Starting phenix.real_space_refine on Fri Mar 15 17:35:36 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w02_32234/03_2024/7w02_32234_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w02_32234/03_2024/7w02_32234.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w02_32234/03_2024/7w02_32234.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w02_32234/03_2024/7w02_32234.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w02_32234/03_2024/7w02_32234_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w02_32234/03_2024/7w02_32234_updated.pdb" } resolution = 3.3 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= 0.006 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: 6 Type Number sf(0) Gaussians P 6 5.49 5 Mg 2 5.21 5 S 68 5.16 5 C 7985 2.51 5 N 2063 2.21 5 O 2202 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 20": "NH1" <-> "NH2" Residue "A TYR 57": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 88": "OD1" <-> "OD2" Residue "A ARG 98": "NH1" <-> "NH2" Residue "A ARG 99": "NH1" <-> "NH2" Residue "A PHE 110": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 123": "OD1" <-> "OD2" Residue "A PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 144": "OE1" <-> "OE2" Residue "A TYR 152": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 160": "NH1" <-> "NH2" Residue "A PHE 185": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 188": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 194": "NH1" <-> "NH2" Residue "A GLU 195": "OE1" <-> "OE2" Residue "A ASP 200": "OD1" <-> "OD2" Residue "A PHE 211": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 220": "NH1" <-> "NH2" Residue "A GLU 224": "OE1" <-> "OE2" Residue "A TYR 225": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 237": "NH1" <-> "NH2" Residue "A ARG 244": "NH1" <-> "NH2" Residue "A ASP 253": "OD1" <-> "OD2" Residue "A PHE 255": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 261": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 288": "NH1" <-> "NH2" Residue "A ARG 289": "NH1" <-> "NH2" Residue "A GLU 292": "OE1" <-> "OE2" Residue "A PHE 322": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 340": "NH1" <-> "NH2" Residue "A PHE 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 384": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 389": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 395": "NH1" <-> "NH2" Residue "A ARG 435": "NH1" <-> "NH2" Residue "A ASP 446": "OD1" <-> "OD2" Residue "A PHE 449": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 459": "OD1" <-> "OD2" Residue "A PHE 486": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 487": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 519": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 522": "OE1" <-> "OE2" Residue "A ASP 525": "OD1" <-> "OD2" Residue "A PHE 539": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 545": "OD1" <-> "OD2" Residue "A ARG 550": "NH1" <-> "NH2" Residue "A TYR 557": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 558": "OE1" <-> "OE2" Residue "A PHE 583": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 591": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 596": "OE1" <-> "OE2" Residue "A GLU 644": "OE1" <-> "OE2" Residue "A ARG 671": "NH1" <-> "NH2" Residue "A ARG 701": "NH1" <-> "NH2" Residue "A ASP 705": "OD1" <-> "OD2" Residue "A ASP 724": "OD1" <-> "OD2" Residue "A GLU 725": "OE1" <-> "OE2" Residue "A ARG 732": "NH1" <-> "NH2" Residue "A TYR 758": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 800": "NH1" <-> "NH2" Residue "A PHE 825": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 834": "OE1" <-> "OE2" Residue "A ARG 838": "NH1" <-> "NH2" Residue "A PHE 912": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 918": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 921": "NH1" <-> "NH2" Residue "A GLU 922": "OE1" <-> "OE2" Residue "A ARG 957": "NH1" <-> "NH2" Residue "A ARG 965": "NH1" <-> "NH2" Residue "A PHE 970": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1011": "NH1" <-> "NH2" Residue "A GLU 1021": "OE1" <-> "OE2" Residue "A GLU 1034": "OE1" <-> "OE2" Residue "A ARG 1081": "NH1" <-> "NH2" Residue "A ARG 1095": "NH1" <-> "NH2" Residue "A ASP 1099": "OD1" <-> "OD2" Residue "A PHE 1106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1110": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1122": "OE1" <-> "OE2" Residue "A ARG 1123": "NH1" <-> "NH2" Residue "A PHE 1141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1149": "OD1" <-> "OD2" Residue "A PHE 1153": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1167": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1225": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1272": "NH1" <-> "NH2" Residue "A TYR 1273": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1293": "OE1" <-> "OE2" Residue "A PHE 1295": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1331": "NH1" <-> "NH2" Residue "A GLU 1385": "OE1" <-> "OE2" Residue "A GLU 1391": "OE1" <-> "OE2" Residue "A GLU 1433": "OE1" <-> "OE2" Residue "A PHE 1441": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1446": "NH1" <-> "NH2" Residue "A ARG 1457": "NH1" <-> "NH2" Residue "A ASP 1465": "OD1" <-> "OD2" Residue "A ARG 1474": "NH1" <-> "NH2" Residue "A GLU 1475": "OE1" <-> "OE2" Residue "A TYR 1480": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1482": "NH1" <-> "NH2" Residue "A ARG 1484": "NH1" <-> "NH2" Residue "A GLU 1488": "OE1" <-> "OE2" Residue "A ARG 1500": "NH1" <-> "NH2" Residue "A ARG 1513": "NH1" <-> "NH2" Residue "A ARG 1521": "NH1" <-> "NH2" Residue "A GLU 1532": "OE1" <-> "OE2" Residue "A GLU 1641": "OE1" <-> "OE2" Residue "A TYR 1650": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1663": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1689": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1692": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 12326 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 12326 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1572, 12326 Unusual residues: {' MG': 2, 'ATP': 2, 'NAG': 2} Classifications: {'peptide': 1566, 'undetermined': 6} Incomplete info: {'truncation_to_alanine': 46} Link IDs: {'PTRANS': 69, 'TRANS': 1496, None: 6} Not linked: pdbres="LEU A1695 " pdbres="ATP A1801 " Not linked: pdbres="ATP A1801 " pdbres="ATP A1802 " Not linked: pdbres="ATP A1802 " pdbres=" MG A1803 " Not linked: pdbres=" MG A1803 " pdbres=" MG A1804 " Not linked: pdbres=" MG A1804 " pdbres="NAG A1805 " Not linked: pdbres="NAG A1805 " pdbres="NAG A1806 " Chain breaks: 8 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 193 Unresolved non-hydrogen angles: 238 Unresolved non-hydrogen dihedrals: 174 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 2, 'HIS:plan': 6, 'PHE:plan': 1, 'GLU:plan': 9, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 110 Time building chain proxies: 6.44, per 1000 atoms: 0.52 Number of scatterers: 12326 At special positions: 0 Unit cell: (97.2, 145.8, 138.24, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 68 16.00 P 6 15.00 Mg 2 11.99 O 2202 8.00 N 2063 7.00 C 7985 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A1274 " - pdb=" SG CYS A1284 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 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 Links applied NAG-ASN " NAG A1805 " - " ASN A 124 " " NAG A1806 " - " ASN A 140 " Time building additional restraints: 4.52 Conformation dependent library (CDL) restraints added in 2.2 seconds 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2932 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 58 helices and 12 sheets defined 45.4% alpha, 8.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.85 Creating SS restraints... Processing helix chain 'A' and resid 2 through 20 removed outlier: 3.991A pdb=" N LEU A 9 " --> pdb=" O ARG A 5 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ARG A 20 " --> pdb=" O THR A 16 " (cutoff:3.500A) Processing helix chain 'A' and resid 22 through 29 Processing helix chain 'A' and resid 33 through 45 removed outlier: 4.411A pdb=" N ILE A 38 " --> pdb=" O LEU A 34 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N LEU A 39 " --> pdb=" O PHE A 35 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ILE A 40 " --> pdb=" O SER A 36 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N LEU A 44 " --> pdb=" O ILE A 40 " (cutoff:3.500A) Processing helix chain 'A' and resid 88 through 100 removed outlier: 3.871A pdb=" N THR A 94 " --> pdb=" O ALA A 90 " (cutoff:3.500A) Processing helix chain 'A' and resid 113 through 121 Processing helix chain 'A' and resid 140 through 142 No H-bonds generated for 'chain 'A' and resid 140 through 142' Processing helix chain 'A' and resid 211 through 226 removed outlier: 3.677A pdb=" N MET A 223 " --> pdb=" O ASP A 219 " (cutoff:3.500A) Processing helix chain 'A' and resid 230 through 236 removed outlier: 3.617A pdb=" N GLN A 236 " --> pdb=" O ARG A 232 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 283 removed outlier: 3.609A pdb=" N LEU A 269 " --> pdb=" O LEU A 265 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N SER A 270 " --> pdb=" O LEU A 266 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N PHE A 271 " --> pdb=" O LEU A 267 " (cutoff:3.500A) removed outlier: 5.448A pdb=" N TYR A 273 " --> pdb=" O LEU A 269 " (cutoff:3.500A) removed outlier: 5.208A pdb=" N THR A 274 " --> pdb=" O SER A 270 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ALA A 279 " --> pdb=" O ALA A 275 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N ARG A 280 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N VAL A 283 " --> pdb=" O ALA A 279 " (cutoff:3.500A) Processing helix chain 'A' and resid 290 through 298 removed outlier: 3.655A pdb=" N MET A 294 " --> pdb=" O LEU A 290 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 327 removed outlier: 3.632A pdb=" N SER A 306 " --> pdb=" O TRP A 302 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ALA A 307 " --> pdb=" O LEU A 303 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N LEU A 314 " --> pdb=" O LEU A 310 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N PHE A 315 " --> pdb=" O LEU A 311 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LEU A 316 " --> pdb=" O PHE A 312 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N THR A 324 " --> pdb=" O ALA A 320 " (cutoff:3.500A) Processing helix chain 'A' and resid 343 through 366 removed outlier: 3.680A pdb=" N SER A 356 " --> pdb=" O CYS A 352 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N SER A 361 " --> pdb=" O THR A 357 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N THR A 366 " --> pdb=" O PHE A 362 " (cutoff:3.500A) Processing helix chain 'A' and resid 371 through 396 removed outlier: 3.853A pdb=" N GLY A 379 " --> pdb=" O ALA A 375 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N PHE A 380 " --> pdb=" O ALA A 376 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LEU A 381 " --> pdb=" O PHE A 377 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N TYR A 382 " --> pdb=" O GLY A 378 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N PHE A 383 " --> pdb=" O GLY A 379 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N TYR A 386 " --> pdb=" O TYR A 382 " (cutoff:3.500A) Proline residue: A 388 - end of helix removed outlier: 4.264A pdb=" N PHE A 391 " --> pdb=" O ILE A 387 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N VAL A 392 " --> pdb=" O PRO A 388 " (cutoff:3.500A) Proline residue: A 394 - end of helix Processing helix chain 'A' and resid 401 through 408 removed outlier: 3.773A pdb=" N SER A 407 " --> pdb=" O GLN A 403 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N CYS A 408 " --> pdb=" O LYS A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 411 through 428 removed outlier: 3.530A pdb=" N GLY A 418 " --> pdb=" O ALA A 414 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N LEU A 421 " --> pdb=" O MET A 417 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLY A 423 " --> pdb=" O ALA A 419 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N LYS A 428 " --> pdb=" O LYS A 424 " (cutoff:3.500A) Processing helix chain 'A' and resid 450 through 473 removed outlier: 3.531A pdb=" N MET A 455 " --> pdb=" O GLN A 451 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N SER A 460 " --> pdb=" O LEU A 456 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N VAL A 461 " --> pdb=" O LEU A 457 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N VAL A 466 " --> pdb=" O LEU A 462 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N TYR A 469 " --> pdb=" O LEU A 465 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLU A 471 " --> pdb=" O THR A 467 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N ALA A 472 " --> pdb=" O TRP A 468 " (cutoff:3.500A) Processing helix chain 'A' and resid 576 through 579 No H-bonds generated for 'chain 'A' and resid 576 through 579' Processing helix chain 'A' and resid 601 through 606 removed outlier: 4.288A pdb=" N LYS A 606 " --> pdb=" O VAL A 602 " (cutoff:3.500A) Processing helix chain 'A' and resid 623 through 634 removed outlier: 3.830A pdb=" N LYS A 634 " --> pdb=" O TYR A 630 " (cutoff:3.500A) Processing helix chain 'A' and resid 641 through 652 Processing helix chain 'A' and resid 669 through 679 Processing helix chain 'A' and resid 697 through 709 removed outlier: 4.217A pdb=" N ALA A 702 " --> pdb=" O ILE A 698 " (cutoff:3.500A) Processing helix chain 'A' and resid 725 through 728 No H-bonds generated for 'chain 'A' and resid 725 through 728' Processing helix chain 'A' and resid 751 through 754 No H-bonds generated for 'chain 'A' and resid 751 through 754' Processing helix chain 'A' and resid 770 through 780 removed outlier: 3.516A pdb=" N LEU A 776 " --> pdb=" O ASP A 772 " (cutoff:3.500A) Processing helix chain 'A' and resid 807 through 815 Processing helix chain 'A' and resid 817 through 820 No H-bonds generated for 'chain 'A' and resid 817 