Starting phenix.real_space_refine on Thu Feb 13 18:24:53 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6wby_21601/02_2025/6wby_21601.cif Found real_map, /net/cci-nas-00/data/ceres_data/6wby_21601/02_2025/6wby_21601.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6wby_21601/02_2025/6wby_21601.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6wby_21601/02_2025/6wby_21601.map" model { file = "/net/cci-nas-00/data/ceres_data/6wby_21601/02_2025/6wby_21601.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6wby_21601/02_2025/6wby_21601.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Ca 2 9.91 5 S 19 5.16 5 C 5848 2.51 5 N 1609 2.21 5 O 1678 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 36 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 9156 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 9154 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1250, 9144 Classifications: {'peptide': 1250} Incomplete info: {'truncation_to_alanine': 44} Link IDs: {'PCIS': 1, 'PTRANS': 104, 'TRANS': 1144} Chain breaks: 13 Unresolved non-hydrogen bonds: 192 Unresolved non-hydrogen angles: 239 Unresolved non-hydrogen dihedrals: 158 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 1, 'HIS:plan': 2, 'ASN:plan1': 1, 'TRP:plan': 1, 'ASP:plan': 6, 'PHE:plan': 1, 'GLU:plan': 7, 'ARG:plan': 11} Unresolved non-hydrogen planarities: 133 Conformer: "B" Number of residues, atoms: 1250, 9144 Classifications: {'peptide': 1250} Incomplete info: {'truncation_to_alanine': 44} Link IDs: {'PCIS': 1, 'PTRANS': 104, 'TRANS': 1144} Chain breaks: 13 Unresolved non-hydrogen bonds: 192 Unresolved non-hydrogen angles: 239 Unresolved non-hydrogen dihedrals: 158 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 1, 'HIS:plan': 2, 'ASN:plan1': 1, 'TRP:plan': 1, 'ASP:plan': 6, 'PHE:plan': 1, 'GLU:plan': 7, 'ARG:plan': 11} Unresolved non-hydrogen planarities: 133 bond proxies already assigned to first conformer: 9353 Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N AHIS A 550 " occ=0.50 ... (18 atoms not shown) pdb=" NE2BHIS A 550 " occ=0.50 Time building chain proxies: 9.81, per 1000 atoms: 1.07 Number of scatterers: 9156 At special positions: 0 Unit cell: (128.321, 89.082, 96.5055, 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 19 16.00 O 1678 8.00 N 1609 7.00 C 5848 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 886 " - pdb=" SG CYS A 895 " distance=2.02 Simple disulfide: pdb=" SG CYS A1104 " - pdb=" SG CYS A1139 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.07 Conformation dependent library (CDL) restraints added in 2.5 seconds 2450 Ramachandran restraints generated. 1225 Oldfield, 0 Emsley, 1225 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2290 Finding SS restraints... Secondary structure from input PDB file: 40 helices and 16 sheets defined 33.7% alpha, 18.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.44 Creating SS restraints... Processing helix chain 'A' and resid 12 through 27 removed outlier: 3.942A pdb=" N ALA A 16 " --> pdb=" O ARG A 12 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N VAL A 17 " --> pdb=" O ARG A 13 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N LEU A 23 " --> pdb=" O ALA A 19 " (cutoff:3.500A) Processing helix chain 'A' and resid 40 through 45 removed outlier: 3.501A pdb=" N ILE A 44 " --> pdb=" O LEU A 40 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 53 removed outlier: 3.602A pdb=" N PHE A 49 " --> pdb=" O ASN A 45 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ALA A 53 " --> pdb=" O PHE A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 79 through 87 Processing helix chain 'A' and resid 92 through 117 removed outlier: 3.523A pdb=" N GLY A 109 " --> pdb=" O ALA A 105 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ARG A 112 " --> pdb=" O TRP A 108 " (cutoff:3.500A) Processing helix chain 'A' and resid 123 through 134 removed outlier: 3.537A pdb=" N ILE A 127 " --> pdb=" O GLY A 123 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ALA A 131 " --> pdb=" O ILE A 127 " (cutoff:3.500A) Processing helix chain 'A' and resid 135 through 140 removed outlier: 3.820A pdb=" N THR A 140 " --> pdb=" O PRO A 136 " (cutoff:3.500A) Processing helix chain 'A' and resid 145 through 148 Processing helix chain 'A' and resid 149 through 154 removed outlier: 3.583A pdb=" N LEU A 154 " --> pdb=" O LEU A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 154 through 166 removed outlier: 3.798A 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 171 through 185 removed outlier: 3.740A pdb=" N SER A 179 " --> pdb=" O ALA A 175 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ALA A 180 " --> pdb=" O ALA A 176 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ALA A 182 " --> pdb=" O LEU A 178 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N VAL A 183 " --> pdb=" O SER A 179 " (cutoff:3.500A) Processing helix chain 'A' and resid 190 through 198 Processing helix chain 'A' and resid 199 through 207 removed outlier: 3.595A pdb=" N TRP A 205 " --> pdb=" O ALA A 201 " (cutoff:3.500A) Processing helix chain 'A' and resid 211 through 229 removed outlier: 3.946A pdb=" N TRP A 220 " --> pdb=" O ARG A 216 " (cutoff:3.500A) Proline residue: A 223 - end of helix Processing helix chain 'A' and resid 232 through 243 removed outlier: 4.072A pdb=" N LYS A 241 " --> pdb=" O LEU A 237 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ILE A 242 " --> pdb=" O ILE A 238 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N SER A 243 " --> pdb=" O PHE A 239 " (cutoff:3.500A) Processing helix chain 'A' and resid 263 through 268 Processing helix chain 'A' and resid 291 through 308 removed outlier: 3.896A pdb=" N ALA A 295 " --> pdb=" O ALA A 291 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N THR A 297 " --> pdb=" O VAL A 293 " (cutoff:3.500A) Processing helix chain 'A' and resid 314 through 328 removed outlier: 3.634A pdb=" N VAL A 319 " --> pdb=" O ARG A 315 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N LEU A 328 " --> pdb=" O ILE A 324 " (cutoff:3.500A) Processing helix chain 'A' and resid 362 through 378 removed outlier: 3.739A pdb=" N ILE A 366 " --> pdb=" O LEU A 362 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N LEU A 368 " --> pdb=" O PRO A 364 " (cutoff:3.500A) Proline residue: A 369 - end of helix removed outlier: 3.672A pdb=" N LEU A 378 " --> pdb=" O LEU A 374 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 419 removed outlier: 3.750A pdb=" N VAL A 410 " --> pdb=" O ALA A 406 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N LEU A 411 " --> pdb=" O PHE A 407 