Starting phenix.real_space_refine on Sun Aug 4 20:18:33 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dtv_30855/08_2024/7dtv_30855.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dtv_30855/08_2024/7dtv_30855.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dtv_30855/08_2024/7dtv_30855.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dtv_30855/08_2024/7dtv_30855.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dtv_30855/08_2024/7dtv_30855.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dtv_30855/08_2024/7dtv_30855.cif" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Ca 4 9.91 5 S 46 5.16 5 C 7126 2.51 5 N 1940 2.21 5 O 2160 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 109": "OE1" <-> "OE2" Residue "A ARG 205": "NH1" <-> "NH2" Residue "A ARG 220": "NH1" <-> "NH2" Residue "A GLU 229": "OE1" <-> "OE2" Residue "A GLU 250": "OE1" <-> "OE2" Residue "A ARG 286": "NH1" <-> "NH2" Residue "A ARG 331": "NH1" <-> "NH2" Residue "A ARG 340": "NH1" <-> "NH2" Residue "A GLU 353": "OE1" <-> "OE2" Residue "A TYR 421": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 441": "NH1" <-> "NH2" Residue "A ARG 551": "NH1" <-> "NH2" Residue "A GLU 558": "OE1" <-> "OE2" Residue "A GLU 567": "OE1" <-> "OE2" Residue "B GLU 109": "OE1" <-> "OE2" Residue "B ARG 205": "NH1" <-> "NH2" Residue "B ARG 220": "NH1" <-> "NH2" Residue "B GLU 229": "OE1" <-> "OE2" Residue "B GLU 250": "OE1" <-> "OE2" Residue "B ARG 286": "NH1" <-> "NH2" Residue "B ARG 331": "NH1" <-> "NH2" Residue "B ARG 340": "NH1" <-> "NH2" Residue "B GLU 353": "OE1" <-> "OE2" Residue "B TYR 421": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 441": "NH1" <-> "NH2" Residue "B ARG 551": "NH1" <-> "NH2" Residue "B GLU 558": "OE1" <-> "OE2" Residue "B GLU 567": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 11276 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 5495 Number of conformers: 1 Conformer: "" Number of residues, atoms: 779, 5495 Classifications: {'peptide': 779} Incomplete info: {'truncation_to_alanine': 206} Link IDs: {'PTRANS': 29, 'TRANS': 749} Chain breaks: 3 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 750 Unresolved non-hydrogen angles: 965 Unresolved non-hydrogen dihedrals: 633 Unresolved non-hydrogen chiralities: 77 Planarities with less than four sites: {'GLN:plan1': 5, 'ASP:plan': 10, 'TYR:plan': 6, 'ASN:plan1': 8, 'TRP:plan': 2, 'HIS:plan': 2, 'PHE:plan': 30, 'GLU:plan': 16, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 413 Chain: "B" Number of atoms: 5495 Number of conformers: 1 Conformer: "" Number of residues, atoms: 779, 5495 Classifications: {'peptide': 779} Incomplete info: {'truncation_to_alanine': 206} Link IDs: {'PTRANS': 29, 'TRANS': 749} Chain breaks: 3 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 750 Unresolved non-hydrogen angles: 965 Unresolved non-hydrogen dihedrals: 633 Unresolved non-hydrogen chiralities: 77 Planarities with less than four sites: {'GLN:plan1': 5, 'ASP:plan': 10, 'TYR:plan': 6, 'ASN:plan1': 8, 'TRP:plan': 2, 'HIS:plan': 2, 'PHE:plan': 30, 'GLU:plan': 16, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 413 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "A" Number of atoms: 59 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 59 Unusual residues: {' CA': 3, 'NAG': 4} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "B" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "B" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 