Starting phenix.real_space_refine (version: dev) on Fri Feb 24 05:01:25 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6bwf_7298/02_2023/6bwf_7298.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6bwf_7298/02_2023/6bwf_7298.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6bwf_7298/02_2023/6bwf_7298.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6bwf_7298/02_2023/6bwf_7298.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6bwf_7298/02_2023/6bwf_7298.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6bwf_7298/02_2023/6bwf_7298.pdb" } resolution = 4.1 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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= 0.004 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 Process input model Symmetric amino acids flipped Residue "A ARG 288": "NH1" <-> "NH2" Residue "A ARG 293": "NH1" <-> "NH2" Residue "A ARG 314": "NH1" <-> "NH2" Residue "A ARG 383": "NH1" <-> "NH2" Residue "A ARG 497": "NH1" <-> "NH2" Residue "A ARG 556": "NH1" <-> "NH2" Residue "A ARG 596": "NH1" <-> "NH2" Residue "A ARG 616": "NH1" <-> "NH2" Residue "A ARG 672": "NH1" <-> "NH2" Residue "A ARG 769": "NH1" <-> "NH2" Residue "A ARG 852": "NH1" <-> "NH2" Residue "B ARG 288": "NH1" <-> "NH2" Residue "B ARG 293": "NH1" <-> "NH2" Residue "B ARG 314": "NH1" <-> "NH2" Residue "B ARG 383": "NH1" <-> "NH2" Residue "B ARG 497": "NH1" <-> "NH2" Residue "B ARG 556": "NH1" <-> "NH2" Residue "B ARG 596": "NH1" <-> "NH2" Residue "B ARG 616": "NH1" <-> "NH2" Residue "B ARG 672": "NH1" <-> "NH2" Residue "B ARG 769": "NH1" <-> "NH2" Residue "B ARG 852": "NH1" <-> "NH2" Residue "C ARG 288": "NH1" <-> "NH2" Residue "C ARG 293": "NH1" <-> "NH2" Residue "C ARG 314": "NH1" <-> "NH2" Residue "C ARG 383": "NH1" <-> "NH2" Residue "C ARG 497": "NH1" <-> "NH2" Residue "C ARG 556": "NH1" <-> "NH2" Residue "C ARG 596": "NH1" <-> "NH2" Residue "C ARG 616": "NH1" <-> "NH2" Residue "C ARG 672": "NH1" <-> "NH2" Residue "C ARG 769": "NH1" <-> "NH2" Residue "C ARG 852": "NH1" <-> "NH2" Residue "D ARG 288": "NH1" <-> "NH2" Residue "D ARG 293": "NH1" <-> "NH2" Residue "D ARG 383": "NH1" <-> "NH2" Residue "D ARG 497": "NH1" <-> "NH2" Residue "D ARG 556": "NH1" <-> "NH2" Residue "D ARG 596": "NH1" <-> "NH2" Residue "D ARG 616": "NH1" <-> "NH2" Residue "D ARG 672": "NH1" <-> "NH2" Residue "D ARG 769": "NH1" <-> "NH2" Residue "D ARG 852": "NH1" <-> "NH2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 22174 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 5546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 766, 5546 Classifications: {'peptide': 766} Incomplete info: {'backbone_only': 4, 'truncation_to_alanine': 234} Link IDs: {'CIS': 43, 'PTRANS': 27, 'TRANS': 695} Chain breaks: 18 Unresolved chain link angles: 7 Unresolved non-hydrogen bonds: 685 Unresolved non-hydrogen angles: 926 Unresolved non-hydrogen dihedrals: 497 Unresolved non-hydrogen chiralities: 42 Planarities with less than four sites: {'GLN:plan1': 6, 'ASN:plan1': 5, 'ASP:plan': 4, 'TYR:plan': 6, 'UNK:plan-1': 120, 'TRP:plan': 2, 'HIS:plan': 5, 'PHE:plan': 2, 'GLU:plan': 6, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 337 Chain: "B" Number of atoms: 5532 Number of conformers: 1 Conformer: "" Number of residues, atoms: 766, 5532 Classifications: {'peptide': 766} Incomplete info: {'backbone_only': 4, 'truncation_to_alanine': 237} Link IDs: {'CIS': 43, 'PTRANS': 27, 'TRANS': 695} Chain breaks: 18 Unresolved chain link angles: 7 Unresolved non-hydrogen bonds: 700 Unresolved non-hydrogen angles: 946 Unresolved non-hydrogen dihedrals: 510 Unresolved non-hydrogen chiralities: 43 Planarities with less than four sites: {'GLN:plan1': 6, 'ASN:plan1': 5, 'ASP:plan': 4, 'TYR:plan': 7, 'UNK:plan-1': 120, 'TRP:plan': 2, 'HIS:plan': 5, 'PHE:plan': 2, 'GLU:plan': 7, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 348 Chain: "C" Number of atoms: 5550 Number of conformers: 1 Conformer: "" Number of residues, atoms: 766, 5550 Classifications: {'peptide': 766} Incomplete info: {'backbone_only': 4, 'truncation_to_alanine': 233} Link IDs: {'CIS': 43, 'PTRANS': 27, 'TRANS': 695} Chain breaks: 18 Unresolved chain link angles: 7 Unresolved non-hydrogen bonds: 681 Unresolved non-hydrogen angles: 922 Unresolved non-hydrogen dihedrals: 493 Unresolved non-hydrogen chiralities: 42 Planarities with less than four sites: {'GLN:plan1': 6, 'ASN:plan1': 5, 'ASP:plan': 4, 'TYR:plan': 6, 'UNK:plan-1': 120, 'TRP:plan': 2, 'HIS:plan': 5, 'PHE:plan': 2, 'GLU:plan': 6, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 337 Chain: "D" Number of atoms: 5546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 766, 5546 Classifications: {'peptide': 766} Incomplete info: {'backbone_only': 4, 'truncation_to_alanine': 234} Link IDs: {'CIS': 43, 'PTRANS': 27, 'TRANS': 695} Chain breaks: 18 Unresolved chain link angles: 7 Unresolved non-hydrogen bonds: 685 Unresolved non-hydrogen angles: 926 Unresolved non-hydrogen dihedrals: 497 Unresolved non-hydrogen chiralities: 42 Planarities with less than four sites: {'GLN:plan1': 6, 'ASN:plan1': 5, 'ASP:plan': 4, 'TYR:plan': 6, 'UNK:plan-1': 120, 'TRP:plan': 2, 'HIS:plan': 5, 'PHE:plan': 2, 'GLU:plan': 6, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 337 Time building chain proxies: 12.19, per 1000 atoms: 0.55 Number of scatterers: 22174 At special positions: 0 Unit cell: (135.3, 135.3, 153.75, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 116 16.00 O 3949 8.00 N 3789 7.00 C 14320 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: 9.04 Conformation dependent library (CDL) restraints added in 3.3 seconds 4992 Ramachandran restraints generated. 2496 Oldfield, 0 Emsley, 2496 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5896 Finding SS restraints... Secondary structure from input PDB file: 161 helices and 0 sheets defined 69.9% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.00 Creating SS restraints... Processing helix chain 'A' and resid 2 through 9 Processing helix chain 'A' and resid 10 through 15 Processing helix chain 'A' and resid 27 through 35 removed outlier: 3.818A pdb=" N UNK A 35 " --> pdb=" O UNK A 31 " (cutoff:3.500A) Processing helix chain 'A' and resid 44 through 48 Processing helix chain 'A' and resid 49 through 52 removed outlier: 4.152A pdb=" N UNK A 52 " --> pdb=" O UNK A 49 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 49 through 52' Processing helix chain 'A' and resid 55 through 64 removed outlier: 3.516A pdb=" N UNK A 64 " --> pdb=" O UNK A 60 " (cutoff:3.500A) Processing helix chain 'A' and resid 90 through 101 Processing helix chain 'A' and resid 123 through 133 removed outlier: 3.689A pdb=" N LEU A 131 " --> pdb=" O ARG A 127 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N ASN A 133 " --> pdb=" O GLU A 129 " (cutoff:3.500A) Processing helix chain 'A' and resid 135 through 140 Processing helix chain 'A' and resid 171 through 176 Processing helix chain 'A' and resid 207 through 212 removed outlier: 4.370A pdb=" N GLN A 211 " --> pdb=" O SER A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 230 through 234 removed outlier: 4.395A pdb=" N HIS A 233 " --> pdb=" O ARG A 230 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 258 Processing helix chain 'A' and resid 275 through 286 removed outlier: 4.982A pdb=" N ILE A 281 " --> pdb=" O ASN A 277 " (cutoff:3.500A) Processing helix chain 'A' and resid 301 through 323 removed outlier: 4.745A pdb=" N LEU A 307 " --> pdb=" O MET A 303 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N VAL A 308 " --> pdb=" O ALA A 304 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N GLN A 322 " --> pdb=" O TYR A 318 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N SER A 323 " --> pdb=" O GLU A 319 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 336 Processing helix chain 'A' and resid 337 through 354 removed outlier: 4.440A pdb=" N LEU A 343 " --> pdb=" O ASP A 339 " (cutoff:3.500A) removed outlier: 4.746A pdb=" N ALA A 344 " --> pdb=" O PHE A 340 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N VAL A 345 " --> pdb=" O GLY A 341 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N GLU A 346 " --> pdb=" O GLN A 342 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N GLN A 354 " --> pdb=" O GLN A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 356 through 361 Processing helix chain 'A' and resid 362 through 364 No H-bonds generated for 'chain 'A' and resid 362 through 364' Processing helix chain 'A' and resid 390 through 397 Processing helix chain 'A' and resid 413 through 421 removed outlier: 3.583A pdb=" N SER A 418 " --> pdb=" O LYS A 414 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LEU A 420 " --> pdb=" O ILE A 416 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N VAL A 421 " --> pdb=" O LEU A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 422 through 429 removed outlier: 4.298A pdb=" N MET A 427 " --> pdb=" O ALA A 424 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N LEU A 428 " --> pdb=" O ILE A 425 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N GLU A 429 " --> pdb=" O LEU A 426 " (cutoff:3.500A) Processing helix chain 'A' and resid 498 through 503 Processing helix chain 'A' and resid 505 through 529 removed outlier: 4.394A pdb=" N LEU A 518 " --> pdb=" O THR A 514 " (cutoff:3.500A) Processing helix chain 'A' and resid 539 through 554 removed outlier: 3.964A pdb=" N VAL A 543 " --> pdb=" O GLN A 539 " (cutoff:3.500A) Processing helix chain 'A' and resid 569 through 574 removed outlier: 4.001A pdb=" N TRP A 573 " --> pdb=" O LYS A 569 " (cutoff:3.500A) Processing helix chain 'A' and resid 578 through 595 removed outlier: 3.525A pdb=" N PHE A 593 " --> pdb=" O PHE A 589 " (cutoff:3.500A) Processing helix chain 'A' and resid 612 through 622 removed outlier: 3.673A pdb=" N ILE A 618 " --> pdb=" O ALA A 614 " (cutoff:3.500A) Processing helix chain 'A' and resid 623 through 627 Processing helix chain 'A' and resid 628 through 633 removed outlier: 3.756A pdb=" N ASP A 632 " --> pdb=" O VAL A 628 " (cutoff:3.500A) Processing helix chain 'A' and resid 639 through 648 removed outlier: 4.237A pdb=" N TYR A 643 " --> pdb=" O GLN A 639 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N GLY A 648 " --> pdb=" O VAL A 644 " (cutoff:3.500A) Processing helix chain 'A' and resid 650 through 677 removed outlier: 6.151A pdb=" N TYR A 656 " --> pdb=" O ALA A 652 " (cutoff:3.500A) removed outlier: 5.749A pdb=" N ILE A 657 " --> pdb=" O ASN A 653 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ILE A 660 " --> pdb=" O TYR A 656 " (cutoff:3.500A) Proline residue: A 671 - end of helix removed outlier: 4.219A pdb=" N ILE A 675 " --> pdb=" O PRO A 671 " (cutoff:3.500A) Processing helix chain 'A' and resid 685 through 696 removed outlier: 3.807A pdb=" N ASP A 689 " --> pdb=" O SER A 685 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N HIS A 693 " --> pdb=" O ASP A 689 " (cutoff:3.500A) Proline residue: A 694 - end of helix Processing helix chain 'A' and resid 703 through 707 removed outlier: 3.556A pdb=" N ILE A 707 " --> pdb=" O ALA A 704 " (cutoff:3.500A) Processing helix chain 'A' and resid 726 through 738 removed outlier: 3.606A pdb=" N ALA A 732 " --> pdb=" O PRO A 728 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N PHE A 736 " --> pdb=" O ALA A 732 " (cutoff:3.500A) Processing helix chain 'A' and resid 744 through 749 Processing helix chain 'A' and resid 754 through 774 removed outlier: 4.059A pdb=" N ILE A 760 " --> pdb=" O GLN A 756 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N ILE A 763 " --> pdb=" O ALA A 759 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N TYR A 770 " --> pdb=" O LYS A 766 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N HIS A 771 " --> pdb=" O TYR A 767 " (cutoff:3.500A) Processing helix chain 'A' and resid 783 through 790 removed outlier: 3.922A pdb=" N LEU A 789 " --> pdb=" O PRO A 785 " (cutoff:3.500A) Processing helix chain 'A' and resid 817 through 844 removed outlier: 4.426A pdb=" N GLU A 833 " --> pdb=" O GLU A 829 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ASP A 840 " --> pdb=" O PHE A 836 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N ASP A 841 " --> pdb=" O ASP A 837 " (cutoff:3.500A) Processing helix chain 'A' and resid 847 through 885 removed outlier: 3.864A pdb=" N ILE A 851 " --> pdb=" O SER A 847 " (cutoff:3.500A) Processing helix chain 'B' and resid 2 through 9 Processing helix chain 'B' and resid 10 through 15 Processing helix chain 'B' and resid 27 through 35 removed outlier: 3.817A pdb=" N UNK B 35 " --> pdb=" O UNK B 31 " (cutoff:3.500A) Processing helix chain 'B' and resid 44 through 48 Processing helix chain 'B' and resid 49 through 52 removed outlier: 4.152A pdb=" N UNK B 52 " --> pdb=" O UNK B 49 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 49 through 52' Processing helix chain 'B' and resid 55 through 64 removed outlier: 3.515A pdb=" N UNK B 64 " --> pdb=" O UNK B 60 " (cutoff:3.500A) Processing helix chain 'B' and resid 90 through 101 Processing helix chain 'B' and resid 123 through 133 removed outlier: 3.689A pdb=" N LEU B 131 " --> pdb=" O ARG B 127 " (cutoff:3.500A) removed outlier: 4.688A pdb=" N ASN B 133 " --> pdb=" O GLU B 129 " (cutoff:3.500A) Processing helix chain 'B' and resid 135 through 140 Processing helix chain 'B' and resid 171 through 176 Processing helix chain 'B' and resid 207 through 212 removed outlier: 4.369A pdb=" N GLN B 211 " --> pdb=" O SER B 207 " (cutoff:3.500A) Processing helix chain 'B' and resid 230 through 234 removed outlier: 4.395A pdb=" N HIS B 233 " --> pdb=" O ARG B 230 " (cutoff:3.500A) Processing helix chain 'B' and resid 251 through 258 Processing helix chain 'B' and resid 275 through 286 removed outlier: 4.983A pdb=" N ILE B 281 " --> pdb=" O ASN B 277 " (cutoff:3.500A) Processing helix chain 'B' and resid 301 through 323 removed outlier: 4.746A pdb=" N LEU B 307 " --> pdb=" O MET B 303 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N VAL B 308 " --> pdb=" O ALA B 304 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N GLN B 322 " --> pdb=" O TYR B 318 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N SER B 323 " --> pdb=" O GLU B 319 " (cutoff:3.500A) Processing helix chain 'B' and resid 331 through 335 Processing helix chain 'B' and resid 336 through 340 Processing helix chain 'B' and resid 341 through 354 removed outlier: 4.008A pdb=" N VAL B 345 " --> pdb=" O GLY B 341 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N GLU B 346 " --> pdb=" O GLN B 342 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N GLN B 354 " --> pdb=" O GLN B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 356 through 361 Processing helix chain 'B' and resid 362 through 364 No H-bonds generated for 'chain 'B' and resid 362 through 364' Processing helix chain 'B' and resid 390 through 397 Processing helix chain 'B' and resid 413 through 421 removed outlier: 3.582A pdb=" N SER B 418 " --> pdb=" O LYS B 414 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEU B 420 " --> pdb=" O ILE B 416 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N VAL B 421 " --> pdb=" O LEU B 417 " (cutoff:3.500A) Processing helix chain 'B' and resid 422 through 429 removed outlier: 4.299A pdb=" N