Starting phenix.real_space_refine on Thu Feb 13 18:33:23 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6wbx_21600/02_2025/6wbx_21600.cif Found real_map, /net/cci-nas-00/data/ceres_data/6wbx_21600/02_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_21600/02_2025/6wbx_21600.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6wbx_21600/02_2025/6wbx_21600.map" model { file = "/net/cci-nas-00/data/ceres_data/6wbx_21600/02_2025/6wbx_21600.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6wbx_21600/02_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-5592/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: 9.85, per 1000 atoms: 1.07 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: 2.14 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: 1.31 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: 3.92 Time building geometry restraints manager: 2.54 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: 1.160 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: 0.350 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 30.940 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.820 ------------------------------------------------------------------------------- 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 9390 Z= 0.785 Angle : 1.069 10.559 12910 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 *********************** 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 : 0.979 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: 0.3078 time to fit residues: 37.1313 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 : 0.972 ------------------------------------------------------------------------------- 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 = 0.088968 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 = 15754.698| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.094175 restraints weight = 8563.765| |-----------------------------------------------------------------------------| r_work (final): 0.3049 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3051 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3051 r_free = 0.3051 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 = 0.3051 r_free = 0.3051 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3051 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8051 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 9390 Z= 0.217 Angle : 0.646 11.548 12910 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 *********************** 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 : 1.134 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: 0.2273 time to fit residues: 24.5889 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 : 1.039 ------------------------------------------------------------------------------- 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: 1.9990 chunk 25 optimal weight: 5.9990 chunk 66 optimal weight: 0.0670 chunk 36 optimal weight: 0.5980 chunk 84 optimal weight: 0.9980 chunk 51 optimal weight: 0.9980 chunk 26 optimal weight: 8.9990 chunk 94 optimal weight: 4.9990 chunk 59 optimal weight: 0.8980 chunk 23 optimal weight: 0.9990 chunk 31 optimal weight: 10.0000 overall best weight: 0.7118 ------------------------------------------------------------------------------- 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 77 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.118675 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.091910 restraints weight = 26883.613| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.094486 restraints weight = 12720.586| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.095690 restraints weight = 6993.270| |-----------------------------------------------------------------------------| r_work (final): 0.3063 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3064 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3064 r_free = 0.3064 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 = 0.3064 r_free = 0.3064 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3064 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8039 moved from start: 0.1744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9390 Z= 0.190 Angle : 0.577 8.891 12910 Z= 0.283 Chirality : 0.043 0.139 1537 Planarity : 0.006 0.058 1681 Dihedral : 4.766 22.424 1340 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer: Outliers : 1.10 % Allowed : 11.54 % Favored : 87.36 % 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: -3.54 (0.21), residues: 1247 helix: -2.71 (0.21), residues: 385 sheet: -1.81 (0.35), residues: 205 loop : -2.27 (0.22), residues: 657 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 246 TYR 0.011 0.001 TYR A 593 ARG 0.004 0.000 ARG A 523 *********************** 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 : 1.014 Fit side-chains REVERT: A 73 TYR cc_start: 0.9072 (m-80) cc_final: 0.8761 (m-80) REVERT: A 421 LEU cc_start: 0.8078 (mp) cc_final: 0.7669 (tp) REVERT: A 648 GLN cc_start: 0.8494 (tp-100) cc_final: 0.8105 (tt0) REVERT: A 1099 LYS cc_start: 0.9014 (tttt) cc_final: 0.8783 (tttm) REVERT: A 1119 MET cc_start: 0.8988 (mtt) cc_final: 0.8593 (mtt) outliers start: 10 outliers final: 9 residues processed: 79 average time/residue: 0.2238 time to fit residues: 25.6529 Evaluate side-chains 69 