydrogen bonds : bond 0.02594 ( 267) hydrogen bonds : angle 4.68414 ( 732) SS BOND : bond 0.00079 ( 2) SS BOND : angle 0.47882 ( 4) covalent geometry : bond 0.00220 ( 9390) covalent geometry : angle 0.52920 (12910) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2494 Ramachandran restraints generated. 1247 Oldfield, 0 Emsley, 1247 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2494 Ramachandran restraints generated. 1247 Oldfield, 0 Emsley, 1247 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 57 time to evaluate : 0.968 Fit side-chains REVERT: A 73 TYR cc_start: 0.9048 (m-80) cc_final: 0.8792 (m-80) REVERT: A 83 LEU cc_start: 0.8705 (OUTLIER) cc_final: 0.8483 (mp) REVERT: A 421 LEU cc_start: 0.8147 (mp) cc_final: 0.7878 (tp) REVERT: A 937 ASP cc_start: 0.7817 (OUTLIER) cc_final: 0.7120 (m-30) REVERT: A 1099 LYS cc_start: 0.8839 (tttm) cc_final: 0.8515 (tptm) REVERT: A 1119 MET cc_start: 0.8987 (mtt) cc_final: 0.8635 (mtt) outliers start: 17 outliers final: 13 residues processed: 70 average time/residue: 0.2332 time to fit residues: 23.4775 Evaluate side-chains 69 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 54 time to evaluate : 0.954 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 SER Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 750 LEU Chi-restraints excluded: chain A residue 761 ASP Chi-restraints excluded: chain A residue 822 THR Chi-restraints excluded: chain A residue 838 THR Chi-restraints excluded: chain A residue 913 LEU Chi-restraints excluded: chain A residue 937 ASP Chi-restraints excluded: chain A residue 954 ILE Chi-restraints excluded: chain A residue 1007 THR Chi-restraints excluded: chain A residue 1036 THR Chi-restraints excluded: chain A residue 1077 VAL Chi-restraints excluded: chain A residue 1078 ILE Chi-restraints excluded: chain A residue 1150 ILE Chi-restraints excluded: chain A residue 1227 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 101 optimal weight: 0.4980 chunk 97 optimal weight: 1.9990 chunk 73 optimal weight: 0.0870 chunk 120 optimal weight: 0.0670 chunk 26 optimal weight: 0.6980 chunk 102 optimal weight: 7.9990 chunk 81 optimal weight: 0.0170 chunk 69 optimal weight: 2.9990 chunk 75 optimal weight: 0.8980 chunk 85 optimal weight: 1.9990 chunk 84 optimal weight: 0.0870 overall best weight: 0.1512 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.118571 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.094508 restraints weight = 31708.842| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.096464 restraints weight = 17412.739| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.097049 restraints weight = 13334.043| |-----------------------------------------------------------------------------| r_work (final): 0.3006 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3007 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3007 r_free = 0.3007 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3007 r_free = 0.3007 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3007 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 moved from start: 0.2777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 9392 Z= 0.082 Angle : 0.513 7.096 12914 Z= 0.244 Chirality : 0.042 0.189 1537 Planarity : 0.005 0.049 1681 Dihedral : 3.741 22.064 1340 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 1.54 % Allowed : 15.82 % Favored : 82.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.96 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.56 (0.23), residues: 1247 helix: -0.20 (0.27), residues: 388 sheet: -1.07 (0.35), residues: 213 loop : -1.53 (0.23), residues: 646 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 205 HIS 0.001 0.000 HIS A 551 PHE 0.012 0.001 PHE A 347 TYR 0.010 0.001 TYR A 593 ARG 0.003 0.000 ARG A 212 Details of bonding type rmsd hydrogen bonds : bond 0.02349 ( 267) hydrogen bonds : angle 4.46453 ( 732) SS BOND : bond 0.00065 ( 2) SS BOND : angle 0.56470 ( 4) covalent geometry : bond 0.00195 ( 9390) covalent geometry : angle 0.51316 (12910) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2494 Ramachandran restraints generated. 1247 Oldfield, 0 Emsley, 1247 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2494 Ramachandran restraints generated. 1247 Oldfield, 0 Emsley, 1247 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 69 time to evaluate : 1.550 Fit side-chains REVERT: A 73 TYR cc_start: 0.9040 (m-80) cc_final: 0.8769 (m-80) REVERT: A 152 MET cc_start: 0.7867 (tmm) cc_final: 0.7346 (tpp) REVERT: A 421 LEU cc_start: 0.8080 (mp) cc_final: 0.7834 (tp) REVERT: A 937 ASP cc_start: 0.7596 (OUTLIER) cc_final: 0.6967 (m-30) REVERT: A 1099 LYS cc_start: 0.8715 (tttm) cc_final: 0.8486 (tptm) REVERT: A 1119 MET cc_start: 0.8928 (mtt) cc_final: 0.8552 (mtt) outliers start: 14 outliers final: 11 residues processed: 79 average time/residue: 0.2301 time to fit residues: 25.9314 Evaluate side-chains 73 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 61 time to evaluate : 0.933 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 SER Chi-restraints excluded: chain A residue 750 LEU Chi-restraints excluded: chain A residue 822 THR Chi-restraints excluded: chain A residue 838 THR Chi-restraints excluded: chain A residue 913 LEU Chi-restraints excluded: chain A residue 937 ASP Chi-restraints excluded: chain A residue 1007 THR Chi-restraints excluded: chain A residue 1036 THR Chi-restraints excluded: chain A residue 1077 VAL Chi-restraints excluded: chain A residue 1078 ILE Chi-restraints excluded: chain A residue 1150 ILE Chi-restraints excluded: chain A residue 1227 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 68 optimal weight: 3.9990 chunk 3 optimal weight: 1.9990 chunk 72 optimal weight: 0.9980 chunk 41 optimal weight: 0.0570 chunk 89 optimal weight: 0.0070 chunk 64 optimal weight: 3.9990 chunk 2 optimal weight: 0.6980 chunk 115 optimal weight: 0.7980 chunk 107 optimal weight: 0.9980 chunk 105 optimal weight: 0.0020 chunk 84 optimal weight: 0.6980 overall best weight: 0.2924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.117984 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.092409 restraints weight = 33952.