Starting phenix.real_space_refine on Sat Aug 23 02:48:21 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6wbx_21600/08_2025/6wbx_21600.cif Found real_map, /net/cci-nas-00/data/ceres_data/6wbx_21600/08_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_21600/08_2025/6wbx_21600.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6wbx_21600/08_2025/6wbx_21600.map" model { file = "/net/cci-nas-00/data/ceres_data/6wbx_21600/08_2025/6wbx_21600.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6wbx_21600/08_2025/6wbx_21600.cif" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: {'ASP:plan': 8, 'ARG:plan': 7, 'GLU:plan': 5, 'TYR:plan': 2, 'GLN:plan1': 3, 'HIS:plan': 3, 'ASN:plan1': 1, 'PHE:plan': 2, 'TRP:plan': 2} 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: {'ASP:plan': 8, 'ARG:plan': 7, 'GLU:plan': 5, 'TYR:plan': 2, 'GLN:plan1': 3, 'HIS:plan': 3, 'ASN:plan1': 1, 'PHE:plan': 2, 'TRP:plan': 2} 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: 4.18, per 1000 atoms: 0.46 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: 0.67 Conformation dependent library (CDL) restraints added in 631.1 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.29 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: 1.51 Time building geometry restraints manager: 0.89 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: 1.090 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: 0.140 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 11.980 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.020 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:1.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.380 ------------------------------------------------------------------------------- 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 : 4.01 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.011 0.001 ARG A1219 TYR 0.018 0.003 TYR A1258 PHE 0.028 0.003 PHE A 433 TRP 0.022 0.003 TRP A 221 HIS 0.010 0.002 HIS A 675 Details of bonding type rmsd covalent geometry : bond 0.01172 ( 9390) covalent geometry : angle 1.06909 (12910) SS BOND : bond 0.00546 ( 2) SS BOND : angle 0.70394 ( 4) hydrogen bonds : bond 0.31484 ( 267) hydrogen bonds : angle 11.60990 ( 732) *********************** 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 : 0.352 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: 0.1171 time to fit residues: 13.8967 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 : 0.290 ------------------------------------------------------------------------------- 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 108 optimal weight: 0.9990 chunk 49 optimal weight: 0.6980 chunk 97 optimal weight: 0.9980 chunk 113 optimal weight: 0.7980 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 5.9990 chunk 123 optimal weight: 0.1980 chunk 65 optimal weight: 0.9990 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 0.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- 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 = 0.3384 r_free = 0.3384 target = 0.117488 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.091150 restraints weight = 28626.203| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.093253 restraints weight = 12978.178| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.094221 restraints weight = 8365.075| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.095136 restraints weight = 5802.534| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.095653 restraints weight = 4917.961| |-----------------------------------------------------------------------------| r_work (final): 0.3067 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3067 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3067 r_free = 0.3067 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 = 0.3067 r_free = 0.3067 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3067 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8030 moved from start: 0.1402 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= 0.135 Angle : 0.634 11.606 12914 Z= 0.316 Chirality : 0.044 0.168 1537 Planarity : 0.007 0.066 1681 Dihedral : 5.391 19.644 1340 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 1.10 % Allowed : 10.88 % Favored : 88.