MET B 427 " --> pdb=" O ALA B 424 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LEU B 428 " --> pdb=" O ILE B 425 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N GLU B 429 " --> pdb=" O LEU B 426 " (cutoff:3.500A) Processing helix chain 'B' and resid 498 through 503 Processing helix chain 'B' and resid 505 through 529 removed outlier: 4.394A pdb=" N LEU B 518 " --> pdb=" O THR B 514 " (cutoff:3.500A) Processing helix chain 'B' and resid 539 through 554 removed outlier: 3.963A pdb=" N VAL B 543 " --> pdb=" O GLN B 539 " (cutoff:3.500A) Processing helix chain 'B' and resid 569 through 574 removed outlier: 4.002A pdb=" N TRP B 573 " --> pdb=" O LYS B 569 " (cutoff:3.500A) Processing helix chain 'B' and resid 578 through 595 removed outlier: 3.524A pdb=" N PHE B 593 " --> pdb=" O PHE B 589 " (cutoff:3.500A) Processing helix chain 'B' and resid 612 through 622 removed outlier: 3.674A pdb=" N ILE B 618 " --> pdb=" O ALA B 614 " (cutoff:3.500A) Processing helix chain 'B' and resid 623 through 627 Processing helix chain 'B' and resid 628 through 633 removed outlier: 3.755A pdb=" N ASP B 632 " --> pdb=" O VAL B 628 " (cutoff:3.500A) Processing helix chain 'B' and resid 639 through 648 removed outlier: 4.237A pdb=" N TYR B 643 " --> pdb=" O GLN B 639 " (cutoff:3.500A) removed outlier: 4.699A pdb=" N GLY B 648 " --> pdb=" O VAL B 644 " (cutoff:3.500A) Processing helix chain 'B' and resid 650 through 677 removed outlier: 6.151A pdb=" N TYR B 656 " --> pdb=" O ALA B 652 " (cutoff:3.500A) removed outlier: 5.748A pdb=" N ILE B 657 " --> pdb=" O ASN B 653 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ILE B 660 " --> pdb=" O TYR B 656 " (cutoff:3.500A) Proline residue: B 671 - end of helix removed outlier: 4.219A pdb=" N ILE B 675 " --> pdb=" O PRO B 671 " (cutoff:3.500A) Processing helix chain 'B' and resid 685 through 696 removed outlier: 3.806A pdb=" N ASP B 689 " --> pdb=" O SER B 685 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N HIS B 693 " --> pdb=" O ASP B 689 " (cutoff:3.500A) Proline residue: B 694 - end of helix Processing helix chain 'B' and resid 703 through 707 removed outlier: 3.556A pdb=" N ILE B 707 " --> pdb=" O ALA B 704 " (cutoff:3.500A) Processing helix chain 'B' and resid 726 through 738 removed outlier: 3.607A pdb=" N ALA B 732 " --> pdb=" O PRO B 728 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N PHE B 736 " --> pdb=" O ALA B 732 " (cutoff:3.500A) Processing helix chain 'B' and resid 744 through 749 Processing helix chain 'B' and resid 754 through 774 removed outlier: 4.059A pdb=" N ILE B 760 " --> pdb=" O GLN B 756 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N ILE B 763 " --> pdb=" O ALA B 759 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N TYR B 770 " --> pdb=" O LYS B 766 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N HIS B 771 " --> pdb=" O TYR B 767 " (cutoff:3.500A) Processing helix chain 'B' and resid 783 through 790 removed outlier: 3.923A pdb=" N LEU B 789 " --> pdb=" O PRO B 785 " (cutoff:3.500A) Processing helix chain 'B' and resid 817 through 844 removed outlier: 4.426A pdb=" N GLU B 833 " --> pdb=" O GLU B 829 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ASP B 840 " --> pdb=" O PHE B 836 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N ASP B 841 " --> pdb=" O ASP B 837 " (cutoff:3.500A) Processing helix chain 'B' and resid 847 through 885 removed outlier: 3.864A pdb=" N ILE B 851 " --> pdb=" O SER B 847 " (cutoff:3.500A) Processing helix chain 'C' and resid 2 through 9 Processing helix chain 'C' and resid 10 through 15 Processing helix chain 'C' and resid 27 through 35 removed outlier: 3.818A pdb=" N UNK C 35 " --> pdb=" O UNK C 31 " (cutoff:3.500A) Processing helix chain 'C' and resid 44 through 48 Processing helix chain 'C' and resid 49 through 52 removed outlier: 4.152A pdb=" N UNK C 52 " --> pdb=" O UNK C 49 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 49 through 52' Processing helix chain 'C' and resid 55 through 64 removed outlier: 3.515A pdb=" N UNK C 64 " --> pdb=" O UNK C 60 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 101 Processing helix chain 'C' and resid 123 through 133 removed outlier: 3.690A pdb=" N LEU C 131 " --> pdb=" O ARG C 127 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N ASN C 133 " --> pdb=" O GLU C 129 " (cutoff:3.500A) Processing helix chain 'C' and resid 135 through 140 Processing helix chain 'C' and resid 171 through 176 Processing helix chain 'C' and resid 207 through 212 removed outlier: 4.369A pdb=" N GLN C 211 " --> pdb=" O SER C 207 " (cutoff:3.500A) Processing helix chain 'C' and resid 230 through 234 removed outlier: 4.394A pdb=" N HIS C 233 " --> pdb=" O ARG C 230 " (cutoff:3.500A) Processing helix chain 'C' and resid 251 through 258 Processing helix chain 'C' and resid 275 through 286 removed outlier: 4.982A pdb=" N ILE C 281 " --> pdb=" O ASN C 277 " (cutoff:3.500A) Processing helix chain 'C' and resid 301 through 323 removed outlier: 4.745A pdb=" N LEU C 307 " --> pdb=" O MET C 303 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N VAL C 308 " --> pdb=" O ALA C 304 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N GLN C 322 " --> pdb=" O TYR C 318 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N SER C 323 " --> pdb=" O GLU C 319 " (cutoff:3.500A) Processing helix chain 'C' and resid 331 through 335 Processing helix chain 'C' and resid 337 through 354 removed outlier: 5.294A pdb=" N LEU C 343 " --> pdb=" O ASP C 339 " (cutoff:3.500A) removed outlier: 4.748A pdb=" N ALA C 344 " --> pdb=" O PHE C 340 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N VAL C 345 " --> pdb=" O GLY C 341 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N GLU C 346 " --> pdb=" O GLN C 342 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N GLN C 354 " --> pdb=" O GLN C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 356 through 361 Processing helix chain 'C' and resid 362 through 364 No H-bonds generated for 'chain 'C' and resid 362 through 364' Processing helix chain 'C' and resid 390 through 397 Processing helix chain 'C' and resid 413 through 421 removed outlier: 3.582A pdb=" N SER C 418 " --> pdb=" O LYS C 414 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LEU C 420 " --> pdb=" O ILE C 416 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N VAL C 421 " --> pdb=" O LEU C 417 " (cutoff:3.500A) Processing helix chain 'C' and resid 422 through 429 removed outlier: 4.299A pdb=" N MET C 427 " --> pdb=" O ALA C 424 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N LEU C 428 " --> pdb=" O ILE C 425 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N GLU C 429 " --> pdb=" O LEU C 426 " (cutoff:3.500A) Processing helix chain 'C' and resid 498 through 503 Processing helix chain 'C' and resid 505 through 529 removed outlier: 4.394A pdb=" N LEU C 518 " --> pdb=" O THR C 514 " (cutoff:3.500A) Processing helix chain 'C' and resid 539 through 554 removed outlier: 3.963A pdb=" N VAL C 543 " --> pdb=" O GLN C 539 " (cutoff:3.500A) Processing helix chain 'C' and resid 569 through 574 removed outlier: 4.001A pdb=" N TRP C 573 " --> pdb=" O LYS C 569 " (cutoff:3.500A) Processing helix chain 'C' and resid 578 through 595 removed outlier: 3.524A pdb=" N PHE C 593 " --> pdb=" O PHE C 589 " (cutoff:3.500A) Processing helix chain 'C' and resid 612 through 622 removed outlier: 3.673A pdb=" N ILE C 618 " --> pdb=" O ALA C 614 " (cutoff:3.500A) Processing helix chain 'C' and resid 623 through 627 Processing helix chain 'C' and resid 628 through 633 removed outlier: 3.755A pdb=" N ASP C 632 " --> pdb=" O VAL C 628 " (cutoff:3.500A) Processing helix chain 'C' and resid 639 through 648 removed outlier: 4.237A pdb=" N TYR C 643 " --> pdb=" O GLN C 639 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N GLY C 648 " --> pdb=" O VAL C 644 " (cutoff:3.500A) Processing helix chain 'C' and resid 650 through 677 removed outlier: 6.151A pdb=" N TYR C 656 " --> pdb=" O ALA C 652 " (cutoff:3.500A) removed outlier: 5.748A pdb=" N ILE C 657 " --> pdb=" O ASN C 653 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ILE C 660 " --> pdb=" O TYR C 656 " (cutoff:3.500A) Proline residue: C 671 - end of helix removed outlier: 4.219A pdb=" N ILE C 675 " --> pdb=" O PRO C 671 " (cutoff:3.500A) Processing helix chain 'C' and resid 685 through 696 removed outlier: 3.807A pdb=" N ASP C 689 " --> pdb=" O SER C 685 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N HIS C 693 " --> pdb=" O ASP C 689 " (cutoff:3.500A) Proline residue: C 694 - end of helix Processing helix chain 'C' and resid 703 through 707 removed outlier: 3.556A pdb=" N ILE C 707 " --> pdb=" O ALA C 704 " (cutoff:3.500A) Processing helix chain 'C' and resid 726 through 738 removed outlier: 3.607A pdb=" N ALA C 732 " --> pdb=" O PRO C 728 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N PHE C 736 " --> pdb=" O ALA C 732 " (cutoff:3.500A) Processing helix chain 'C' and resid 744 through 749 Processing helix chain 'C' and resid 754 through 774 removed outlier: 4.060A pdb=" N ILE C 760 " --> pdb=" O GLN C 756 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N ILE C 763 " --> pdb=" O ALA C 759 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N TYR C 770 " --> pdb=" O LYS C 766 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N HIS C 771 " --> pdb=" O TYR C 767 " (cutoff:3.500A) Processing helix chain 'C' and resid 783 through 790 removed outlier: 3.923A pdb=" N LEU C 789 " --> pdb=" O PRO C 785 " (cutoff:3.500A) Processing helix chain 'C' and resid 817 through 844 removed outlier: 4.426A pdb=" N GLU C 833 " --> pdb=" O GLU C 829 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ASP C 840 " --> pdb=" O PHE C 836 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N ASP C 841 " --> pdb=" O ASP C 837 " (cutoff:3.500A) Processing helix chain 'C' and resid 847 through 885 removed outlier: 3.865A pdb=" N ILE C 851 " --> pdb=" O SER C 847 " (cutoff:3.500A) Processing helix chain 'D' and resid 2 through 9 Processing helix chain 'D' and resid 10 through 15 Processing helix chain 'D' and resid 27 through 35 removed outlier: 3.818A pdb=" N UNK D 35 " --> pdb=" O UNK D 31 " (cutoff:3.500A) Processing helix chain 'D' and resid 44 through 48 Processing helix chain 'D' and resid 49 through 52 removed outlier: 4.152A pdb=" N UNK D 52 " --> pdb=" O UNK D 49 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 49 through 52' Processing helix chain 'D' and resid 55 through 64 removed outlier: 3.515A pdb=" N UNK D 64 " --> pdb=" O UNK D 60 " (cutoff:3.500A) Processing helix chain 'D' and resid 90 through 101 Processing helix chain 'D' and resid 123 through 133 removed outlier: 3.690A pdb=" N LEU D 131 " --> pdb=" O ARG D 127 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N ASN D 133 " --> pdb=" O GLU D 129 " (cutoff:3.500A) Processing helix chain 'D' and resid 135 through 140 Processing helix chain 'D' and resid 171 through 176 Processing helix chain 'D' and resid 207 through 212 removed outlier: 4.369A pdb=" N GLN D 211 " --> pdb=" O SER D 207 " (cutoff:3.500A) Processing helix chain 'D' and resid 230 through 234 removed outlier: 4.395A pdb=" N HIS D 233 " --> pdb=" O ARG D 230 " (cutoff:3.500A) Processing helix chain 'D' and resid 251 through 258 Processing helix chain 'D' and resid 275 through 286 removed outlier: 4.983A pdb=" N ILE D 281 " --> pdb=" O ASN D 277 " (cutoff:3.500A) Processing helix chain 'D' and resid 301 through 323 removed outlier: 4.745A pdb=" N LEU D 307 " --> pdb=" O MET D 303 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N VAL D 308 " --> pdb=" O ALA D 304 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N GLN D 322 " --> pdb=" O TYR D 318 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N SER D 323 " --> pdb=" O GLU D 319 " (cutoff:3.500A) Processing helix chain 'D' and resid 331 through 336 Processing helix chain 'D' and resid 337 through 354 removed outlier: 5.295A pdb=" N LEU D 343 " --> pdb=" O ASP D 339 " (cutoff:3.500A) removed outlier: 4.746A pdb=" N ALA D 344 " --> pdb=" O PHE D 340 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N VAL D 345 " --> pdb=" O GLY D 341 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N GLU D 346 " --> pdb=" O GLN D 342 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N GLN D 354 " --> pdb=" O GLN D 350 " (cutoff:3.500A) Processing helix chain 'D' and resid 356 through 361 Processing helix chain 'D' and resid 362 through 364 No H-bonds generated for 'chain 'D' and resid 362 through 364' Processing helix chain 'D' and resid 390 through 397 Processing helix chain 'D' and resid 413 through 421 removed outlier: 3.583A pdb=" N SER D 418 " --> pdb=" O LYS D 414 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEU D 420 " --> pdb=" O ILE D 416 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N VAL D 421 " --> pdb=" O LEU D 417 " (cutoff:3.500A) Processing helix chain 'D' and resid 422 through 429 removed outlier: 4.299A pdb=" N MET D 427 " --> pdb=" O ALA D 424 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N LEU D 428 " --> pdb=" O ILE D 425 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N GLU D 429 " --> pdb=" O LEU D 426 " (cutoff:3.500A) Processing helix chain 'D' and resid 498 through 503 Processing helix chain 'D' and resid 505 through 529 removed outlier: 4.393A pdb=" N LEU D 518 " --> pdb=" O THR D 514 " (cutoff:3.500A) Processing helix chain 'D' and resid 539 through 554 removed outlier: 3.963A pdb=" N VAL D 543 " --> pdb=" O GLN D 539 " (cutoff:3.500A) Processing helix chain 'D' and resid 569 through 574 removed outlier: 4.001A pdb=" N TRP D 573 " --> pdb=" O LYS D 569 " (cutoff:3.500A) Processing helix chain 'D' and resid 578 through 595 removed outlier: 3.524A pdb=" N PHE D 593 " --> pdb=" O PHE D 589 " (cutoff:3.500A) Processing helix chain 'D' and resid 612 through 622 removed outlier: 3.673A pdb=" N ILE D 618 " --> pdb=" O ALA D 614 " (cutoff:3.500A) Processing helix chain 'D' and resid 623 through 627 Processing helix chain 'D' and resid 628 through 633 removed outlier: 3.756A pdb=" N ASP D 632 " --> pdb=" O VAL D 628 " (cutoff:3.500A) Processing helix chain 'D' and resid 639 through 648 removed outlier: 4.237A pdb=" N TYR D 643 " --> pdb=" O GLN D 639 " (cutoff:3.500A) removed outlier: 4.701A pdb=" N GLY D 648 " --> pdb=" O VAL D 644 " (cutoff:3.500A) Processing helix chain 'D' and resid 650 through 677 removed outlier: 6.151A pdb=" N TYR D 656 " --> pdb=" O ALA D 652 " (cutoff:3.500A) removed outlier: 5.749A pdb=" N ILE D 657 " --> pdb=" O ASN D 653 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ILE D 660 " --> pdb=" O TYR D 656 " (cutoff:3.500A) Proline residue: D 671 - end of helix removed outlier: 4.219A pdb=" N ILE D 675 " --> pdb=" O PRO D 671 " (cutoff:3.500A) Processing helix chain 'D' and resid 685 through 696 removed outlier: 3.807A pdb=" N ASP D 689 " --> pdb=" O SER D 685 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N HIS D 693 " --> pdb=" O ASP D 689 " (cutoff:3.500A) Proline residue: D 694 - end of helix Processing helix chain 'D' and resid 703 through 707 removed outlier: 3.556A pdb=" N ILE D 707 " --> pdb=" O ALA D 704 " (cutoff:3.500A) Processing helix chain 'D' and resid 726 through 738 removed outlier: 