57 Unusual residues: {' CA': 1, 'NAG': 4} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 7.13, per 1000 atoms: 0.63 Number of scatterers: 11276 At special positions: 0 Unit cell: (90.246, 94.302, 179.478, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Ca 4 19.99 S 46 16.00 O 2160 8.00 N 1940 7.00 C 7126 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=18, symmetry=0 Simple disulfide: pdb=" SG CYS A 60 " - pdb=" SG CYS A 101 " distance=2.03 Simple disulfide: pdb=" SG CYS A 236 " - pdb=" SG CYS A 561 " distance=2.14 Simple disulfide: pdb=" SG CYS A 358 " - pdb=" SG CYS A 395 " distance=2.20 Simple disulfide: pdb=" SG CYS A 437 " - pdb=" SG CYS A 449 " distance=2.03 Simple disulfide: pdb=" SG CYS A 542 " - pdb=" SG CYS A 562 " distance=2.02 Simple disulfide: pdb=" SG CYS A 546 " - pdb=" SG CYS A 565 " distance=2.02 Simple disulfide: pdb=" SG CYS A 568 " - pdb=" SG CYS A 582 " distance=2.03 Simple disulfide: pdb=" SG CYS A 585 " - pdb=" SG CYS A 598 " distance=2.03 Simple disulfide: pdb=" SG CYS A 677 " - pdb=" SG CYS A 765 " distance=2.03 Simple disulfide: pdb=" SG CYS B 60 " - pdb=" SG CYS B 101 " distance=2.03 Simple disulfide: pdb=" SG CYS B 236 " - pdb=" SG CYS B 561 " distance=2.14 Simple disulfide: pdb=" SG CYS B 358 " - pdb=" SG CYS B 395 " distance=2.20 Simple disulfide: pdb=" SG CYS B 437 " - pdb=" SG CYS B 449 " distance=2.03 Simple disulfide: pdb=" SG CYS B 542 " - pdb=" SG CYS B 562 " distance=2.02 Simple disulfide: pdb=" SG CYS B 546 " - pdb=" SG CYS B 565 " distance=2.02 Simple disulfide: pdb=" SG CYS B 568 " - pdb=" SG CYS B 582 " distance=2.03 Simple disulfide: pdb=" SG CYS B 585 " - pdb=" SG CYS B 598 " distance=2.03 Simple disulfide: pdb=" SG CYS B 677 " - pdb=" SG CYS B 765 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " " NAG D 2 " - " NAG D 3 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " NAG F 3 " NAG-ASN " NAG A1104 " - " ASN A 261 " " NAG A1105 " - " ASN A 287 " " NAG A1106 " - " ASN A 446 " " NAG A1107 " - " ASN A 468 " " NAG B1103 " - " ASN B 261 " " NAG B1104 " - " ASN B 287 " " NAG B1105 " - " ASN B 446 " " NAG B1106 " - " ASN B 468 " " NAG C 1 " - " ASN A 488 " " NAG D 1 " - " ASN A 541 " " NAG E 1 " - " ASN B 488 " " NAG F 1 " - " ASN B 541 " Time building additional restraints: 4.25 Conformation dependent library (CDL) restraints added in 2.3 seconds 3084 Ramachandran restraints generated. 1542 Oldfield, 0 Emsley, 1542 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2932 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 18 sheets defined 41.7% alpha, 7.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.37 Creating SS restraints... Processing helix chain 'A' and resid 64 through 84 removed outlier: 3.524A pdb=" N ALA A 77 " --> pdb=" O ALA A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 103 through 115 removed outlier: 3.648A pdb=" N ALA A 110 " --> pdb=" O LYS A 106 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N SER A 113 " --> pdb=" O GLU A 109 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N VAL A 115 " --> pdb=" O THR A 111 " (cutoff:3.500A) Processing helix chain 'A' and resid 149 through 154 Processing helix chain 'A' and resid 172 through 176 removed outlier: 3.526A pdb=" N SER A 175 " --> pdb=" O ARG A 172 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ASN A 176 " --> pdb=" O LEU