through 820' Processing helix chain 'A' and resid 832 through 842 removed outlier: 3.520A pdb=" N PHE A 836 " --> pdb=" O MET A 832 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N LEU A 837 " --> pdb=" O GLU A 833 " (cutoff:3.500A) Processing helix chain 'A' and resid 901 through 921 removed outlier: 3.790A pdb=" N TRP A 909 " --> pdb=" O CYS A 905 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N TYR A 918 " --> pdb=" O LYS A 914 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N SER A 919 " --> pdb=" O LYS A 915 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N TRP A 920 " --> pdb=" O ALA A 916 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ARG A 921 " --> pdb=" O ALA A 917 " (cutoff:3.500A) Processing helix chain 'A' and resid 923 through 935 Proline residue: A 933 - end of helix Processing helix chain 'A' and resid 942 through 945 No H-bonds generated for 'chain 'A' and resid 942 through 945' Processing helix chain 'A' and resid 980 through 993 removed outlier: 3.958A pdb=" N HIS A 985 " --> pdb=" O GLN A 981 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N GLN A 991 " --> pdb=" O LYS A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 1004 through 1021 removed outlier: 3.862A pdb=" N GLY A1016 " --> pdb=" O ALA A1012 " (cutoff:3.500A) removed outlier: 7.186A pdb=" N GLY A1017 " --> pdb=" O SER A1013 " (cutoff:3.500A) removed outlier: 7.774A pdb=" N GLY A1018 " --> pdb=" O VAL A1014 " (cutoff:3.500A) removed outlier: 4.890A pdb=" N PHE A1019 " --> pdb=" O GLU A1015 " (cutoff:3.500A) removed outlier: 4.807A pdb=" N ASN A1020 " --> pdb=" O GLY A1016 " (cutoff:3.500A) removed outlier: 4.748A pdb=" N GLU A1021 " --> pdb=" O GLY A1017 " (cutoff:3.500A) Processing helix chain 'A' and resid 1049 through 1065 removed outlier: 3.518A pdb=" N LEU A1060 " --> pdb=" O VAL A1056 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N LEU A1065 " --> pdb=" O LEU A1061 " (cutoff:3.500A) Processing helix chain 'A' and resid 1096 through 1124 removed outlier: 4.020A pdb=" N ILE A1100 " --> pdb=" O LYS A1096 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ALA A1107 " --> pdb=" O ASN A1103 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N PHE A1110 " --> pdb=" O PHE A1106 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N SER A1113 " --> pdb=" O ALA A1109 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N THR A1114 " --> pdb=" O PHE A1110 " (cutoff:3.500A) removed outlier: 4.784A pdb=" N PHE A1115 " --> pdb=" O LEU A1111 " (cutoff:3.500A) removed outlier: 5.709A pdb=" N SER A1116 " --> pdb=" O ALA A1112 " (cutoff:3.500A) removed outlier: 4.793A pdb=" N ILE A1117 " --> pdb=" O SER A1113 " (cutoff:3.500A) removed outlier: 5.196A pdb=" N LEU A1118 " --> pdb=" O THR A1114 " (cutoff:3.500A) removed outlier: 5.317A pdb=" N ALA A1119 " --> pdb=" O PHE A1115 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N ARG A1123 " --> pdb=" O ALA A1119 " (cutoff:3.500A) Processing helix chain 'A' and resid 1127 through 1133 removed outlier: 3.656A pdb=" N GLN A1131 " --> pdb=" O ALA A1127 " (cutoff:3.500A) Processing helix chain 'A' and resid 1138 through 1167 removed outlier: 3.785A pdb=" N SER A1144 " --> pdb=" O SER A1140 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ALA A1145 " --> pdb=" O PHE A1141 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ILE A1155 " --> pdb=" O ILE A1151 " (cutoff:3.500A) Proline residue: A1156 - end of helix removed outlier: 4.101A pdb=" N LEU A1161 " --> pdb=" O SER A1157 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N VAL A1162 " --> pdb=" O LEU A1158 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N VAL A1163 " --> pdb=" O LEU A1159 " (cutoff:3.500A) Processing helix chain 'A' and resid 1170 through 1172 No H-bonds generated for 'chain 'A' and resid 1170 through 1172' Processing helix chain 'A' and resid 1177 through 1201 removed outlier: 3.701A pdb=" N ILE A1193 " --> pdb=" O GLY A1189 " (cutoff:3.500A) Proline residue: A1194 - end of helix removed outlier: 3.717A pdb=" N ASN A1200 " --> pdb=" O MET A1196 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N PHE A1201 " --> pdb=" O TYR A1197 " (cutoff:3.500A) Processing helix chain 'A' and resid 1207 through 1219 removed outlier: 3.828A pdb=" N THR A1211 " --> pdb=" O ALA A1207 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N ARG A1212 " --> pdb=" O THR A1208 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N ILE A1215 " --> pdb=" O THR A1211 " (cutoff:3.500A) Processing helix chain 'A' and resid 1222 through 1232 removed outlier: 3.562A pdb=" N ARG A1232 " --> pdb=" O VAL A1228 " (cutoff:3.500A) Processing helix chain 'A' and