Starting phenix.real_space_refine on Tue Mar 19 01:48:31 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lqz_23492/03_2024/7lqz_23492_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lqz_23492/03_2024/7lqz_23492.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.41 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lqz_23492/03_2024/7lqz_23492.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lqz_23492/03_2024/7lqz_23492.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lqz_23492/03_2024/7lqz_23492_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lqz_23492/03_2024/7lqz_23492_trim_updated.pdb" } resolution = 3.41 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= 0.013 sd= 0.092 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 32 5.49 5 S 124 5.16 5 Na 1 4.78 5 C 15024 2.51 5 N 3476 2.21 5 O 4108 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 116": "NH1" <-> "NH2" Residue "A ARG 117": "NH1" <-> "NH2" Residue "A ARG 142": "NH1" <-> "NH2" Residue "A ARG 144": "NH1" <-> "NH2" Residue "A ARG 213": "NH1" <-> "NH2" Residue "A PHE 249": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 365": "NH1" <-> "NH2" Residue "A ARG 411": "NH1" <-> "NH2" Residue "A ARG 422": "NH1" <-> "NH2" Residue "A PHE 431": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 434": "NH1" <-> "NH2" Residue "A ARG 476": "NH1" <-> "NH2" Residue "A ARG 581": "NH1" <-> "NH2" Residue "A PHE 651": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 655": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 703": "NH1" <-> "NH2" Residue "A ARG 723": "NH1" <-> "NH2" Residue "A ARG 741": "NH1" <-> "NH2" Residue "A ARG 745": "NH1" <-> "NH2" Residue "A ARG 773": "NH1" <-> "NH2" Residue "B ARG 116": "NH1" <-> "NH2" Residue "B ARG 117": "NH1" <-> "NH2" Residue "B ARG 142": "NH1" <-> "NH2" Residue "B ARG 144": "NH1" <-> "NH2" Residue "B ARG 213": "NH1" <-> "NH2" Residue "B PHE 249": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 365": "NH1" <-> "NH2" Residue "B ARG 411": "NH1" <-> "NH2" Residue "B ARG 422": "NH1" <-> "NH2" Residue "B PHE 431": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 434": "NH1" <-> "NH2" Residue "B ARG 476": "NH1" <-> "NH2" Residue "B ARG 581": "NH1" <-> "NH2" Residue "B PHE 651": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 655": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 703": "NH1" <-> "NH2" Residue "B ARG 723": "NH1" <-> "NH2" Residue "B ARG 741": "NH1" <-> "NH2" Residue "B ARG 745": "NH1" <-> "NH2" Residue "B ARG 773": "NH1" <-> "NH2" Residue "C ARG 116": "NH1" <-> "NH2" Residue "C ARG 117": "NH1" <-> "NH2" Residue "C ARG 142": "NH1" <-> "NH2" Residue "C ARG 144": "NH1" <-> "NH2" Residue "C ARG 213": "NH1" <-> "NH2" Residue "C PHE 249": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 365": "NH1" <-> "NH2" Residue "C ARG 411": "NH1" <-> "NH2" Residue "C ARG 422": "NH1" <-> "NH2" Residue "C PHE 431": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 434": "NH1" <-> "NH2" Residue "C ARG 476": "NH1" <-> "NH2" Residue "C ARG 581": "NH1" <-> "NH2" Residue "C PHE 651": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 655": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 703": "NH1" <-> "NH2" Residue "C ARG 723": "NH1" <-> "NH2" Residue "C ARG 741": "NH1" <-> "NH2" Residue "C ARG 745": "NH1" <-> "NH2" Residue "C ARG 773": "NH1" <-> "NH2" Residue "D ARG 116": "NH1" <-> "NH2" Residue "D ARG 117": "NH1" <-> "NH2" Residue "D ARG 142": "NH1" <-> "NH2" Residue "D ARG 144": "NH1" <-> "NH2" Residue "D ARG 213": "NH1" <-> "NH2" Residue "D PHE 249": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 365": "NH1" <-> "NH2" Residue "D ARG 411": "NH1" <-> "NH2" Residue "D ARG 422": "NH1" <-> "NH2" Residue "D PHE 431": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 434": "NH1" <-> "NH2" Residue "D ARG 476": "NH1" <-> "NH2" Residue "D ARG 581": "NH1" <-> "NH2" Residue "D PHE 651": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 655": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 703": "NH1" <-> "NH2" Residue "D ARG 723": "NH1" <-> "NH2" Residue "D ARG 741": "NH1" <-> "NH2" Residue "D ARG 745": "NH1" <-> "NH2" Residue "D ARG 773": "NH1" <-> "NH2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 22765 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 5250 Number of conformers: 1 Conformer: "" Number of residues, atoms: 651, 5250 Classifications: {'peptide': 651} Link IDs: {'PTRANS': 19, 'TRANS': 631} Chain breaks: 1 Chain: "B" Number of atoms: 5250 Number of conformers: 1 Conformer: "" Number of residues, atoms: 651, 5250 Classifications: {'peptide': 651} Link IDs: {'PTRANS': 19, 'TRANS': 631} Chain breaks: 1 Chain: "C" Number of atoms: 5250 Number of conformers: 1 Conformer: "" Number of residues, atoms: 651, 5250 Classifications: {'peptide': 651} Link IDs: {'PTRANS': 19, 'TRANS': 631} Chain breaks: 1 Chain: "D" Number of atoms: 5250 Number of conformers: 1 Conformer: "" Number of residues, atoms: 651, 5250 Classifications: {'peptide': 651} Link IDs: {'PTRANS': 19, 'TRANS': 631} Chain breaks: 1 Chain: "A" Number of atoms: 442 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 442 Unusual residues: {' NA': 1, '6EU': 1, 'POV': 8} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 21 Chain: "B" Number of atoms: 441 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 441 Unusual residues: {'6EU': 1, 'POV': 8} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 21 Chain: "C" Number of atoms: 441 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 441 Unusual residues: {'6EU': 1, 'POV': 8} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 21 Chain: "D" Number of atoms: 441 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 441 Unusual residues: {'6EU': 1, 'POV': 8} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 21 Time building chain proxies: 12.70, per 1000 atoms: 0.56 Number of scatterers: 22765 At special positions: 0 Unit cell: (137.75, 137.75, 124.45, 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 124 16.00 P 32 15.00 Na 1 11.00 O 4108 8.00 N 3476 7.00 C 15024 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: 8.84 Conformation dependent library (CDL) restraints added in 3.5 seconds 5176 Ramachandran restraints generated. 2588 Oldfield, 0 Emsley, 2588 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4928 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 124 helices and 4 sheets defined 49.6% alpha, 1.