A 173 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 172 through 176' Processing helix chain 'A' and resid 192 through 204 removed outlier: 3.728A pdb=" N ALA A 198 " --> pdb=" O ALA A 194 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ILE A 201 " --> pdb=" O MET A 197 " (cutoff:3.500A) Processing helix chain 'A' and resid 219 through 230 removed outlier: 3.728A pdb=" N GLU A 224 " --> pdb=" O ARG A 220 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N LYS A 225 " --> pdb=" O PRO A 221 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N PHE A 226 " --> pdb=" O GLY A 222 " (cutoff:3.500A) Processing helix chain 'A' and resid 248 through 261 Processing helix chain 'A' and resid 276 through 287 removed outlier: 3.516A pdb=" N GLU A 282 " --> pdb=" O PRO A 278 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 311 Processing helix chain 'A' and resid 329 through 335 removed outlier: 3.721A pdb=" N LYS A 335 " --> pdb=" O ARG A 331 " (cutoff:3.500A) Processing helix chain 'A' and resid 347 through 357 Processing helix chain 'A' and resid 415 through 436 removed outlier: 3.672A pdb=" N ASN A 419 " --> pdb=" O ARG A 415 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ASP A 433 " --> pdb=" O HIS A 429 " (cutoff:3.500A) Processing helix chain 'A' and resid 444 through 448 Processing helix chain 'A' and resid 456 through 466 removed outlier: 3.597A pdb=" N VAL A 460 " --> pdb=" O GLU A 456 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N HIS A 466 " --> pdb=" O LYS A 462 " (cutoff:3.500A) Processing helix chain 'A' and resid 529 through 533 removed outlier: 3.617A pdb=" N PHE A 533 " --> pdb=" O TRP A 530 " (cutoff:3.500A) Processing helix chain 'A' and resid 613 through 637 removed outlier: 3.537A pdb=" N VAL A 630 " --> pdb=" O LEU A 626 " (cutoff:3.500A) Processing helix chain 'A' and resid 652 through 664 removed outlier: 4.534A pdb=" N LEU A 658 " --> pdb=" O LEU A 654 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N PHE A 662 " --> pdb=" O LEU A 658 " (cutoff:3.500A) Processing helix chain 'A' and resid 665 through 667 No H-bonds generated for 'chain 'A' and resid 665 through 667' Processing helix chain 'A' and resid 673 through 679 Processing helix chain 'A' and resid 681 through 691 removed outlier: 4.320A pdb=" N SER A 687 " --> pdb=" O ALA A 683 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N VAL A 689 " --> pdb=" O GLY A 685 " (cutoff:3.500A) Processing helix chain 'A' and resid 692 through 697 Processing helix chain 'A' and resid 727 through 730 Processing helix chain 'A' and resid 731 through 746 removed outlier: 4.839A pdb=" N TYR A 744 " --> pdb=" O VAL A 740 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N THR A 745 " --> pdb=" O ILE A 741 " (cutoff:3.500A) Processing helix chain 'A' and resid 770 through 780 Processing helix chain 'A' and resid 782 through 787 Processing helix chain 'A' and resid 787 through 792 Processing helix chain 'A' and resid 802 through 827 removed outlier: 4.252A pdb=" N ILE A 822 " --> pdb=" O TRP A 818 " (cutoff:3.500A) Proline residue: A 823 - end of helix Processing helix chain 'A' and resid 830 through 835 removed outlier: 3.849A pdb=" N SER A 834 " --> pdb=" O GLY A 830 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N ALA A 835 " --> pdb=" O LYS A 831 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 830 through 835' Processing helix chain 