Starting phenix.real_space_refine on Sat Aug 3 18:44:11 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wiw_32538/08_2024/7wiw_32538.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wiw_32538/08_2024/7wiw_32538.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.12 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wiw_32538/08_2024/7wiw_32538.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wiw_32538/08_2024/7wiw_32538.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wiw_32538/08_2024/7wiw_32538.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wiw_32538/08_2024/7wiw_32538.cif" } resolution = 3.12 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= 0.057 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 3 5.21 5 S 15 5.16 5 C 5473 2.51 5 N 1547 2.21 5 O 1559 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B ASP 12": "OD1" <-> "OD2" Residue "B PHE 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 80": "OE1" <-> "OE2" Residue "B ASP 95": "OD1" <-> "OD2" Residue "B ASP 103": "OD1" <-> "OD2" Residue "B PHE 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 179": "NH1" <-> "NH2" Residue "B ARG 180": "NH1" <-> "NH2" Residue "B ASP 182": "OD1" <-> "OD2" Residue "B ARG 195": "NH1" <-> "NH2" Residue "B GLU 198": "OE1" <-> "OE2" Residue "B PHE 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 207": "NH1" <-> "NH2" Residue "B GLU 213": "OE1" <-> "OE2" Residue "B ARG 232": "NH1" <-> "NH2" Residue "B TYR 283": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 298": "OE1" <-> "OE2" Residue "B ARG 324": "NH1" <-> "NH2" Residue "B ASP 336": "OD1" <-> "OD2" Residue "B TYR 341": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 350": "OD1" <-> "OD2" Residue "B ARG 424": "NH1" <-> "NH2" Residue "B PHE 439": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 447": "NH1" <-> "NH2" Residue "B ARG 454": "NH1" <-> "NH2" Residue "B ARG 482": "NH1" <-> "NH2" Residue "B ASP 501": "OD1" <-> "OD2" Residue "B GLU 503": "OE1" <-> "OE2" Residue "B ARG 527": "NH1" <-> "NH2" Residue "B ARG 532": "NH1" <-> "NH2" Residue "B ASP 535": "OD1" <-> "OD2" Residue "B PHE 539": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 542": "OD1" <-> "OD2" Residue "B ARG 544": "NH1" <-> "NH2" Residue "B PHE 561": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 566": "NH1" <-> "NH2" Residue "A ARG 284": "NH1" <-> "NH2" Residue "A ARG 329": "NH1" <-> "NH2" Residue "A PHE 331": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 382": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 385": "NH1" <-> "NH2" Residue "A ASP 397": "OD1" <-> "OD2" Residue "A ASP 430": "OD1" <-> "OD2" Residue "A PHE 438": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 464": "NH1" <-> "NH2" Residue "A TYR 476": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 478": "OE1" <-> "OE2" Residue "A ARG 496": "NH1" <-> "NH2" Residue "A GLU 499": "OE1" <-> "OE2" Residue "A ARG 509": "NH1" <-> "NH2" Residue "A ARG 523": "NH1" <-> "NH2" Residue "A ARG 543": "NH1" <-> "NH2" Residue "A PHE 552": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 554": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 595": "NH1" <-> "NH2" Residue "A ARG 599": "NH1" <-> "NH2" Residue "A GLU 600": "OE1" <-> "OE2" Residue "A ASP 603": "OD1" <-> "OD2" Residue "A PHE 612": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 619": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 628": "OD1" <-> "OD2" Residue "A ARG 658": "NH1" <-> "NH2" Residue "A ASP 673": "OD1" <-> "OD2" Residue "A ARG 685": "NH1" <-> "NH2" Residue "A PHE 688": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 702": "OE1" <-> "OE2" Residue "A GLU 714": "OE1" <-> "OE2" Residue "A ARG 721": "NH1" <-> "NH2" Residue "A GLU 722": "OE1" <-> "OE2" Residue "A ARG 728": "NH1" <-> "NH2" Residue "A ARG 753": "NH1" <-> "NH2" Residue "A ARG 758": "NH1" <-> "NH2" Residue "A ASP 770": "OD1" <-> "OD2" Residue "A PHE 775": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 777": "OD1" <-> "OD2" Residue "A ARG 793": "NH1" <-> "NH2" Residue "A ARG 809": "NH1" <-> "NH2" Residue "A ASP 811": "OD1" <-> "OD2" Residue "A ARG 836": "NH1" <-> "NH2" Residue "A TYR 837": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 839": "NH1" <-> "NH2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 