resid 1241 through 1244 No H-bonds generated for 'chain 'A' and resid 1241 through 1244' Processing helix chain 'A' and resid 1249 through 1251 No H-bonds generated for 'chain 'A' and resid 1249 through 1251' Processing helix chain 'A' and resid 1253 through 1273 removed outlier: 3.733A pdb=" N LEU A1257 " --> pdb=" O PRO A1253 " (cutoff:3.500A) Processing helix chain 'A' and resid 1278 through 1286 removed outlier: 4.238A pdb=" N TYR A1283 " --> pdb=" O VAL A1279 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LYS A1285 " --> pdb=" O ALA A1281 " (cutoff:3.500A) Processing helix chain 'A' and resid 1305 through 1324 removed outlier: 3.822A pdb=" N GLY A1314 " --> pdb=" O MET A1310 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N CYS A1315 " --> pdb=" O ALA A1311 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ALA A1316 " --> pdb=" O ALA A1312 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LEU A1320 " --> pdb=" O ALA A1316 " (cutoff:3.500A) Processing helix chain 'A' and resid 1359 through 1367 removed outlier: 3.610A pdb=" N GLU A1364 " --> pdb=" O ASP A1360 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ARG A1365 " --> pdb=" O VAL A1361 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N THR A1366 " --> pdb=" O ALA A1362 " (cutoff:3.500A) Processing helix chain 'A' and resid 1422 through 1430 removed outlier: 3.779A pdb=" N MET A1428 " --> pdb=" O THR A1424 " (cutoff:3.500A) Processing helix chain 'A' and resid 1473 through 1483 removed outlier: 3.520A pdb=" N LEU A1477 " --> pdb=" O GLY A1473 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N TYR A1480 " --> pdb=" O MET A1476 " (cutoff:3.500A) Processing helix chain 'A' and resid 1488 through 1502 removed outlier: 3.698A pdb=" N ILE A1491 " --> pdb=" O GLU A1488 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N GLY A1492 " --> pdb=" O ARG A1489 " (cutoff:3.500A) removed outlier: 5.205A pdb=" N ALA A1493 " --> pdb=" O HIS A1490 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N ASN A1497 " --> pdb=" O CYS A1494 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N ARG A1500 " --> pdb=" O ASN A1497 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N GLY A1501 " --> pdb=" O THR A1498 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LEU A1502 " --> pdb=" O LEU A1499 " (cutoff:3.500A) Processing helix chain 'A' and resid 1511 through 1513 No H-bonds generated for 'chain 'A' and resid 1511 through 1513' Processing helix chain 'A' and resid 1519 through 1528 removed outlier: 3.756A pdb=" N LEU A1523 " --> pdb=" O ASN A1519 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ALA A1528 " --> pdb=" O SER A1524 " (cutoff:3.500A) Processing helix chain 'A' and resid 1547 through 1561 removed outlier: 3.519A pdb=" N TRP A1554 " --> pdb=" O ARG A1550 " (cutoff:3.500A) Processing helix chain 'A' and resid 1598 through 1602 Processing helix chain 'A' and resid 1622 through 1634 removed outlier: 3.553A pdb=" N ALA A1629 " --> pdb=" O GLU A1625 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N PHE A1630 " --> pdb=" O GLU A1626 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N VAL A1631 " --> pdb=" O PHE A1627 " (cutoff:3.500A) Processing helix chain 'A' and resid 1660 through 1663 No H-bonds generated for 'chain 'A' and resid 1660 through 1663' Processing helix chain 'A' and resid 1665 through 1667 No H-bonds generated for 'chain 'A' and resid 1665 through 1667' Processing helix chain 'A' and resid 1685 through 1692 removed outlier: 3.953A pdb=" N PHE A1692 " --> pdb=" O VAL A1688 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 105 through 107 removed outlier: 7.117A pdb=" N TRP A 78 " --> pdb=" O ARG A 106 " (cutoff:3.500A) removed outlier: 7.783A pdb=" N ALA A 81 " --> pdb=" O LEU A 130 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N ALA A 132 " --> pdb=" O ALA A 81 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N VAL A 134 " --> pdb=" O HIS A 153 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU A 154 " --> pdb=" O SER A1075 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 238 through 241 removed outlier: 6.634A pdb=" N THR A1036 " --> pdb=" O THR A 239 " (cutoff:3.500A) removed outlier: 7.728A pdb=" N THR A 241 " --> pdb=" O THR A1036 " (cutoff:3.500A) removed outlier: 5.846A pdb=" N VAL A1038 " --> pdb=" O THR A 241 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 589 through 591 removed outlier: 6.495A pdb=" N LEU A 556 " --> pdb=" O GLY A 529 " (cutoff:3.500A) removed outlier: 4.795A pdb=" N LYS A 531 " --> pdb=" O LEU A 554 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N LEU A 554 " --> pdb=" O LYS A 531 