Starting phenix.real_space_refine on Thu Mar 13 21:33:56 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6wby_21601/03_2025/6wby_21601.cif Found real_map, /net/cci-nas-00/data/ceres_data/6wby_21601/03_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_21601/03_2025/6wby_21601.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6wby_21601/03_2025/6wby_21601.map" model { file = "/net/cci-nas-00/data/ceres_data/6wby_21601/03_2025/6wby_21601.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6wby_21601/03_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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/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: 10.02, per 1000 atoms: 1.09 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: 2.12 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: 1.34 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: 3.84 Time building geometry restraints manager: 2.54 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 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: 0.850 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: 0.090 Process input model: 31.010 Find NCS groups from input model: 0.160 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:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.450 ------------------------------------------------------------------------------- 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 : 0.998 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: 0.2813 time to fit residues: 33.2122 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 : 0.928 ------------------------------------------------------------------------------- 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 = 0.3835 r_free = 0.3835 target = 0.151432 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.124644 restraints weight = 22121.089| |-----------------------------------------------------------------------------| r_work (start): 0.3496 rms_B_bonded: 2.66 r_work: 0.3331 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work (final): 0.3331 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2816 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2816 r_free = 0.2816 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2816 r_free = 0.2816 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2816 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8443 moved from start: 0.1319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9377 Z= 0.196 Angle : 0.621 8.815 12892 Z= 0.310 Chirality : 0.044 0.380 1546 Planarity : 0.006 0.056 1661 Dihedral : 5.284 33.299 1322 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 4.54 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: -3.54 (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 : 0.964 Fit side-chains REVERT: A 309 MET cc_start: 0.8237 (mtt) cc_final: 0.8023 (mtt) REVERT: A 739 ARG cc_start: 0.7930 (mpt-90) cc_final: 0.7672 (mpt180) REVERT: A 1034 ASP cc_start: 0.7254 (m-30) cc_final: 0.6938 (m-30) outliers start: 10 outliers final: 7 residues processed: 83 average time/residue: 0.2581 time to fit residues: 31.3599 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 : 0.911 ------------------------------------------------------------------------------- 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: 7.9990 chunk 22 optimal weight: 0.9980 chunk 77 optimal weight: 0.9990 chunk 86 optimal weight: 0.7980 chunk 82 optimal weight: 0.8980 chunk 121 optimal weight: 5.9990 chunk 41 optimal weight: 0.9990 chunk 44 optimal weight: 3.9990 chunk 29 optimal weight: 0.0270 chunk 21 optimal weight: 1.9990 chunk 113 optimal weight: 0.7980 overall best weight: 0.7038 ------------------------------------------------------------------------------- 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 = 0.3845 r_free = 0.3845 target = 0.152424 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.125769 restraints weight = 34786.413| |-----------------------------------------------------------------------------| r_work (start): 0.3503 rms_B_bonded: 3.90 r_work: 0.3287 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.3287 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3277 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3277 r_free = 0.3277 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 = 0.3277 r_free = 0.3277 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3277 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8476 moved from start: 0.1627 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= 0.198 Angle : 0.593 8.958 12892 Z= 0.288 Chirality : 0.045 0.444 1546 Planarity : 0.005 0.053 1661 Dihedral : 4.776 34.948 1322 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 1.29 % Allowed : 9.57 % Favored : 89.