'A' and resid 836 through 851 removed outlier: 3.543A pdb=" N GLY A 847 " --> pdb=" O ALA A 843 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N LEU A 849 " --> pdb=" O SER A 845 " (cutoff:3.500A) Processing helix chain 'A' and resid 852 through 858 Processing helix chain 'B' and resid 64 through 84 removed outlier: 3.524A pdb=" N ALA B 77 " --> pdb=" O ALA B 73 " (cutoff:3.500A) Processing helix chain 'B' and resid 103 through 115 removed outlier: 3.648A pdb=" N ALA B 110 " --> pdb=" O LYS B 106 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N SER B 113 " --> pdb=" O GLU B 109 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N VAL B 115 " --> pdb=" O THR B 111 " (cutoff:3.500A) Processing helix chain 'B' and resid 149 through 154 Processing helix chain 'B' and resid 172 through 176 removed outlier: 3.526A pdb=" N SER B 175 " --> pdb=" O ARG B 172 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ASN B 176 " --> pdb=" O LEU B 173 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 172 through 176' Processing helix chain 'B' and resid 192 through 204 removed outlier: 3.727A pdb=" N ALA B 198 " --> pdb=" O ALA B 194 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ILE B 201 " --> pdb=" O MET B 197 " (cutoff:3.500A) Processing helix chain 'B' and resid 219 through 230 removed outlier: 3.728A pdb=" N GLU B 224 " --> pdb=" O ARG B 220 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N LYS B 225 " --> pdb=" O PRO B 221 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N PHE B 226 " --> pdb=" O GLY B 222 " (cutoff:3.500A) Processing helix chain 'B' and resid 248 through 261 Processing helix chain 'B' and resid 276 through 287 removed outlier: 3.517A pdb=" N GLU B 282 " --> pdb=" O PRO B 278 " (cutoff:3.500A) Processing helix chain 'B' and resid 307 through 311 Processing helix chain 'B' and resid 329 through 335 removed outlier: 3.722A pdb=" N LYS B 335 " --> pdb=" O ARG B 331 " (cutoff:3.500A) Processing helix chain 'B' and resid 347 through 357 Processing helix chain 'B' and resid 415 through 436 removed outlier: 3.672A pdb=" N ASN B 419 " --> pdb=" O ARG B 415 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ASP B 433 " --> pdb=" O HIS B 429 " (cutoff:3.500A) Processing helix chain 'B' and resid 444 through 448 Processing helix chain 'B' and resid 456 through 466 removed outlier: 3.598A pdb=" N VAL B 460 " --> pdb=" O GLU B 456 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N HIS B 466 " --> pdb=" O LYS B 462 " (cutoff:3.500A) Processing helix chain 'B' and resid 529 through 533 removed outlier: 3.617A pdb=" N PHE B 533 " --> pdb=" O TRP B 530 " (cutoff:3.500A) Processing helix chain 'B' and resid 613 through 637 removed outlier: 3.537A pdb=" N VAL B 630 " --> pdb=" O LEU B 626 " (cutoff:3.500A) Processing helix chain 'B' and resid 652 through 664 removed outlier: 4.534A pdb=" N LEU B 658 " --> pdb=" O LEU B 654 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N PHE B 662 " --> pdb=" O LEU B 658 " (cutoff:3.500A) Processing helix chain 'B' and resid 665 through 667 No H-bonds generated for 'chain 'B' and resid 665 through 667' Processing helix chain 'B' and resid 673 through 679 Processing helix chain 'B' and resid 681 through 691 removed outlier: 4.321A pdb=" N SER B 687 " --> pdb=" O ALA B 683 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N VAL B 689 " --> pdb=" O GLY B 685 " (cutoff:3.500A) Processing