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 741 through 745 removed outlier: 6.681A pdb=" N ILE A 735 " --> pdb=" O GLN A 742 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N CYS A 744 " --> pdb=" O ILE A 733 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N ILE A 733 " --> pdb=" O CYS A 744 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ARG A 732 " --> pdb=" O ILE A 561 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N ILE A 716 " --> pdb=" O THR A 562 " (cutoff:3.500A) removed outlier: 7.769A pdb=" N LEU A 564 " --> pdb=" O ILE A 716 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N LEU A 718 " --> pdb=" O LEU A 564 " (cutoff:3.500A) removed outlier: 8.332A pdb=" N GLY A 566 " --> pdb=" O LEU A 718 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 826 through 828 removed outlier: 3.659A pdb=" N LEU A 798 " --> pdb=" O TYR A 758 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N MET A 760 " --> pdb=" O PHE A 796 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N THR A 785 " --> pdb=" O ILE A 797 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 967 through 970 removed outlier: 6.751A pdb=" N GLU A 996 " --> pdb=" O VAL A 968 " (cutoff:3.500A) removed outlier: 7.760A pdb=" N PHE A 970 " --> pdb=" O GLU A 996 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N ARG A 998 " --> pdb=" O PHE A 970 " (cutoff:3.500A) No H-bonds generated for sheet with id= F Processing sheet with id= G, first strand: chain 'A' and resid 1404 through 1406 removed outlier: 3.743A pdb=" N LEU A1381 " --> pdb=" O VAL A1406 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'A' and resid 1458 through 1461 removed outlier: 6.940A pdb=" N VAL A1535 " --> pdb=" O GLY A1459 " (cutoff:3.500A) removed outlier: 8.583A pdb=" N CYS A1461 " --> pdb=" O VAL A1535 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N PHE A1537 " --> pdb=" O CYS A1461 " (cutoff:3.500A) No H-bonds generated for sheet with id= H Processing sheet with id= I, first strand: chain 'A' and resid 1610 through 1614 removed outlier: 3.543A pdb=" N SER A1681 " --> pdb=" O SER A1610 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N ASP A1677 " --> pdb=" O LYS A1614 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'A' and resid 535 through 537 removed outlier: 7.326A pdb=" N LYS A 537 " --> pdb=" O ARG A 550 " (cutoff:3.500A) removed outlier: 5.265A pdb=" N ARG A 550 " --> pdb=" O LYS A 537 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'A' and resid 1386 through 1390 removed outlier: 3.516A pdb=" N LYS A1388 " --> pdb=" O VAL A1399 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N TYR A1390 " --> pdb=" O LEU A1397 " (cutoff:3.500A) removed outlier: 5.825A pdb=" N LEU A1397 " --> pdb=" O TYR A1390 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'A' and resid 1586 through 1588 removed outlier: 3.558A pdb=" N CYS A1594 " --> pdb=" O ILE A1586 " (cutoff:3.500A) removed outlier: 5.823A pdb=" N VAL A1588 " --> pdb=" O PHE A1592 " (cutoff:3.500A) removed outlier: 5.293A pdb=" N PHE A1592 " --> pdb=" O VAL A1588 " (cutoff:3.500A) 402 hydrogen bonds defined for protein. 1161 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: 4.34 Time building geometry restraints manager: 4.97 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3886 1.34 - 1.46: 2654 1.46 - 1.58: 5957 1.58 - 1.69: 10 1.69 - 1.81: 112 Bond restraints: 12619 Sorted by residual: bond pdb=" C4 ATP A1802 " pdb=" C5 ATP A1802 " ideal model delta sigma weight residual 1.388 1.466 -0.078 1.00e-02 1.00e+04 6.01e+01 bond pdb=" C4 ATP A1801 " pdb=" C5 ATP A1801 " ideal model delta sigma weight residual 1.388 1.464 -0.076 1.00e-02 1.00e+04 5.79e+01 bond pdb=" C5 ATP A1801 " pdb=" C6 ATP A1801 " ideal model delta sigma weight residual 1.409 1.477 -0.068 1.00e-02 1.00e+04 4.56e+01 bond pdb=" C5 ATP A1802 " pdb=" C6 ATP A1802 " ideal model delta sigma weight residual 1.409 1.475 -0.066 1.00e-02 1.00e+04 4.38e+01 bond pdb=" C4 ATP A1801 " pdb=" N9 ATP A1801 " ideal model delta sigma weight residual 1.374 1.327 0.047 1.00e-02 1.00e+04 2.18e+01 ... (remaining 12614 not shown) Histogram of bond angle deviations from ideal: 98.46 - 106.01: 282 106.01 - 113.55: 7010 113.55 - 121.10: 6522 121.10 - 128.64: 3217 128.64 - 136.19: 102 Bond angle restraints: 17133 Sorted by residual: angle pdb=" PB ATP A1801 " pdb=" O3B ATP A1801 " pdb=" PG ATP A1801 " ideal model delta sigma weight residual 139.87 119.58 20.29 1.00e+00 1.00e+00 4.12e+02 angle pdb=" PB ATP A1802 " pdb=" O3B ATP A1802 " pdb=" PG ATP A1802 " ideal model delta sigma weight residual 139.87 120.09 19.78 1.00e+00 1.00e+00 3.91e+02 angle pdb=" PA ATP A1802 " pdb=" O3A ATP A1802 " pdb=" PB