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.96 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.42 (0.19), residues: 1247 helix: -3.82 (0.16), residues: 378 sheet: -2.00 (0.35), residues: 207 loop : -2.69 (0.20), residues: 662 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 523 TYR 0.012 0.001 TYR A 593 PHE 0.011 0.001 PHE A 246 TRP 0.015 0.001 TRP A 205 HIS 0.004 0.001 HIS A 675 Details of bonding type rmsd covalent geometry : bond 0.00315 ( 9390) covalent geometry : angle 0.63367 (12910) SS BOND : bond 0.00197 ( 2) SS BOND : angle 0.35569 ( 4) hydrogen bonds : bond 0.04462 ( 267) hydrogen bonds : angle 6.36551 ( 732) *********************** 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 77 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 67 time to evaluate : 0.385 Fit side-chains REVERT: A 648 GLN cc_start: 0.8517 (tp-100) cc_final: 0.8093 (tt0) REVERT: A 1061 ARG cc_start: 0.7070 (mmm160) cc_final: 0.6615 (tpt170) REVERT: A 1119 MET cc_start: 0.9022 (mtt) cc_final: 0.8627 (mtt) outliers start: 10 outliers final: 6 residues processed: 74 average time/residue: 0.1010 time to fit residues: 10.5455 Evaluate side-chains 64 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 58 time to evaluate : 0.348 ------------------------------------------------------------------------------- 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 112 optimal weight: 3.9990 chunk 12 optimal weight: 0.6980 chunk 92 optimal weight: 10.0000 chunk 87 optimal weight: 0.0370 chunk 6 optimal weight: 0.6980 chunk 113 optimal weight: 0.9980 chunk 118 optimal weight: 1.9990 chunk 63 optimal weight: 0.3980 chunk 11 optimal weight: 5.9990 chunk 39 optimal weight: 2.9990 chunk 25 optimal weight: 10.0000 overall best weight: 0.5658 ------------------------------------------------------------------------------- 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 A 534 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.118294 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.091328 restraints weight = 34997.455| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.094009 restraints weight = 14355.150| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.095883 restraints weight = 7630.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.096054 restraints weight = 5998.586| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.096377 restraints weight = 5137.159| |-----------------------------------------------------------------------------| r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3088 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3088 r_free = 0.3088 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3088 r_free = 0.3088 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3088 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 moved from start: 0.1752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9392 Z= 0.109 Angle : 0.572 8.843 12914 Z= 0.280 Chirality : 0.042 0.142 1537 Planarity : 0.006 0.057 1681 Dihedral : 4.739 22.210 1340 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer: Outliers : 0.99 % Allowed : 11.87 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.53 (0.21), residues: 1247 helix: -2.74 (0.21), residues: 384 sheet: -1.79 (0.35), residues: 205 loop : -2.25 (0.22), residues: 658 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 212 TYR 0.011 0.001 TYR A 593 PHE 0.009 0.001 PHE A 246 TRP 0.014 0.001 TRP A 205 HIS 0.002 0.000 HIS A 551 Details of bonding type rmsd covalent geometry : bond 0.00258 ( 9390) covalent geometry : angle 0.57145 (12910) SS BOND : bond 0.00057 ( 2) SS BOND : angle 1.11726 ( 4) hydrogen bonds : bond 0.03450 ( 267) hydrogen bonds : angle 5.51404 ( 732) *********************** 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 80 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 71 time to evaluate : 0.336 Fit side-chains REVERT: A 73 TYR cc_start: 0.9065 (m-80) cc_final: 0.8738 (m-80) REVERT: A 421 LEU cc_start: 0.8093 (mp) cc_final: 0.7712 (tp) REVERT: A 648 GLN cc_start: 0.8478 (tp-100) cc_final: 0.8100 (tt0) REVERT: A 1099 LYS cc_start: 0.9035 (tttt) cc_final: 0.8802 (tttm) REVERT: A 1119 MET cc_start: 0.9006 (mtt) cc_final: 0.8609 (mtt) outliers start: 9 outliers final: 8 residues processed: 78 average time/residue: 0.1031 time to fit residues: 11.5438 Evaluate side-chains 69 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 61 time to evaluate : 0.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 41 optimal weight: 0.7980 chunk 104 optimal weight: 1.9990 chunk 76 optimal weight: 2.9990 chunk 98 optimal weight: 0.7980 chunk 112 optimal weight: 1.9990 chunk 21 optimal weight: 0.4980 chunk 91 optimal weight: 6.9990 chunk 118 optimal weight: 0.9990 chunk 78 optimal weight: 3.9990 chunk 27 optimal weight: 5.9990 chunk 109 optimal weight: 2.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- 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 = 0.3252 r_free = 0.3252 target = 0.112298 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2885 r_free = 0.2885 target = 0.085944 restraints weight = 28887.194| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2913 r_free = 0.2913 target = 0.088221 restraints weight = 14214.759| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2922 r_free = 0.2922 target = 0.088838 restraints weight = 8994.