3.606A pdb=" N ALA D 732 " --> pdb=" O PRO D 728 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N PHE D 736 " --> pdb=" O ALA D 732 " (cutoff:3.500A) Processing helix chain 'D' and resid 744 through 749 Processing helix chain 'D' and resid 754 through 774 removed outlier: 4.059A pdb=" N ILE D 760 " --> pdb=" O GLN D 756 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N ILE D 763 " --> pdb=" O ALA D 759 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N TYR D 770 " --> pdb=" O LYS D 766 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N HIS D 771 " --> pdb=" O TYR D 767 " (cutoff:3.500A) Processing helix chain 'D' and resid 783 through 790 removed outlier: 3.922A pdb=" N LEU D 789 " --> pdb=" O PRO D 785 " (cutoff:3.500A) Processing helix chain 'D' and resid 817 through 844 removed outlier: 4.425A pdb=" N GLU D 833 " --> pdb=" O GLU D 829 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ASP D 840 " --> pdb=" O PHE D 836 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N ASP D 841 " --> pdb=" O ASP D 837 " (cutoff:3.500A) Processing helix chain 'D' and resid 847 through 885 removed outlier: 3.865A pdb=" N ILE D 851 " --> pdb=" O SER D 847 " (cutoff:3.500A) 974 hydrogen bonds defined for protein. 2808 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: 5.58 Time building geometry restraints manager: 9.82 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6355 1.34 - 1.45: 4381 1.45 - 1.57: 11665 1.57 - 1.69: 0 1.69 - 1.81: 200 Bond restraints: 22601 Sorted by residual: bond pdb=" C ARG C 242 " pdb=" N PRO C 243 " ideal model delta sigma weight residual 1.332 1.378 -0.046 8.90e-03 1.26e+04 2.66e+01 bond pdb=" C ARG B 242 " pdb=" N PRO B 243 " ideal model delta sigma weight residual 1.332 1.378 -0.045 8.90e-03 1.26e+04 2.61e+01 bond pdb=" C ARG D 242 " pdb=" N PRO D 243 " ideal model delta sigma weight residual 1.332 1.378 -0.045 8.90e-03 1.26e+04 2.60e+01 bond pdb=" C ARG A 242 " pdb=" N PRO A 243 " ideal model delta sigma weight residual 1.332 1.377 -0.044 8.90e-03 1.26e+04 2.50e+01 bond pdb=" C GLN A 239 " pdb=" N PRO A 240 " ideal model delta sigma weight residual 1.337 1.376 -0.040 1.11e-02 8.12e+03 1.29e+01 ... (remaining 22596 not shown) Histogram of bond angle deviations from ideal: 96.92 - 104.71: 334 104.71 - 112.50: 11049 112.50 - 120.29: 10239 120.29 - 128.08: 8779 128.08 - 135.86: 295 Bond angle restraints: 30696 Sorted by residual: angle pdb=" N HIS A 777 " pdb=" CA HIS A 777 " pdb=" C HIS A 777 " ideal model delta sigma weight residual 110.80 127.91 -17.11 2.13e+00 2.20e-01 6.46e+01 angle pdb=" N HIS B 777 " pdb=" CA HIS B 777 " pdb=" C HIS B 777 " ideal model delta sigma weight residual 110.80 127.90 -17.10 2.13e+00 2.20e-01 6.44e+01 angle pdb=" N HIS D 777 " pdb=" CA HIS D 777 " pdb=" C HIS D 777 " ideal model delta sigma weight residual 110.80 127.87 -17.07 2.13e+00 2.20e-01 6.43e+01 angle pdb=" N HIS C 777 " pdb=" CA HIS C 777 " pdb=" C HIS C 777 " ideal model delta sigma weight residual 110.80 127.86 -17.06 2.13e+00 2.20e-01 6.41e+01 angle pdb=" N PRO D 812 " pdb=" CA PRO D 812 " pdb=" CB PRO D 812 " ideal model delta sigma weight residual 103.25 111.24 -7.99 1.05e+00 9.07e-01 5.79e+01 ... (remaining 30691 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.67: 12933 26.67 - 53.34: 319 53.34 - 80.00: 24 80.00 - 106.67: 0 106.67 - 133.34: 8 Dihedral angle restraints: 13284 sinusoidal: 4269 harmonic: 9015 Sorted by residual: dihedral pdb=" CA TYR C 776 " pdb=" C TYR C 776 " pdb=" N HIS C 777 " pdb=" CA HIS C 777 " ideal model delta harmonic sigma weight residual -180.00 -46.66 -133.34 0 5.00e+00 4.00e-02 7.11e+02 dihedral pdb=" CA TYR B 776 " pdb=" C TYR B 776 " pdb=" N HIS B 777 " pdb=" CA HIS B 777 " ideal model delta harmonic sigma weight residual -180.00 -46.68 -133.32 0 5.00e+00 4.00e-02 7.11e+02 dihedral pdb=" CA TYR A 776 " pdb=" C TYR A 776 " pdb=" N HIS A 777 " pdb=" CA HIS A 777 " ideal model delta harmonic sigma weight residual -180.00 -46.69 -133.31 0 5.00e+00 4.00e-02 7.11e+02 ... (remaining 13281 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.093: 3077 0.093 - 0.186: 380 0.186 - 0.279: 58 0.279 - 0.372: 9 0.372 - 0.465: 7 Chirality restraints: 3531 Sorted by residual: chirality pdb=" CA HIS D 777 " pdb=" N HIS D 777 " pdb=" C HIS D 777 " pdb=" CB HIS D 777 " both_signs ideal model delta sigma weight residual False 2.51 2.05 0.46 2.00e-01 2.50e+01 5.40e+00 chirality pdb=" CA HIS B 777 " pdb=" N HIS B 777 " pdb=" C HIS B 777 " pdb=" CB HIS B 777 " both_signs ideal model delta sigma weight residual False 2.51 2.05 0.46 2.00e-01 2.50e+01 5.36e+00 chirality pdb=" CA HIS C 777 " pdb=" N HIS C 777 " pdb=" C HIS C 777 " pdb=" CB HIS C 777 " both_signs ideal model delta sigma weight residual False 2.51 2.05 0.46 2.00e-01 2.50e+01 5.35e+00 ... (remaining 3528 not shown) Planarity restraints: 3910 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE D 512 " -0.033 2.00e-02 2.50e+03 3.18e-02 1.76e+01 pdb=" CG PHE D 512 " 0.071 2.00e-02 2.50e+03 pdb=" CD1 PHE D 512 " -0.020 2.00e-02 2.50e+03 pdb=" CD2 PHE D 512 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 PHE D 512 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE D 512 " -0.022 2.00e-02 2.50e+03 pdb=" CZ PHE D 512 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE C 512 " 0.033 2.00e-02 2.50e+03 3.18e-02 1.76e+01 pdb=" CG PHE C 512 " -0.071 2.00e-02 2.50e+03 pdb=" CD1 PHE C 512 " 0.020 2.00e-02 2.50e+03 pdb=" CD2 PHE C 512 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 PHE C 512 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE C 512 " 0.023 2.00e-02 2.50e+03 pdb=" CZ PHE C 512 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 512 " -0.033 2.00e-02 2.50e+03 3.17e-02 1.75e+01 pdb=" CG PHE A 512 " 0.071 2.00e-02 2.50e+03 pdb=" CD1 PHE A 512 " -0.020 2.00e-02 2.50e+03 pdb=" CD2 PHE A 512 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 PHE A 512 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE A 512 " -0.022 2.00e-02 2.50e+03 pdb=" CZ PHE A 512 " 0.005 2.00e-02 2.50e+03 ... (remaining 3907 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 5649 2.79 - 3.32: 21152 3.32 - 3.85: 34490 3.85 - 4.37: 38935 4.37 - 4.90: 62040 Nonbonded interactions: 162266 Sorted by model distance: nonbonded pdb=" O SER B 337 " pdb=" N ASP B 339 " model vdw 2.263 2.520 nonbonded pdb=" O PHE B 578 " pdb=" OG SER B 581 " model vdw 2.272 2.440 nonbonded pdb=" O PHE C 578 " pdb=" OG SER C 581 " model vdw 2.272 2.440 nonbonded pdb=" O PHE A 578 " pdb=" OG SER A 581 " model vdw 2.273 2.440 nonbonded pdb=" O PHE D 578 " pdb=" OG SER D 581 " model vdw 2.273 2.440 ... (remaining 162261 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 1 through 331 or (resid 332 through 334 and (name N or nam \ e CA or name C or name O or name CB )) or resid 335 or (resid 336 and (name N or \ name CA or name C or name O or name CB )) or resid 337 through 886)) selection = chain 'B' selection = (chain 'C' and (resid 1 through 331 or (resid 332 through 334 and (name N or nam \ e CA or name C or name O or name CB )) or resid 335 or (resid 336 and (name N or \ name CA or name C or name O or name CB )) or resid 337 through 886)) selection = (chain 'D' and (resid 1 through 331 or (resid 332 through 334 and (name N or nam \ e CA or name C or name O or name CB )) or resid 335 or (resid 336 and (name N or \ name CA or name C or name O or name CB )) or resid 337 through 886)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 116 5.16 5 C 14320 2.51 5 N 3789 2.21 5 O 3949 1.98 5 sf(0) = scattering factor at diffraction angle 0. 