ATP A1802 " ideal model delta sigma weight residual 136.83 121.88 14.95 1.00e+00 1.00e+00 2.23e+02 angle pdb=" PA ATP A1801 " pdb=" O3A ATP A1801 " pdb=" PB ATP A1801 " ideal model delta sigma weight residual 136.83 122.86 13.97 1.00e+00 1.00e+00 1.95e+02 angle pdb=" C5 ATP A1801 " pdb=" C4 ATP A1801 " pdb=" N3 ATP A1801 " ideal model delta sigma weight residual 126.80 118.97 7.83 1.00e+00 1.00e+00 6.13e+01 ... (remaining 17128 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 6682 17.97 - 35.94: 665 35.94 - 53.91: 135 53.91 - 71.88: 23 71.88 - 89.85: 12 Dihedral angle restraints: 7517 sinusoidal: 2976 harmonic: 4541 Sorted by residual: dihedral pdb=" CA ARG A1174 " pdb=" C ARG A1174 " pdb=" N ASP A1175 " pdb=" CA ASP A1175 " ideal model delta harmonic sigma weight residual -180.00 -142.34 -37.66 0 5.00e+00 4.00e-02 5.67e+01 dihedral pdb=" CA ARG A1401 " pdb=" C ARG A1401 " pdb=" N LEU A1402 " pdb=" CA LEU A1402 " ideal model delta harmonic sigma weight residual 180.00 154.95 25.05 0 5.00e+00 4.00e-02 2.51e+01 dihedral pdb=" CA LEU A1001 " pdb=" C LEU A1001 " pdb=" N GLY A1002 " pdb=" CA GLY A1002 " ideal model delta harmonic sigma weight residual -180.00 -156.03 -23.97 0 5.00e+00 4.00e-02 2.30e+01 ... (remaining 7514 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.067: 1673 0.067 - 0.134: 265 0.134 - 0.201: 9 0.201 - 0.268: 2 0.268 - 0.334: 2 Chirality restraints: 1951 Sorted by residual: chirality pdb=" C1 NAG A1805 " pdb=" ND2 ASN A 124 " pdb=" C2 NAG A1805 " pdb=" O5 NAG A1805 " both_signs ideal model delta sigma weight residual False -2.40 -2.07 -0.33 2.00e-01 2.50e+01 2.80e+00 chirality pdb=" C1 NAG A1806 " pdb=" ND2 ASN A 140 " pdb=" C2 NAG A1806 " pdb=" O5 NAG A1806 " both_signs ideal model delta sigma weight residual False -2.40 -2.10 -0.30 2.00e-01 2.50e+01 2.22e+00 chirality pdb=" CB ILE A 829 " pdb=" CA ILE A 829 " pdb=" CG1 ILE A 829 " pdb=" CG2 ILE A 829 " both_signs ideal model delta sigma weight residual False 2.64 2.41 0.24 2.00e-01 2.50e+01 1.38e+00 ... (remaining 1948 not shown) Planarity restraints: 2150 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE A 110 " -0.033 5.00e-02 4.00e+02 4.96e-02 3.94e+00 pdb=" N PRO A 111 " 0.086 5.00e-02 4.00e+02 pdb=" CA PRO A 111 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 111 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP A1546 " 0.030 5.00e-02 4.00e+02 4.62e-02 3.41e+00 pdb=" N PRO A1547 " -0.080 5.00e-02 4.00e+02 pdb=" CA PRO A1547 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO A1547 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 31 " 0.030 5.00e-02 4.00e+02 4.47e-02 3.20e+00 pdb=" N PRO A 32 " -0.077 5.00e-02 4.00e+02 pdb=" CA PRO A 32 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 32 " 0.025 5.00e-02 4.00e+02 ... (remaining 2147 not shown) Histogram of nonbonded interaction distances: 1.89 - 2.49: 54 2.49 - 3.10: 8609 3.10 - 3.70: 17271 3.70 - 4.30: 25301 4.30 - 4.90: 43406 Nonbonded interactions: 94641 Sorted by model distance: nonbonded pdb=" OE1 GLN A 613 " pdb="MG MG A1803 " model vdw 1.892 2.170 nonbonded pdb=" O2B ATP A1801 " pdb="MG MG A1803 " model vdw 2.000 2.170 nonbonded pdb=" OG1 THR A1423 " pdb="MG MG A1804 " model vdw 2.052 2.170 nonbonded pdb=" OD2 ASP A1149 " pdb=" OH TYR A1197 " model vdw 2.054 2.440 nonbonded pdb=" O2B ATP A1802 " pdb="MG MG A1804 " model vdw 2.061 2.170 ... (remaining 94636 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=1.00 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: 3.720 Check model and map are aligned: 0.170 Set scattering table: 0.120 Process input model: 34.320 Find NCS groups from input model: 0.460 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8515 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 : 0.007 0.078 12619 Z= 0.447 Angle : 0.888 20.293 17133 Z= 0.554 Chirality : 0.049 0.334 1951 Planarity : 0.004 0.050 2148 Dihedral : 15.175 89.849 4582 Min Nonbonded Distance : 1.892 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.06 % Allowed : 10.85 % Favored : 89.08 % Rotamer: Outliers : 0.23 % Allowed : 0.70 % Favored : 99.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -3.18 (0.20), residues: 1548 helix: -1.38 (0.18), residues: 776 sheet: -2.40 (0.45), residues: 123 loop : -2.93 (0.21), residues: 649 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 658 HIS 0.006 0.001 HIS A 304 PHE 0.024 0.002 PHE A 156 TYR 0.012 0.002 TYR A 386 ARG 0.008 0.001 ARG A1305 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1334 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 136 time to evaluate : 1.301 Fit side-chains REVERT: A 417 MET cc_start: 0.9019 (mtm) cc_final: 0.8751 (mtm) REVERT: A 1231 MET cc_start: 0.9122 (ttp) cc_final: 0.8794 (ttp) outliers start: 3 outliers final: 0 residues processed: 138 average time/residue: 0.2530 time to fit residues: 51.2315 Evaluate side-chains 110 residues out of total 1334 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 110 time to evaluate : 1.