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.44 Creating SS restraints... Processing helix chain 'A' and resid 116 through 124 Processing helix chain 'A' and resid 134 through 140 Processing helix chain 'A' and resid 159 through 165 removed outlier: 3.512A pdb=" N LEU A 165 " --> pdb=" O LEU A 161 " (cutoff:3.500A) Processing helix chain 'A' and resid 175 through 184 removed outlier: 3.621A pdb=" N GLN A 184 " --> pdb=" O ASP A 180 " (cutoff:3.500A) Processing helix chain 'A' and resid 188 through 192 Processing helix chain 'A' and resid 199 through 201 No H-bonds generated for 'chain 'A' and resid 199 through 201' Processing helix chain 'A' and resid 207 through 210 No H-bonds generated for 'chain 'A' and resid 207 through 210' Processing helix chain 'A' and resid 216 through 225 removed outlier: 3.602A pdb=" N GLU A 224 " --> pdb=" O THR A 220 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ASN A 225 " --> pdb=" O LEU A 221 " (cutoff:3.500A) Processing helix chain 'A' and resid 253 through 259 Processing helix chain 'A' and resid 263 through 268 removed outlier: 3.667A pdb=" N LYS A 267 " --> pdb=" O LEU A 263 " (cutoff:3.500A) Processing helix chain 'A' and resid 289 through 295 removed outlier: 3.868A pdb=" N VAL A 294 " --> pdb=" O LEU A 290 " (cutoff:3.500A) Processing helix chain 'A' and resid 301 through 321 removed outlier: 3.597A pdb=" N LYS A 305 " --> pdb=" O ALA A 301 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N PHE A 306 " --> pdb=" O ASP A 302 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N THR A 308 " --> pdb=" O THR A 304 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ILE A 314 " --> pdb=" O MET A 310 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N LEU A 315 " --> pdb=" O TYR A 311 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ILE A 316 " --> pdb=" O ASN A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 327 through 329 No H-bonds generated for 'chain 'A' and resid 327 through 329' Processing helix chain 'A' and resid 338 through 344 removed outlier: 3.562A pdb=" N ALA A 342 " --> pdb=" O PRO A 338 " (cutoff:3.500A) Processing helix chain 'A' and resid 349 through 355 Processing helix chain 'A' and resid 397 through 402 removed outlier: 3.772A pdb=" N ALA A 402 " --> pdb=" O LEU A 398 " (cutoff:3.500A) Processing helix chain 'A' and resid 413 through 415 No H-bonds generated for 'chain 'A' and resid 413 through 415' Processing helix chain 'A' and resid 418 through 421 No H-bonds generated for 'chain 'A' and resid 418 through 421' Processing helix chain 'A' and resid 424 through 428 Processing helix chain 'A' and resid 433 through 455 removed outlier: 3.501A pdb=" N ILE A 448 " --> pdb=" O CYS A 444 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N VAL A 449 " --> pdb=" O LEU A 445 " (cutoff:3.500A) Processing helix chain 'A' and resid 471 through 498 removed outlier: 3.618A pdb=" N PHE A 475 " --> pdb=" O VAL A 471 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N GLY A 486 " --> pdb=" O LEU A 482 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N TYR A 497 " --> pdb=" O ARG A 493 " (cutoff:3.500A) Processing helix chain 'A' and resid 506 through 510 removed outlier: 4.032A pdb=" N VAL A 510 " --> pdb=" O THR A 507 " (cutoff:3.500A) Processing helix chain 'A' and resid 513 through 532 removed outlier: 3.962A pdb=" N PHE A 518 " --> pdb=" O SER A 514 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N SER A 522 " --> pdb=" O PHE A 518 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N VAL A 529 " --> pdb=" O MET A 525 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N VAL A 530 " --> pdb=" O LEU A 526 " (cutoff:3.500A) Processing helix chain 'A' and resid 537 through 541 removed outlier: 3.738A pdb=" N VAL A 540 " --> pdb=" O LYS A 537 " (cutoff:3.500A) Processing helix chain 'A' and resid 543 through 556 removed outlier: 3.812A pdb=" N THR A 552 " --> pdb=" O ALA A 548 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N MET A 554 " --> pdb=" O GLY A 550 " (cutoff:3.500A) removed outlier: 4.734A pdb=" N LEU A 555 " --> pdb=" O TRP A 551 " (cutoff:3.500A) removed outlier: 5.012A pdb=" N TYR A 556 " --> pdb=" O THR A 552 " (cutoff:3.500A) Processing helix chain 'A' and resid 562 through 573 removed outlier: 4.118A pdb=" N TYR A 567 " --> pdb=" O GLN A 563 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ALA A 568 " --> pdb=" O MET A 564 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N MET A 570 " --> pdb=" O ILE A 566 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ILE A 571 " --> pdb=" O TYR A 567 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N GLU A 572 " --> pdb=" O ALA A 568 " (cutoff:3.500A) Processing helix chain 'A' and resid 579 through 600 removed outlier: 3.971A pdb=" N PHE A 584 " --> pdb=" O CYS A 580 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N VAL A 585 " --> pdb=" O ARG A 581 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N LEU A 587 " --> pdb=" O MET A 583 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N THR A 595 " --> pdb=" O PHE A 591 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N VAL A 598 " --> pdb=" O SER A 594 " (cutoff:3.500A) Processing helix chain 'A' and resid 632 through 638 Processing helix chain 'A' and resid 658 through 672 Processing helix chain 'A' and resid 676 through 712 removed outlier: 3.754A pdb=" N ILE A 681 " --> pdb=" O LEU A 677 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ALA A 682 " --> pdb=" O ASN A 678 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ASN A 689 " --> pdb=" O GLY A 685 " (cutoff:3.500A) removed outlier: 4.847A pdb=" N GLN A 693 " --> pdb=" O ASN A 689 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N GLU A 694 " --> pdb=" O LYS A 690 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N LYS A 696 " --> pdb=" O ALA A 692 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ASN A 697 " --> pdb=" O GLN A 693 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LYS A 700 " --> pdb=" O LYS A 696 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N LEU A 701 " --> pdb=" O ASN A 697 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N THR A 706 " --> pdb=" O GLN A 702 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ILE A 707 " --> pdb=" O ARG A 703 " (cutoff:3.500A) Processing helix chain 'A' and resid 715 through 718 No H-bonds generated for 'chain 'A' and resid 715 through 718' Processing helix chain 'B' and resid 116 through 124 Processing helix chain 'B' and resid 134 through 140 Processing helix chain 'B' and resid 159 through 165 removed outlier: 3.512A pdb=" N LEU B 165 " --> pdb=" O LEU B 161 " (cutoff:3.500A) Processing helix chain 'B' and resid 175 through 184 removed outlier: 3.620A pdb=" N GLN B 184 " --> pdb=" O ASP B 180 " (cutoff:3.500A) Processing helix chain 'B' and resid 188 through 192 Processing helix chain 'B' and resid 199 through 201 No H-bonds generated for 'chain 'B' and resid 199 through 201' Processing helix chain 'B' and resid 207 through 210 No H-bonds generated for 'chain 'B' and resid 207 through 210' Processing helix chain 'B' and resid 216 through 225 removed outlier: 3.601A pdb=" N GLU B 224 " --> pdb=" O THR B 220 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N ASN B 225 " --> pdb=" O LEU B 221 " (cutoff:3.500A) Processing helix chain 'B' and resid 253 through 259 Processing helix chain 'B' and resid 263 through 268 removed outlier: 3.666A pdb=" N LYS B 267 " --> pdb=" O LEU B 263 " (cutoff:3.500A) Processing helix chain 'B' and resid 289 through 295 removed outlier: 3.868A pdb=" N VAL B 294 " --> pdb=" O LEU B 290 " (cutoff:3.500A) Processing helix chain 'B' and resid 301 through 321 