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.730 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: 5.460 Check model and map are aligned: 0.330 Process input model: 53.460 Find NCS groups from input model: 1.550 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Set scattering table: 0.210 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:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 64.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7101 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 : 0.008 0.081 22601 Z= 0.481 Angle : 1.491 17.114 30696 Z= 0.848 Chirality : 0.070 0.465 3531 Planarity : 0.008 0.076 3910 Dihedral : 12.820 133.338 7388 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 12.32 Ramachandran Plot: Outliers : 1.32 % Allowed : 12.10 % Favored : 86.58 % Rotamer Outliers : 0.59 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 4.93 % Twisted Proline : 11.11 % Twisted General : 2.80 % 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: -5.34 (0.14), residues: 2496 helix: -3.42 (0.10), residues: 1504 sheet: None (None), residues: 0 loop : -3.57 (0.19), residues: 992 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4992 Ramachandran restraints generated. 2496 Oldfield, 0 Emsley, 2496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4992 Ramachandran restraints generated. 2496 Oldfield, 0 Emsley, 2496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 814 residues out of total 2340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 803 time to evaluate : 2.415 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: 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 outliers start: 11 outliers final: 0 residues processed: 814 average time/residue: 0.3274 time to fit residues: 411.2879 Evaluate side-chains 513 residues out of total 2340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 513 time to evaluate : 2.327 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.2286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 256 optimal weight: 0.9990 chunk 230 optimal weight: 9.9990 chunk 127 optimal weight: 3.9990 chunk 78 optimal weight: 10.0000 chunk 155 optimal weight: 10.0000 chunk 123 optimal weight: 5.9990 chunk 238 optimal weight: 10.0000 chunk 92 optimal weight: 10.0000 chunk 144 optimal weight: 0.0030 chunk 177 optimal weight: 0.5980 chunk 276 optimal weight: 0.6980 overall best weight: 1.2594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 394 GLN A 406 ASN A 504 HIS ** A 751 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 771 HIS A 821 GLN ** B 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 406 ASN B 504 HIS ** B 751 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 777 HIS B 821 GLN B 873 ASN C 390 HIS ** C 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 406 ASN C 568 GLN ** C 751 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 821 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 825 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 406 ASN D 504 HIS ** D 738 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 771 HIS D 821 GLN D 864 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7278 moved from start: 0.3767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.048 22601 Z= 0.270 Angle : 1.047 19.218 30696 Z= 0.481 Chirality : 0.046 0.255 3531 Planarity : 0.005 0.068 3910 Dihedral : 8.213 57.786 3211 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 16.04 Ramachandran Plot: Outliers : 0.48 % Allowed : 10.30 % Favored : 89.22 % Rotamer Outliers : 0.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 5.92 % Twisted Proline : 8.33 % Twisted General : 0.95 % 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: -3.52 (0.16), residues: 2496 helix: -1.63 (0.12), residues: 1580 sheet: None (None), residues: 0 loop : -3.52 (0.20), residues: 916 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4992 Ramachandran restraints generated. 2496 Oldfield, 0 Emsley, 2496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4992 Ramachandran restraints generated. 2496 Oldfield, 0 Emsley, 2496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 643 residues out of total 2340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 634 time to evaluate : 2.205 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 outliers start: 9 outliers final: 4 residues processed: 641 average time/residue: 0.3208 time to fit residues: 318.8514 Evaluate side-chains 473 residues out of total 2340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 469 time to evaluate : 2.265 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.2114 time to fit residues: 4.6303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 153 optimal weight: 10.0000 chunk 85 optimal weight: 10.0000 chunk 229 optimal weight: 10.0000 chunk 187 optimal weight: 2.9990 chunk 76 optimal weight: 10.0000 chunk 276 optimal weight: 1.9990 chunk 298 optimal weight: 4.9990 chunk 246 optimal weight: 9.9990 chunk 274 optimal weight: 0.0030 chunk 94 optimal weight: 8.9990 chunk 221 optimal weight: 1.9990 overall best weight: 2.3998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 394 GLN ** A 738 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 751 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 864 GLN A 873 ASN C 192 ASN ** C 622 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 751 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 821 GLN C 825 HIS C 864 GLN ** D 731 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 738 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7511 moved from start: 0.5198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.055 22601 Z= 0.389 Angle : 1.114 18.566 30696 Z= 0.513 Chirality : 0.049 0.249 3531 Planarity : 0.005 0.062 3910 Dihedral : 7.793 43.579 3211 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 18.46 Ramachandran Plot: Outliers : 0.48 % Allowed : 11.10 % Favored : 88.42 % Rotamer Outliers : 0.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 5.92 % Twisted Proline : 8.33 % Twisted General : 0.86 % 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: -3.21 (0.16), residues: 2496 helix: -1.30 (0.12), residues: 1636 sheet: None (None), residues: 0 loop : -3.71 (0.20), residues: 860 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4992 Ramachandran restraints generated. 2496 Oldfield, 0 Emsley, 2496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4992 Ramachandran restraints generated. 2496 Oldfield, 0 Emsley, 2496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 583 residues out of total 2340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 579 time to evaluate : 2.409 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 outliers start: 4 outliers final: 2 residues processed: 582 average time/residue: 0.3223 time to fit residues: 295.0587 Evaluate side-chains 470 residues out of total 2340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 468 time to evaluate : 2.668 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.2198 time to fit residues: 4.4141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 273 optimal weight: 0.8980 chunk 207 optimal weight: 0.8980 chunk 143 optimal weight: 1.9990 chunk 30 optimal weight: 0.9980 chunk 131 optimal weight: 0.8980 chunk 185 optimal weight: 1.9990 chunk 277 optimal weight: 0.5980 chunk 293 optimal weight: 0.7980 chunk 145 optimal weight: 2.9990 chunk 263 optimal weight: 0.9990 chunk 79 optimal weight: 10.0000 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 622 ASN A 731 GLN A 738 GLN A 744 ASN ** A 751 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 771 HIS A 777 HIS ** A 830 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 864 GLN ** B 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 622 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 751 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 830 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 622 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 731 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 751 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 771 HIS ** C 830 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 731 GLN D 771 HIS D 777 HIS ** D 830 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7385 moved from start: 0.5731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.050 22601 Z= 0.217 Angle : 1.006 18.883 30696 Z= 0.446 Chirality : 0.044 0.247 3531 Planarity : 0.004 0.055 3910 Dihedral : 6.845 40.516 3211 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 16.36 Ramachandran Plot: Outliers : 0.48 % Allowed : 9.90 % Favored : 89.62 % Rotamer Outliers : 0.