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 60 time to evaluate : 0.909 ------------------------------------------------------------------------------- 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: 0.9990 chunk 60 optimal weight: 2.9990 chunk 16 optimal weight: 3.9990 chunk 123 optimal weight: 7.9990 chunk 80 optimal weight: 0.6980 chunk 17 optimal weight: 0.6980 chunk 120 optimal weight: 0.0170 chunk 65 optimal weight: 0.2980 chunk 73 optimal weight: 6.9990 chunk 88 optimal weight: 0.0870 overall best weight: 0.3596 ------------------------------------------------------------------------------- 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 = 0.3292 r_free = 0.3292 target = 0.115290 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2936 r_free = 0.2936 target = 0.089395 restraints weight = 42829.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.091496 restraints weight = 20163.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.092248 restraints weight = 13224.147| |-----------------------------------------------------------------------------| r_work (final): 0.2925 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2930 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2930 r_free = 0.2930 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2930 r_free = 0.2930 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2930 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.2099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 9390 Z= 0.150 Angle : 0.539 7.869 12910 Z= 0.260 Chirality : 0.042 0.144 1537 Planarity : 0.005 0.053 1681 Dihedral : 4.336 22.869 1340 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 1.54 % Allowed : 12.86 % 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: -2.88 (0.22), residues: 1247 helix: -1.92 (0.24), residues: 385 sheet: -1.59 (0.34), residues: 213 loop : -1.98 (0.23), residues: 649 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 *********************** 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 82 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 68 time to evaluate : 0.918 Fit side-chains REVERT: A 73 TYR cc_start: 0.9005 (m-80) cc_final: 0.8739 (m-80) REVERT: A 421 LEU cc_start: 0.8154 (mp) cc_final: 0.7792 (tp) REVERT: A 1099 LYS cc_start: 0.8935 (tttt) cc_final: 0.8682 (tttm) REVERT: A 1119 MET cc_start: 0.8945 (mtt) cc_final: 0.8552 (mtt) outliers start: 14 outliers final: 12 residues processed: 77 average time/residue: 0.2261 time to fit residues: 24.9116 Evaluate side-chains 69 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 57 time to evaluate : 0.990 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 SER Chi-restraints excluded: chain A residue 323 LEU 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 48 optimal weight: 2.9990 chunk 8 optimal weight: 0.9980 chunk 16 optimal weight: 1.9990 chunk 110 optimal weight: 0.8980 chunk 33 optimal weight: 7.9990 chunk 87 optimal weight: 0.1980 chunk 53 optimal weight: 0.9980 chunk 49 optimal weight: 0.0670 chunk 75 optimal weight: 5.9990 chunk 114 optimal weight: 0.4980 chunk 101 optimal weight: 0.6980 overall best weight: 0.4718 ------------------------------------------------------------------------------- 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 = 0.3282 r_free = 0.3282 target = 0.114640 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2940 r_free = 0.2940 target = 0.089616 restraints weight = 40773.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2954 r_free = 0.2954 target = 0.091266 restraints weight = 21214.570| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.092258 restraints weight = 13660.246| |-----------------------------------------------------------------------------| r_work (final): 0.2946 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2953 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2953 r_free = 0.2953 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2953 r_free = 0.2953 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2953 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8163 moved from start: 0.2216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 9390 Z= 0.159 Angle : 0.540 7.412 12910 Z= 0.260 Chirality : 0.042 0.204 1537 Planarity : 0.005 0.053 1681 Dihedral : 4.170 22.891 1340 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 1.98 % Allowed : 13.74 % 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: -2.51 (0.22), residues: 1247 helix: -1.44 (0.25), residues: 385 sheet: -1.47 (0.35), residues: 213 loop : -1.84 (0.23), residues: 649 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 205 HIS 0.001 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 *********************** 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 80 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 62 time to evaluate : 0.933 Fit side-chains REVERT: A 73 TYR cc_start: 0.9026 (m-80) cc_final: 0.8773 (m-80) REVERT: A 83 LEU cc_start: 0.8704 (OUTLIER) cc_final: 0.8492 (mp) REVERT: A 152 MET cc_start: 0.8039 (tmm) cc_final: 0.7480 (tpp) REVERT: A 421 LEU cc_start: 0.8149 (mp) cc_final: 0.7833 (tp) REVERT: A 1099 LYS cc_start: 0.8899 (tttt) cc_final: 0.8642 (tttm) REVERT: A 1119 MET cc_start: 0.8991 (mtt) cc_final: 0.8605 (mtt) outliers start: 18 outliers final: 12 residues processed: 