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2931 r_free = 0.2931 target = 0.089565 restraints weight = 7102.196| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.089765 restraints weight = 6291.403| |-----------------------------------------------------------------------------| r_work (final): 0.2905 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2914 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2914 r_free = 0.2914 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 = 0.2914 r_free = 0.2914 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2914 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8205 moved from start: 0.1851 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= 0.141 Angle : 0.583 8.244 12914 Z= 0.283 Chirality : 0.044 0.144 1537 Planarity : 0.005 0.052 1681 Dihedral : 4.617 23.517 1340 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer: Outliers : 1.43 % Allowed : 13.52 % Favored : 85.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.96 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.04 (0.22), residues: 1247 helix: -2.12 (0.23), residues: 385 sheet: -1.69 (0.34), residues: 213 loop : -2.03 (0.23), residues: 649 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 523 TYR 0.011 0.001 TYR A 593 PHE 0.009 0.001 PHE A 433 TRP 0.015 0.001 TRP A 205 HIS 0.002 0.001 HIS A 551 Details of bonding type rmsd covalent geometry : bond 0.00338 ( 9390) covalent geometry : angle 0.58272 (12910) SS BOND : bond 0.00139 ( 2) SS BOND : angle 0.77134 ( 4) hydrogen bonds : bond 0.03288 ( 267) hydrogen bonds : angle 5.24199 ( 732) *********************** 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 77 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 64 time to evaluate : 0.281 Fit side-chains REVERT: A 73 TYR cc_start: 0.9035 (m-80) cc_final: 0.8805 (m-80) REVERT: A 421 LEU cc_start: 0.8169 (mp) cc_final: 0.7805 (tp) REVERT: A 1099 LYS cc_start: 0.8956 (tttt) cc_final: 0.8662 (tttm) REVERT: A 1119 MET cc_start: 0.9021 (mtt) cc_final: 0.8663 (mtt) outliers start: 13 outliers final: 12 residues processed: 75 average time/residue: 0.0959 time to fit residues: 10.0508 Evaluate side-chains 70 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 58 time to evaluate : 0.299 ------------------------------------------------------------------------------- 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 105 optimal weight: 0.8980 chunk 122 optimal weight: 0.9990 chunk 74 optimal weight: 4.9990 chunk 67 optimal weight: 3.9990 chunk 90 optimal weight: 1.9990 chunk 97 optimal weight: 0.5980 chunk 115 optimal weight: 1.9990 chunk 107 optimal weight: 0.6980 chunk 51 optimal weight: 0.1980 chunk 58 optimal weight: 1.9990 chunk 64 optimal weight: 5.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 69 GLN A1092 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.113012 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2893 r_free = 0.2893 target = 0.086419 restraints weight = 29774.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2921 r_free = 0.2921 target = 0.088780 restraints weight = 14807.559| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2934 r_free = 0.2934 target = 0.089687 restraints weight = 8664.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2936 r_free = 0.2936 target = 0.089839 restraints weight = 6979.291| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2953 r_free = 0.2953 target = 0.091071 restraints weight = 6334.924| |-----------------------------------------------------------------------------| r_work (final): 0.2939 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2940 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2940 r_free = 0.2940 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 = 0.2940 r_free = 0.2940 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2940 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 moved from start: 0.2059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9392 Z= 0.111 Angle : 0.555 7.988 12914 Z= 0.267 Chirality : 0.043 0.165 1537 Planarity : 0.005 0.054 1681 Dihedral : 4.364 22.620 1340 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 1.65 % Allowed : 14.62 % Favored : 83.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.96 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.66 (0.22), residues: 1247 helix: -1.63 (0.25), residues: 386 sheet: -1.58 (0.34), residues: 213 loop : -1.88 (0.23), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 212 TYR 0.011 0.001 TYR A 593 PHE 0.010 0.001 PHE A 347 TRP 0.015 0.001 TRP A 205 HIS 0.002 0.000 HIS A 551 Details of bonding type rmsd covalent geometry : bond 0.00268 ( 9390) covalent geometry : angle 0.55478 (12910) SS BOND : bond 0.00132 ( 2) SS BOND : angle 0.57161 ( 4) hydrogen bonds : bond 0.02909 ( 267) hydrogen bonds : angle 5.01404 ( 732) *********************** 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: 15 poor density : 62 