removed outlier: 3.596A pdb=" N LYS B 305 " --> pdb=" O ALA B 301 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N PHE B 306 " --> pdb=" O ASP B 302 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N THR B 308 " --> pdb=" O THR B 304 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ILE B 314 " --> pdb=" O MET B 310 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N LEU B 315 " --> pdb=" O TYR B 311 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ILE B 316 " --> pdb=" O ASN B 312 " (cutoff:3.500A) Processing helix chain 'B' and resid 327 through 329 No H-bonds generated for 'chain 'B' and resid 327 through 329' Processing helix chain 'B' and resid 338 through 344 removed outlier: 3.562A pdb=" N ALA B 342 " --> pdb=" O PRO B 338 " (cutoff:3.500A) Processing helix chain 'B' and resid 349 through 355 Processing helix chain 'B' and resid 397 through 402 removed outlier: 3.773A pdb=" N ALA B 402 " --> pdb=" O LEU B 398 " (cutoff:3.500A) Processing helix chain 'B' and resid 413 through 415 No H-bonds generated for 'chain 'B' and resid 413 through 415' Processing helix chain 'B' and resid 418 through 421 No H-bonds generated for 'chain 'B' and resid 418 through 421' Processing helix chain 'B' and resid 424 through 428 Processing helix chain 'B' and resid 433 through 455 removed outlier: 3.501A pdb=" N ILE B 448 " --> pdb=" O CYS B 444 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N VAL B 449 " --> pdb=" O LEU B 445 " (cutoff:3.500A) Processing helix chain 'B' and resid 471 through 498 removed outlier: 3.618A pdb=" N PHE B 475 " --> pdb=" O VAL B 471 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N GLY B 486 " --> pdb=" O LEU B 482 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N TYR B 497 " --> pdb=" O ARG B 493 " (cutoff:3.500A) Processing helix chain 'B' and resid 506 through 510 removed outlier: 4.033A pdb=" N VAL B 510 " --> pdb=" O THR B 507 " (cutoff:3.500A) Processing helix chain 'B' and resid 513 through 532 removed outlier: 3.963A pdb=" N PHE B 518 " --> pdb=" O SER B 514 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N SER B 522 " --> pdb=" O PHE B 518 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N VAL B 529 " --> pdb=" O MET B 525 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N VAL B 530 " --> pdb=" O LEU B 526 " (cutoff:3.500A) Processing helix chain 'B' and resid 537 through 541 removed outlier: 3.737A pdb=" N VAL B 540 " --> pdb=" O LYS B 537 " (cutoff:3.500A) Processing helix chain 'B' and resid 543 through 556 removed outlier: 3.810A pdb=" N THR B 552 " --> pdb=" O ALA B 548 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N MET B 554 " --> pdb=" O GLY B 550 " (cutoff:3.500A) removed outlier: 4.734A pdb=" N LEU B 555 " --> pdb=" O TRP B 551 " (cutoff:3.500A) removed outlier: 5.012A pdb=" N TYR B 556 " --> pdb=" O THR B 552 " (cutoff:3.500A) Processing helix chain 'B' and resid 562 through 573 removed outlier: 4.117A pdb=" N TYR B 567 " --> pdb=" O GLN B 563 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ALA B 568 " --> pdb=" O MET B 564 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N MET B 570 " --> pdb=" O ILE B 566 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ILE B 571 " --> pdb=" O TYR B 567 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N GLU B 572 " --> pdb=" O ALA B 568 " (cutoff:3.500A) Processing helix chain 'B' and resid 579 through 600 removed outlier: 3.971A pdb=" N PHE B 584 " --> pdb=" O CYS B 580 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N VAL B 585 " --> pdb=" O ARG B 581 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LEU B 587 " --> pdb=" O MET B 583 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N THR B 595 " --> pdb=" O PHE B 591 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N VAL B 598 " --> pdb=" O SER B 594 " (cutoff:3.500A) Processing helix chain 'B' and resid 632 through 638 Processing helix chain 'B' and resid 658 through 672 Processing helix chain 'B' and resid 676 through 712 removed outlier: 3.754A pdb=" N ILE B 681 " --> pdb=" O LEU B 677 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ALA B 682 " --> pdb=" O ASN B 678 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ASN B 689 " --> pdb=" O GLY B 685 " (cutoff:3.500A) removed outlier: 4.847A pdb=" N GLN B 693 " --> pdb=" O ASN B 689 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N GLU B 694 " --> pdb=" O LYS B 690 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N LYS B 696 " --> pdb=" O ALA B 692 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ASN B 697 " --> pdb=" O GLN B 693 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LYS B 700 " --> pdb=" O LYS B 696 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N LEU B 701 " --> pdb=" O ASN B 697 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N THR B 706 " --> pdb=" O GLN B 702 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ILE B 707 " --> pdb=" O ARG B 703 " (cutoff:3.500A) Processing helix chain 'B' and resid 715 through 718 No H-bonds generated for 'chain 'B' and resid 715 through 718' Processing helix chain 'C' and resid 116 through 124 Processing helix chain 'C' and resid 134 through 140 Processing helix chain 'C' and resid 159 through 165 removed outlier: 3.512A pdb=" N LEU C 165 " --> pdb=" O LEU C 161 " (cutoff:3.500A) Processing helix chain 'C' and resid 175 through 184 removed outlier: 3.621A pdb=" N GLN C 184 " --> pdb=" O ASP C 180 " (cutoff:3.500A) Processing helix chain 'C' and resid 188 through 192 Processing helix chain 'C' and resid 199 through 201 No H-bonds generated for 'chain 'C' and resid 199 through 201' Processing helix chain 'C' and resid 207 through 210 No H-bonds generated for 'chain 'C' and resid 207 through 210' Processing helix chain 'C' and resid 216 through 225 removed outlier: 3.601A pdb=" N GLU C 224 " --> pdb=" O THR C 220 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N ASN C 225 " --> pdb=" O LEU C 221 " (cutoff:3.500A) Processing helix chain 'C' and resid 253 through 259 Processing helix chain 'C' and resid 263 through 268 removed outlier: 3.666A pdb=" N LYS C 267 " --> pdb=" O LEU C 263 " (cutoff:3.500A) Processing helix chain 'C' and resid 289 through 295 removed outlier: 3.869A pdb=" N VAL C 294 " --> pdb=" O LEU C 290 " (cutoff:3.500A) Processing helix chain 'C' and resid 301 through 321 removed outlier: 3.596A pdb=" N LYS C 305 " --> pdb=" O ALA C 301 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N PHE C 306 " --> pdb=" O ASP C 302 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N THR C 308 " --> pdb=" O THR C 304 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ILE C 314 " --> pdb=" O MET C 310 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N LEU C 315 " --> pdb=" O TYR C 311 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ILE C 316 " --> pdb=" O ASN C 312 " (cutoff:3.500A) Processing helix chain 'C' and resid 327 through 329 No H-bonds generated for 'chain 'C' and resid 327 through 329' Processing helix chain 'C' and resid 338 through 344 removed outlier: 3.563A