76 average time/residue: 0.2215 time to fit residues: 24.2058 Evaluate side-chains 70 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 57 time to evaluate : 0.938 ------------------------------------------------------------------------------- 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 610 ASP Chi-restraints excluded: chain A residue 750 LEU Chi-restraints excluded: chain A residue 822 THR 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 103 optimal weight: 5.9990 chunk 112 optimal weight: 0.9980 chunk 82 optimal weight: 2.9990 chunk 76 optimal weight: 5.9990 chunk 53 optimal weight: 2.9990 chunk 125 optimal weight: 30.0000 chunk 57 optimal weight: 0.6980 chunk 8 optimal weight: 0.0270 chunk 111 optimal weight: 2.9990 chunk 43 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 overall best weight: 1.5442 ------------------------------------------------------------------------------- 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 = 0.3408 r_free = 0.3408 target = 0.124019 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.102389 restraints weight = 31004.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.106385 restraints weight = 21645.147| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.105110 restraints weight = 11643.252| |-----------------------------------------------------------------------------| r_work (final): 0.2880 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2888 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2888 r_free = 0.2888 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2888 r_free = 0.2888 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2888 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 moved from start: 0.2020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 9390 Z= 0.311 Angle : 0.613 9.806 12910 Z= 0.298 Chirality : 0.045 0.155 1537 Planarity : 0.005 0.049 1681 Dihedral : 4.520 23.522 1340 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.95 % Favored : 94.05 % Rotamer: Outliers : 1.65 % Allowed : 14.95 % Favored : 83.41 % 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: -2.38 (0.23), residues: 1247 helix: -1.25 (0.26), residues: 380 sheet: -1.55 (0.35), residues: 206 loop : -1.76 (0.23), residues: 661 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 205 HIS 0.003 0.001 HIS A 858 PHE 0.013 0.002 PHE A 433 TYR 0.011 0.001 TYR A 439 ARG 0.004 0.000 ARG A 523 *********************** 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 70 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 55 time to evaluate : 0.976 Fit side-chains REVERT: A 73 TYR cc_start: 0.9031 (m-80) cc_final: 0.8828 (m-80) REVERT: A 421 LEU cc_start: 0.8184 (mp) cc_final: 0.7867 (tp) REVERT: A 1119 MET cc_start: 0.8977 (mtt) cc_final: 0.8603 (mtt) outliers start: 15 outliers final: 13 residues processed: 66 average time/residue: 0.2320 time to fit residues: 21.8283 Evaluate side-chains 66 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 53 time to evaluate : 0.982 ------------------------------------------------------------------------------- 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 63 optimal weight: 0.7980 chunk 50 optimal weight: 4.9990 chunk 49 optimal weight: 0.7980 chunk 116 optimal weight: 0.5980 chunk 93 optimal weight: 1.9990 chunk 4 optimal weight: 0.7980 chunk 112 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 51 optimal weight: 0.9990 chunk 70 optimal weight: 2.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- 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 = 0.3436 r_free = 0.3436 target = 0.126152 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.105515 restraints weight = 38049.865| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.107284 restraints weight = 51856.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.108738 restraints weight = 17175.971| |-----------------------------------------------------------------------------| r_work (final): 0.2970 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2967 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2967 r_free = 0.2967 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 = 0.2967 r_free = 0.2967 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2967 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.2168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9390 Z= 0.194 Angle : 0.562 8.541 12910 Z= 0.270 Chirality : 0.043 0.258 1537 Planarity : 0.005 0.049 1681 Dihedral : 4.338 22.094 1340 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 1.87 % Allowed : 15.38 % Favored : 82.75 % 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: -2.20 (0.23), residues: 1247 helix: -1.04 (0.26), residues: 388 sheet: -1.39 (0.35), residues: 213 loop : -1.71 (0.24), residues: 646 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 0.003 0.000 ARG A 523 *********************** 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 : 1.048 Fit side-chains REVERT: A 73 TYR cc_start: 0.9008 (m-80) cc_final: 0.8807 (m-80) REVERT: A 304 MET cc_start: 0.8033 (mmm) cc_final: 0.7709 (tmm) REVERT: A 1099 LYS cc_start: 0.8705 (tttm) cc_final: 0.8489 (tptm) REVERT: A 1119 MET cc_start: 0.8953 (mtt) cc_final: 0.8565 (mtt) outliers start: 17 outliers final: 15 residues processed: 69 average time/residue: 0.2332 time