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ALA A 414 " --> pdb=" O VAL A 410 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ALA A 416 " --> pdb=" O LEU A 412 " (cutoff:3.500A) Processing helix chain 'A' and resid 419 through 424 removed outlier: 3.873A pdb=" N TRP A 423 " --> pdb=" O THR A 419 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N THR A 424 " --> pdb=" O SER A 420 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 419 through 424' Processing helix chain 'A' and resid 437 through 448 removed outlier: 3.682A pdb=" N ASN A 441 " --> pdb=" O PRO A 437 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N THR A 443 " --> pdb=" O TYR A 439 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ALA A 444 " --> pdb=" O TRP A 440 " (cutoff:3.500A) Processing helix chain 'A' and resid 495 through 503 removed outlier: 3.534A pdb=" N ALA A 501 " --> pdb=" O GLU A 497 " (cutoff:3.500A) Processing helix chain 'A' and resid 505 through 512 removed outlier: 3.646A pdb=" N PHE A 509 " --> pdb=" O VAL A 505 " (cutoff:3.500A) Processing helix chain 'A' and resid 517 through 525 removed outlier: 3.639A pdb=" N THR A 521 " --> pdb=" O GLY A 517 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N ARG A 523 " --> pdb=" O ALA A 519 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N GLU A 524 " --> pdb=" O ASP A 520 " (cutoff:3.500A) Processing helix chain 'A' and resid 545 through 554 removed outlier: 3.547A pdb=" N AHIS A 550 " --> pdb=" O PRO A 546 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N HIS A 551 " --> pdb=" O ILE A 547 " (cutoff:3.500A) removed outlier: 3.575A 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 618 through 620 No H-bonds generated for 'chain 'A' and resid 618 through 620' Processing helix chain 'A' and resid 621 through 632 removed outlier: 3.574A pdb=" N ARG A 630 " --> pdb=" O ASN A 626 " (cutoff:3.500A) Processing helix chain 'A' and resid 644 through 649 removed outlier: 3.699A pdb=" N ALA A 649 " --> pdb=" O ASP A 645 " (cutoff:3.500A) Processing helix chain 'A' and resid 728 through 732 removed outlier: 3.506A pdb=" N THR A 731 " --> pdb=" O ALA A 728 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N SER A 732 " --> pdb=" O PRO A 729 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 728 through 732' Processing helix chain 'A' and resid 934 through 940 removed outlier: 4.217A pdb=" N LEU A 938 " --> pdb=" O GLN A 934 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ILE A 939 " --> pdb=" O LEU A 935 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLN A 940 " --> pdb=" O ARG A 936 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 934 through 940' Processing helix chain 'A' and resid 959 through 964 removed outlier: 3.649A pdb=" N ALA A 963 " --> pdb=" O SER A 960 " (cutoff:3.500A) Processing helix chain 'A' and resid 1091 through 1096 removed outlier: 3.543A pdb=" N ASN A1095 " --> pdb=" O ASP A1091 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N SER A1096 " --> pdb=" O ASN A1092 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1091 through 1096' Processing helix chain 'A' and resid 1125 through 1130 removed outlier: 3.741A pdb=" N ASP A1130 " --> pdb=" O ARG A1126 " (cutoff:3.500A) Processing helix chain 'A' and resid 1255 through 1264 removed outlier: 3.712A pdb=" N GLY A1261 " --> pdb=" O TRP A1257 " (cutoff:3.500A) Processing helix chain 'A' and resid 1268 through 1278 Processing helix chain 'A' and resid 1296 through 1307 removed outlier: 3.513A pdb=" N VAL A1300 " --> pdb=" O PRO A1296 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N ALA A1301 " --> pdb=" O ALA A1297 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N LEU A1303 " --> pdb=" O GLY A1299 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ALA A1305 " --> pdb=" O ALA A1301 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N THR A1307 " --> pdb=" O LEU A1303 " (cutoff:3.500A) Processing helix chain 'A' and resid 1336 through 1356 removed outlier: 3.684A pdb=" N TYR A1341 " --> pdb=" O ALA A1337 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N SER A1346 " --> pdb=" O LEU A1342 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N LEU A1347 " --> pdb=" O ALA A1343 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LEU A1349 " --> pdb=" O GLY A1345 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N LEU A1354 " --> pdb=" O ALA A1350 " (cutoff:3.500A) Processing helix chain 'A' and resid 1369 through 1385 removed outlier: 3.894A pdb=" N GLN A1373 " --> pdb=" O SER A1369 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LEU A1374 " --> pdb=" O TRP A1370 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N SER A1379 " --> pdb=" O LEU A1375 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N VAL A1383 " --> pdb=" O SER A1379 " (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: 6.697A pdb=" N ARG A 455 " --> pdb=" O SER A 528 " (cutoff:3.500A) removed outlier: 5.959A pdb=" N LEU A 530 " --> pdb=" O ARG A 455 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N LEU A 457 " --> pdb=" O LEU A 530 " (cutoff:3.500A) removed outlier: 5.227A pdb=" N VAL A 532 " --> pdb=" O LEU A 457 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N VAL A 459 " --> pdb=" O VAL A 532 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N SER A 528 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N VAL A 595 " --> pdb=" O SER A 528 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N GLY A 566 " --> pdb=" O PRO A 588 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N VAL A 590 " --> pdb=" O GLN A 564 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N GLN A 564 " --> pdb=" O VAL A 590 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N ILE A 592 " --> pdb=" O VAL A 562 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 577 through 579 removed outlier: 7.041A 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: 3.506A pdb=" N GLN A1236 " --> pdb=" O VAL A1208 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N THR A1227 " --> pdb=" O VAL A1239 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 641 through 642 removed outlier: 7.578A pdb=" N ARG A 614 " --> pdb=" O VAL A 657 " (cutoff:3.500A) removed outlier: 7.605A pdb=" N THR A 659 " --> pdb=" O ARG A 614 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N GLY A 873 " --> pdb=" O ALA A 656 " (cutoff:3.500A) removed outlier: 5.528A pdb=" N VAL A1163 " --> pdb=" O ARG A 928 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N ARG A 928 " --> pdb=" O VAL A1163 " (cutoff:3.500A) removed outlier: 3.507A 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: 6.835A pdb=" N THR A 817 " --> pdb=" O