pdb=" N ALA C 342 " --> pdb=" O PRO C 338 " (cutoff:3.500A) Processing helix chain 'C' and resid 349 through 355 Processing helix chain 'C' and resid 397 through 402 removed outlier: 3.772A pdb=" N ALA C 402 " --> pdb=" O LEU C 398 " (cutoff:3.500A) Processing helix chain 'C' and resid 413 through 415 No H-bonds generated for 'chain 'C' and resid 413 through 415' Processing helix chain 'C' and resid 418 through 421 No H-bonds generated for 'chain 'C' and resid 418 through 421' Processing helix chain 'C' and resid 424 through 428 Processing helix chain 'C' and resid 433 through 455 removed outlier: 3.739A pdb=" N VAL C 449 " --> pdb=" O LEU C 445 " (cutoff:3.500A) Processing helix chain 'C' and resid 471 through 498 removed outlier: 3.617A pdb=" N PHE C 475 " --> pdb=" O VAL C 471 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N GLY C 486 " --> pdb=" O LEU C 482 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N TYR C 497 " --> pdb=" O ARG C 493 " (cutoff:3.500A) Processing helix chain 'C' and resid 506 through 510 removed outlier: 4.033A pdb=" N VAL C 510 " --> pdb=" O THR C 507 " (cutoff:3.500A) Processing helix chain 'C' and resid 513 through 532 removed outlier: 3.963A pdb=" N PHE C 518 " --> pdb=" O SER C 514 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N SER C 522 " --> pdb=" O PHE C 518 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N VAL C 529 " --> pdb=" O MET C 525 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N VAL C 530 " --> pdb=" O LEU C 526 " (cutoff:3.500A) Processing helix chain 'C' and resid 537 through 541 removed outlier: 3.737A pdb=" N VAL C 540 " --> pdb=" O LYS C 537 " (cutoff:3.500A) Processing helix chain 'C' and resid 543 through 556 removed outlier: 3.811A pdb=" N THR C 552 " --> pdb=" O ALA C 548 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N MET C 554 " --> pdb=" O GLY C 550 " (cutoff:3.500A) removed outlier: 4.735A pdb=" N LEU C 555 " --> pdb=" O TRP C 551 " (cutoff:3.500A) removed outlier: 5.012A pdb=" N TYR C 556 " --> pdb=" O THR C 552 " (cutoff:3.500A) Processing helix chain 'C' and resid 562 through 573 removed outlier: 4.117A pdb=" N TYR C 567 " --> pdb=" O GLN C 563 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ALA C 568 " --> pdb=" O MET C 564 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N MET C 570 " --> pdb=" O ILE C 566 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ILE C 571 " --> pdb=" O TYR C 567 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N GLU C 572 " --> pdb=" O ALA C 568 " (cutoff:3.500A) Processing helix chain 'C' and resid 579 through 600 removed outlier: 3.971A pdb=" N PHE C 584 " --> pdb=" O CYS C 580 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N VAL C 585 " --> pdb=" O ARG C 581 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N LEU C 587 " --> pdb=" O MET C 583 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N THR C 595 " --> pdb=" O PHE C 591 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N VAL C 598 " --> pdb=" O SER C 594 " (cutoff:3.500A) Processing helix chain 'C' and resid 632 through 638 Processing helix chain 'C' and resid 658 through 672 Processing helix chain 'C' and resid 676 through 712 removed outlier: 3.754A pdb=" N ILE C 681 " --> pdb=" O LEU C 677 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ALA C 682 " --> pdb=" O ASN C 678 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ASN C 689 " --> pdb=" O GLY C 685 " (cutoff:3.500A) removed outlier: 4.847A pdb=" N GLN C 693 " --> pdb=" O ASN C 689 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N GLU C 694 " --> pdb=" O LYS C 690 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N LYS C 696 " --> pdb=" O ALA C 692 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ASN C 697 " --> pdb=" O GLN C 693 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LYS C 700 " --> pdb=" O LYS C 696 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N LEU C 701 " --> pdb=" O ASN C 697 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N THR C 706 " --> pdb=" O GLN C 702 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ILE C 707 " --> pdb=" O ARG C 703 " (cutoff:3.500A) Processing helix chain 'C' and resid 715 through 718 No H-bonds generated for 'chain 'C' and resid 715 through 718' Processing helix chain 'D' and resid 116 through 124 Processing helix chain 'D' and resid 134 through 140 Processing helix chain 'D' and resid 159 through 165 removed outlier: 3.512A pdb=" N LEU D 165 " --> pdb=" O LEU D 161 " (cutoff:3.500A) Processing helix chain 'D' and resid 175 through 184 removed outlier: 3.622A pdb=" N GLN D 184 " --> pdb=" O ASP D 180 " (cutoff:3.500A) Processing helix chain 'D' and resid 188 through 192 Processing helix chain 'D' and resid 199 through 201 No H-bonds generated for 'chain 'D' and resid 199 through 201' Processing helix chain 'D' and resid 207 through 210 No H-bonds generated for 'chain 'D' and resid 207 through 210' Processing helix chain 'D' and resid 216 through 225 removed outlier: 3.602A pdb=" N GLU D 224 " --> pdb=" O THR D 220 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N ASN D 225 " --> pdb=" O LEU D 221 " (cutoff:3.500A) Processing helix chain 'D' and resid 253 through 259 Processing helix chain 'D' and resid 263 through 268 removed outlier: 3.666A pdb=" N LYS D 267 " --> pdb=" O LEU D 263 " (cutoff:3.500A) Processing helix chain 'D' and resid 289 through 295 removed outlier: 3.868A pdb=" N VAL D 294 " --> pdb=" O LEU D 290 " (cutoff:3.500A) Processing helix chain 'D' and resid 301 through 321 removed outlier: 3.598A pdb=" N LYS D 305 " --> pdb=" O ALA D 301 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N PHE D 306 " --> pdb=" O ASP D 302 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N THR D 308 " --> pdb=" O THR D 304 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ILE D 314 " --> pdb=" O MET D 310 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N LEU D 315 " --> pdb=" O TYR D 311 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ILE D 316 " --> pdb=" O ASN D 312 " (cutoff:3.500A) Processing helix chain 'D' and resid 327 through 329 No H-bonds generated for 'chain 'D' and resid 327 through 329' Processing helix chain 'D' and resid 338 through 344 removed outlier: 3.563A pdb=" N ALA D 342 " --> pdb=" O PRO D 338 " (cutoff:3.500A) Processing helix chain 'D' and resid 349 through 355 Processing helix chain 'D' and resid 397 through 402 removed outlier: 3.772A pdb=" N ALA D 402 " --> pdb=" O LEU D 398 " (cutoff:3.500A) Processing helix chain 'D' and resid 413 through 415 No H-bonds generated for 'chain 'D' and resid 413 through 415' Processing helix chain 'D' and resid 418 through 421 No H-bonds generated for 'chain 'D' and resid 418 through 421' Processing helix chain 'D' and resid 424 through 428 Processing helix chain 'D' and resid 433 through 455 removed outlier: 3.501A pdb=" N ILE D 448 " --> pdb=" O CYS D 444 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N VAL D 449 " --> pdb=" O LEU D 445 " (cutoff:3.500A) Processing helix chain 'D' and resid 471 