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.96 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.57 (0.22), residues: 1225 helix: -1.85 (0.24), residues: 375 sheet: -1.19 (0.35), residues: 198 loop : -1.74 (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 0.022 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 85 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 73 time to evaluate : 0.903 Fit side-chains REVERT: A 739 ARG cc_start: 0.8060 (mpt-90) cc_final: 0.7844 (mpt180) REVERT: A 1034 ASP cc_start: 0.7333 (m-30) cc_final: 0.7001 (m-30) outliers start: 12 outliers final: 9 residues processed: 79 average time/residue: 0.2273 time to fit residues: 26.5105 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 : 1.038 ------------------------------------------------------------------------------- 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: 0.9990 chunk 35 optimal weight: 0.0370 chunk 26 optimal weight: 10.0000 chunk 56 optimal weight: 0.5980 chunk 74 optimal weight: 1.9990 chunk 4 optimal weight: 0.9990 chunk 11 optimal weight: 3.9990 chunk 85 optimal weight: 2.9990 chunk 15 optimal weight: 2.9990 chunk 41 optimal weight: 0.6980 chunk 88 optimal weight: 4.9990 overall best weight: 0.6662 ------------------------------------------------------------------------------- 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 = 0.3844 r_free = 0.3844 target = 0.152038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.125951 restraints weight = 39412.631| |-----------------------------------------------------------------------------| r_work (start): 0.3513 rms_B_bonded: 4.89 r_work: 0.3235 rms_B_bonded: 4.58 restraints_weight: 0.5000 r_work (final): 0.3235 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3198 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3198 r_free = 0.3198 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3198 r_free = 0.3198 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3198 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8512 moved from start: 0.1828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9377 Z= 0.186 Angle : 0.568 8.501 12892 Z= 0.276 Chirality : 0.045 0.510 1546 Planarity : 0.005 0.050 1661 Dihedral : 4.543 35.243 1322 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 1.72 % Allowed : 10.32 % Favored : 87.96 % 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: -1.94 (0.23), residues: 1225 helix: -1.14 (0.26), residues: 376 sheet: -0.86 (0.36), residues: 197 loop : -1.47 (0.24), residues: 652 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 0.012 0.001 PHE A 246 TYR 0.011 0.001 TYR A 439 ARG 0.006 0.000 ARG A 523 *********************** 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 83 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 67 time to evaluate : 1.049 Fit side-chains REVERT: A 115 GLU cc_start: 0.8205 (mt-10) cc_final: 0.7964 (mt-10) REVERT: A 1034 ASP cc_start: 0.7411 (m-30) cc_final: 0.7118 (m-30) outliers start: 16 outliers final: 14 residues processed: 78 average time/residue: 0.2004 time to fit residues: 23.1361 Evaluate side-chains 72 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 58 time to evaluate : 0.936 ------------------------------------------------------------------------------- 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 106 optimal weight: 3.9990 chunk 57 optimal weight: 0.0770 chunk 18 optimal weight: 0.8980 chunk 113 optimal weight: 0.0470 chunk 93 optimal weight: 0.6980 chunk 4 optimal weight: 0.1980 chunk 65 optimal weight: 0.0870 chunk 40 optimal weight: 0.4980 chunk 30 optimal weight: 2.9990 chunk 67 optimal weight: 3.9990 chunk 83 optimal weight: 0.8980 overall best weight: 0.1814 ------------------------------------------------------------------------------- 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 = 0.3875 r_free = 0.3875 target = 0.152651 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.128223 restraints weight = 22238.571| |-----------------------------------------------------------------------------| r_work (start): 0.3578 rms_B_bonded: 2.48 r_work: 0.3424 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3282 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3282 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3300 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3300 r_free = 0.3300 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3300 r_free = 0.3300 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3300 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8483 moved from start: 0.2170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 9377 Z= 0.140 Angle : 0.536 8.201 12892 Z= 0.259 Chirality : 0.044 0.544 1546 Planarity : 0.005 0.045 1661 Dihedral : 4.186 34.028 1322 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 1.61 % Allowed : 10.86 % Favored : 87.