LEU A 762 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N GLY A 794 " --> pdb=" O THR A 791 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 745 through 746 removed outlier: 6.797A pdb=" N THR A 774 " --> pdb=" O THR A 838 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N LEU A 840 " --> pdb=" O THR A 772 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N THR A 772 " --> pdb=" O LEU A 840 " (cutoff:3.500A) removed outlier: 4.905A pdb=" N LEU A 842 " --> pdb=" O ILE A 770 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N ILE A 770 " --> pdb=" O LEU A 842 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 745 through 746 removed outlier: 4.678A pdb=" N LEU A 842 " --> pdb=" O VAL A 854 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 860 through 862 removed outlier: 4.253A pdb=" N ALA A 860 " --> pdb=" O ILE A 910 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N THR A 914 " --> pdb=" O VAL A 862 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 860 through 862 removed outlier: 4.253A pdb=" N ALA A 860 " --> pdb=" O ILE A 910 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N THR A 914 " --> pdb=" O VAL A 862 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 886 through 887 Processing sheet with id=AB4, first strand: chain 'A' and resid 946 through 948 Processing sheet with id=AB5, first strand: chain 'A' and resid 1036 through 1037 removed outlier: 3.597A pdb=" N LEU A1002 " --> pdb=" O THR A1036 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ILE A1078 " --> pdb=" O ARG A1001 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 1027 through 1028 removed outlier: 3.773A pdb=" N ARG A1027 " --> pdb=" O VAL A1016 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N ASP A1054 " --> pdb=" O LYS A1014 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 1185 through 1186 removed outlier: 3.522A pdb=" N ARG A1219 " --> pdb=" O THR A1249 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N THR A1251 " --> pdb=" O ALA A1217 " (cutoff:3.500A) 321 hydrogen bonds defined for protein. 876 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.01 Time building geometry restraints manager: 2.40 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2824 1.33 - 1.45: 1376 1.45 - 1.57: 5147 1.57 - 1.69: 0 1.69 - 1.81: 30 Bond restraints: 9377 Sorted by residual: bond pdb=" CB VAL A1229 " pdb=" CG2 VAL A1229 " ideal model delta sigma weight residual 1.521 1.421 0.100 3.30e-02 9.18e+02 9.10e+00 bond pdb=" CG LEU A 559 " pdb=" CD2 LEU A 559 " ideal model delta sigma weight residual 1.521 1.436 0.085 3.30e-02 9.18e+02 6.62e+00 bond pdb=" CB VAL A1239 " pdb=" CG2 VAL A1239 " ideal model delta sigma weight residual 1.521 1.448 0.073 3.30e-02 9.18e+02 4.93e+00 bond pdb=" C VAL A1009 " pdb=" N PRO A1010 " ideal model delta sigma weight residual 1.334 1.377 -0.043 2.34e-02 1.83e+03 3.39e+00 bond pdb=" C ILE A 34 " pdb=" N SER A 35 " ideal model delta sigma weight residual 1.329 1.295 0.034 1.86e-02 2.89e+03 3.29e+00 ... (remaining 9372 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.50: 12465 2.50 - 5.00: 371 5.00 - 7.50: 45 7.50 - 9.99: 8 9.99 - 12.49: 3 Bond angle restraints: 12892 Sorted by residual: angle pdb=" C ASP A 37 " pdb=" N THR A 38 " pdb=" CA THR A 38 " ideal model delta sigma weight residual 121.54 132.02 -10.48 1.91e+00 2.74e-01 3.01e+01 angle pdb=" N THR A 661 " pdb=" CA THR A 661 " pdb=" C THR A 661 " ideal model delta sigma weight residual 109.81 120.36 -10.55 2.21e+00 2.05e-01 2.28e+01 angle pdb=" C VAL A1117 " pdb=" CA VAL A1117 " pdb=" CB VAL A1117 " ideal model delta sigma weight residual 111.08 115.07 -3.99 9.50e-01 1.11e+00 1.77e+01 angle pdb=" CA PRO A1010 " pdb=" N PRO A1010 " pdb=" CD PRO A1010 " ideal model delta sigma weight residual 112.00 106.79 5.21 1.40e+00 5.10e-01 1.39e+01 angle pdb=" CA VAL A1009 " pdb=" C VAL A1009 " pdb=" N PRO A1010 " ideal model delta sigma weight residual 118.88 124.45 -5.57 1.54e+00 4.22e-01 1.31e+01 ... (remaining 12887 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.82: 5111 17.82 - 35.64: 377 35.64 - 53.47: 51 53.47 - 71.29: 4 71.29 - 89.11: 5 Dihedral angle restraints: 5548 sinusoidal: 2007 harmonic: 3541 Sorted by residual: dihedral pdb=" CA GLU A1008 " pdb=" C GLU A1008 " pdb=" N VAL A1009 " pdb=" CA VAL A1009 " ideal model delta harmonic sigma weight residual -180.00 -151.26 -28.74 0 5.00e+00 4.00e-02 3.30e+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 -152.12 -27.88 0 5.00e+00 4.00e-02 3.11e+01 dihedral pdb=" CA PRO A1010 " pdb=" C PRO A1010 " pdb=" N ALA A1011 " pdb=" CA ALA A1011 " ideal model delta harmonic sigma weight residual 180.00 -153.41 -26.59 0 5.00e+00 4.00e-02 2.83e+01 ... (remaining 5545 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.118: 1451 0.118 - 0.235: 89 0.235 - 0.353: 5 0.353 - 0.470: 0 0.470 - 0.588: 1 Chirality restraints: 1546 Sorted by residual: chirality pdb=" CB ILE A 145 " pdb=" CA ILE A 145 " pdb=" CG1 ILE A 145 " pdb=" CG2 ILE A 145 " both_signs ideal model delta sigma weight residual False 2.64 2.06 0.59 2.00e-01 2.50e+01 8.64e+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 2.18 0.34 2.00e-01 2.50e+01 2.94e+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 2.34 0.30 2.00e-01 2.50e+01 2.31e+00 ... (remaining 1543 not shown) Planarity restraints: 1661 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA A 155 " -0.048 5.00e-02 4.00e+02 7.12e-02 8.11e+00 pdb=" N PRO A 156 " 0.123 5.00e-02 4.00e+02 pdb=" CA PRO A 156 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO A 156 " -0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA A 974 " 0.047 5.00e-02 4.00e+02 7.12e-02 8.11e+00 pdb=" N PRO A 975 " -0.123 5.00e-02 4.00e+02 pdb=" CA PRO A 975 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO A 975 " 0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASP A 37 " -0.014 2.00e-02 2.50e+03 2.81e-02 7.90e+00 pdb=" C ASP A 37 " 0.049 2.00e-02 2.50e+03 pdb=" O ASP A 37 " -0.019 2.00e-02 2.50e+03 pdb=" N THR A 38 " -0.016 2.00e-02 2.50e+03 ... (remaining 1658 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.61: 94 2.61 - 3.19: 7338 3.19 - 3.76: 13386 3.76 - 4.33: 18552 4.33 - 4.90: 32385 Nonbonded interactions: 71755 Sorted by model distance: nonbonded pdb=" O THR A 838 " pdb=" OE2 GLU A 839 " model vdw 2.042 3.040 nonbonded pdb=" O ALA A 962 " pdb="CA CA A2002 " model vdw 2.067 2.510 nonbonded pdb=" OG SER A 715 " pdb=" OE1 GLN A 756 " model vdw 2.243 3.040 nonbonded pdb=" O ASP A 967 " pdb="CA CA A2002 " model vdw 2.263 2.510 nonbonded pdb=" O THR A 970 " pdb="CA CA A2002 " model vdw 2.296 2.510 ... (remaining 71750 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.720 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: 0.380 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 31.030 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.060 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:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8410 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 : 0.010 0.100 9377 Z= 0.671 Angle : 1.037 12.493 12892 Z= 0.579 Chirality : 0.063 0.588 1546 Planarity : 0.009 0.071 1661 Dihedral : 12.683 89.109 3252 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 3.28 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.30 % Favored : 93.62 % Rotamer: Outliers : 0.32 % Allowed : 6.13 % Favored : 93.