through 498 removed outlier: 3.619A pdb=" N PHE D 475 " --> pdb=" O VAL D 471 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N GLY D 486 " --> pdb=" O LEU D 482 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N TYR D 497 " --> pdb=" O ARG D 493 " (cutoff:3.500A) Processing helix chain 'D' and resid 506 through 510 removed outlier: 4.032A pdb=" N VAL D 510 " --> pdb=" O THR D 507 " (cutoff:3.500A) Processing helix chain 'D' and resid 513 through 532 removed outlier: 3.963A pdb=" N PHE D 518 " --> pdb=" O SER D 514 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N SER D 522 " --> pdb=" O PHE D 518 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N VAL D 529 " --> pdb=" O MET D 525 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N VAL D 530 " --> pdb=" O LEU D 526 " (cutoff:3.500A) Processing helix chain 'D' and resid 537 through 541 removed outlier: 3.737A pdb=" N VAL D 540 " --> pdb=" O LYS D 537 " (cutoff:3.500A) Processing helix chain 'D' and resid 543 through 556 removed outlier: 3.812A pdb=" N THR D 552 " --> pdb=" O ALA D 548 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N MET D 554 " --> pdb=" O GLY D 550 " (cutoff:3.500A) removed outlier: 4.735A pdb=" N LEU D 555 " --> pdb=" O TRP D 551 " (cutoff:3.500A) removed outlier: 5.011A pdb=" N TYR D 556 " --> pdb=" O THR D 552 " (cutoff:3.500A) Processing helix chain 'D' and resid 562 through 573 removed outlier: 4.118A pdb=" N TYR D 567 " --> pdb=" O GLN D 563 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ALA D 568 " --> pdb=" O MET D 564 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N MET D 570 " --> pdb=" O ILE D 566 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ILE D 571 " --> pdb=" O TYR D 567 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N GLU D 572 " --> pdb=" O ALA D 568 " (cutoff:3.500A) Processing helix chain 'D' and resid 579 through 600 removed outlier: 3.971A pdb=" N PHE D 584 " --> pdb=" O CYS D 580 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N VAL D 585 " --> pdb=" O ARG D 581 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N LEU D 587 " --> pdb=" O MET D 583 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N THR D 595 " --> pdb=" O PHE D 591 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N VAL D 598 " --> pdb=" O SER D 594 " (cutoff:3.500A) Processing helix chain 'D' and resid 632 through 638 Processing helix chain 'D' and resid 658 through 672 Processing helix chain 'D' and resid 676 through 712 removed outlier: 3.754A pdb=" N ILE D 681 " --> pdb=" O LEU D 677 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ALA D 682 " --> pdb=" O ASN D 678 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ASN D 689 " --> pdb=" O GLY D 685 " (cutoff:3.500A) removed outlier: 4.847A pdb=" N GLN D 693 " --> pdb=" O ASN D 689 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N GLU D 694 " --> pdb=" O LYS D 690 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N LYS D 696 " --> pdb=" O ALA D 692 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ASN D 697 " --> pdb=" O GLN D 693 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LYS D 700 " --> pdb=" O LYS D 696 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N LEU D 701 " --> pdb=" O ASN D 697 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N THR D 706 " --> pdb=" O GLN D 702 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ILE D 707 " --> pdb=" O ARG D 703 " (cutoff:3.500A) Processing helix chain 'D' and resid 715 through 718 No H-bonds generated for 'chain 'D' and resid 715 through 718' Processing sheet with id= A, first strand: chain 'A' and resid 746 through 748 removed outlier: 3.521A pdb=" N SER A 382 " --> pdb=" O VAL A 746 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N TRP A 374 " --> pdb=" O SER A 381 " (cutoff:3.500A) removed outlier: 5.880A pdb=" N LEU A 383 " --> pdb=" O THR A 372 " (cutoff:3.500A) removed outlier: 5.298A pdb=" N THR A 372 " --> pdb=" O LEU A 383 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 746 through 748 removed outlier: 3.521A pdb=" N SER B 382 " --> pdb=" O VAL B 746 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N TRP B 374 " --> pdb=" O SER B 381 " (cutoff:3.500A) removed outlier: 5.879A pdb=" N LEU B 383 " --> pdb=" O THR B 372 " (cutoff:3.500A) removed outlier: 5.298A pdb=" N THR B 372 " --> pdb=" O LEU B 383 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'C' and resid 746 through 748 removed outlier: 3.522A pdb=" N SER C 382 " --> pdb=" O VAL C 746 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N TRP C 374 " --> pdb=" O SER C 381 " (cutoff:3.500A) removed outlier: 5.880A pdb=" N LEU C 383 " --> pdb=" O THR C 372 " (cutoff:3.500A) removed outlier: 5.297A pdb=" N THR C 372 " --> pdb=" O LEU C 383 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'D' and resid 746 through 748 removed outlier: 3.521A pdb=" N SER D 382 " --> pdb=" O VAL D 746 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N TRP D 374 " --> pdb=" O SER D 381 " (cutoff:3.500A) removed outlier: 5.881A pdb=" N LEU D 383 " --> pdb=" O THR D 372 " (cutoff:3.500A) removed outlier: 5.298A pdb=" N THR D 372 " --> pdb=" O LEU D 383 " (cutoff:3.500A) 641 hydrogen bonds defined for protein. 1875 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: 6.03 Time building geometry restraints manager: 9.51 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 3428 1.31 - 1.44: 6289 1.44 - 1.56: 13215 1.56 - 1.69: 88 1.69 - 1.82: 200 Bond restraints: 23220 Sorted by residual: bond pdb=" CAV 6EU A 902 " pdb=" CBB 6EU A 902 " ideal model delta sigma weight residual 1.330 1.523 -0.193 2.00e-02 2.50e+03 9.35e+01 bond pdb=" CAV 6EU B 903 " pdb=" CBB 6EU B 903 " ideal model delta sigma weight residual 1.330 1.523 -0.193 2.00e-02 2.50e+03 9.34e+01 bond pdb=" CAV 6EU C 903 " pdb=" CBB 6EU C 903 " ideal model delta sigma weight residual 1.330 1.523 -0.193 2.00e-02 2.50e+03 9.28e+01 bond pdb=" CAV 6EU D 906 " pdb=" CBB 6EU D 906 " ideal model delta sigma weight residual 1.330 1.522 -0.192 2.00e-02 2.50e+03 9.25e+01 bond pdb=" CAR 6EU C 903 " pdb=" CAZ 6EU C 903 " ideal model delta sigma weight residual 1.538 1.372 0.166 2.00e-02 2.50e+03 6.91e+01 ... (remaining 23215 not shown) Histogram of bond angle deviations from ideal: 98.57 - 105.68: 424 105.68 - 112.78: 12332 112.78 - 119.88: 8069 119.88 - 126.98: 10123 126.98 - 134.08: 228 Bond angle restraints: 31176 Sorted by residual: angle pdb=" N ILE D 575 " pdb=" CA ILE D 575 " pdb=" C ILE D 575 " ideal model delta sigma weight residual 113.20 104.22 8.98 9.60e-01 1.09e+00 8.76e+01 angle pdb=" N ILE C 575 " pdb=" CA ILE C 575 " pdb=" C ILE C 575 " ideal model delta sigma weight residual 113.20 104.22 8.98 9.60e-01 1.09e+00 8.74e+01 angle pdb=" N ILE B 575 " pdb=" CA ILE B 575 " pdb=" C ILE B 575 " ideal model delta sigma weight residual 113.20 104.23 8.97 9.60e-01 1.09e+00 8.73e+01 angle pdb=" N ILE A 575 " pdb=" CA ILE A 575 " pdb=" C ILE A 575 " ideal model delta sigma weight residual 113.20 104.24 8.96 9.60e-01 1.09e+00 8.71e+01 angle pdb=" C ARG D 430 " pdb=" N