helix chain 'B' and resid 692 through 697 Processing helix chain 'B' and resid 727 through 730 Processing helix chain 'B' and resid 731 through 746 removed outlier: 4.839A pdb=" N TYR B 744 " --> pdb=" O VAL B 740 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N THR B 745 " --> pdb=" O ILE B 741 " (cutoff:3.500A) Processing helix chain 'B' and resid 770 through 780 Processing helix chain 'B' and resid 782 through 787 Processing helix chain 'B' and resid 787 through 792 Processing helix chain 'B' and resid 802 through 827 removed outlier: 4.252A pdb=" N ILE B 822 " --> pdb=" O TRP B 818 " (cutoff:3.500A) Proline residue: B 823 - end of helix Processing helix chain 'B' and resid 830 through 835 removed outlier: 3.849A pdb=" N SER B 834 " --> pdb=" O GLY B 830 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N ALA B 835 " --> pdb=" O LYS B 831 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 830 through 835' Processing helix chain 'B' and resid 836 through 851 removed outlier: 3.543A pdb=" N GLY B 847 " --> pdb=" O ALA B 843 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N LEU B 849 " --> pdb=" O SER B 845 " (cutoff:3.500A) Processing helix chain 'B' and resid 852 through 858 Processing sheet with id=AA1, first strand: chain 'A' and resid 26 through 28 removed outlier: 6.256A pdb=" N ILE A 32 " --> pdb=" O GLY A 94 " (cutoff:3.500A) removed outlier: 7.746A pdb=" N ARG A 96 " --> pdb=" O ILE A 32 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 26 through 28 removed outlier: 6.331A pdb=" N GLY A 36 " --> pdb=" O PHE A 98 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 164 through 166 removed outlier: 5.727A pdb=" N GLN A 164 " --> pdb=" O LEU A 184 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 237 through 243 removed outlier: 7.822A pdb=" N VAL A 209 " --> pdb=" O ASP A 238 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N SER A 240 " --> pdb=" O VAL A 209 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N THR A 211 " --> pdb=" O SER A 240 " (cutoff:3.500A) removed outlier: 5.969A pdb=" N LEU A 242 " --> pdb=" O THR A 211 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N ALA A 213 " --> pdb=" O LEU A 242 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N GLY A 210 " --> pdb=" O VAL A 268 " (cutoff:3.500A) removed outlier: 7.681A pdb=" N PHE A 270 " --> pdb=" O GLY A 210 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N ILE A 212 " --> pdb=" O PHE A 270 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 469 through 470 removed outlier: 3.541A pdb=" N PHE A 469 " --> pdb=" O VAL A 477 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 492 through 495 Processing sheet with id=AA7, first strand: chain 'A' and resid 509 through 511 removed outlier: 3.664A pdb=" N PHE A 522 " --> pdb=" O TYR A 510 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 553 through 554 Processing sheet with id=AA9, first strand: chain 'A' and resid 589 through 590 removed outlier: 3.815A pdb=" N ALA A 600 " --> pdb=" O TRP A 590 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 26 through 28 removed outlier: 6.256A pdb=" N ILE B 32 " --> pdb=" O GLY B 94 " (cutoff:3.500A) removed outlier: 7.746A pdb=" N ARG B 96 " --> pdb=" O ILE B 32 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 26 through 28 removed outlier: 6.331A pdb=" N GLY B 36 " --> pdb=" O PHE B 98 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 