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.96 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.12 (0.18), residues: 1225 helix: -4.98 (0.08), residues: 382 sheet: -2.14 (0.32), residues: 197 loop : -2.77 (0.20), residues: 646 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.003 TRP A 221 HIS 0.014 0.002 HIS A 675 PHE 0.025 0.003 PHE A 433 TYR 0.014 0.002 TYR A1258 ARG 0.005 0.001 ARG A 687 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2450 Ramachandran restraints generated. 1225 Oldfield, 0 Emsley, 1225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2450 Ramachandran restraints generated. 1225 Oldfield, 0 Emsley, 1225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 85 time to evaluate : 1.027 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 309 MET cc_start: 0.8288 (mtt) cc_final: 0.8074 (mtt) REVERT: A 739 ARG cc_start: 0.7207 (mpt-90) cc_final: 0.6968 (mpt180) REVERT: A 1034 ASP cc_start: 0.7167 (m-30) cc_final: 0.6960 (m-30) outliers start: 3 outliers final: 2 residues processed: 88 average time/residue: 0.2826 time to fit residues: 33.2063 Evaluate side-chains 63 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 61 time to evaluate : 1.010 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 703 VAL Chi-restraints excluded: chain A residue 830 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 105 optimal weight: 0.8980 chunk 94 optimal weight: 7.9990 chunk 52 optimal weight: 0.6980 chunk 32 optimal weight: 0.0370 chunk 63 optimal weight: 0.8980 chunk 50 optimal weight: 0.9990 chunk 97 optimal weight: 2.9990 chunk 37 optimal weight: 0.6980 chunk 59 optimal weight: 0.6980 chunk 72 optimal weight: 1.9990 chunk 113 optimal weight: 2.9990 overall best weight: 0.6058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 551 HIS A1151 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.148318 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.123152 restraints weight = 21355.133| |-----------------------------------------------------------------------------| r_work (start): 0.3509 rms_B_bonded: 2.50 r_work: 0.3365 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3225 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3225 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3218 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3218 r_free = 0.3218 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3218 r_free = 0.3218 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3218 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8539 moved from start: 0.1321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9377 Z= 0.196 Angle : 0.621 8.806 12892 Z= 0.311 Chirality : 0.044 0.383 1546 Planarity : 0.006 0.056 1661 Dihedral : 5.283 33.323 1322 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 1.08 % Allowed : 8.60 % Favored : 90.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.96 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.55 (0.20), residues: 1225 helix: -3.15 (0.19), residues: 376 sheet: -1.55 (0.34), residues: 197 loop : -2.08 (0.22), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 214 HIS 0.003 0.001 HIS A 675 PHE 0.015 0.001 PHE A 246 TYR 0.011 0.001 TYR A 439 ARG 0.004 0.000 ARG A1061 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2450 Ramachandran restraints generated. 1225 Oldfield, 0 Emsley, 1225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2450 Ramachandran restraints generated. 1225 Oldfield, 0 Emsley, 1225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 79 time to evaluate : 0.930 Fit side-chains REVERT: A 309 MET cc_start: 0.8308 (mtt) cc_final: 0.8097 (mtt) REVERT: A 739 ARG cc_start: 0.8062 (mpt-90) cc_final: 0.7818 (mpt180) REVERT: A 1034 ASP cc_start: 0.7368 (m-30) cc_final: 0.7056 (m-30) outliers start: 10 outliers final: 7 residues processed: 83 average time/residue: 0.2224 time to fit residues: 26.3346 Evaluate side-chains 67 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 60 time to evaluate : 1.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 661 THR Chi-restraints excluded: chain A residue 703 VAL Chi-restraints excluded: chain A residue 713 THR Chi-restraints excluded: chain A residue 830 THR Chi-restraints excluded: chain A residue 1015 GLN Chi-restraints excluded: chain A residue 1053 THR Chi-restraints excluded: chain A residue 1152 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 123 optimal weight: 0.8980 chunk 22 optimal weight: 0.7980 chunk 77 optimal weight: 0.7980 chunk 86 optimal weight: 0.9980 chunk 82 optimal weight: 0.9990 chunk 121 optimal weight: 2.9990 chunk 41 optimal weight: 0.8980 chunk 44 optimal weight: 3.9990 chunk 29 optimal weight: 0.0470 chunk 21 optimal weight: 1.9990 chunk 113 optimal weight: 0.8980 overall best weight: 0.6878 ------------------------------------------------------------------------------- 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 = 0.3820 r_free = 0.3820 target = 0.148429 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.123992 restraints weight = 33549.432| |-----------------------------------------------------------------------------| r_work (start): 0.3513 rms_B_bonded: 4.29 r_work: 0.3284 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.3284 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2755 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2755 r_free = 0.2755 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2755 r_free = 0.2755 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2755 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8490 moved from start: 0.1619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9377 Z= 0.197 Angle : 0.594 9.005 12892 Z= 0.289 Chirality : 0.045 0.448 1546 Planarity : 0.005 0.052 1661 Dihedral : 4.786 34.865 1322 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 1.29 % Allowed : 9.78 % Favored : 88.