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 6.09 % Twisted Proline : 3.70 % Twisted General : 0.33 % 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: -2.46 (0.17), residues: 2496 helix: -0.61 (0.13), residues: 1548 sheet: None (None), residues: 0 loop : -3.39 (0.20), residues: 948 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4992 Ramachandran restraints generated. 2496 Oldfield, 0 Emsley, 2496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4992 Ramachandran restraints generated. 2496 Oldfield, 0 Emsley, 2496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 581 residues out of total 2340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 576 time to evaluate : 2.394 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 outliers start: 5 outliers final: 2 residues processed: 578 average time/residue: 0.3147 time to fit residues: 287.2945 Evaluate side-chains 466 residues out of total 2340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 464 time to evaluate : 2.507 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.2162 time to fit residues: 4.3733 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 244 optimal weight: 5.9990 chunk 166 optimal weight: 0.5980 chunk 4 optimal weight: 10.0000 chunk 218 optimal weight: 1.9990 chunk 121 optimal weight: 0.5980 chunk 250 optimal weight: 5.9990 chunk 203 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 150 optimal weight: 2.9990 chunk 263 optimal weight: 1.9990 chunk 74 optimal weight: 0.9990 overall best weight: 1.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 622 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 751 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 777 HIS ** A 830 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 864 GLN B 231 HIS ** B 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 622 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 830 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 751 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 821 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 830 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 830 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7427 moved from start: 0.6176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.052 22601 Z= 0.247 Angle : 1.002 18.564 30696 Z= 0.447 Chirality : 0.045 0.256 3531 Planarity : 0.004 0.054 3910 Dihedral : 6.627 37.156 3211 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 16.72 Ramachandran Plot: Outliers : 0.48 % Allowed : 9.70 % Favored : 89.82 % Rotamer Outliers : 0.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 6.09 % Twisted Proline : 0.00 % Twisted General : 0.33 % 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: -2.21 (0.17), residues: 2496 helix: -0.35 (0.14), residues: 1548 sheet: None (None), residues: 0 loop : -3.43 (0.19), residues: 948 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4992 Ramachandran restraints generated. 2496 Oldfield, 0 Emsley, 2496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4992 Ramachandran restraints generated. 2496 Oldfield, 0 Emsley, 2496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 540 residues out of total 2340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 538 time to evaluate : 2.617 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 outliers start: 2 outliers final: 1 residues processed: 538 average time/residue: 0.3091 time to fit residues: 266.8125 Evaluate side-chains 450 residues out of total 2340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 449 time to evaluate : 2.508 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.2314 time to fit residues: 3.7717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 98 optimal weight: 0.0970 chunk 264 optimal weight: 4.9990 chunk 58 optimal weight: 0.0030 chunk 172 optimal weight: 7.9990 chunk 72 optimal weight: 7.9990 chunk 294 optimal weight: 0.6980 chunk 244 optimal weight: 0.0470 chunk 136 optimal weight: 1.9990 chunk 24 optimal weight: 0.1980 chunk 97 optimal weight: 0.6980 chunk 154 optimal weight: 9.9990 overall best weight: 0.2086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 622 ASN ** A 751 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 830 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 864 GLN B 298 HIS ** B 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 622 ASN ** B 751 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 830 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 821 GLN C 830 GLN ** D 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 731 GLN ** D 777 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 830 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7280 moved from start: 0.6481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.044 22601 Z= 0.174 Angle : 0.962 19.238 30696 Z= 0.420 Chirality : 0.042 0.212 3531 Planarity : 0.004 0.058 3910 Dihedral : 6.060 34.329 3211 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 14.60 Ramachandran Plot: Outliers : 0.48 % Allowed : 9.33 % Favored : 90.18 % Rotamer Outliers : 0.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 6.09 % Twisted Proline : 2.78 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.90 (0.17), residues: 2496 helix: -0.01 (0.14), residues: 1524 sheet: None (None), residues: 0 loop : -3.41 (0.19), residues: 972 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4992 Ramachandran restraints generated. 2496 Oldfield, 0 Emsley, 2496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4992 Ramachandran restraints generated. 