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.96 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.42 (0.24), residues: 1225 helix: -0.53 (0.27), residues: 384 sheet: -0.47 (0.36), residues: 207 loop : -1.32 (0.24), residues: 634 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 0.005 0.001 PHE A 433 TYR 0.018 0.001 TYR A 71 ARG 0.004 0.000 ARG A 764 *********************** 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 86 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 71 time to evaluate : 0.937 Fit side-chains REVERT: A 115 GLU cc_start: 0.8107 (mt-10) cc_final: 0.7875 (mt-10) REVERT: A 312 MET cc_start: 0.8243 (ttt) cc_final: 0.7961 (tpt) REVERT: A 1034 ASP cc_start: 0.7348 (m-30) cc_final: 0.7013 (m-30) outliers start: 15 outliers final: 13 residues processed: 80 average time/residue: 0.2073 time to fit residues: 24.4822 Evaluate side-chains 77 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 64 time to evaluate : 0.905 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 464 PHE Chi-restraints excluded: chain A residue 610 ASP 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 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: 0.9990 chunk 71 optimal weight: 5.9990 chunk 115 optimal weight: 2.9990 chunk 26 optimal weight: 10.0000 chunk 83 optimal weight: 2.9990 chunk 68 optimal weight: 0.6980 chunk 89 optimal weight: 0.0060 chunk 29 optimal weight: 0.0070 chunk 79 optimal weight: 0.6980 chunk 23 optimal weight: 0.0050 chunk 40 optimal weight: 3.9990 overall best weight: 0.2828 ------------------------------------------------------------------------------- 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 = 0.3905 r_free = 0.3905 target = 0.157404 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.130621 restraints weight = 25713.193| |-----------------------------------------------------------------------------| r_work (start): 0.3563 rms_B_bonded: 3.06 r_work: 0.3389 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3389 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3405 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3405 r_free = 0.3405 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3405 r_free = 0.3405 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3405 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8395 moved from start: 0.2314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 9377 Z= 0.144 Angle : 0.532 8.195 12892 Z= 0.257 Chirality : 0.044 0.559 1546 Planarity : 0.004 0.044 1661 Dihedral : 4.036 34.215 1322 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 1.51 % Allowed : 12.26 % Favored : 86.24 % 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: -1.03 (0.24), residues: 1225 helix: -0.09 (0.27), residues: 388 sheet: -0.24 (0.36), residues: 207 loop : -1.18 (0.24), residues: 630 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 0.010 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 79 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 65 time to evaluate : 0.995 Fit side-chains REVERT: A 312 MET cc_start: 0.8242 (ttt) cc_final: 0.7959 (tpt) REVERT: A 1034 ASP cc_start: 0.7136 (m-30) cc_final: 0.6821 (m-30) outliers start: 14 outliers final: 14 residues processed: 73 average time/residue: 0.2114 time to fit residues: 22.6857 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 : 0.973 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 LEU Chi-restraints excluded: chain A residue 464 PHE Chi-restraints excluded: chain A residue 610 ASP 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 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: 0.9990 chunk 31 optimal weight: 4.9990 chunk 123 optimal weight: 3.9990 chunk 110 optimal weight: 0.9990 chunk 103 optimal weight: 0.9990 chunk 117 optimal weight: 0.3980 chunk 19 optimal weight: 2.9990 chunk 75 optimal weight: 0.6980 chunk 27 optimal weight: 0.7980 chunk 88 optimal weight: 0.8980 chunk 21 optimal weight: 2.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- 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 = 0.3848 r_free = 0.3848 target = 0.150459 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.125656 restraints weight = 32396.736| |-----------------------------------------------------------------------------| r_work (start): 0.3541 rms_B_bonded: 3.77 r_work: 0.3337 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3337 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3346 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3346 r_free = 0.3346 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3346 r_free = 0.3346 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3346 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8451 moved from start: 0.2258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9377 Z= 0.188 Angle : 0.543 8.334 12892 Z= 0.262 Chirality : 0.045 0.538 1546 Planarity : 0.004 0.044 1661 Dihedral : 4.116 35.173 1322 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 4.21 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: -0.84 (0.24), residues: 1225 helix: 0.12 (0.27), residues: 388 sheet: -0.12 (0.37), residues: 207 loop : -1.11 (0.25), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 214 HIS 0.003 0.001 HIS A 675 PHE 0.009 0.001 PHE A 433 TYR 0.012 0.001 TYR A 439 ARG 0.003 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 78 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 62 time to evaluate : 1.333 Fit side-chains REVERT: A 312 MET cc_start: 0.8259 (ttt) cc_final: 0.7986 (tpt) REVERT: A 1034 ASP cc_start: 0.7214 (m-30) cc_final: 0.6902 (m-30) outliers start: 16 outliers final: 15 residues processed: 72 average time/residue: 0.2628 time to fit residues: 27.9513 Evaluate side-chains 74 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 59 time to evaluate : 1.