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.96 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.59 (0.22), residues: 1225 helix: -1.87 (0.24), residues: 375 sheet: -1.20 (0.35), residues: 198 loop : -1.75 (0.23), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 214 HIS 0.003 0.001 HIS A 675 PHE 0.021 0.001 PHE A 246 TYR 0.011 0.001 TYR A 439 ARG 0.006 0.000 ARG A1106 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2450 Ramachandran restraints generated. 1225 Oldfield, 0 Emsley, 1225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2450 Ramachandran restraints generated. 1225 Oldfield, 0 Emsley, 1225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 72 time to evaluate : 1.024 Fit side-chains REVERT: A 739 ARG cc_start: 0.8064 (mpt-90) cc_final: 0.7851 (mpt180) REVERT: A 1034 ASP cc_start: 0.7356 (m-30) cc_final: 0.7018 (m-30) outliers start: 12 outliers final: 9 residues processed: 78 average time/residue: 0.1850 time to fit residues: 21.5580 Evaluate side-chains 73 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 64 time to evaluate : 1.055 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 464 PHE Chi-restraints excluded: chain A residue 661 THR Chi-restraints excluded: chain A residue 703 VAL Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 830 THR Chi-restraints excluded: chain A residue 1015 GLN Chi-restraints excluded: chain A residue 1053 THR Chi-restraints excluded: chain A residue 1152 ASP Chi-restraints excluded: chain A residue 1336 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 46 optimal weight: 0.8980 chunk 35 optimal weight: 0.0020 chunk 26 optimal weight: 10.0000 chunk 56 optimal weight: 0.0370 chunk 74 optimal weight: 0.5980 chunk 4 optimal weight: 0.9980 chunk 11 optimal weight: 0.6980 chunk 85 optimal weight: 0.9990 chunk 15 optimal weight: 2.9990 chunk 41 optimal weight: 0.8980 chunk 88 optimal weight: 0.0870 overall best weight: 0.2844 ------------------------------------------------------------------------------- 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 = 0.3863 r_free = 0.3863 target = 0.151757 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.127633 restraints weight = 38007.494| |-----------------------------------------------------------------------------| r_work (start): 0.3562 rms_B_bonded: 4.75 r_work: 0.3308 rms_B_bonded: 4.18 restraints_weight: 0.5000 r_work (final): 0.3308 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3322 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3322 r_free = 0.3322 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3322 r_free = 0.3322 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3322 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8463 moved from start: 0.1998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 9377 Z= 0.146 Angle : 0.549 8.168 12892 Z= 0.266 Chirality : 0.044 0.517 1546 Planarity : 0.005 0.047 1661 Dihedral : 4.364 34.365 1322 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 1.51 % Allowed : 10.43 % Favored : 88.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.96 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.82 (0.23), residues: 1225 helix: -1.02 (0.26), residues: 376 sheet: -0.76 (0.37), residues: 196 loop : -1.43 (0.24), residues: 653 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 98 HIS 0.002 0.000 HIS A 551 PHE 0.010 0.001 PHE A 246 TYR 0.009 0.001 TYR A 439 ARG 0.003 0.000 ARG A1106 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2450 Ramachandran restraints generated. 1225 Oldfield, 0 Emsley, 1225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2450 Ramachandran restraints generated. 1225 Oldfield, 0 Emsley, 1225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 77 time to evaluate : 1.058 Fit side-chains REVERT: A 115 GLU cc_start: 0.8139 (mt-10) cc_final: 0.7856 (mt-10) REVERT: A 1034 ASP cc_start: 0.7372 (m-30) cc_final: 0.7090 (m-30) outliers start: 14 outliers final: 12 residues processed: 86 average time/residue: 0.2197 time to fit residues: 27.3723 Evaluate side-chains 75 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 63 time to evaluate : 0.953 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 464 PHE Chi-restraints excluded: chain A residue 661 THR Chi-restraints excluded: chain A residue 703 VAL Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 830 THR Chi-restraints excluded: chain A residue 913 LEU Chi-restraints excluded: chain A residue 1015 GLN Chi-restraints excluded: chain A residue 1053 THR Chi-restraints excluded: chain A residue 1064 LEU Chi-restraints excluded: chain A residue 1077 VAL Chi-restraints excluded: chain A residue 1152 ASP Chi-restraints excluded: chain A residue 1336 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 106 optimal weight: 1.9990 chunk 57 optimal weight: 3.9990 chunk 18 optimal weight: 0.9990 chunk 113 optimal weight: 0.8980 chunk 93 optimal weight: 5.9990 chunk 4 optimal weight: 0.0060 chunk 65 optimal weight: 0.0000 chunk 40 optimal weight: 2.9990 chunk 30 optimal weight: 0.9980 chunk 67 optimal weight: 5.9990 chunk 83 optimal weight: 2.9990 overall best weight: 0.5802 ------------------------------------------------------------------------------- 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 = 0.3849 r_free = 0.3849 target = 0.150492 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.125842 restraints weight = 22352.573| |-----------------------------------------------------------------------------| r_work (start): 0.3550 rms_B_bonded: 2.56 r_work: 0.3393 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3251 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3251 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3263 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3263 r_free = 0.3263 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3263 r_free = 0.3263 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3263 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8517 moved from start: 0.2078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9377 Z= 0.177 Angle : 0.553 8.362 12892 Z= 0.268 Chirality : 0.045 0.539 1546 Planarity : 0.005 0.046 1661 Dihedral : 4.270 34.751 1322 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 1.51 % Allowed : 11.08 % Favored : 87.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.96 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.51 (0.24), residues: 1225 helix: -0.60 (0.27), residues: 384 sheet: -0.57 (0.37), residues: 196 loop : -1.35 (0.24), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 214 HIS 0.003 0.001 HIS A 675 PHE 0.008 0.001 PHE A 433 TYR 0.011 0.001 TYR A 439 ARG 0.005 0.000 ARG A 523 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2450 Ramachandran restraints generated. 