time to evaluate : 0.388 Fit side-chains REVERT: A 73 TYR cc_start: 0.9046 (m-80) cc_final: 0.8795 (m-80) REVERT: A 304 MET cc_start: 0.8300 (mmm) cc_final: 0.7859 (tmm) REVERT: A 421 LEU cc_start: 0.8203 (mp) cc_final: 0.7897 (tp) REVERT: A 1061 ARG cc_start: 0.7059 (mmm160) cc_final: 0.6603 (tpt170) REVERT: A 1099 LYS cc_start: 0.8927 (tttt) cc_final: 0.8607 (tttm) REVERT: A 1119 MET cc_start: 0.9003 (mtt) cc_final: 0.8624 (mtt) outliers start: 15 outliers final: 11 residues processed: 73 average time/residue: 0.0927 time to fit residues: 9.7712 Evaluate side-chains 69 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 58 time to evaluate : 0.279 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 80 optimal weight: 0.5980 chunk 91 optimal weight: 0.9980 chunk 36 optimal weight: 0.8980 chunk 49 optimal weight: 0.9990 chunk 62 optimal weight: 1.9990 chunk 113 optimal weight: 1.9990 chunk 107 optimal weight: 0.5980 chunk 11 optimal weight: 4.9990 chunk 31 optimal weight: 8.9990 chunk 45 optimal weight: 2.9990 chunk 88 optimal weight: 1.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- 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 = 0.3257 r_free = 0.3257 target = 0.112761 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2914 r_free = 0.2914 target = 0.087943 restraints weight = 33322.790| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2913 r_free = 0.2913 target = 0.088373 restraints weight = 16429.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2928 r_free = 0.2928 target = 0.089502 restraints weight = 13257.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.2942 r_free = 0.2942 target = 0.090496 restraints weight = 8134.140| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.090994 restraints weight = 7360.977| |-----------------------------------------------------------------------------| 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 = 0.50 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 = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2926 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8184 moved from start: 0.2125 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 : 0.562 7.710 12914 Z= 0.270 Chirality : 0.043 0.157 1537 Planarity : 0.005 0.054 1681 Dihedral : 4.289 22.918 1340 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 1.98 % Allowed : 15.49 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.38 (0.23), residues: 1247 helix: -1.25 (0.26), residues: 385 sheet: -1.43 (0.35), residues: 213 loop : -1.81 (0.23), residues: 649 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 523 TYR 0.011 0.001 TYR A 593 PHE 0.010 0.001 PHE A 347 TRP 0.013 0.001 TRP A 205 HIS 0.002 0.000 HIS A 551 Details of bonding type rmsd covalent geometry : bond 0.00294 ( 9390) covalent geometry : angle 0.56160 (12910) SS BOND : bond 0.00159 ( 2) SS BOND : angle 0.49281 ( 4) hydrogen bonds : bond 0.02915 ( 267) hydrogen bonds : angle 4.98352 ( 732) *********************** 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 79 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 61 time to evaluate : 0.348 Fit side-chains REVERT: A 73 TYR cc_start: 0.9038 (m-80) cc_final: 0.8803 (m-80) REVERT: A 304 MET cc_start: 0.8327 (mmm) cc_final: 0.7932 (tmm) REVERT: A 421 LEU cc_start: 0.8180 (mp) cc_final: 0.7874 (tp) REVERT: A 1099 LYS cc_start: 0.8900 (tttt) cc_final: 0.8547 (tttm) REVERT: A 1119 MET cc_start: 0.9028 (mtt) cc_final: 0.8664 (mtt) outliers start: 18 outliers final: 14 residues processed: 74 average time/residue: 0.1016 time to fit residues: 10.6066 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 : 0.347 ------------------------------------------------------------------------------- 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 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 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 64 optimal weight: 5.9990 chunk 47 optimal weight: 0.7980 chunk 116 optimal weight: 1.9990 chunk 16 optimal weight: 0.0170 chunk 21 optimal weight: 0.7980 chunk 42 optimal weight: 0.0170 chunk 32 optimal weight: 0.1980 chunk 80 optimal weight: 0.9990 chunk 35 optimal weight: 0.0980 chunk 1 optimal weight: 1.9990 chunk 108 optimal weight: 0.0370 overall best weight: 0.0734 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 208 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.116861 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.091047 restraints weight = 40267.299| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.094505 restraints weight = 19943.218| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.094677 restraints weight = 12422.960| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.095625 restraints weight = 7800.