2496 Oldfield, 0 Emsley, 2496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 554 residues out of total 2340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 553 time to evaluate : 2.504 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 outliers start: 1 outliers final: 0 residues processed: 553 average time/residue: 0.3555 time to fit residues: 314.9576 Evaluate side-chains 454 residues out of total 2340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 454 time to evaluate : 2.444 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.2973 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 283 optimal weight: 0.8980 chunk 33 optimal weight: 0.4980 chunk 167 optimal weight: 0.7980 chunk 214 optimal weight: 1.9990 chunk 166 optimal weight: 7.9990 chunk 247 optimal weight: 0.9990 chunk 164 optimal weight: 6.9990 chunk 293 optimal weight: 2.9990 chunk 183 optimal weight: 3.9990 chunk 178 optimal weight: 0.6980 chunk 135 optimal weight: 0.0570 overall best weight: 0.5898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 731 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 751 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 830 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 297 GLN ** B 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 622 ASN ** B 751 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 830 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 731 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 830 GLN ** D 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 731 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 830 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7308 moved from start: 0.6699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.041 22601 Z= 0.188 Angle : 0.955 18.708 30696 Z= 0.417 Chirality : 0.043 0.194 3531 Planarity : 0.004 0.053 3910 Dihedral : 5.901 31.057 3211 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 14.87 Ramachandran Plot: Outliers : 0.44 % Allowed : 9.25 % Favored : 90.30 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 6.09 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.71 (0.17), residues: 2496 helix: 0.16 (0.14), residues: 1504 sheet: None (None), residues: 0 loop : -3.29 (0.19), residues: 992 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4992 Ramachandran restraints generated. 2496 Oldfield, 0 Emsley, 2496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4992 Ramachandran restraints generated. 2496 Oldfield, 0 Emsley, 2496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 522 residues out of total 2340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 522 time to evaluate : 2.316 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 522 average time/residue: 0.3244 time to fit residues: 268.8184 Evaluate side-chains 437 residues out of total 2340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 437 time to evaluate : 2.334 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.3086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 181 optimal weight: 4.9990 chunk 117 optimal weight: 1.9990 chunk 174 optimal weight: 0.4980 chunk 88 optimal weight: 5.9990 chunk 57 optimal weight: 0.3980 chunk 56 optimal weight: 0.6980 chunk 186 optimal weight: 0.8980 chunk 199 optimal weight: 0.7980 chunk 144 optimal weight: 4.9990 chunk 27 optimal weight: 1.9990 chunk 230 optimal weight: 9.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 622 ASN A 744 ASN ** A 751 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 830 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 860 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 622 ASN B 744 ASN ** B 751 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 830 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 622 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 821 GLN C 830 GLN D 297 GLN D 298 HIS ** D 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 830 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7306 moved from start: 0.6926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.040 22601 Z= 0.191 Angle : 0.952 18.695 30696 Z= 0.415 Chirality : 0.043 0.197 3531 Planarity : 0.004 0.052 3910 Dihedral : 5.835 31.009 3211 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 14.65 Ramachandran Plot: Outliers : 0.32 % Allowed : 9.58 % Favored : 90.10 % Rotamer Outliers : 0.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 6.09 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.72 (0.17), residues: 2496 helix: 0.14 (0.14), residues: 1528 sheet: None (None), residues: 0 loop : -3.36 (0.19), residues: 968 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4992 Ramachandran restraints generated. 2496 Oldfield, 0 Emsley, 2496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4992 Ramachandran restraints generated. 2496 Oldfield, 0 Emsley, 2496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 513 residues out of total 2340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 512 time to evaluate : 2.390 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 512 average time/residue: 0.3046 time to fit residues: 250.2771 Evaluate side-chains 432 residues out of total 2340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 432 time to evaluate : 2.316 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.2952 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/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-4877/modules/cctbx_project/iotbx/cli_parser.py", line 865, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/phenix/phenix/programs/real_space_refine.py", line 192, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 297, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 673, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 736, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/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-4877/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-4877/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-4877/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-4877/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-4877/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-4877/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/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-4877/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-4877/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-4877/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-4877/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: 68.0434 > 50: distance: 18 - 24: 12.547 distance: 24 - 25: 22.981 distance: 25 - 26: 22.253 distance: 25 - 28: 20.628 distance: 26 - 27: 39.077 distance: 26 - 33: 55.747 distance: 28 - 29: 9.569 distance: 29 - 30: 33.118 distance: 30 - 31: 34.508 distance: 33 - 34: 41.649 distance: 34 - 35: 30.254 distance: 34 - 37: 18.680 distance: 35 - 36: 26.835 distance: 35 - 42: 33.914 distance: 37 - 38: 11.668 distance: 38 - 39: 11.823 distance: 39 - 40: 16.968 distance: 39 - 41: 15.723 distance: 43 - 44: 5.063 distance: 43 - 46: 34.958 distance: 44 - 45: 34.557 distance: 46 - 47: 37.204 distance: 47 - 48: 50.794 distance: 47 - 49: 8.361 distance: 50 - 51: 12.695 distance: 50 - 56: 34.816 distance: 51 - 52: 23.671 distance: 51 - 54: 30.943 distance: 52 - 53: 16.785 distance: 52 - 57: 10.661 distance: 54 - 55: 10.547 distance: 57 - 58: 3.377 distance: 58 - 59: 15.209 distance: 58 - 61: 5.427 distance: 59 - 60: 38.451 distance: 59 - 63: 7.372 distance: 61 - 62: 21.131 distance: 63 - 64: 23.643 distance: 64 - 65: 22.636 distance: 64 - 67: 32.015 distance: 65 - 70: 22.030 distance: 67 - 68: 12.411 distance: 67 - 69: 29.601 distance: 70 - 71: 14.572 distance: 71 - 72: 17.167 distance: 71 - 74: 16.752 distance: 72 - 73: 12.766 distance: 72 - 79: 14.316 distance: 74 - 75: 15.339 distance: 75 - 76: 31.946 distance: 76 - 77: 25.952 distance: 76 - 78: 12.472 distance: 79 - 80: 5.696 distance: 80 - 81: 8.064 distance: 80 - 83: 20.284 distance: 81 - 82: 16.009 distance: 81 - 88: 12.505 distance: 82 - 117: 13.109 distance: 83 - 84: 13.107 distance: 84 - 85: 23.348 distance: 85 - 87: 4.686 distance: 88 - 89: 5.120 distance: 89 - 90: 5.795 distance: 89 - 92: 11.304 distance: 90 - 91: 17.308 distance: 90 - 102: 14.930 distance: 91 - 125: 29.283 distance: 93 - 94: 6.113 distance: 94 - 96: 5.602 distance: 95 - 97: 15.949 distance: 96 - 97: 17.143 distance: 97 - 99: 9.717 distance: 98 - 100: 7.337 distance: 99 - 101: 9.749 distance: 100 - 101: 6.298 distance: 102 - 103: 5.982 distance: 103 - 104: 6.698 distance: 103 - 106: 4.843 distance: 104 - 105: 14.491 distance: 104 - 110: 10.225 distance: 105 - 130: 7.180 distance: 106 - 107: 14.630 distance: 106 - 108: 14.010 distance: 107 - 109: 11.406