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 LEU 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 91 optimal weight: 7.9990 chunk 15 optimal weight: 0.7980 chunk 76 optimal weight: 4.9990 chunk 2 optimal weight: 3.9990 chunk 100 optimal weight: 3.9990 chunk 36 optimal weight: 0.6980 chunk 110 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 chunk 6 optimal weight: 0.0980 chunk 70 optimal weight: 2.9990 chunk 81 optimal weight: 1.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- 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 = 0.3847 r_free = 0.3847 target = 0.152475 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.126207 restraints weight = 33684.169| |-----------------------------------------------------------------------------| r_work (start): 0.3504 rms_B_bonded: 4.15 r_work: 0.3294 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3294 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3306 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3306 r_free = 0.3306 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3306 r_free = 0.3306 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3306 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8479 moved from start: 0.2156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 9377 Z= 0.250 Angle : 0.572 8.609 12892 Z= 0.276 Chirality : 0.046 0.584 1546 Planarity : 0.005 0.046 1661 Dihedral : 4.327 36.063 1322 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % 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: -0.81 (0.24), residues: 1225 helix: 0.28 (0.28), residues: 377 sheet: -0.30 (0.37), residues: 197 loop : -1.08 (0.24), residues: 651 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 214 HIS 0.004 0.001 HIS A 675 PHE 0.011 0.001 PHE A 433 TYR 0.013 0.001 TYR A 439 ARG 0.003 0.000 ARG A 764 *********************** 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 72 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 57 time to evaluate : 1.146 Fit side-chains REVERT: A 312 MET cc_start: 0.8346 (ttt) cc_final: 0.8040 (tpt) REVERT: A 1034 ASP cc_start: 0.7065 (m-30) cc_final: 0.6784 (m-30) outliers start: 15 outliers final: 13 residues processed: 68 average time/residue: 0.2848 time to fit residues: 28.4843 Evaluate side-chains 70 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 57 time to evaluate : 0.798 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 LEU 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 1336 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 63 optimal weight: 0.6980 chunk 120 optimal weight: 8.9990 chunk 96 optimal weight: 5.9990 chunk 14 optimal weight: 0.5980 chunk 114 optimal weight: 0.4980 chunk 13 optimal weight: 0.9990 chunk 108 optimal weight: 5.9990 chunk 34 optimal weight: 4.9990 chunk 43 optimal weight: 0.9980 chunk 122 optimal weight: 9.9990 chunk 83 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.153796 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.127037 restraints weight = 31959.677| |-----------------------------------------------------------------------------| r_work (start): 0.3520 rms_B_bonded: 3.77 r_work: 0.3313 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3313 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3326 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3326 r_free = 0.3326 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 = 0.3326 r_free = 0.3326 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3326 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8458 moved from start: 0.2239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9377 Z= 0.191 Angle : 0.548 8.425 12892 Z= 0.265 Chirality : 0.045 0.588 1546 Planarity : 0.004 0.044 1661 Dihedral : 4.234 35.495 1322 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 1.51 % Allowed : 12.80 % Favored : 85.70 % 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: -0.68 (0.24), residues: 1225 helix: 0.45 (0.28), residues: 372 sheet: -0.26 (0.37), residues: 197 loop : -1.03 (0.24), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 214 HIS 0.002 0.001 HIS A 551 PHE 0.008 0.001 PHE A 75 TYR 0.011 0.001 TYR A 439 ARG 0.003 0.000 ARG A 523 *********************** 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 74 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 60 time to evaluate : 0.915 Fit side-chains REVERT: A 312 MET cc_start: 0.8319 (ttt) cc_final: 0.8005 (tpt) REVERT: A 1034 ASP cc_start: 0.7056 (m-30) cc_final: 0.6795 (m-30) outliers start: 14 outliers final: 13 residues processed: 70 average