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.094165 restraints weight = 17094.754| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.095760 restraints weight = 10978.669| |-----------------------------------------------------------------------------| r_work (final): 0.2990 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2991 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2991 r_free = 0.2991 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2991 r_free = 0.2991 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2991 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8130 moved from start: 0.2834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 9392 Z= 0.084 Angle : 0.515 6.895 12914 Z= 0.244 Chirality : 0.042 0.158 1537 Planarity : 0.005 0.049 1681 Dihedral : 3.693 22.313 1340 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 1.43 % Allowed : 16.04 % Favored : 82.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.96 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.41 (0.23), residues: 1247 helix: -0.04 (0.27), residues: 389 sheet: -0.99 (0.35), residues: 213 loop : -1.46 (0.24), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 205 HIS 0.001 0.000 HIS A 85 PHE 0.012 0.001 PHE A 347 TYR 0.011 0.001 TYR A 593 ARG 0.003 0.000 ARG A1061 Details of bonding type rmsd hydrogen bonds : bond 0.02448 ( 267) hydrogen bonds : angle 4.42676 ( 732) SS BOND : bond 0.00078 ( 2) SS BOND : angle 0.47939 ( 4) covalent geometry : bond 0.00202 ( 9390) covalent geometry : angle 0.51542 (12910) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2494 Ramachandran restraints generated. 1247 Oldfield, 0 Emsley, 1247 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2494 Ramachandran restraints generated. 1247 Oldfield, 0 Emsley, 1247 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 63 time to evaluate : 1.056 Fit side-chains REVERT: A 73 TYR cc_start: 0.9040 (m-80) cc_final: 0.8781 (m-80) REVERT: A 152 MET cc_start: 0.7895 (tmm) cc_final: 0.7347 (tpp) REVERT: A 170 MET cc_start: 0.7519 (ttp) cc_final: 0.7276 (ttp) REVERT: A 421 LEU cc_start: 0.8082 (mp) cc_final: 0.7818 (tp) REVERT: A 937 ASP cc_start: 0.7619 (OUTLIER) cc_final: 0.7002 (m-30) REVERT: A 1099 LYS cc_start: 0.8706 (tttm) cc_final: 0.8479 (tptm) REVERT: A 1119 MET cc_start: 0.8941 (mtt) cc_final: 0.8563 (mtt) outliers start: 13 outliers final: 12 residues processed: 72 average time/residue: 0.2390 time to fit residues: 25.1255 Evaluate side-chains 73 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 60 time to evaluate : 1.071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 SER Chi-restraints excluded: chain A residue 750 LEU Chi-restraints excluded: chain A residue 822 THR Chi-restraints excluded: chain A residue 838 THR Chi-restraints excluded: chain A residue 913 LEU Chi-restraints excluded: chain A residue 937 ASP Chi-restraints excluded: chain A residue 1007 THR Chi-restraints excluded: chain A residue 1036 THR Chi-restraints excluded: chain A residue 1077 VAL Chi-restraints excluded: chain A residue 1078 ILE Chi-restraints excluded: chain A residue 1150 ILE Chi-restraints excluded: chain A residue 1153 VAL Chi-restraints excluded: chain A residue 1227 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 109 optimal weight: 3.9990 chunk 107 optimal weight: 2.9990 chunk 122 optimal weight: 2.9990 chunk 59 optimal weight: 0.0010 chunk 74 optimal weight: 0.8980 chunk 37 optimal weight: 0.9990 chunk 43 optimal weight: 2.9990 chunk 64 optimal weight: 5.9990 chunk 102 optimal weight: 2.9990 chunk 58 optimal weight: 0.1980 chunk 63 optimal weight: 0.0470 overall best weight: 0.4286 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.116370 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.090321 restraints weight = 30898.875| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.092250 restraints weight = 15971.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.093407 restraints weight = 10548.965| |-----------------------------------------------------------------------------| r_work (final): 0.3187 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3187 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3187 r_free = 0.3187 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3187 r_free = 0.3187 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3187 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8209 moved from start: 0.2839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 9392 Z= 0.091 Angle : 0.527 9.202 12914 Z= 0.249 Chirality : 0.042 0.147 1537 Planarity : 0.005 0.047 1681 Dihedral : 3.720 22.240 1340 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 1.65 % Allowed : 16.15 % Favored : 82.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.96 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.26 (0.24), residues: 1247 helix: 0.15 (0.28), residues: 387 sheet: -0.95 (0.35), residues: 213 loop : -1.40 (0.24), residues: 647 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 205 HIS 0.001 0.000 HIS A 551 PHE 0.011 0.001 PHE A 347 TYR 0.011 0.001 TYR A 593 ARG 0.003 0.000 ARG A1061 Details of bonding type rmsd hydrogen bonds : bond 0.02495 ( 267) hydrogen bonds : angle 4.41695 ( 732) SS BOND : bond 0.00084 ( 2) SS BOND : angle 0.49281 ( 4) covalent geometry : bond 0.00221 ( 9390) covalent geometry : angle 0.52696 (12910) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3685.10 seconds wall clock time: 68 minutes 2.09 seconds (4082.09 seconds total)