1225 Oldfield, 0 Emsley, 1225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2450 Ramachandran restraints generated. 1225 Oldfield, 0 Emsley, 1225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 65 time to evaluate : 0.923 Fit side-chains REVERT: A 115 GLU cc_start: 0.8135 (mt-10) cc_final: 0.7911 (mt-10) REVERT: A 312 MET cc_start: 0.8303 (ttt) cc_final: 0.8042 (tpt) REVERT: A 1034 ASP cc_start: 0.7391 (m-30) cc_final: 0.7079 (m-30) outliers start: 14 outliers final: 13 residues processed: 73 average time/residue: 0.2142 time to fit residues: 22.5701 Evaluate side-chains 74 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 61 time to evaluate : 0.922 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 464 PHE Chi-restraints excluded: chain A residue 703 VAL Chi-restraints excluded: chain A residue 713 THR Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 830 THR Chi-restraints excluded: chain A residue 913 LEU Chi-restraints excluded: chain A residue 988 VAL Chi-restraints excluded: chain A residue 1015 GLN Chi-restraints excluded: chain A residue 1053 THR Chi-restraints excluded: chain A residue 1064 LEU Chi-restraints excluded: chain A residue 1077 VAL Chi-restraints excluded: chain A residue 1152 ASP Chi-restraints excluded: chain A residue 1336 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 17 optimal weight: 0.8980 chunk 71 optimal weight: 5.9990 chunk 115 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 chunk 83 optimal weight: 0.9990 chunk 68 optimal weight: 0.7980 chunk 89 optimal weight: 0.8980 chunk 29 optimal weight: 0.0030 chunk 79 optimal weight: 0.8980 chunk 23 optimal weight: 0.0970 chunk 40 optimal weight: 2.9990 overall best weight: 0.5388 ------------------------------------------------------------------------------- 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 = 0.3856 r_free = 0.3856 target = 0.151084 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.126110 restraints weight = 24793.388| |-----------------------------------------------------------------------------| r_work (start): 0.3553 rms_B_bonded: 2.76 r_work: 0.3385 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work (final): 0.3385 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3397 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3397 r_free = 0.3397 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3397 r_free = 0.3397 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3397 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8415 moved from start: 0.2191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 9377 Z= 0.167 Angle : 0.543 8.247 12892 Z= 0.262 Chirality : 0.044 0.552 1546 Planarity : 0.005 0.045 1661 Dihedral : 4.183 34.825 1322 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 1.72 % Allowed : 12.37 % Favored : 85.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.96 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.14 (0.24), residues: 1225 helix: -0.15 (0.27), residues: 384 sheet: -0.42 (0.37), residues: 196 loop : -1.22 (0.24), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 423 HIS 0.002 0.001 HIS A 675 PHE 0.010 0.001 PHE A1066 TYR 0.011 0.001 TYR A 439 ARG 0.004 0.000 ARG A 523 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2450 Ramachandran restraints generated. 1225 Oldfield, 0 Emsley, 1225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2450 Ramachandran restraints generated. 1225 Oldfield, 0 Emsley, 1225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 66 time to evaluate : 0.942 Fit side-chains REVERT: A 115 GLU cc_start: 0.8037 (mt-10) cc_final: 0.7799 (mt-10) REVERT: A 312 MET cc_start: 0.8212 (ttt) cc_final: 0.7946 (tpt) REVERT: A 1034 ASP cc_start: 0.7052 (m-30) cc_final: 0.6757 (m-30) outliers start: 16 outliers final: 15 residues processed: 74 average time/residue: 0.2075 time to fit residues: 22.4756 Evaluate side-chains 77 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 62 time to evaluate : 1.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 610 ASP Chi-restraints excluded: chain A residue 703 VAL Chi-restraints excluded: chain A residue 713 THR Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 766 ILE Chi-restraints excluded: chain A residue 830 THR Chi-restraints excluded: chain A residue 841 SER Chi-restraints excluded: chain A residue 913 LEU Chi-restraints excluded: chain A residue 988 VAL Chi-restraints excluded: chain A residue 1015 GLN Chi-restraints excluded: chain A residue 1053 THR Chi-restraints excluded: chain A residue 1064 LEU Chi-restraints excluded: chain A residue 1077 VAL Chi-restraints excluded: chain A residue 1152 ASP Chi-restraints excluded: chain A residue 1336 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 67 optimal weight: 1.9990 chunk 31 optimal weight: 4.9990 chunk 123 optimal weight: 8.9990 chunk 110 optimal weight: 0.9990 chunk 103 optimal weight: 0.8980 chunk 117 optimal weight: 0.3980 chunk 19 optimal weight: 2.9990 chunk 75 optimal weight: 0.5980 chunk 27 optimal weight: 0.8980 chunk 88 optimal weight: 0.0470 chunk 21 optimal weight: 1.9990 overall best weight: 0.5678 ------------------------------------------------------------------------------- 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 = 0.3852 r_free = 0.3852 target = 0.150723 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.126209 restraints weight = 32384.206| |-----------------------------------------------------------------------------| r_work (start): 0.3551 rms_B_bonded: 3.64 r_work: 0.3347 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3347 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3360 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3360 r_free = 0.3360 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3360 r_free = 0.3360 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3360 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8439 moved from start: 0.2256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9377 Z= 0.170 Angle : 0.538 8.251 12892 Z= 0.260 Chirality : 0.045 0.572 1546 Planarity : 0.004 0.045 1661 Dihedral : 4.125 34.929 1322 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 1.61 % Allowed : 12.90 % Favored : 85.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.96 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.87 (0.24), residues: 1225 helix: 0.20 (0.28), residues: 382 sheet: -0.28 (0.37), residues: 196 loop : -1.13 (0.24), residues: 647 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 214 HIS 0.002 0.001 HIS A 675 PHE 0.007 0.001 PHE A 433 TYR 0.011 0.001 TYR A 439 ARG 0.004 0.000 ARG A 523 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2450 Ramachandran restraints generated. 