PHE D 431 " pdb=" CA PHE D 431 " ideal model delta sigma weight residual 121.54 133.92 -12.38 1.91e+00 2.74e-01 4.20e+01 ... (remaining 31171 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.32: 13611 33.32 - 66.65: 678 66.65 - 99.97: 106 99.97 - 133.30: 24 133.30 - 166.62: 25 Dihedral angle restraints: 14444 sinusoidal: 6788 harmonic: 7656 Sorted by residual: dihedral pdb=" CA LEU D 462 " pdb=" C LEU D 462 " pdb=" N PRO D 463 " pdb=" CA PRO D 463 " ideal model delta harmonic sigma weight residual -180.00 -152.37 -27.63 0 5.00e+00 4.00e-02 3.05e+01 dihedral pdb=" CA LEU B 462 " pdb=" C LEU B 462 " pdb=" N PRO B 463 " pdb=" CA PRO B 463 " ideal model delta harmonic sigma weight residual -180.00 -152.37 -27.63 0 5.00e+00 4.00e-02 3.05e+01 dihedral pdb=" CA LEU C 462 " pdb=" C LEU C 462 " pdb=" N PRO C 463 " pdb=" CA PRO C 463 " ideal model delta harmonic sigma weight residual -180.00 -152.38 -27.62 0 5.00e+00 4.00e-02 3.05e+01 ... (remaining 14441 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.079: 2906 0.079 - 0.158: 356 0.158 - 0.237: 46 0.237 - 0.316: 24 0.316 - 0.395: 8 Chirality restraints: 3340 Sorted by residual: chirality pdb=" CAR 6EU B 903 " pdb=" CAO 6EU B 903 " pdb=" CAU 6EU B 903 " pdb=" CAZ 6EU B 903 " both_signs ideal model delta sigma weight residual False 2.83 2.44 0.40 2.00e-01 2.50e+01 3.90e+00 chirality pdb=" CAR 6EU D 906 " pdb=" CAO 6EU D 906 " pdb=" CAU 6EU D 906 " pdb=" CAZ 6EU D 906 " both_signs ideal model delta sigma weight residual False 2.83 2.44 0.39 2.00e-01 2.50e+01 3.88e+00 chirality pdb=" CAR 6EU C 903 " pdb=" CAO 6EU C 903 " pdb=" CAU 6EU C 903 " pdb=" CAZ 6EU C 903 " both_signs ideal model delta sigma weight residual False 2.83 2.44 0.39 2.00e-01 2.50e+01 3.87e+00 ... (remaining 3337 not shown) Planarity restraints: 3756 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE C 431 " 0.012 2.00e-02 2.50e+03 1.74e-02 5.33e+00 pdb=" CG PHE C 431 " -0.040 2.00e-02 2.50e+03 pdb=" CD1 PHE C 431 " 0.011 2.00e-02 2.50e+03 pdb=" CD2 PHE C 431 " 0.016 2.00e-02 2.50e+03 pdb=" CE1 PHE C 431 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 PHE C 431 " -0.001 2.00e-02 2.50e+03 pdb=" CZ PHE C 431 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 431 " 0.012 2.00e-02 2.50e+03 1.74e-02 5.27e+00 pdb=" CG PHE B 431 " -0.040 2.00e-02 2.50e+03 pdb=" CD1 PHE B 431 " 0.011 2.00e-02 2.50e+03 pdb=" CD2 PHE B 431 " 0.016 2.00e-02 2.50e+03 pdb=" CE1 PHE B 431 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 PHE B 431 " -0.001 2.00e-02 2.50e+03 pdb=" CZ PHE B 431 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 431 " -0.013 2.00e-02 2.50e+03 1.73e-02 5.25e+00 pdb=" CG PHE A 431 " 0.040 2.00e-02 2.50e+03 pdb=" CD1 PHE A 431 " -0.011 2.00e-02 2.50e+03 pdb=" CD2 PHE A 431 " -0.016 2.00e-02 2.50e+03 pdb=" CE1 PHE A 431 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 PHE A 431 " 0.001 2.00e-02 2.50e+03 pdb=" CZ PHE A 431 " 0.001 2.00e-02 2.50e+03 ... (remaining 3753 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 3679 2.75 - 3.29: 20449 3.29 - 3.82: 34445 3.82 - 4.36: 43599 4.36 - 4.90: 73811 Nonbonded interactions: 175983 Sorted by model distance: nonbonded pdb=" O PRO B 765 " pdb=" OH TYR C 201 " model vdw 2.211 2.440 nonbonded pdb=" O PRO C 765 " pdb=" OH TYR D 201 " model vdw 2.256 2.440 nonbonded pdb=" O VAL D 400 " pdb=" OG SER D 404 " model vdw 2.276 2.440 nonbonded pdb=" O VAL A 400 " pdb=" OG SER A 404 " model vdw 2.276 2.440 nonbonded pdb=" O VAL B 400 " pdb=" OG SER B 404 " model vdw 2.276 2.440 ... (remaining 175978 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 111 through 779 or resid 901 or (resid 904 and (name N or \ name C1 or name C11 or name C12 or name C13 or name C14 or name C15 or name C2 o \ r name C21 or name C22 or name C23 or name C24 or name C25 or name C26 or name C \ 27 or name C28 or name C29 or name C3 or name C31 or name C32 or name C33 or nam \ e C34 or name C35 or name C36 or name C37 or name C38 or name C39 or name O11 or \ name O12 or name O13 or name O14 or name O21 or name O22 or name O31 or name O3 \ 2 or name P or name C210 or name C211 or name C212 or name C213 or name C214 or \ name C215 or name C216 or name C217 or name C218 or name C310 or name C311)) or \ resid 905 or resid 907 through 908 or (resid 909 and (name N or name C1 or name \ C11 or name C12 or name C13 or name C14 or name C15 or name C2 or name C21 or na \ me C22 or name C23 or name C24 or name C25 or name C26 or name C27 or name C28 o \ r name C29 or name C3 or name C31 or name C32 or name C33 or name C34 or name C3 \ 5 or name C36 or name C37 or name C38 or name O11 or name O12 or name O13 or nam \ e O14 or name O21 or name O22 or name O31 or name O32 or name P or name C210 or \ name C211 or name C212 or name C213 or name C214 or name C215 or name C216 or na \ me C217 or name C218)))) selection = (chain 'B' and (resid 111 through 779 or (resid 901 and (name N or name C1 or na \ me C11 or name C12 or name C13 or name C14 or name C15 or name C2 or name C21 or \ name C22 or name C23 or name C24 or name C25 or name C26 or name C27 or name C2 \ 8 or name C29 or name C3 or name C31 or name C32 or name C33 or name C34 or name \ C35 or name C36 or name C37 or name C38 or name O11 or name O12 or name O13 or \ name O14 or name O21 or name O22 or name O31 or name O32 or name P or name C210 \ or name C211 or name C212 or name C213 or name C214 or name C215 or name C216 or \ name C217 or name C218)) or (resid 904 and (name N or name C1 or name C11 or na \ me C12 or name C13 or name C14 or name C15 or name C2 or name C21 or name C22 or \ name C23 or name C24 or name C25 or name C26 or name C27 or name C28 or name C2 \ 9 or name C3 or name C31 or name C32 or name C33 or name C34 or name C35 or name \ C36 or name C37 or name C38 or name C39 or name O11 or name O12 or name O13 or \ name O14 or name O21 or name O22 or name O31 or name O32 or name P or name C210 \ or name C211 or name C212 or name C213 or name C214 or name C215 or name C216 or \ name C217 or name C218 or name C310 or name C311)) or (resid 905 and (name N or \ name C1 or name C11 or name C12 or name C13 or name C14 or name C15 or name C2 \ or name C21 or name C22 or name C23 or name C24 or name C25 or name C26 or name \ C27 or name C28 or name C29 or name C3 or name C31 or name C32 or name C33 or na \ me C34 or name C35 or name C36 or name C37 or name C38 or name O11 or name O12 o \ r name O13 or name O14 or name O21 or name O22 or name O31 or name O32 or name P \ or name C210 or name C211 or name C212 or name C213 or name C214 or name C215 o \ r name C216 or name C217 or name C218)) or resid 907 through 908 or (resid 909 a \ nd (name N or name C1 or name C11 or name C12 or name C13 or name C14 or name C1 \ 5 or name C2 or name C21 or name C22 or name C23 or name C24 or name C25 or name \ C26 or name C27 or name C28 or name C29 or name C3 or name C31 or name C32 or n \ ame C33 or name C34 or name C35 or name C36 or name C37 or name C38 or name O11 \ or name O12 or name O13 or name O14 or name O21 or name O22 or name O31 or