8603 Number of models: 1 Model: "" Number of chains: 4 Chain: "B" Number of atoms: 4198 Number of conformers: 1 Conformer: "" Number of residues, atoms: 567, 4198 Classifications: {'peptide': 567} Link IDs: {'PTRANS': 25, 'TRANS': 541} Chain: "A" Number of atoms: 4340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 570, 4340 Classifications: {'peptide': 570} Link IDs: {'PTRANS': 25, 'TRANS': 544} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 2, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 6.01, per 1000 atoms: 0.70 Number of scatterers: 8603 At special positions: 0 Unit cell: (66.42, 91.02, 137.76, 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 15 16.00 P 6 15.00 Mg 3 11.99 O 1559 8.00 N 1547 7.00 C 5473 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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 Time building additional restraints: 3.90 Conformation dependent library (CDL) restraints added in 1.5 seconds 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2084 Finding SS restraints... Secondary structure from input PDB file: 50 helices and 6 sheets defined 54.9% alpha, 7.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.97 Creating SS restraints... Processing helix chain 'B' and resid 19 through 37 removed outlier: 3.922A pdb=" N LEU B 23 " --> pdb=" O GLY B 19 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N PHE B 25 " --> pdb=" O ALA B 21 " (cutoff:3.500A) Processing helix chain 'B' and resid 37 through 45 removed outlier: 3.696A pdb=" N LEU B 41 " --> pdb=" O LEU B 37 " (cutoff:3.500A) Processing helix chain 'B' and resid 49 through 54 removed outlier: 3.764A pdb=" N ARG B 52 " --> pdb=" O ALA B 49 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N TRP B 54 " --> pdb=" O GLN B 51 " (cutoff:3.500A) Processing helix chain 'B' and resid 56 through 83 removed outlier: 3.666A pdb=" N LEU B 60 " --> pdb=" O TRP B 56 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N ILE B 79 " --> pdb=" O ALA B 75 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N GLU B 80 " --> pdb=" O ARG B 76 " (cutoff:3.500A) Processing helix chain 'B' and resid 85 through 97 Processing helix chain 'B' and resid 98 through 100 No H-bonds generated for 'chain 'B' and resid 98 through 100' Processing helix chain 'B' and resid 107 through 119 removed outlier: 4.056A pdb=" N ALA B 111 " --> pdb=" O ALA B 107 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N THR B 112 " --> pdb=" O GLU B 108 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ALA B 113 " --> pdb=" O ASN B 109 " (cutoff:3.500A) Processing helix chain 'B' and resid 131 through 150 Proline residue: B 142 - end of helix Processing helix chain 'B' and resid 153 through 162 removed outlier: 3.743A pdb=" N ALA B 162 " --> pdb=" O VAL B 158 " (cutoff:3.500A) Processing helix chain 'B' and resid 162 through 202 removed outlier: 4.261A pdb=" N LEU B 166 " --> pdb=" O ALA B 162 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ALA B 178 " --> pdb=" O SER B 174 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ARG B 179 " --> pdb=" O ALA B 175 " (cutoff:3.500A) removed outlier: 5.368A pdb=" N ARG B 180 " --> pdb=" O ALA B 176 " (cutoff:3.500A) removed outlier: 5.446A pdb=" N ALA B 181 " --> pdb=" O PHE B 177 " (cutoff:3.500A) Processing helix chain 'B' and resid 202 through 209 removed outlier: 3.780A pdb=" N LEU B 206 " --> pdb=" O THR B 202 " (cutoff:3.500A) Processing helix chain 'B' and resid 217 through 265 removed outlier: 3.834A pdb=" N ASN B 221 " --> pdb=" O SER B 217 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ALA B 222 " --> pdb=" O LEU B 218 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N ILE B 238 " --> pdb=" O LEU B 234 " (cutoff:3.500A) Proline residue: B 239 - end of helix Processing helix chain 'B' and resid 269 through 312 removed outlier: 3.748A pdb=" N ALA B 275 " --> pdb=" O PRO B 271 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N VAL B 278 " --> pdb=" O ILE B 274 " (cutoff:3.500A) Proline residue: B 286 - end of helix removed outlier: 3.849A pdb=" N SER B 291 " --> pdb=" O PHE B 287 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N GLU B 292 " --> pdb=" O THR B 288 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N