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.096753 restraints weight = 6674.774| |-----------------------------------------------------------------------------| r_work (final): 0.3018 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3025 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3025 r_free = 0.3025 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3025 r_free = 0.3025 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3025 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 moved from start: 0.2507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 9392 Z= 0.084 Angle : 0.528 7.286 12914 Z= 0.252 Chirality : 0.042 0.250 1537 Planarity : 0.005 0.052 1681 Dihedral : 3.951 22.077 1340 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 5.17 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.98 (0.23), residues: 1247 helix: -0.71 (0.27), residues: 376 sheet: -1.30 (0.35), residues: 213 loop : -1.67 (0.23), residues: 658 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 691 TYR 0.010 0.001 TYR A 593 PHE 0.011 0.001 PHE A 347 TRP 0.014 0.001 TRP A 205 HIS 0.002 0.000 HIS A 551 Details of bonding type rmsd covalent geometry : bond 0.00198 ( 9390) covalent geometry : angle 0.52829 (12910) SS BOND : bond 0.00029 ( 2) SS BOND : angle 0.47512 ( 4) hydrogen bonds : bond 0.02482 ( 267) hydrogen bonds : angle 4.74176 ( 732) *********************** 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 81 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 64 time to evaluate : 0.354 Fit side-chains REVERT: A 73 TYR cc_start: 0.9015 (m-80) cc_final: 0.8756 (m-80) REVERT: A 421 LEU cc_start: 0.8149 (mp) cc_final: 0.7898 (tp) REVERT: A 937 ASP cc_start: 0.7790 (OUTLIER) cc_final: 0.7067 (m-30) REVERT: A 1099 LYS cc_start: 0.8866 (tttt) cc_final: 0.8547 (tttm) REVERT: A 1119 MET cc_start: 0.8985 (mtt) cc_final: 0.8605 (mtt) outliers start: 17 outliers final: 11 residues processed: 76 average time/residue: 0.1007 time to fit residues: 10.8737 Evaluate side-chains 68 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 56 time to evaluate : 0.329 ------------------------------------------------------------------------------- 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 761 ASP 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 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 81 optimal weight: 0.1980 chunk 105 optimal weight: 0.8980 chunk 82 optimal weight: 0.2980 chunk 114 optimal weight: 2.9990 chunk 113 optimal weight: 0.9990 chunk 84 optimal weight: 0.7980 chunk 9 optimal weight: 0.6980 chunk 77 optimal weight: 2.9990 chunk 2 optimal weight: 0.8980 chunk 53 optimal weight: 2.9990 chunk 110 optimal weight: 8.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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 = 0.3293 r_free = 0.3293 target = 0.115351 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2929 r_free = 0.2929 target = 0.088709 restraints weight = 31448.660| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.091000 restraints weight = 15830.933| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.091688 restraints weight = 9635.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.092440 restraints weight = 7621.647| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.092535 restraints weight = 6666.026| |-----------------------------------------------------------------------------| r_work (final): 0.2963 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2963 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2963 r_free = 0.2963 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 = 0.2963 r_free = 0.2963 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2963 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 moved from start: 0.2487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 9392 Z= 0.102 Angle : 0.540 6.828 12914 Z= 0.258 Chirality : 0.043 0.183 1537 Planarity : 0.005 0.054 1681 Dihedral : 3.953 22.642 1340 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 1.43 % Allowed : 16.26 % Favored : 82.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.96 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.88 (0.23), residues: 1247 helix: -0.65 (0.27), residues: 396 sheet: -1.18 (0.35), residues: 213 loop : -1.63 (0.24), residues: 638 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 523 TYR 0.011 0.001 TYR A 593 PHE 0.011 0.001 PHE A 347 TRP 0.013 0.001 TRP A 205 HIS 0.001 0.000 HIS A 85 Details of bonding type rmsd covalent geometry : bond 0.00246 ( 9390) covalent geometry : angle 0.53975 (12910) SS BOND : bond 0.00117 ( 2) SS BOND : angle 0.43298 ( 4) hydrogen bonds : bond 0.02639 ( 267) hydrogen bonds : angle 4.69500 ( 732) *********************** 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 67 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 54 time to evaluate : 0.350 Fit side-chains REVERT: A 73 TYR cc_start: 0.9058 (m-80) cc_final: 0.8781 (m-80) REVERT: A 421 LEU cc_start: 0.8162 (mp) cc_final: 0.7878 (tp) REVERT: A 1099 LYS cc_start: 0.8844 (tttt) cc_final: 0.8502 (tttm) REVERT: A 1119 MET cc_start: 0.9005 (mtt) cc_final: 0.8636 (mtt) outliers start: 13 outliers final: 11 residues processed: 64 average time/residue: 0.1035 time to fit residues: 9.3674 Evaluate side-chains 64 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 53 time to evaluate : 0.284 ------------------------------------------------------------------------------- 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 761 ASP Chi-restraints excluded: chain A residue 822 THR Chi-restraints excluded: chain A residue 913 LEU 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 15 optimal weight: 0.5980 chunk 18 optimal weight: 0.7980 chunk 87 optimal weight: 0.4980 chunk 55 optimal weight: 0.6980 chunk 110 optimal weight: 2.9990 chunk 124 optimal weight: 30.0000 chunk 105 optimal weight: 0.6980 chunk 6 optimal weight: 0.6980 chunk 27 optimal weight: 0.7980 chunk 114 optimal weight: 3.9990 chunk 7 optimal weight: 0.7980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 = 0.3298 r_free = 0.3298 target = 0.115624 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2944 r_free = 0.2944 target = 0.089867 restraints weight = 37167.479| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.091949 restraints weight = 18631.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.092140 restraints weight = 15116.222| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.094436 restraints weight = 8541.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.094415 restraints weight = 6519.573| |-----------------------------------------------------------------------------| r_work (final): 0.2962 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2964 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2964 r_free = 0.2964 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 = 0.2964 r_free = 0.2964 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2964 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8103 moved from start: 0.2517 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= 0.106 Angle : 0.542 6.948 12914 Z= 0.260 Chirality : 0.043 0.174 1537 Planarity : 0.005 0.049 1681 Dihedral : 3.964 22.289 1340 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 1.32 % Allowed : 16.37 % Favored : 82.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.96 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.68 (0.23), residues: 1247 helix: -0.42 (0.27), residues: 390 sheet: -1.10 (0.35), residues: 213 loop : -1.52 (0.24), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 169 TYR 0.011 0.001 TYR A 593 PHE 0.011 0.001 PHE A 347 TRP 0.012 0.001 TRP A 205 HIS 0.001 0.000 HIS A 551 Details of bonding type rmsd covalent geometry : bond 0.00255 ( 9390) covalent geometry : angle 0.54199 (12910) SS BOND : bond 0.00131 ( 2) SS BOND : angle 0.46582 ( 4) hydrogen bonds : bond 0.02687 ( 267) hydrogen bonds : angle 4.66366 ( 732) *********************** 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 66 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 54 time to evaluate : 0.255 Fit side-chains REVERT: A 73 TYR cc_start: 0.9070 (m-80) cc_final: 0.8787 (m-80) REVERT: A 421 LEU cc_start: 0.8145 (mp) cc_final: 0.7850 (tp) REVERT: A 1099 LYS cc_start: 0.8860 (tttt) cc_final: 0.8613 (tttm) REVERT: A 1119 MET cc_start: 0.9003 (mtt) cc_final: 0.8606 (mtt) outliers start: 12 outliers final: 11 residues processed: 64 average time/residue: 0.1083 time to fit residues: 9.5083 Evaluate side-chains 64 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 53 time to evaluate : 0.322 ------------------------------------------------------------------------------- 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 761 ASP Chi-restraints excluded: chain A residue 822 THR Chi-restraints excluded: chain A residue 913 LEU 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 64 optimal weight: 6.9990 chunk 49 optimal weight: 0.0770 chunk 76 optimal weight: 1.9990 chunk 22 optimal weight: 0.9990 chunk 91 optimal weight: 0.9990 chunk 80 optimal weight: 0.9990 chunk 121 optimal weight: 0.0470 chunk 13 optimal weight: 0.0970 chunk 2 optimal weight: 0.9990 chunk 93 optimal weight: 2.9990 chunk 102 optimal weight: 0.9980 overall best weight: 0.4436 ------------------------------------------------------------------------------- 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 = 0.3301 r_free = 0.3301 target = 0.115909 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.091475 restraints weight = 35027.758| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.093340 restraints weight = 20524.917| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.094064 restraints weight = 14480.251| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.094786 restraints weight = 8451.