164 through 166 removed outlier: 5.727A pdb=" N GLN B 164 " --> pdb=" O LEU B 184 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'B' and resid 237 through 243 removed outlier: 7.822A pdb=" N VAL B 209 " --> pdb=" O ASP B 238 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N SER B 240 " --> pdb=" O VAL B 209 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N THR B 211 " --> pdb=" O SER B 240 " (cutoff:3.500A) removed outlier: 5.968A pdb=" N LEU B 242 " --> pdb=" O THR B 211 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N ALA B 213 " --> pdb=" O LEU B 242 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N GLY B 210 " --> pdb=" O VAL B 268 " (cutoff:3.500A) removed outlier: 7.681A pdb=" N PHE B 270 " --> pdb=" O GLY B 210 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N ILE B 212 " --> pdb=" O PHE B 270 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 469 through 470 removed outlier: 3.541A pdb=" N PHE B 469 " --> pdb=" O VAL B 477 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 492 through 495 Processing sheet with id=AB7, first strand: chain 'B' and resid 509 through 511 removed outlier: 3.664A pdb=" N PHE B 522 " --> pdb=" O TYR B 510 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 553 through 554 Processing sheet with id=AB9, first strand: chain 'B' and resid 589 through 590 removed outlier: 3.815A pdb=" N ALA B 600 " --> pdb=" O TRP B 590 " (cutoff:3.500A) 398 hydrogen bonds defined for protein. 1134 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.56 Time building geometry restraints manager: 4.70 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: 3683 1.34 - 1.46: 2278 1.46 - 1.58: 5489 1.58 - 1.69: 0 1.69 - 1.81: 54 Bond restraints: 11504 Sorted by residual: bond pdb=" C1 NAG B1105 " pdb=" O5 NAG B1105 " ideal model delta sigma weight residual 1.406 1.463 -0.057 2.00e-02 2.50e+03 7.99e+00 bond pdb=" C1 NAG A1106 " pdb=" O5 NAG A1106 " ideal model delta sigma weight residual 1.406 1.463 -0.057 2.00e-02 2.50e+03 7.99e+00 bond pdb=" C1 NAG A1104 " pdb=" O5 NAG A1104 " ideal model delta sigma weight residual 1.406 1.448 -0.042 2.00e-02 2.50e+03 4.38e+00 bond pdb=" C1 NAG B1103 " pdb=" O5 NAG B1103 " ideal model delta sigma weight residual 1.406 1.448 -0.042 2.00e-02 2.50e+03 4.38e+00 bond pdb=" C1 NAG D 3 " pdb=" O5 NAG D 3 " ideal model delta sigma weight residual 1.406 1.446 -0.040 2.00e-02 2.50e+03 4.04e+00 ... (remaining 11499 not shown) Histogram of bond angle deviations from ideal: 99.62 - 106.53: 306 106.53 - 113.44: 6242 113.44 - 120.34: 4424 120.34 - 127.25: 4613 127.25 - 134.16: 119 Bond angle restraints: 15704 Sorted by residual: angle pdb=" N ASP B 570 " pdb=" CA ASP B 570 " pdb=" C ASP B 570 " ideal model delta sigma weight residual 111.02 120.03 -9.01 1.25e+00 6.40e-01 5.19e+01 angle pdb=" N ASP A 570 " pdb=" CA ASP A 570 " pdb=" C ASP A 570 " ideal model delta sigma weight residual 111.02 120.01 -8.99 1.25e+00 6.40e-01 5.18e+01 angle pdb=" N PHE B 128 " pdb=" CA PHE B 128 " pdb=" C PHE B 128 " ideal model delta sigma weight residual 111.37 120.19 -8.82 1.64e+00 3.72e-01 2.89e+01 angle pdb=" N PHE A 128 " pdb=" CA PHE A 128 " pdb=" C PHE A 128 " ideal model delta sigma weight residual 111.37 120.17 -8.80 1.64e+00 3.72e-01 2.88e+01 angle pdb=" N GLU B 127 " pdb=" CA GLU B 127 " pdb=" C GLU B 127 " ideal model delta sigma weight residual 110.80 100.68 10.12 