LEU B 293 " --> pdb=" O ALA B 289 " (cutoff:3.500A) Proline residue: B 295 - end of helix Processing helix chain 'B' and resid 374 through 381 Processing helix chain 'B' and resid 398 through 400 No H-bonds generated for 'chain 'B' and resid 398 through 400' Processing helix chain 'B' and resid 422 through 429 Processing helix chain 'B' and resid 435 through 446 removed outlier: 3.701A pdb=" N PHE B 439 " --> pdb=" O SER B 435 " (cutoff:3.500A) Processing helix chain 'B' and resid 448 through 453 Processing helix chain 'B' and resid 471 through 485 removed outlier: 3.631A pdb=" N GLN B 476 " --> pdb=" O GLY B 472 " (cutoff:3.500A) Processing helix chain 'B' and resid 501 through 514 removed outlier: 3.520A pdb=" N ALA B 506 " --> pdb=" O ALA B 502 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ALA B 507 " --> pdb=" O GLU B 503 " (cutoff:3.500A) Processing helix chain 'B' and resid 550 through 555 removed outlier: 3.942A pdb=" N LEU B 555 " --> pdb=" O ILE B 551 " (cutoff:3.500A) Processing helix chain 'B' and resid 559 through 564 removed outlier: 3.667A pdb=" N GLN B 563 " --> pdb=" O GLY B 559 " (cutoff:3.500A) Processing helix chain 'A' and resid 309 through 322 removed outlier: 3.631A pdb=" N GLU A 316 " --> pdb=" O VAL A 312 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N VAL A 322 " --> pdb=" O SER A 318 " (cutoff:3.500A) Processing helix chain 'A' and resid 327 through 347 removed outlier: 4.261A pdb=" N THR A 332 " --> pdb=" O HIS A 328 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N VAL A 333 " --> pdb=" O ARG A 329 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N ALA A 336 " --> pdb=" O THR A 332 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ALA A 337 " --> pdb=" O VAL A 333 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLY A 339 " --> pdb=" O PHE A 335 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N LEU A 340 " --> pdb=" O ALA A 336 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N LEU A 341 " --> pdb=" O ALA A 337 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N GLY A 342 " --> pdb=" O VAL A 338 " (cutoff:3.500A) Processing helix chain 'A' and resid 350 through 371 removed outlier: 3.508A pdb=" N TRP A 354 " --> pdb=" O ALA A 350 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N HIS A 356 " --> pdb=" O THR A 352 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N PHE A 362 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ARG A 364 " --> pdb=" O ALA A 360 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ARG A 369 " --> pdb=" O ALA A 365 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N LEU A 371 " --> pdb=" O ARG A 367 " (cutoff:3.500A) Processing helix chain 'A' and resid 378 through 380 No H-bonds generated for 'chain 'A' and resid 378 through 380' Processing helix chain 'A' and resid 381 through 386 removed outlier: 3.840A pdb=" N ARG A 385 " --> pdb=" O TRP A 381 " (cutoff:3.500A) Processing helix chain 'A' and resid 387 through 396 removed outlier: 3.593A pdb=" N LEU A 393 " --> pdb=" O SER A 389 " (cutoff:3.500A) Processing helix chain 'A' and resid 401 through 406 Processing helix chain 'A' and resid 408 through 418 removed outlier: 4.121A pdb=" N VAL A 416 " --> pdb=" O ALA A 412 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N VAL A 417 " --> pdb=" O VAL A 413 " (cutoff:3.500A) Processing helix chain 'A' and resid 418 through 423 Processing helix chain 'A' and resid 424 through 430 removed outlier: 3.671A pdb=" N VAL A 428 " --> pdb=" O VAL A 424 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N VAL A 429 " --> pdb=" O TYR A 425 " (cutoff:3.500A) Processing helix chain 'A' and resid 430 through 435 Processing helix chain 'A' and resid 437 through 453 removed outlier: 3.825A pdb=" N VAL A 441 " --> pdb=" O LEU A 437 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N THR A 446 " --> pdb=" O LEU A 442 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N LEU A 451 " --> pdb=" O ILE A 447 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N THR A 452 " --> pdb=" O THR A 448 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ILE A 453 " --> pdb=" O SER A 449 " (cutoff:3.500A) Processing helix chain 'A' and resid 462 through 479 removed outlier: 3.561A pdb=" N GLU A 