1225 Oldfield, 0 Emsley, 1225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2450 Ramachandran restraints generated. 1225 Oldfield, 0 Emsley, 1225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 64 time to evaluate : 1.041 Fit side-chains REVERT: A 312 MET cc_start: 0.8245 (ttt) cc_final: 0.7996 (tpt) REVERT: A 1034 ASP cc_start: 0.7160 (m-30) cc_final: 0.6855 (m-30) outliers start: 15 outliers final: 13 residues processed: 72 average time/residue: 0.2428 time to fit residues: 25.0236 Evaluate side-chains 75 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 62 time to evaluate : 0.890 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 610 ASP Chi-restraints excluded: chain A residue 703 VAL Chi-restraints excluded: chain A residue 713 THR Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 766 ILE Chi-restraints excluded: chain A residue 830 THR Chi-restraints excluded: chain A residue 913 LEU Chi-restraints excluded: chain A residue 988 VAL Chi-restraints excluded: chain A residue 1015 GLN Chi-restraints excluded: chain A residue 1053 THR Chi-restraints excluded: chain A residue 1077 VAL Chi-restraints excluded: chain A residue 1152 ASP Chi-restraints excluded: chain A residue 1336 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 91 optimal weight: 0.0270 chunk 15 optimal weight: 0.9980 chunk 76 optimal weight: 4.9990 chunk 2 optimal weight: 1.9990 chunk 100 optimal weight: 3.9990 chunk 36 optimal weight: 0.5980 chunk 110 optimal weight: 1.9990 chunk 18 optimal weight: 0.9990 chunk 6 optimal weight: 0.0030 chunk 70 optimal weight: 3.9990 chunk 81 optimal weight: 1.9990 overall best weight: 0.5250 ------------------------------------------------------------------------------- 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 = 0.3858 r_free = 0.3858 target = 0.151267 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.126597 restraints weight = 32275.341| |-----------------------------------------------------------------------------| r_work (start): 0.3552 rms_B_bonded: 3.72 r_work: 0.3355 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3355 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3367 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3367 r_free = 0.3367 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3367 r_free = 0.3367 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3367 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8436 moved from start: 0.2336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 9377 Z= 0.164 Angle : 0.534 8.252 12892 Z= 0.257 Chirality : 0.044 0.571 1546 Planarity : 0.004 0.044 1661 Dihedral : 4.072 34.906 1322 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 1.72 % Allowed : 12.80 % Favored : 85.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.96 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.63 (0.24), residues: 1225 helix: 0.49 (0.28), residues: 377 sheet: -0.11 (0.37), residues: 207 loop : -1.06 (0.25), residues: 641 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 214 HIS 0.002 0.000 HIS A 675 PHE 0.011 0.001 PHE A1066 TYR 0.010 0.001 TYR A 439 ARG 0.004 0.000 ARG A 523 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2450 Ramachandran restraints generated. 1225 Oldfield, 0 Emsley, 1225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2450 Ramachandran restraints generated. 1225 Oldfield, 0 Emsley, 1225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 64 time to evaluate : 1.065 Fit side-chains REVERT: A 312 MET cc_start: 0.8228 (ttt) cc_final: 0.7940 (tpt) REVERT: A 1034 ASP cc_start: 0.7147 (m-30) cc_final: 0.6855 (m-30) outliers start: 16 outliers final: 14 residues processed: 74 average time/residue: 0.2162 time to fit residues: 23.6618 Evaluate side-chains 77 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 63 time to evaluate : 1.005 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 610 ASP Chi-restraints excluded: chain A residue 703 VAL Chi-restraints excluded: chain A residue 713 THR Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 766 ILE Chi-restraints excluded: chain A residue 830 THR Chi-restraints excluded: chain A residue 841 SER Chi-restraints excluded: chain A residue 913 LEU Chi-restraints excluded: chain A residue 988 VAL Chi-restraints excluded: chain A residue 1015 GLN Chi-restraints excluded: chain A residue 1053 THR Chi-restraints excluded: chain A residue 1077 VAL Chi-restraints excluded: chain A residue 1152 ASP Chi-restraints excluded: chain A residue 1336 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 63 optimal weight: 0.7980 chunk 120 optimal weight: 0.5980 chunk 96 optimal weight: 3.9990 chunk 14 optimal weight: 0.9980 chunk 114 optimal weight: 0.8980 chunk 13 optimal weight: 0.0050 chunk 108 optimal weight: 2.9990 chunk 34 optimal weight: 2.9990 chunk 43 optimal weight: 0.8980 chunk 122 optimal weight: 8.9990 chunk 83 optimal weight: 2.9990 overall best weight: 0.6394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 626 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.151244 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.126957 restraints weight = 30704.685| |-----------------------------------------------------------------------------| r_work (start): 0.3556 rms_B_bonded: 3.50 r_work: 0.3355 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3355 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3366 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3366 r_free = 0.3366 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3366 r_free = 0.3366 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3366 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8436 moved from start: 0.2353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9377 Z= 0.177 Angle : 0.537 8.291 12892 Z= 0.259 Chirality : 0.045 0.592 1546 Planarity : 0.004 0.044 1661 Dihedral : 4.076 35.114 1322 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 3.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 1.61 % Allowed : 12.80 % Favored : 85.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.96 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.58 (0.24), residues: 1225 helix: 0.64 (0.28), residues: 377 sheet: -0.22 (0.37), residues: 196 loop : -1.05 (0.24), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 214 HIS 0.002 0.001 HIS A 675 PHE 0.008 0.001 PHE A 433 TYR 0.011 0.001 TYR A 439 ARG 0.004 0.000 ARG A 764 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2450 Ramachandran restraints generated. 