name \ O32 or name P or name C210 or name C211 or name C212 or name C213 or name C214 o \ r name C215 or name C216 or name C217 or name C218)))) selection = (chain 'C' and (resid 111 through 779 or (resid 901 and (name N or name C1 or na \ me C11 or name C12 or name C13 or name C14 or name C15 or name C2 or name C21 or \ name C22 or name C23 or name C24 or name C25 or name C26 or name C27 or name C2 \ 8 or name C29 or name C3 or name C31 or name C32 or name C33 or name C34 or name \ C35 or name C36 or name C37 or name C38 or name O11 or name O12 or name O13 or \ name O14 or name O21 or name O22 or name O31 or name O32 or name P or name C210 \ or name C211 or name C212 or name C213 or name C214 or name C215 or name C216 or \ name C217 or name C218)) or (resid 904 and (name N or name C1 or name C11 or na \ me C12 or name C13 or name C14 or name C15 or name C2 or name C21 or name C22 or \ name C23 or name C24 or name C25 or name C26 or name C27 or name C28 or name C2 \ 9 or name C3 or name C31 or name C32 or name C33 or name C34 or name C35 or name \ C36 or name C37 or name C38 or name C39 or name O11 or name O12 or name O13 or \ name O14 or name O21 or name O22 or name O31 or name O32 or name P or name C210 \ or name C211 or name C212 or name C213 or name C214 or name C215 or name C216 or \ name C217 or name C218 or name C310 or name C311)) or (resid 905 and (name N or \ name C1 or name C11 or name C12 or name C13 or name C14 or name C15 or name C2 \ or name C21 or name C22 or name C23 or name C24 or name C25 or name C26 or name \ C27 or name C28 or name C29 or name C3 or name C31 or name C32 or name C33 or na \ me C34 or name C35 or name C36 or name C37 or name C38 or name O11 or name O12 o \ r name O13 or name O14 or name O21 or name O22 or name O31 or name O32 or name P \ or name C210 or name C211 or name C212 or name C213 or name C214 or name C215 o \ r name C216 or name C217 or name C218)) or resid 907 through 908 or (resid 909 a \ nd (name N or name C1 or name C11 or name C12 or name C13 or name C14 or name C1 \ 5 or name C2 or name C21 or name C22 or name C23 or name C24 or name C25 or name \ C26 or name C27 or name C28 or name C29 or name C3 or name C31 or name C32 or n \ ame C33 or name C34 or name C35 or name C36 or name C37 or name C38 or name O11 \ or name O12 or name O13 or name O14 or name O21 or name O22 or name O31 or name \ O32 or name P or name C210 or name C211 or name C212 or name C213 or name C214 o \ r name C215 or name C216 or name C217 or name C218)))) selection = (chain 'D' and (resid 111 through 779 or (resid 901 and (name N or name C1 or na \ me C11 or name C12 or name C13 or name C14 or name C15 or name C2 or name C21 or \ name C22 or name C23 or name C24 or name C25 or name C26 or name C27 or name C2 \ 8 or name C29 or name C3 or name C31 or name C32 or name C33 or name C34 or name \ C35 or name C36 or name C37 or name C38 or name O11 or name O12 or name O13 or \ name O14 or name O21 or name O22 or name O31 or name O32 or name P or name C210 \ or name C211 or name C212 or name C213 or name C214 or name C215 or name C216 or \ name C217 or name C218)) or resid 904 through 905 or resid 907 through 909)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.45 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: 2.280 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: 0.020 Extract box with map and model: 7.020 Check model and map are aligned: 0.370 Set scattering table: 0.220 Process input model: 57.500 Find NCS groups from input model: 1.600 Set up NCS constraints: 0.130 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:2.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 72.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7654 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 : 0.013 0.193 23220 Z= 0.800 Angle : 1.554 14.412 31176 Z= 0.726 Chirality : 0.062 0.395 3340 Planarity : 0.007 0.053 3756 Dihedral : 20.374 166.620 9516 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.26 % Favored : 92.74 % Rotamer: Outliers : 0.35 % Allowed : 6.98 % Favored : 92.68 % 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: -5.71 (0.11), residues: 2588 helix: -4.44 (0.05), residues: 1472 sheet: -3.92 (0.40), residues: 84 loop : -2.42 (0.17), residues: 1032 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.004 TRP C 751 HIS 0.010 0.003 HIS C 366 PHE 0.040 0.003 PHE C 431 TYR 0.025 0.003 TYR A 465 ARG 0.010 0.001 ARG C 703 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5176 Ramachandran restraints generated. 2588 Oldfield, 0 Emsley, 2588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5176 Ramachandran restraints generated. 2588 Oldfield, 0 Emsley, 2588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 357 residues out of total 2308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 349 time to evaluate : 2.369 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 166 ASN cc_start: 0.8232 (m-40) cc_final: 0.8031 (m-40) REVERT: A 184 GLN cc_start: 0.8646 (mm-40) cc_final: 0.8341 (tp40) REVERT: A 207 LEU cc_start: 0.7924 (tp) cc_final: 0.7721 (tp) REVERT: A 222 LEU cc_start: 0.8461 (mt) cc_final: 0.7987 (tp) REVERT: A 380 HIS cc_start: 0.6734 (t-90) cc_final: 0.6373 (t-90) REVERT: A 483 SER cc_start: 0.8344 (m) cc_final: 0.7979 (p) REVERT: A 655 TYR cc_start: 0.8722 (p90) cc_final: 0.7977 (p90) REVERT: B 162 LYS cc_start: 0.5915 (tptm) cc_final: 0.5604 (tttp) REVERT: B 222 LEU cc_start: 0.8479 (mt) cc_final: 0.8047 (tp) REVERT: B 380 HIS cc_start: 0.6810 (t-90) cc_final: 0.6343 (t-90) REVERT: B 418 GLU cc_start: 0.7773 (mm-30) cc_final: 0.7061 (tp30) REVERT: B 483 SER cc_start: 0.8383 (m) cc_final: 0.8023 (p) REVERT: C 115 ASP cc_start: 0.8096 (p0) cc_final: 0.7872 (p0) REVERT: C 166 ASN cc_start: 0.8169 (m-40) cc_final: 0.7935 (m-40) REVERT: C 168 HIS cc_start: 0.7109 (m170) cc_final: 0.6721 (m170) REVERT: C 169 ASN cc_start: 0.8097 (t160) cc_final: 0.7866 (t0) REVERT: C 207 LEU cc_start: 0.7804 (tp) cc_final: 0.7594 (tp) REVERT: C 222 LEU cc_start: 0.8436 (mt) cc_final: 0.7939 (tp) REVERT: C 380 HIS cc_start: 0.6666 (t-90) cc_final: 0.6275 (t-90) REVERT: C 483 SER cc_start: 0.8387 (m) cc_final: 0.7929 (p) REVERT: D 162 LYS cc_start: 0.5916 (tptm) cc_final: 0.5655 (tttp) REVERT: D 166 ASN cc_start: 0.7992 (m-40) cc_final: 0.7764 (p0) REVERT: D 380 HIS cc_start: 0.6548 (t-90) cc_final: 0.6105 (t-90) REVERT: D 483 SER cc_start: 0.8189 (m) cc_final: 0.7956 (p) REVERT: D 748 GLU cc_start: 0.6862 (mp0) cc_final: 0.6470 (mp0) outliers start: 8 outliers final: 4 residues processed: 357 average time/residue: 0.3619 time to fit residues: 195.5751 Evaluate side-chains 207 residues out of total 2308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 203 time to evaluate : 2.616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain B residue 727 LEU Chi-restraints excluded: chain C residue 727 LEU Chi-restraints excluded: chain D residue 727 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 219 optimal weight: 0.9980 chunk 197 optimal weight: 20.0000 chunk 109 optimal weight: 0.6980 chunk 