467 " --> pdb=" O GLN A 463 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LYS A 468 " --> pdb=" O ARG A 464 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N GLY A 471 " --> pdb=" O GLU A 467 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLU A 472 " --> pdb=" O LYS A 468 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N GLY A 479 " --> pdb=" O SER A 475 " (cutoff:3.500A) Processing helix chain 'A' and resid 479 through 484 Processing helix chain 'A' and resid 487 through 489 No H-bonds generated for 'chain 'A' and resid 487 through 489' Processing helix chain 'A' and resid 490 through 495 Processing helix chain 'A' and resid 497 through 515 removed outlier: 3.606A pdb=" N ALA A 506 " --> pdb=" O GLY A 502 " (cutoff:3.500A) Proline residue: A 510 - end of helix removed outlier: 3.846A pdb=" N GLY A 513 " --> pdb=" O ARG A 509 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N LYS A 514 " --> pdb=" O PRO A 510 " (cutoff:3.500A) Processing helix chain 'A' and resid 516 through 521 removed outlier: 3.642A pdb=" N ALA A 521 " --> pdb=" O LEU A 517 " (cutoff:3.500A) Processing helix chain 'A' and resid 523 through 539 removed outlier: 3.569A pdb=" N PHE A 527 " --> pdb=" O ARG A 523 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N TRP A 529 " --> pdb=" O ALA A 525 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ALA A 532 " --> pdb=" O LEU A 528 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N THR A 536 " --> pdb=" O ALA A 532 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N LEU A 537 " --> pdb=" O ALA A 533 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N LEU A 538 " --> pdb=" O THR A 534 " (cutoff:3.500A) Processing helix chain 'A' and resid 545 through 548 Processing helix chain 'A' and resid 549 through 554 removed outlier: 3.725A pdb=" N PHE A 554 " --> pdb=" O LEU A 550 " (cutoff:3.500A) Processing helix chain 'A' and resid 558 through 568 removed outlier: 4.337A pdb=" N ARG A 562 " --> pdb=" O THR A 558 " (cutoff:3.500A) Processing helix chain 'A' and resid 569 through 587 removed outlier: 3.628A pdb=" N LEU A 573 " --> pdb=" O GLY A 569 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N LEU A 577 " --> pdb=" O LEU A 573 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLN A 584 " --> pdb=" O ALA A 580 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N THR A 586 " --> pdb=" O HIS A 582 " (cutoff:3.500A) Processing helix chain 'A' and resid 649 through 657 Processing helix chain 'A' and resid 715 through 723 Processing helix chain 'A' and resid 725 through 730 Processing helix chain 'A' and resid 734 through 738 Processing helix chain 'A' and resid 752 through 761 removed outlier: 3.516A pdb=" N ALA A 757 " --> pdb=" O ARG A 753 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ALA A 759 " --> pdb=" O THR A 755 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 349 through 355 removed outlier: 6.404A pdb=" N ASP B 350 " --> pdb=" O ALA B 338 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N ALA B 338 " --> pdb=" O ASP B 350 " (cutoff:3.500A) removed outlier: 5.148A pdb=" N VAL B 352 " --> pdb=" O ASP B 336 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ASP B 336 " --> pdb=" O VAL B 352 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N VAL B 337 " --> pdb=" O ARG B 387 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N ARG B 387 " --> pdb=" O VAL B 337 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 410 through 412 removed outlier: 6.247A pdb=" N THR B 362 " --> pdb=" O ILE B 523 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N ALA B 363 " --> pdb=" O LEU B 538 " (cutoff:3.500A) removed outlier: 7.109A pdb=" N VAL B 540 " --> pdb=" O ALA B 363 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N VAL B 365 " --> pdb=" O VAL B 540 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N GLU B 547 " --> pdb=" O PHE B 539 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N ASP B 541 " --> pdb=" O VAL B 545 " (cutoff:3.500A) removed outlier: 5.343A pdb=" N VAL B 545 " --> pdb=" O ASP B 541 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 626 through 629 removed outlier: 5.522A pdb=" N VAL A 615 " --> pdb=" O ASP A 628 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 626 through 