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 132 optimal weight: 10.0000 chunk 118 optimal weight: 0.6980 chunk 66 optimal weight: 5.9990 chunk 40 optimal weight: 0.6980 chunk 80 optimal weight: 6.9990 chunk 63 optimal weight: 0.7980 chunk 123 optimal weight: 1.9990 chunk 47 optimal weight: 4.9990 chunk 74 optimal weight: 0.9980 chunk 91 optimal weight: 4.9990 chunk 142 optimal weight: 0.0570 overall best weight: 0.6498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 553 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8441 moved from start: 0.0920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 12619 Z= 0.154 Angle : 0.616 12.883 17133 Z= 0.311 Chirality : 0.044 0.523 1951 Planarity : 0.004 0.053 2148 Dihedral : 7.951 89.458 1797 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.04 % Favored : 90.96 % Rotamer: Outliers : 0.85 % Allowed : 7.30 % Favored : 91.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -2.58 (0.20), residues: 1548 helix: -0.77 (0.19), residues: 765 sheet: -1.92 (0.45), residues: 141 loop : -2.81 (0.21), residues: 642 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 658 HIS 0.009 0.001 HIS A 141 PHE 0.009 0.001 PHE A 583 TYR 0.015 0.001 TYR A1283 ARG 0.008 0.000 ARG A 670 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1334 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 128 time to evaluate : 1.442 Fit side-chains REVERT: A 455 MET cc_start: 0.8738 (mmm) cc_final: 0.8478 (mmm) outliers start: 11 outliers final: 5 residues processed: 132 average time/residue: 0.2407 time to fit residues: 47.3014 Evaluate side-chains 114 residues out of total 1334 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 109 time to evaluate : 1.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 950 LEU Chi-restraints excluded: chain A residue 1219 LEU Chi-restraints excluded: chain A residue 1512 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/iotbx/cli_parser.py", line 944, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/programs/real_space_refine.py", line 189, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 700, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 764, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 50.486 > 50: distance: 90 - 96: 10.746 distance: 96 - 97: 7.597 distance: 97 - 98: 7.100 distance: 97 - 100: 15.418 distance: 98 - 99: 18.221 distance: 98 - 104: 24.404 distance: 100 - 101: 17.894 distance: 101 - 102: 23.682 distance: 101 - 103: 11.819 distance: 104 - 105: 31.830 distance: 105 - 106: 15.585 distance: 105 - 108: 19.366 distance: 106 - 107: 27.529 distance: 106 - 113: 6.015 distance: 108 - 109: 15.581 distance: 109 - 110: 11.015 distance: 110 - 111: 5.370 distance: 110 - 112: 6.186 distance: 113 - 114: 14.844 distance: 113 - 119: 28.990 distance: 114 - 115: 11.130 distance: 114 - 117: 23.560 distance: 115 - 116: 9.613 distance: 115 - 120: 5.366 distance: 117 - 118: 12.215 distance: 118 - 119: 11.926 distance: 120 - 121: 19.805 distance: 121 - 122: 16.146 distance: 121 - 124: 16.762 distance: 122 - 123: 4.316 distance: 122 - 126: 15.626 distance: 124 - 125: 32.170 distance: 126 - 127: 17.651 distance: 127 - 128: 14.035 distance: 127 - 130: 19.860 distance: 128 - 129: 21.918 distance: 128 - 133: 16.282 distance: 130 - 131: 24.714 distance: 130 - 132: 17.706 distance: 133 - 134: 9.196 distance: 134 - 135: 14.952 distance: 135 - 136: 25.047 distance: 135 - 137: 20.768 distance: 137 - 138: 15.628 distance: 138 - 139: 13.659 distance: 138 - 141: 18.218 distance: 139 - 140: 13.089 distance: 139 - 145: 8.618 distance: 141 - 142: 16.461 distance: 142 - 143: 4.587 distance: 143 - 144: 12.147 distance: 145 - 146: 13.905 distance: 146 - 147: 9.058 distance: 146 - 149: 5.664 distance: 147 - 148: 22.045 distance: 147 - 153: 9.948 distance: 149 - 150: 7.127 distance: 150 - 151: 17.816 distance: 150 - 152: 16.947 distance: 153 - 154: 18.851 distance: 153 - 159: 15.642 distance: 154 - 155: 11.355 distance: 154 - 157: 33.320 distance: 155 - 156: 18.551 distance: 155 - 160: 17.747 distance: 156 - 182: 20.997 distance: 157 - 158: 13.819 distance: 158 - 159: 37.957 distance: 160 - 161: 14.013 distance: 161 - 162: 9.196 distance: 161 - 164: 10.154 distance: 162 - 163: 7.303 distance: 162 - 167: 15.085 distance: 163 - 190: 14.663 distance: 164 - 165: 18.224 distance: 164 - 166: 7.896