time/residue: 0.2145 time to fit residues: 21.8959 Evaluate side-chains 71 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 58 time to evaluate : 0.913 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 LEU 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 1336 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 99 optimal weight: 0.6980 chunk 105 optimal weight: 0.0040 chunk 48 optimal weight: 0.9990 chunk 18 optimal weight: 0.9980 chunk 109 optimal weight: 0.4980 chunk 112 optimal weight: 0.7980 chunk 17 optimal weight: 2.9990 chunk 78 optimal weight: 0.8980 chunk 31 optimal weight: 2.9990 chunk 111 optimal weight: 0.9990 chunk 59 optimal weight: 0.8980 overall best weight: 0.5792 ------------------------------------------------------------------------------- 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 = 0.3854 r_free = 0.3854 target = 0.150890 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.126151 restraints weight = 28704.995| |-----------------------------------------------------------------------------| r_work (start): 0.3551 rms_B_bonded: 3.25 r_work: 0.3351 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3351 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3358 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3358 r_free = 0.3358 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3358 r_free = 0.3358 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3358 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8440 moved from start: 0.2325 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= 0.172 Angle : 0.539 8.244 12892 Z= 0.260 Chirality : 0.045 0.602 1546 Planarity : 0.004 0.043 1661 Dihedral : 4.139 35.061 1322 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 1.29 % Allowed : 13.23 % 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: -0.56 (0.24), residues: 1225 helix: 0.47 (0.28), residues: 384 sheet: -0.08 (0.37), residues: 208 loop : -0.97 (0.25), residues: 633 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 214 HIS 0.003 0.001 HIS A 675 PHE 0.011 0.001 PHE A1066 TYR 0.011 0.001 TYR A 439 ARG 0.003 0.000 ARG A 523 ********************** 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 73 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 61 time to evaluate : 0.906 Fit side-chains REVERT: A 312 MET cc_start: 0.8247 (ttt) cc_final: 0.7962 (tpt) REVERT: A 1034 ASP cc_start: 0.6965 (m-30) cc_final: 0.6685 (m-30) outliers start: 12 outliers final: 11 residues processed: 70 average time/residue: 0.2692 time to fit residues: 27.6160 Evaluate side-chains 73 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 62 time to evaluate : 0.944 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 LEU Chi-restraints excluded: chain A residue 610 ASP 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 841 SER Chi-restraints excluded: chain A residue 913 LEU Chi-restraints excluded: chain A residue 988 VAL Chi-restraints excluded: chain A residue 1053 THR Chi-restraints excluded: chain A residue 1077 VAL 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: 2.9990 chunk 34 optimal weight: 0.0040 chunk 75 optimal weight: 1.9990 chunk 64 optimal weight: 4.9990 chunk 70 optimal weight: 0.9990 chunk 66 optimal weight: 0.9980 chunk 23 optimal weight: 0.0770 chunk 18 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 chunk 82 optimal weight: 0.0070 chunk 65 optimal weight: 1.9990 overall best weight: 0.4170 ------------------------------------------------------------------------------- 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 = 0.3867 r_free = 0.3867 target = 0.151905 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.127251 restraints weight = 28201.359| |-----------------------------------------------------------------------------| r_work (start): 0.3566 rms_B_bonded: 3.07 r_work: 0.3365 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3365 ------------------------------------------------------------------------------- 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 = 0.50 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 = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3382 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8422 moved from start: 0.2452 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= 0.153 Angle : 0.527 8.187 12892 Z= 0.254 Chirality : 0.044 0.600 1546 Planarity : 0.004 0.043 1661 Dihedral : 4.009 34.563 1322 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 1.40 % Allowed : 13.23 % Favored : 85.38 % 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: -0.41 (0.24), residues: 1225 helix: 0.73 (0.28), residues: 383 sheet: -0.19 (0.36), residues: 207 loop : -0.89 (0.25), residues: 635 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 214 HIS 0.001 0.000 HIS A 551 PHE 0.008 0.001 PHE A 75 TYR 0.010 0.001 TYR A 439 ARG 0.004 0.000 ARG A 523 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4502.48 seconds wall clock time: 80 minutes 42.86 seconds (4842.86 seconds total)