629 removed outlier: 5.522A pdb=" N VAL A 615 " --> pdb=" O ASP A 628 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N VAL A 615 " --> pdb=" O ARG A 664 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N ARG A 664 " --> pdb=" O VAL A 615 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N GLN A 672 " --> pdb=" O VAL A 669 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 638 through 639 removed outlier: 6.799A pdb=" N THR A 639 " --> pdb=" O VAL A 799 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N GLY A 687 " --> pdb=" O ILE A 768 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 813 through 817 removed outlier: 4.160A pdb=" N GLU A 823 " --> pdb=" O VAL A 815 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N ASP A 817 " --> pdb=" O ILE A 821 " (cutoff:3.500A) removed outlier: 5.466A pdb=" N ILE A 821 " --> pdb=" O ASP A 817 " (cutoff:3.500A) 371 hydrogen bonds defined for protein. 1080 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: 2.66 Time building geometry restraints manager: 4.25 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.15 - 1.28: 1385 1.28 - 1.41: 2087 1.41 - 1.54: 5245 1.54 - 1.67: 22 1.67 - 1.81: 25 Bond restraints: 8764 Sorted by residual: bond pdb=" C4 ATP B 601 " pdb=" C5 ATP B 601 " ideal model delta sigma weight residual 1.388 1.466 -0.078 1.00e-02 1.00e+04 6.06e+01 bond pdb=" C4 ATP A 901 " pdb=" C5 ATP A 901 " ideal model delta sigma weight residual 1.388 1.465 -0.077 1.00e-02 1.00e+04 5.95e+01 bond pdb=" C VAL B 493 " pdb=" O VAL B 493 " ideal model delta sigma weight residual 1.238 1.152 0.085 1.17e-02 7.31e+03 5.31e+01 bond pdb=" C5 ATP A 901 " pdb=" C6 ATP A 901 " ideal model delta sigma weight residual 1.409 1.478 -0.069 1.00e-02 1.00e+04 4.76e+01 bond pdb=" C5 ATP B 601 " pdb=" C6 ATP B 601 " ideal model delta sigma weight residual 1.409 1.475 -0.066 1.00e-02 1.00e+04 4.38e+01 ... (remaining 8759 not shown) Histogram of bond angle deviations from ideal: 99.92 - 107.18: 307 107.18 - 114.43: 5284 114.43 - 121.69: 4345 121.69 - 128.94: 1966 128.94 - 136.20: 82 Bond angle restraints: 11984 Sorted by residual: angle pdb=" PB ATP B 601 " pdb=" O3B ATP B 601 " pdb=" PG ATP B 601 " ideal model delta sigma weight residual 139.87 119.13 20.74 1.00e+00 1.00e+00 4.30e+02 angle pdb=" PA ATP B 601 " pdb=" O3A ATP B 601 " pdb=" PB ATP B 601 " ideal model delta sigma weight residual 136.83 122.08 14.75 1.00e+00 1.00e+00 2.18e+02 angle pdb=" C5 ATP B 601 " pdb=" C4 ATP B 601 " pdb=" N3 ATP B 601 " ideal model delta sigma weight residual 126.80 118.68 8.12 1.00e+00 1.00e+00 6.60e+01 angle pdb=" C5 ATP A 901 " pdb=" C4 ATP A 901 " pdb=" N3 ATP A 901 " ideal model delta sigma weight residual 126.80 118.76 8.04 1.00e+00 1.00e+00 6.46e+01 angle pdb=" PB ATP A 901 " pdb=" O3B ATP A 901 " pdb=" PG ATP A 901 " ideal model delta sigma weight residual 139.87 132.41 7.46 1.00e+00 1.00e+00 5.56e+01 ... (remaining 11979 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.73: 4719 17.73 - 35.46: 390 35.46 - 53.19: 92 53.19 - 70.92: 17 70.92 - 88.65: 10 Dihedral angle restraints: 5228 sinusoidal: 1995 harmonic: 3233 Sorted by residual: dihedral pdb=" CA ALA A 711 " pdb=" C ALA A 711 " pdb=" N PRO A 712 " pdb=" CA PRO A 712 " ideal model delta harmonic sigma weight residual 180.00 -152.63 -27.37 0 5.00e+00 4.00e-02 3.00e+01 dihedral pdb=" CA PRO A 712 " pdb=" C PRO A 712 " pdb=" N ALA A 713 " pdb=" CA ALA A 713 " ideal model delta harmonic sigma weight residual 180.00 157.75 22.25 0 5.00e+00 4.00e-02 1.98e+01 dihedral pdb=" N VAL B 493 " pdb=" C VAL B 493 " pdb=" CA VAL B 493 " pdb=" CB VAL B 493 " ideal model delta harmonic sigma weight residual 123.40 113.54 9.86 0 2.50e+00 1.60e-01 1.55e+01 ... (remaining 5225 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.091: 1381 0.091 - 0.182: 71 0.182 - 0.272: 5 0.272 - 0.363: 1 0.363 - 0.454: 2 Chirality restraints: 1460 Sorted by residual: chirality pdb=" CB VAL B 328 " pdb=" CA VAL B 328 " pdb=" CG1 VAL B 328 " pdb=" CG2 VAL B 328 " both_signs ideal model delta sigma weight residual False -2.63 -2.18 -0.45 2.00e-01 2.50e+01 5.16e+00 chirality pdb=" CA VAL B 493 " pdb=" N VAL B 493 " pdb=" C VAL B 493 " pdb=" CB VAL B 493 " both_signs ideal model delta sigma weight residual False 2.44 