2.13e+00 2.20e-01 2.26e+01 ... (remaining 15699 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.46: 6219 17.46 - 34.92: 643 34.92 - 52.38: 130 52.38 - 69.84: 32 69.84 - 87.30: 8 Dihedral angle restraints: 7032 sinusoidal: 2508 harmonic: 4524 Sorted by residual: dihedral pdb=" CB CYS B 677 " pdb=" SG CYS B 677 " pdb=" SG CYS B 765 " pdb=" CB CYS B 765 " ideal model delta sinusoidal sigma weight residual -86.00 -162.61 76.61 1 1.00e+01 1.00e-02 7.38e+01 dihedral pdb=" CB CYS A 677 " pdb=" SG CYS A 677 " pdb=" SG CYS A 765 " pdb=" CB CYS A 765 " ideal model delta sinusoidal sigma weight residual -86.00 -162.61 76.61 1 1.00e+01 1.00e-02 7.38e+01 dihedral pdb=" CB CYS A 568 " pdb=" SG CYS A 568 " pdb=" SG CYS A 582 " pdb=" CB CYS A 582 " ideal model delta sinusoidal sigma weight residual 93.00 157.37 -64.37 1 1.00e+01 1.00e-02 5.45e+01 ... (remaining 7029 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.256: 1838 0.256 - 0.511: 6 0.511 - 0.767: 0 0.767 - 1.023: 0 1.023 - 1.278: 2 Chirality restraints: 1846 Sorted by residual: chirality pdb=" C1 NAG C 1 " pdb=" ND2 ASN A 488 " pdb=" C2 NAG C 1 " pdb=" O5 NAG C 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.12 -1.28 2.00e-01 2.50e+01 4.09e+01 chirality pdb=" C1 NAG E 1 " pdb=" ND2 ASN B 488 " pdb=" C2 NAG E 1 " pdb=" O5 NAG E 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.12 -1.28 2.00e-01 2.50e+01 4.08e+01 chirality pdb=" CA CYS A 765 " pdb=" N CYS A 765 " pdb=" C CYS A 765 " pdb=" CB CYS A 765 " both_signs ideal model delta sigma weight residual False 2.51 2.13 0.38 2.00e-01 2.50e+01 3.53e+00 ... (remaining 1843 not shown) Planarity restraints: 2058 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU B 797 " 0.052 5.00e-02 4.00e+02 7.86e-02 9.89e+00 pdb=" N PRO B 798 " -0.136 5.00e-02 4.00e+02 pdb=" CA PRO B 798 " 0.041 5.00e-02 4.00e+02 pdb=" CD PRO B 798 " 0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 797 " -0.052 5.00e-02 4.00e+02 7.84e-02 9.84e+00 pdb=" N PRO A 798 " 0.136 5.00e-02 4.00e+02 pdb=" CA PRO A 798 " -0.041 5.00e-02 4.00e+02 pdb=" CD PRO A 798 " -0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU A 610 " 0.042 5.00e-02 4.00e+02 6.43e-02 6.63e+00 pdb=" N PRO A 611 " -0.111 5.00e-02 4.00e+02 pdb=" CA PRO A 611 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO A 611 " 0.035 5.00e-02 4.00e+02 ... (remaining 2055 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 879 2.73 - 3.27: 10480 3.27 - 3.82: 17494 3.82 - 4.36: 20337 4.36 - 4.90: 35982 Nonbonded interactions: 85172 Sorted by model distance: nonbonded pdb=" OE2 GLU B 282 " pdb=" CD ARG B 286 " model vdw 2.189 3.440 nonbonded pdb=" OE2 GLU A 282 " pdb=" CD ARG A 286 " model vdw 2.189 3.440 nonbonded pdb=" O ALA A 144 " pdb=" OG SER A 150 " model vdw 2.207 3.040 nonbonded pdb=" O ALA B 144 " pdb=" OG SER B 150 " model vdw 2.207 3.040 nonbonded pdb=" OH TYR B 218 " pdb=" OG SER B 296 " model vdw 2.215 3.040 ... (remaining 85167 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 20 through 859 or resid 1101 or resid 1102 or resid 1104 t \ hrough 1106)) selection = (chain 'B' and (resid 20 through 859 or resid 1101 or resid 1102 or resid 1104 t \ hrough 1106)) } ncs_group { reference = chain 'C' selection = chain 'E' } ncs_group { reference = chain 'D' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 2.500 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: 0.000 Extract box with