67 optimal weight: 9.9990 chunk 132 optimal weight: 0.0000 chunk 105 optimal weight: 0.8980 chunk 203 optimal weight: 7.9990 chunk 78 optimal weight: 0.0670 chunk 123 optimal weight: 0.9980 chunk 151 optimal weight: 0.9980 chunk 236 optimal weight: 0.8980 overall best weight: 0.5122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 166 ASN A 215 ASN A 225 ASN A 230 GLN A 261 ASN A 291 HIS A 312 ASN A 366 HIS A 421 ASN A 630 ASN A 750 ASN A 755 ASN A 762 ASN A 767 ASN B 166 ASN B 215 ASN B 225 ASN B 230 GLN B 261 ASN B 291 HIS B 312 ASN B 366 HIS B 421 ASN B 630 ASN B 750 ASN B 755 ASN B 762 ASN B 767 ASN C 169 ASN C 215 ASN C 225 ASN C 230 GLN C 261 ASN C 291 HIS C 312 ASN C 366 HIS C 421 ASN C 630 ASN C 729 GLN C 750 ASN C 755 ASN C 767 ASN D 166 ASN D 215 ASN D 225 ASN D 230 GLN D 261 ASN D 291 HIS D 312 ASN D 366 HIS D 421 ASN D 630 ASN D 750 ASN D 755 ASN D 762 ASN D 767 ASN Total number of N/Q/H flips: 56 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7549 moved from start: 0.2316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 23220 Z= 0.140 Angle : 0.564 8.004 31176 Z= 0.299 Chirality : 0.037 0.158 3340 Planarity : 0.004 0.039 3756 Dihedral : 21.478 154.888 4524 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 1.47 % Allowed : 9.71 % Favored : 88.82 % 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: -3.43 (0.14), residues: 2588 helix: -2.33 (0.11), residues: 1436 sheet: -3.60 (0.42), residues: 84 loop : -1.84 (0.18), residues: 1068 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 374 HIS 0.002 0.001 HIS D 412 PHE 0.019 0.001 PHE D 191 TYR 0.014 0.001 TYR A 673 ARG 0.008 0.000 ARG D 411 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5176 Ramachandran restraints generated. 2588 Oldfield, 0 Emsley, 2588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5176 Ramachandran restraints generated. 2588 Oldfield, 0 Emsley, 2588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 2308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 247 time to evaluate : 2.315 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 162 LYS cc_start: 0.5782 (tptm) cc_final: 0.5479 (tttp) REVERT: A 168 HIS cc_start: 0.6774 (m170) cc_final: 0.6376 (m170) REVERT: A 169 ASN cc_start: 0.7627 (t0) cc_final: 0.7269 (t0) REVERT: A 171 GLN cc_start: 0.8353 (OUTLIER) cc_final: 0.7529 (pp30) REVERT: A 184 GLN cc_start: 0.8651 (mm-40) cc_final: 0.8430 (tp40) REVERT: A 207 LEU cc_start: 0.7998 (tp) cc_final: 0.7771 (tp) REVERT: A 222 LEU cc_start: 0.8536 (mt) cc_final: 0.8269 (tp) REVERT: A 418 GLU cc_start: 0.7388 (mm-30) cc_final: 0.7091 (tp30) REVERT: A 426 ASP cc_start: 0.7483 (m-30) cc_final: 0.7033 (t0) REVERT: A 718 MET cc_start: 0.6750 (mtp) cc_final: 0.6514 (mtm) REVERT: B 162 LYS cc_start: 0.5877 (tptm) cc_final: 0.5586 (tttp) REVERT: B 169 ASN cc_start: 0.7487 (t0) cc_final: 0.7235 (t0) REVERT: B 418 GLU cc_start: 0.7605 (mm-30) cc_final: 0.7160 (tp30) REVERT: B 426 ASP cc_start: 0.7482 (m-30) cc_final: 0.6782 (t0) REVERT: B 655 TYR cc_start: 0.8509 (p90) cc_final: 0.8008 (p90) REVERT: C 115 ASP cc_start: 0.8083 (p0) cc_final: 0.7807 (p0) REVERT: C 162 LYS cc_start: 0.5850 (tptt) cc_final: 0.4958 (tttp) REVERT: C 168 HIS cc_start: 0.7087 (m170) cc_final: 0.6818 (m170) REVERT: C 193 ASN cc_start: 0.7649 (m-40) cc_final: 0.6790 (t0) REVERT: C 222 LEU cc_start: 0.8461 (mt) cc_final: 0.8184 (tp) REVERT: C 655 TYR cc_start: 0.8534 (p90) cc_final: 0.8150 (p90) REVERT: D 162 LYS cc_start: 0.5854 (tptm) cc_final: 0.5623 (tttp) REVERT: D 426 ASP cc_start: 0.7316 (m-30) cc_final: 0.6911 (t0) outliers start: 34 outliers final: 15 residues processed: 275 average time/residue: 0.3265 time to fit residues: 142.0186 Evaluate side-chains 202 residues out of total 2308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 186 time to evaluate : 1.972 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 GLN Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 363 GLU Chi-restraints excluded: chain A residue 522 SER Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain B residue 171 GLN Chi-restraints excluded: chain B residue 363 GLU Chi-restraints excluded: chain B residue 397 VAL Chi-restraints excluded: chain B residue 522 SER Chi-restraints excluded: chain B residue 727 LEU Chi-restraints excluded: chain C residue 363 GLU Chi-restraints excluded: chain C residue 397 VAL Chi-restraints excluded: chain C residue 522 SER Chi-restraints excluded: chain C residue 727 LEU Chi-restraints excluded: chain D residue 363 GLU Chi-restraints excluded: chain D residue 727 LEU 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: 69.4824 > 50: distance: 48 - 52: 20.802 distance: 52 - 53: 25.172 distance: 53 - 54: 44.788 distance: 53 - 56: 56.008 distance: 54 - 55: 43.369 distance: 54 - 61: 10.760 distance: 56 - 57: 50.857 distance: 57 - 58: 47.934 distance: 58 - 59: 30.949 distance: 58 - 60: 28.705 distance: 61 - 62: 51.339 distance: 62 - 63: 4.831 distance: 62 - 65: 68.199 distance: 63 - 64: 67.080 distance: 63 - 72: 41.360 distance: 65 - 66: 39.592 distance: 66 - 67: 27.811 distance: 67 - 68: 42.616 distance: 68 - 69: 14.960 distance: 69 - 70: 24.288 distance: 69 - 71: 37.574 distance: 72 - 73: 39.402 distance: 73 - 74: 27.644 distance: 73 - 76: 68.295 distance: 74 - 75: 18.693 distance: 74 - 83: 12.971 distance: 76 - 77: 43.663 distance: 77 - 78: 46.983 distance: 78 - 79: 21.016 distance: 79 - 80: 11.171 distance: 80 - 81: 31.310 distance: 80 - 82: 34.516 distance: 83 - 84: 62.140 distance: 83 - 89: 40.035 distance: 84 - 85: 37.789 distance: 84 - 87: 19.089 distance: 85 - 86: 12.319 distance: 85 - 90: 27.330 distance: 87 - 88: 41.262 distance: 88 - 89: 43.673 distance: 90 - 91: 45.430 distance: 91 - 92: 27.714 distance: 91 - 94: 61.830 distance: 92 - 93: 18.633 distance: 92 - 96: 45.173 distance: 94 - 95: 56.983 distance: 96 - 97: 14.689 distance: 97 - 98: 31.316 distance: 97 - 100: 44.754 distance: 98 - 99: 22.070 distance: 98 - 104: 37.482 distance: 100 - 101: 21.113 distance: 101 - 102: 25.447 distance: 102 - 103: 32.939 distance: 104 - 105: 42.136 distance: 105 - 106: 34.477 distance: 105 - 108: 25.046 distance: 106 - 107: 15.233 distance: 106 - 113: 41.379 distance: 107 - 128: 50.735 distance: 108 - 109: 57.147 distance: 109 - 110: 46.705 distance: 110 - 111: 14.843 distance: 111 - 112: 35.954 distance: 113 - 114: 41.785 distance: 114 - 115: 17.479 distance: 114 - 117: 38.922 distance: 115 - 116: 39.143 distance: 115 - 120: 44.778 distance: 117 - 118: 52.789 distance: 117 - 119: 40.030 distance: 120 - 121: 16.226 distance: 121 - 122: 46.253 distance: 121 - 124: 37.229 distance: 122 - 123: 57.257 distance: 122 - 128: 50.414 distance: 124 - 125: 39.185 distance: 125 - 126: 41.644 distance: 125 - 127: 6.360 distance: 128 - 129: 21.872 distance: 129 - 130: 12.145 distance: 129 - 132: 17.674 distance: 130 - 131: 11.336 distance: 130 - 139: 10.500 distance: 132 - 133: 15.169 distance: 133 - 134: 8.118 distance: 133 - 135: 11.813 distance: 134 - 136: 5.762 distance: 135 - 137: 23.115 distance: 136 - 138: 3.000 distance: 137 - 138: 16.567