2.86 -0.42 2.00e-01 2.50e+01 4.40e+00 chirality pdb=" CA ASP B 325 " pdb=" N ASP B 325 " pdb=" C ASP B 325 " pdb=" CB ASP B 325 " both_signs ideal model delta sigma weight residual False 2.51 2.82 -0.31 2.00e-01 2.50e+01 2.44e+00 ... (remaining 1457 not shown) Planarity restraints: 1522 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA HIS A 827 " 0.019 2.00e-02 2.50e+03 3.73e-02 1.39e+01 pdb=" C HIS A 827 " -0.065 2.00e-02 2.50e+03 pdb=" O HIS A 827 " 0.024 2.00e-02 2.50e+03 pdb=" N GLU A 828 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA HIS A 402 " 0.018 2.00e-02 2.50e+03 3.71e-02 1.37e+01 pdb=" C HIS A 402 " -0.064 2.00e-02 2.50e+03 pdb=" O HIS A 402 " 0.024 2.00e-02 2.50e+03 pdb=" N TYR A 403 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG B 324 " -0.017 2.00e-02 2.50e+03 3.36e-02 1.13e+01 pdb=" C ARG B 324 " 0.058 2.00e-02 2.50e+03 pdb=" O ARG B 324 " -0.022 2.00e-02 2.50e+03 pdb=" N ASP B 325 " -0.019 2.00e-02 2.50e+03 ... (remaining 1519 not shown) Histogram of nonbonded interaction distances: 1.89 - 2.49: 54 2.49 - 3.09: 6046 3.09 - 3.70: 12692 3.70 - 4.30: 18891 4.30 - 4.90: 32238 Nonbonded interactions: 69921 Sorted by model distance: nonbonded pdb=" OE1 GLN B 414 " pdb="MG MG B 602 " model vdw 1.891 2.170 nonbonded pdb=" OE1 GLN A 691 " pdb="MG MG A 902 " model vdw 1.895 2.170 nonbonded pdb=" OG SER A 650 " pdb="MG MG A 902 " model vdw 1.987 2.170 nonbonded pdb=" OG SER B 373 " pdb="MG MG B 602 " model vdw 2.110 2.170 nonbonded pdb=" O2B ATP B 601 " pdb="MG MG B 602 " model vdw 2.132 2.170 ... (remaining 69916 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== 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: 2.990 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: 0.330 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 28.020 Find NCS groups from input model: 0.150 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:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8630 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 : 0.006 0.085 8764 Z= 0.410 Angle : 0.987 20.743 11984 Z= 0.666 Chirality : 0.049 0.454 1460 Planarity : 0.006 0.075 1522 Dihedral : 14.745 88.649 3144 Min Nonbonded Distance : 1.891 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.62 % Allowed : 7.06 % Favored : 92.32 % Rotamer: Outliers : 1.03 % Allowed : 6.86 % Favored : 92.11 % Cbeta Deviations : 0.10 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.54 (0.21), residues: 1133 helix: -2.55 (0.17), residues: 701 sheet: -2.40 (0.84), residues: 33 loop : -3.70 (0.24), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 154 HIS 0.009 0.001 HIS A 407 PHE 0.011 0.001 PHE B 199 TYR 0.010 0.001 TYR B 283 ARG 0.002 0.000 ARG A 574 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 874 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 95 time to evaluate : 0.912 Fit side-chains REVERT: A 407 HIS cc_start: 0.8931 (OUTLIER) cc_final: 0.8412 (p90) REVERT: A 714 GLU cc_start: 0.7495 (tm-30) cc_final: 0.7028 (tm-30) outliers start: 9 outliers final: 3 residues processed: 101 average time/residue: 0.2900 time to fit residues: 38.0271 Evaluate side-chains 77 residues out of total 874 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 73 time to evaluate : 1.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 495 GLN Chi-restraints excluded: chain A residue 407 HIS Chi-restraints excluded: chain A residue 630 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 95 optimal weight: 0.1980 chunk 85 optimal weight: 2.9990 chunk 47 optimal weight: 0.9980 chunk 29 optimal weight: 1.9990 chunk 57 optimal weight: 1.9990 chunk 45 optimal weight: 0.6980 chunk 88 optimal weight: 0.0000 chunk 34 optimal weight: 0.7980 chunk 53 optimal weight: 3.9990 chunk 65 optimal weight: 0.7980 chunk 102 optimal weight: 0.9990 overall best weight: 0.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 109 ASN B 203 GLN B 438 GLN B 476 GLN B 526 HIS A 480 GLN A 582 HIS A 717 GLN A 752 GLN A 827 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8559 moved from start: 0.1443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8764 Z= 0.166 Angle : 0.619 8.119 11984 Z= 0.318 Chirality : 0.041 0.168 1460 Planarity : 0.005 0.078 1522 Dihedral : 9.369 88.606 1313 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.26 % Allowed : 7.06 % Favored : 92.67 % Rotamer: Outliers : 1.83 % Allowed : 10.64 % Favored : 87.