map and model: 0.380 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 33.230 Find NCS groups from input model: 0.670 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 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 0.079 11504 Z= 0.533 Angle : 0.937 10.120 15704 Z= 0.528 Chirality : 0.074 1.278 1846 Planarity : 0.007 0.079 2046 Dihedral : 14.961 87.299 4046 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.13 % Allowed : 9.79 % Favored : 90.08 % Rotamer: Outliers : 0.00 % Allowed : 17.58 % Favored : 82.42 % 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: -4.67 (0.17), residues: 1542 helix: -2.99 (0.15), residues: 604 sheet: -3.32 (0.35), residues: 158 loop : -3.15 (0.19), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 299 HIS 0.003 0.001 HIS A 312 PHE 0.014 0.002 PHE A 539 TYR 0.013 0.002 TYR A 63 ARG 0.002 0.000 ARG B 220 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3084 Ramachandran restraints generated. 1542 Oldfield, 0 Emsley, 1542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3084 Ramachandran restraints generated. 1542 Oldfield, 0 Emsley, 1542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 1356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 114 time to evaluate : 1.483 Fit side-chains REVERT: A 74 MET cc_start: 0.8954 (ttt) cc_final: 0.8717 (ttt) REVERT: B 74 MET cc_start: 0.8961 (ttt) cc_final: 0.8720 (ttt) outliers start: 0 outliers final: 0 residues processed: 114 average time/residue: 0.2350 time to fit residues: 38.8199 Evaluate side-chains 79 residues out of total 1356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 79 time to evaluate : 1.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 766, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 71.4586 > 50: distance: 22 - 27: 30.819 distance: 27 - 28: 7.627 distance: 28 - 29: 57.322 distance: 28 - 31: 9.065 distance: 29 - 33: 38.038 distance: 31 - 32: 45.123 distance: 32 - 115: 31.391 distance: 33 - 34: 42.279 distance: 34 - 35: 40.159 distance: 34 - 37: 56.282 distance: 35 - 36: 39.292 distance: 38 - 39: 40.457 distance: 38 - 40: 39.691 distance: 41 - 42: 38.867 distance: 41 - 47: 68.612 distance: 43 - 48: 56.425 distance: 45 - 46: 39.902 distance: 46 - 47: 40.377 distance: 49 - 50: 12.036 distance: 50 - 51: 48.634 distance: 52 - 53: 51.724 distance: 53 - 54: 6.245 distance: 53 - 56: 13.344 distance: 54 - 55: 51.336 distance: 54 - 63: 7.521 distance: 56 - 57: 40.437 distance: 58 - 59: 42.175 distance: 59 - 60: 50.748 distance: 60 - 61: 57.304 distance: 60 - 62: 56.969 distance: 64 - 65: 12.858 distance: 65 - 66: 9.521 distance: 65 - 67: 25.678 distance: 67 - 68: 15.639 distance: 68 - 69: 15.027 distance: 68 - 71: 31.353 distance: 69 - 70: 40.644 distance: 69 - 75: 39.787 distance: 71 - 72: 14.296 distance: 72 - 73: 18.538 distance: 72 - 74: 10.950 distance: 75 - 76: 59.686 distance: 76 - 77: 24.373 distance: 76 - 79: 19.535 distance: 77 - 78: 29.535 distance: 77 - 86: 29.582 distance: 78 - 101: 35.562 distance: 80 - 82: 39.291 distance: 81 - 83: 46.675 distance: 82 - 84: 37.465 distance: 83 - 85: 14.100 distance: 84 - 85: 49.363 distance: 87 - 88: 40.708 distance: 87 - 90: 40.230 distance: 88 - 89: 40.807 distance: 89 - 105: 32.581 distance: 90 - 91: 39.637 distance: 90 - 92: 56.532 distance: 94 - 97: 38.735 distance: 95 - 101: 33.862 distance: 97 - 98: 57.736 distance: 98 - 99: 40.274 distance: 100 - 146: 34.026