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.095692 restraints weight = 7670.925| |-----------------------------------------------------------------------------| r_work (final): 0.2992 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2990 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2990 r_free = 0.2990 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2990 r_free = 0.2990 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2990 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8132 moved from start: 0.2636 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= 0.092 Angle : 0.531 6.954 12914 Z= 0.253 Chirality : 0.042 0.155 1537 Planarity : 0.005 0.047 1681 Dihedral : 3.858 22.194 1340 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 1.32 % Allowed : 16.26 % Favored : 82.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.96 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.50 (0.23), residues: 1247 helix: -0.17 (0.27), residues: 384 sheet: -1.06 (0.35), residues: 213 loop : -1.47 (0.24), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1061 TYR 0.011 0.001 TYR A 593 PHE 0.011 0.001 PHE A 347 TRP 0.012 0.001 TRP A 205 HIS 0.001 0.000 HIS A 551 Details of bonding type rmsd covalent geometry : bond 0.00223 ( 9390) covalent geometry : angle 0.53125 (12910) SS BOND : bond 0.00092 ( 2) SS BOND : angle 0.50512 ( 4) hydrogen bonds : bond 0.02561 ( 267) hydrogen bonds : angle 4.57186 ( 732) ********************** 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 71 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 59 time to evaluate : 0.360 Fit side-chains REVERT: A 73 TYR cc_start: 0.9038 (m-80) cc_final: 0.8779 (m-80) REVERT: A 421 LEU cc_start: 0.8122 (mp) cc_final: 0.7882 (tp) REVERT: A 937 ASP cc_start: 0.7657 (OUTLIER) cc_final: 0.7020 (m-30) REVERT: A 1099 LYS cc_start: 0.8799 (tttt) cc_final: 0.8571 (tttm) REVERT: A 1119 MET cc_start: 0.8981 (mtt) cc_final: 0.8605 (mtt) outliers start: 12 outliers final: 11 residues processed: 67 average time/residue: 0.1053 time to fit residues: 9.8977 Evaluate side-chains 68 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 56 time to evaluate : 0.242 ------------------------------------------------------------------------------- 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 33 optimal weight: 5.9990 chunk 117 optimal weight: 0.5980 chunk 3 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 chunk 79 optimal weight: 0.5980 chunk 53 optimal weight: 0.0870 chunk 91 optimal weight: 0.9990 chunk 89 optimal weight: 0.7980 chunk 121 optimal weight: 0.0870 chunk 112 optimal weight: 0.0370 chunk 17 optimal weight: 0.9990 overall best weight: 0.2814 ------------------------------------------------------------------------------- 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 = 0.3456 r_free = 0.3456 target = 0.122562 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.096119 restraints weight = 37979.819| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.098091 restraints weight = 14026.905| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.099588 restraints weight = 9201.406| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.099986 restraints weight = 6609.126| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.100548 restraints weight = 5915.762| |-----------------------------------------------------------------------------| r_work (final): 0.3148 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3146 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3146 r_free = 0.3146 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3146 r_free = 0.3146 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3146 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 moved from start: 0.2754 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= 0.085 Angle : 0.526 6.955 12914 Z= 0.250 Chirality : 0.042 0.150 1537 Planarity : 0.005 0.049 1681 Dihedral : 3.773 22.307 1340 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 1.43 % Allowed : 16.26 % Favored : 82.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.96 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.35 (0.24), residues: 1247 helix: 0.02 (0.28), residues: 384 sheet: -0.98 (0.36), residues: 213 loop : -1.41 (0.24), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 169 TYR 0.011 0.001 TYR A 593 PHE 0.011 0.001 PHE A 347 TRP 0.012 0.001 TRP A 205 HIS 0.001 0.000 HIS A 85 Details of bonding type rmsd covalent geometry : bond 0.00205 ( 9390) covalent geometry : angle 0.52580 (12910) SS BOND : bond 0.00069 ( 2) SS BOND : angle 0.49226 ( 4) hydrogen bonds : bond 0.02482 ( 267) hydrogen bonds : angle 4.49557 ( 732) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1511.22 seconds wall clock time: 26 minutes 36.63 seconds (1596.63 seconds total)