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -3.10 (0.24), residues: 1133 helix: -1.44 (0.20), residues: 689 sheet: -2.22 (0.85), residues: 33 loop : -2.98 (0.26), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 154 HIS 0.003 0.001 HIS A 407 PHE 0.015 0.001 PHE A 612 TYR 0.009 0.001 TYR B 283 ARG 0.003 0.000 ARG B 301 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 874 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 87 time to evaluate : 0.908 Fit side-chains REVERT: B 372 LYS cc_start: 0.8664 (mtmt) cc_final: 0.8453 (mtmm) REVERT: A 286 LEU cc_start: 0.8705 (pp) cc_final: 0.8495 (pp) REVERT: A 714 GLU cc_start: 0.7372 (tm-30) cc_final: 0.6918 (tm-30) outliers start: 16 outliers final: 7 residues processed: 99 average time/residue: 0.2260 time to fit residues: 31.0048 Evaluate side-chains 81 residues out of total 874 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 74 time to evaluate : 1.003 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 397 VAL Chi-restraints excluded: chain B residue 542 ASP Chi-restraints excluded: chain A residue 407 HIS Chi-restraints excluded: chain A residue 662 VAL Chi-restraints excluded: chain A residue 766 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 57 optimal weight: 0.0870 chunk 31 optimal weight: 0.4980 chunk 85 optimal weight: 4.9990 chunk 69 optimal weight: 0.7980 chunk 28 optimal weight: 0.8980 chunk 102 optimal weight: 3.9990 chunk 111 optimal weight: 2.9990 chunk 91 optimal weight: 2.9990 chunk 101 optimal weight: 0.9980 chunk 35 optimal weight: 1.9990 chunk 82 optimal weight: 2.9990 overall best weight: 0.6558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8562 moved from start: 0.1701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8764 Z= 0.180 Angle : 0.587 7.828 11984 Z= 0.300 Chirality : 0.041 0.143 1460 Planarity : 0.005 0.073 1522 Dihedral : 8.771 89.258 1309 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.26 % Allowed : 6.27 % Favored : 93.47 % Rotamer: Outliers : 2.40 % Allowed : 13.16 % Favored : 84.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.47 (0.25), residues: 1133 helix: -0.96 (0.21), residues: 701 sheet: -2.19 (0.77), residues: 32 loop : -2.69 (0.27), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 154 HIS 0.003 0.001 HIS A 407 PHE 0.015 0.001 PHE A 612 TYR 0.010 0.001 TYR B 283 ARG 0.002 0.000 ARG B 301 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 874 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 79 time to evaluate : 1.002 Fit side-chains REVERT: B 372 LYS cc_start: 0.8730 (mtmt) cc_final: 0.8517 (mtmm) outliers start: 21 outliers final: 13 residues processed: 96 average time/residue: 0.2412 time to fit residues: 32.1786 Evaluate side-chains 85 residues out of total 874 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 72 time to evaluate : 0.889 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 174 SER Chi-restraints excluded: chain B residue 250 LEU Chi-restraints excluded: chain B residue 352 VAL Chi-restraints excluded: chain B residue 542 ASP Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 407 HIS Chi-restraints excluded: chain A residue 422 VAL Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 766 VAL Chi-restraints excluded: chain A residue 816 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 101 optimal weight: 0.0770 chunk 77 optimal weight: 3.9990 chunk 53 optimal weight: 4.9990 chunk 11 optimal weight: 1.9990 chunk 49 optimal weight: 4.9990 chunk 69 optimal weight: 2.9990 chunk 103 optimal weight: 0.6980 chunk 109 optimal weight: 0.0870 chunk 97 optimal weight: 0.7980 chunk 29 optimal weight: 6.9990 chunk 90 optimal weight: 4.9990 overall best weight: 0.7318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8564 moved from start: 0.1835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8764 Z= 0.187 Angle : 0.575 7.413 11984 Z= 0.292 Chirality : 0.041 0.138 1460 Planarity : 0.005 0.070 1522 Dihedral : 8.594 87.639 1309 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.26 % Allowed : 6.35 % Favored : 93.38 % Rotamer: Outliers : 2.86 % Allowed : 13.39 % Favored : 83.