to fit residues: 23.1175 Evaluate side-chains 67 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 52 time to evaluate : 0.971 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 SER Chi-restraints excluded: chain A residue 370 LEU 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 822 THR Chi-restraints excluded: chain A residue 913 LEU 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: 0.7980 chunk 51 optimal weight: 0.1980 chunk 2 optimal weight: 2.9990 chunk 122 optimal weight: 0.5980 chunk 73 optimal weight: 0.0370 chunk 101 optimal weight: 0.0000 chunk 36 optimal weight: 0.9980 chunk 21 optimal weight: 0.4980 chunk 112 optimal weight: 0.6980 chunk 47 optimal weight: 0.0980 chunk 93 optimal weight: 1.9990 overall best weight: 0.1662 ------------------------------------------------------------------------------- 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 = 0.3305 r_free = 0.3305 target = 0.116246 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.091589 restraints weight = 31955.778| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.092984 restraints weight = 15970.321| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.093362 restraints weight = 14602.067| |-----------------------------------------------------------------------------| r_work (final): 0.2958 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2960 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2960 r_free = 0.2960 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2960 r_free = 0.2960 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2960 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 moved from start: 0.2538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 9390 Z= 0.136 Angle : 0.529 7.478 12910 Z= 0.252 Chirality : 0.042 0.196 1537 Planarity : 0.005 0.054 1681 Dihedral : 3.973 21.997 1340 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 1.87 % Allowed : 15.16 % Favored : 82.97 % 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: -1.87 (0.23), residues: 1247 helix: -0.59 (0.27), residues: 386 sheet: -1.27 (0.35), residues: 213 loop : -1.61 (0.24), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 205 HIS 0.001 0.000 HIS A 551 PHE 0.011 0.001 PHE A 347 TYR 0.010 0.001 TYR A 593 ARG 0.002 0.000 ARG A 523 *********************** 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 77 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 60 time to evaluate : 0.893 Fit side-chains REVERT: A 73 TYR cc_start: 0.9003 (m-80) cc_final: 0.8770 (m-80) REVERT: A 152 MET cc_start: 0.7935 (tmm) cc_final: 0.7398 (tpp) REVERT: A 964 THR cc_start: 0.8852 (p) cc_final: 0.8650 (p) REVERT: A 1099 LYS cc_start: 0.8768 (tttm) cc_final: 0.8461 (tptm) REVERT: A 1119 MET cc_start: 0.8939 (mtt) cc_final: 0.8555 (mtt) outliers start: 17 outliers final: 14 residues processed: 71 average time/residue: 0.2358 time to fit residues: 23.9658 Evaluate side-chains 69 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 55 time to evaluate : 0.982 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 SER Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 370 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 101 optimal weight: 3.9990 chunk 97 optimal weight: 4.9990 chunk 73 optimal weight: 0.0050 chunk 120 optimal weight: 0.8980 chunk 26 optimal weight: 6.9990 chunk 102 optimal weight: 2.9990 chunk 81 optimal weight: 0.9990 chunk 69 optimal weight: 0.9990 chunk 75 optimal weight: 0.8980 chunk 85 optimal weight: 2.9990 chunk 84 optimal weight: 0.2980 overall best weight: 0.6196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1092 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.115325 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.090030 restraints weight = 31950.266| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.091705 restraints weight = 15524.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.092658 restraints weight = 11703.107| |-----------------------------------------------------------------------------| r_work (final): 0.2955 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2949 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2949 r_free = 0.2949 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2949 r_free = 0.2949 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2949 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 moved from start: 0.2499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 9390 Z= 0.167 Angle : 0.536 7.436 12910 Z= 0.256 Chirality : 0.043 0.168 1537 Planarity : 0.005 0.049 1681 Dihedral : 3.969 22.631 1340 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 1.65 % Allowed : 15.60 % Favored : 82.75 % 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: -1.74 (0.23), residues: 1247 helix: -0.49 (0.27), residues: 390 sheet: -1.16 (0.35), residues: 213 loop : -1.55 (0.24), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 205 HIS 0.001 0.000 HIS A 858 PHE 0.011 0.001 PHE A 347 TYR 0.011 0.001 TYR A 593 ARG 0.003 0.000 ARG A 523 *********************** 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 68 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 53 time to evaluate : 1.115 Fit side-chains REVERT: A 73 TYR cc_start: 0.9041 (m-80) cc_final: 0.8781 (m-80) REVERT: A 152 MET cc_start: 0.7969 (tmm) cc_final: 0.7410 (tpp) REVERT: A 964 THR cc_start: 0.8896 (p) cc_final: 0.8685 (p) REVERT: A 1099 LYS cc_start: 0.8765 (tttm) cc_final: 0.8524 (tptm) REVERT: A 1119 MET cc_start: 0.9001 (mtt) cc_final: 0.8626 (mtt) outliers start: 15 outliers final: 14 residues processed: 65 average time/residue: 0.2471 time to fit residues: 22.7773 Evaluate side-chains 66 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 52 time to evaluate : 1.071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 SER Chi-restraints excluded: chain A residue 370 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 68 optimal weight: 3.9990 chunk 3 optimal weight: 2.9990 chunk 72 optimal weight: 0.6980 chunk 41 optimal weight: 1.9990 chunk 89 optimal weight: 0.0050 chunk 64 optimal weight: 3.9990 chunk 2 optimal weight: 0.8980 chunk 115 optimal weight: 0.0770 chunk 107 optimal weight: 0.0570 chunk 105 optimal weight: 0.9980 chunk 84 optimal weight: 0.9990 overall best weight: 0.3470 ------------------------------------------------------------------------------- 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 = 0.3304 r_free = 0.3304 target = 0.116149 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.091864 restraints weight = 34195.116| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.093750 restraints weight = 19220.110| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.094243 restraints weight = 14644.346| |-----------------------------------------------------------------------------| r_work (final): 0.2966 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3133 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3133 r_free = 0.3133 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3133 r_free = 0.3133 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3133 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8163 moved from start: 0.2650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 9390 Z= 0.139 Angle : 0.523 7.204 12910 Z= 0.249 Chirality : 0.042 0.166 1537 Planarity : 0.005 0.048 1681 Dihedral : 3.874 21.908 1340 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 1.43 % Allowed : 15.82 % Favored : 82.75 % 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: -1.58 (0.23), residues: 1247 helix: -0.32 (0.27), residues: 390 sheet: -1.06 (0.35), residues: 213 loop : -1.48 (0.24), residues: 644 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 0.011 0.001 TYR A 593 ARG 0.002 0.000 ARG A 523 ********************** 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 70 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 57 time to evaluate : 0.986 Fit side-chains REVERT: A 73 TYR cc_start: 0.9029 (m-80) cc_final: 0.8773 (m-80) REVERT: A 152 MET cc_start: 0.7933 (tmm) cc_final: 0.7380 (tpp) REVERT: A 304 MET cc_start: 0.8111 (mmm) cc_final: 0.7886 (mmm) REVERT: A 1099 LYS cc_start: 0.8721 (tttm) cc_final: 0.8484 (tptm) REVERT: A 1119 MET cc_start: 0.8950 (mtt) cc_final: 0.8582 (mtt) outliers start: 13 outliers final: 13 residues processed: 66 average time/residue: 0.2474 time to fit residues: 23.1329 Evaluate side-chains 67 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 54 time to evaluate : 1.011 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 SER Chi-restraints excluded: chain A residue 370 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 913 LEU 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 109 optimal weight: 0.7980 chunk 107 optimal weight: 0.9990 chunk 122 optimal weight: 0.0170 chunk 59 optimal weight: 0.5980 chunk 74 optimal weight: 1.9990 chunk 37 optimal weight: 0.8980 chunk 43 optimal weight: 0.6980 chunk 64 optimal weight: 5.9990 chunk 102 optimal weight: 1.9990 chunk 58 optimal weight: 0.0070 chunk 63 optimal weight: 0.3980 overall best weight: 0.3436 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1092 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.116594 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.090605 restraints weight = 30846.646| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.092903 restraints weight = 14346.018| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.093209 restraints weight = 11338.596| |-----------------------------------------------------------------------------| r_work (final): 0.2964 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2967 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2967 r_free = 0.2967 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2967 r_free = 0.2967 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2967 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 moved from start: 0.2741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 9390 Z= 0.138 Angle : 0.518 7.135 12910 Z= 0.246 Chirality : 0.042 0.159 1537 Planarity : 0.005 0.049 1681 Dihedral : 3.789 22.344 1340 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 1.65 % Allowed : 15.60 % Favored : 82.75 % 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: -1.40 (0.24), residues: 1247 helix: -0.06 (0.28), residues: 384 sheet: -1.00 (0.35), residues: 213 loop : -1.42 (0.24), residues: 650 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 0.011 0.001 TYR A 593 ARG 0.003 0.000 ARG A 523 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2956.83 seconds wall clock time: 53 minutes 34.08 seconds (3214.08 seconds total)