1225 Oldfield, 0 Emsley, 1225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2450 Ramachandran restraints generated. 1225 Oldfield, 0 Emsley, 1225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 66 time to evaluate : 1.024 Fit side-chains REVERT: A 312 MET cc_start: 0.8229 (ttt) cc_final: 0.7940 (tpt) REVERT: A 1034 ASP cc_start: 0.6988 (m-30) cc_final: 0.6726 (m-30) outliers start: 15 outliers final: 14 residues processed: 74 average time/residue: 0.2175 time to fit residues: 23.6029 Evaluate side-chains 75 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 61 time to evaluate : 1.019 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 610 ASP Chi-restraints excluded: chain A residue 703 VAL Chi-restraints excluded: chain A residue 713 THR Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 766 ILE Chi-restraints excluded: chain A residue 830 THR Chi-restraints excluded: chain A residue 841 SER Chi-restraints excluded: chain A residue 913 LEU Chi-restraints excluded: chain A residue 988 VAL Chi-restraints excluded: chain A residue 1015 GLN Chi-restraints excluded: chain A residue 1053 THR Chi-restraints excluded: chain A residue 1077 VAL Chi-restraints excluded: chain A residue 1152 ASP Chi-restraints excluded: chain A residue 1336 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 99 optimal weight: 0.0270 chunk 105 optimal weight: 0.0170 chunk 48 optimal weight: 0.8980 chunk 18 optimal weight: 0.9990 chunk 109 optimal weight: 0.8980 chunk 112 optimal weight: 0.9990 chunk 17 optimal weight: 0.9990 chunk 78 optimal weight: 3.9990 chunk 31 optimal weight: 4.9990 chunk 111 optimal weight: 2.9990 chunk 59 optimal weight: 0.2980 overall best weight: 0.4276 ------------------------------------------------------------------------------- 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 = 0.3874 r_free = 0.3874 target = 0.152477 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.127501 restraints weight = 28647.666| |-----------------------------------------------------------------------------| r_work (start): 0.3571 rms_B_bonded: 3.20 r_work: 0.3374 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3374 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3382 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3382 r_free = 0.3382 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3382 r_free = 0.3382 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3382 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8415 moved from start: 0.2464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 9377 Z= 0.154 Angle : 0.528 8.201 12892 Z= 0.254 Chirality : 0.044 0.612 1546 Planarity : 0.004 0.043 1661 Dihedral : 3.988 34.670 1322 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 1.51 % Allowed : 13.01 % Favored : 85.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.96 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.34 (0.24), residues: 1225 helix: 0.91 (0.28), residues: 377 sheet: -0.06 (0.37), residues: 207 loop : -0.97 (0.25), residues: 641 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 214 HIS 0.002 0.000 HIS A 675 PHE 0.009 0.001 PHE A1066 TYR 0.010 0.001 TYR A 439 ARG 0.009 0.000 ARG A 764 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2450 Ramachandran restraints generated. 1225 Oldfield, 0 Emsley, 1225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2450 Ramachandran restraints generated. 1225 Oldfield, 0 Emsley, 1225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 64 time to evaluate : 0.925 Fit side-chains REVERT: A 312 MET cc_start: 0.8204 (ttt) cc_final: 0.7942 (tpt) REVERT: A 1034 ASP cc_start: 0.6930 (m-30) cc_final: 0.6653 (m-30) outliers start: 14 outliers final: 13 residues processed: 72 average time/residue: 0.1979 time to fit residues: 21.7612 Evaluate side-chains 74 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 61 time to evaluate : 0.937 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 610 ASP Chi-restraints excluded: chain A residue 703 VAL Chi-restraints excluded: chain A residue 713 THR Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 830 THR Chi-restraints excluded: chain A residue 841 SER Chi-restraints excluded: chain A residue 913 LEU Chi-restraints excluded: chain A residue 988 VAL Chi-restraints excluded: chain A residue 1015 GLN Chi-restraints excluded: chain A residue 1053 THR Chi-restraints excluded: chain A residue 1077 VAL Chi-restraints excluded: chain A residue 1152 ASP Chi-restraints excluded: chain A residue 1336 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 43 optimal weight: 1.9990 chunk 34 optimal weight: 0.5980 chunk 75 optimal weight: 1.9990 chunk 64 optimal weight: 4.9990 chunk 70 optimal weight: 0.9990 chunk 66 optimal weight: 0.9990 chunk 23 optimal weight: 0.3980 chunk 18 optimal weight: 4.9990 chunk 35 optimal weight: 0.0470 chunk 82 optimal weight: 1.9990 chunk 65 optimal weight: 0.1980 overall best weight: 0.4480 ------------------------------------------------------------------------------- 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 = 0.3874 r_free = 0.3874 target = 0.152555 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.127769 restraints weight = 28185.654| |-----------------------------------------------------------------------------| r_work (start): 0.3572 rms_B_bonded: 3.06 r_work: 0.3377 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3377 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3391 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3391 r_free = 0.3391 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3391 r_free = 0.3391 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3391 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8411 moved from start: 0.2512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 9377 Z= 0.156 Angle : 0.527 8.214 12892 Z= 0.253 Chirality : 0.045 0.608 1546 Planarity : 0.004 0.042 1661 Dihedral : 3.940 34.664 1322 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 1.72 % Allowed : 12.80 % Favored : 85.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.96 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.24 (0.25), residues: 1225 helix: 1.00 (0.28), residues: 383 sheet: 0.01 (0.37), residues: 207 loop : -0.93 (0.25), residues: 635 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 214 HIS 0.002 0.000 HIS A 675 PHE 0.007 0.001 PHE A 75 TYR 0.010 0.001 TYR A 439 ARG 0.009 0.000 ARG A 764 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4204.20 seconds wall clock time: 75 minutes 8.92 seconds (4508.92 seconds total)