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.14 (0.25), residues: 1133 helix: -0.73 (0.21), residues: 704 sheet: -1.93 (0.79), residues: 32 loop : -2.50 (0.27), residues: 397 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 154 HIS 0.002 0.001 HIS A 407 PHE 0.014 0.001 PHE A 612 TYR 0.010 0.001 TYR B 283 ARG 0.002 0.000 ARG A 753 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 874 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 77 time to evaluate : 0.956 Fit side-chains REVERT: A 376 ARG cc_start: 0.8472 (ptp90) cc_final: 0.8254 (ptt90) outliers start: 25 outliers final: 15 residues processed: 97 average time/residue: 0.2250 time to fit residues: 30.0246 Evaluate side-chains 88 residues out of total 874 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 73 time to evaluate : 0.947 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 127 LEU Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 174 SER Chi-restraints excluded: chain B residue 250 LEU Chi-restraints excluded: chain B residue 352 VAL Chi-restraints excluded: chain B residue 397 VAL Chi-restraints excluded: chain B residue 542 ASP Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 379 LEU Chi-restraints excluded: chain A residue 407 HIS Chi-restraints excluded: chain A residue 522 THR Chi-restraints excluded: chain A residue 766 VAL Chi-restraints excluded: chain A residue 816 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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-5409/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 766, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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-5409/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-5409/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-5409/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-5409/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-5409/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-5409/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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-5409/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-5409/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-5409/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-5409/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: 68.8038 > 50: distance: 29 - 57: 28.965 distance: 34 - 40: 29.031 distance: 35 - 65: 26.645 distance: 40 - 41: 41.443 distance: 41 - 42: 63.343 distance: 41 - 44: 39.986 distance: 42 - 43: 51.892 distance: 42 - 49: 39.931 distance: 44 - 45: 39.744 distance: 45 - 46: 8.207 distance: 46 - 47: 34.017 distance: 46 - 48: 33.723 distance: 49 - 50: 22.133 distance: 50 - 51: 34.402 distance: 50 - 53: 23.996 distance: 51 - 52: 55.670 distance: 51 - 57: 23.976 distance: 53 - 54: 39.454 distance: 54 - 55: 41.529 distance: 54 - 56: 18.263 distance: 57 - 58: 43.024 distance: 58 - 59: 44.904 distance: 58 - 61: 14.928 distance: 59 - 60: 22.367 distance: 59 - 65: 34.426 distance: 61 - 62: 15.405 distance: 61 - 63: 59.057 distance: 62 - 64: 25.703 distance: 65 - 66: 8.593 distance: 66 - 67: 37.146 distance: 66 - 69: 23.429 distance: 67 - 68: 12.857 distance: 67 - 70: 26.154 distance: 70 - 71: 20.670 distance: 71 - 72: 29.324 distance: 71 - 74: 20.269 distance: 72 - 73: 20.384 distance: 72 - 81: 43.517 distance: 74 - 75: 24.664 distance: 75 - 76: 12.537 distance: 76 - 77: 25.305 distance: 77 - 78: 23.158 distance: 78 - 79: 29.538 distance: 78 - 80: 11.420 distance: 81 - 82: 11.335 distance: 82 - 83: 42.782 distance: 82 - 85: 16.124 distance: 83 - 84: 42.732 distance: 83 - 89: 29.571 distance: 85 - 86: 20.595 distance: 86 - 87: 51.453 distance: 86 - 88: 51.690 distance: 89 - 90: 29.401 distance: 89 - 95: 4.297 distance: 90 - 91: 11.437 distance: 90 - 93: 53.931 distance: 91 - 92: 18.242 distance: 91 - 96: 23.229 distance: 93 - 94: 57.603 distance: 94 - 95: 33.239 distance: 96 - 97: 7.073 distance: 97 - 98: 8.921 distance: 97 - 100: 33.289 distance: 98 - 104: 42.409 distance: 100 - 101: 29.878 distance: 101 - 102: 28.965 distance: 104 - 105: 25.744 distance: 105 - 106: 3.510 distance: 106 - 107: 40.660 distance: 106 - 108: 42.445 distance: 108 - 109: 29.161 distance: 109 - 110: 26.959 distance: 110 - 111: 31.969 distance: 110 - 113: 25.785