Starting phenix.real_space_refine (version: dev) on Fri Mar 17 20:59:08 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tys_26193/03_2023/7tys_26193_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tys_26193/03_2023/7tys_26193.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.41 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tys_26193/03_2023/7tys_26193.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tys_26193/03_2023/7tys_26193.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tys_26193/03_2023/7tys_26193_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tys_26193/03_2023/7tys_26193_updated.pdb" } resolution = 3.41 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= 1.000 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 PHE 333": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 326": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 258": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4893/modules/chem_data/mon_lib" Total number of atoms: 21286 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 2660 Number of conformers: 1 Conformer: "" Number of residues, atoms: 361, 2660 Classifications: {'peptide': 361} Incomplete info: {'truncation_to_alanine': 53} Link IDs: {'PTRANS': 16, 'TRANS': 344} Unresolved non-hydrogen bonds: 194 Unresolved non-hydrogen angles: 241 Unresolved non-hydrogen dihedrals: 153 Unresolved non-hydrogen chiralities: 14 Planarities with less than four sites: {'TYR:plan': 2, 'GLU:plan': 14, 'ARG:plan': 8, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 125 Chain: "B" Number of atoms: 2531 Number of conformers: 1 Conformer: "" Number of residues, atoms: 333, 2531 Classifications: {'peptide': 333} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'PTRANS': 13, 'TRANS': 319} Unresolved non-hydrogen bonds: 82 Unresolved non-hydrogen angles: 103 Unresolved non-hydrogen dihedrals: 61 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLU:plan': 9, 'ARG:plan': 2, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 61 Chain: "C" Number of atoms: 2515 Number of conformers: 1 Conformer: "" Number of residues, atoms: 332, 2515 Classifications: {'peptide': 332} Incomplete info: {'truncation_to_alanine': 27} Link IDs: {'PTRANS': 13, 'TRANS': 318} Unresolved non-hydrogen bonds: 94 Unresolved non-hydrogen angles: 119 Unresolved non-hydrogen dihedrals: 71 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLU:plan': 9, 'ARG:plan': 2, 'ASP:plan': 4, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 63 Chain: "D" Number of atoms: 2511 Number of conformers: 1 Conformer: "" Number of residues, atoms: 331, 2511 Classifications: {'peptide': 331} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PTRANS': 13, 'TRANS': 317} Unresolved non-hydrogen bonds: 89 Unresolved non-hydrogen angles: 110 Unresolved non-hydrogen dihedrals: 68 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 9, 'ARG:plan': 2, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 62 Chain: "E" Number of atoms: 10155 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1431, 10155 Classifications: {'peptide': 1431} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 335} Link IDs: {'PTRANS': 48, 'TRANS': 1382} Chain breaks: 4 Unresolved non-hydrogen bonds: 1180 Unresolved non-hydrogen angles: 1469 Unresolved non-hydrogen dihedrals: 954 Unresolved non-hydrogen chiralities: 112 Planarities with less than four sites: {'GLN:plan1': 18, 'HIS:plan': 7, 'TYR:plan': 1, 'ASN:plan1': 6, 'TRP:plan': 2, 'ASP:plan': 30, 'PHE:plan': 16, 'GLU:plan': 37, 'ARG:plan': 27} Unresolved non-hydrogen planarities: 620 Chain: "F" 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 chiralities: 2 Chain: "A" Number of atoms: 177 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 177 Unusual residues: {' K': 2, 'ATP': 1, 'POV': 1} Classifications: {'peptide': 2, 'undetermined': 4} Link IDs: {'TRANS': 1, None: 4} Not linked: pdbres="ATP A 401 " pdbres=" K A 402 " Not linked: pdbres=" K A 402 " pdbres=" K A 403 " Not linked: pdbres=" K A 403 " pdbres="POV A 404 " Not linked: pdbres="POV A 404 " pdbres="P5S A 405 " Chain breaks: 1 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'POV:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 121 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 121 Unusual residues: {'ATP': 1, 'POV': 1} Classifications: {'peptide': 1, 'undetermined': 2} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'POV:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "C" Number of atoms: 121 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 121 Unusual residues: {'ATP': 1, 'POV': 1} Classifications: {'peptide': 1, 'undetermined': 2} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'POV:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "D" Number of atoms: 121 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 121 Unusual residues: {'ATP': 1, 'POV': 1} Classifications: {'peptide': 1, 'undetermined': 2} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'POV:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "E" Number of atoms: 346 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 346 Unusual residues: {'65I': 6, 'ATP': 1, 'BJX': 1, 'POV': 1} Classifications: {'peptide': 1, 'undetermined': 9} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'POV:plan-1': 1} Unresolved non-hydrogen planarities: 1 Time building chain proxies: 13.78, per 1000 atoms: 0.65 Number of scatterers: 21286 At special positions: 0 Unit cell: (165.11, 107.635, 145.255, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) K 2 19.00 S 109 16.00 P 32 15.00 O 3778 8.00 N 3588 7.00 C 13777 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 110 " - pdb=" SG CYS A 142 " distance=2.03 Simple disulfide: pdb=" SG CYS B 110 " - pdb=" SG CYS B 142 " distance=2.03 Simple disulfide: pdb=" SG CYS C 110 " - pdb=" SG CYS C 142 " distance=2.03 Simple disulfide: pdb=" SG CYS D 110 " - pdb=" SG CYS D 142 " distance=2.03 Simple disulfide: pdb=" SG CYS E 6 " - pdb=" SG CYS E 26 " 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 F 1 " - " NAG F 2 " NAG-ASN " NAG F 1 " - " ASN E 10 " Time building additional restraints: 9.54 Conformation dependent library (CDL) restraints added in 3.4 seconds 5540 Ramachandran restraints generated. 2770 Oldfield, 0 Emsley, 2770 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5266 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 93 helices and 25 sheets defined 47.8% alpha, 8.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 26.49 Creating SS restraints... Processing helix chain 'A' and resid 26 through 29 removed outlier: 3.523A pdb=" N ARG A 29 " --> pdb=" O TYR A 26 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 26 through 29' Processing helix chain 'A' and resid 54 through 57 No H-bonds generated for 'chain 'A' and resid 54 through 57' Processing helix chain 'A' and resid 59 through 65 removed outlier: 3.663A pdb=" N VAL A 64 " --> pdb=" O PHE A 60 " (cutoff:3.500A) Processing helix chain 'A' and resid 68 through 97 removed outlier: 3.569A pdb=" N SER A 82 " --> pdb=" O SER A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 128 Processing helix chain 'A' and resid 143 through 171 removed outlier: 3.693A pdb=" N LEU A 147 " --> pdb=" O PRO A 143 " (cutoff:3.500A) Processing helix chain 'A' and resid 178 through 180 No H-bonds generated for 'chain 'A' and resid 178 through 180' Processing helix chain 'A' and resid 272 through 274 No H-bonds generated for 'chain 'A' and resid 272 through 274' Processing helix chain 'A' and resid 306 through 308 No H-bonds generated for 'chain 'A' and resid 306 through 308' Processing helix chain 'A' and resid 330 through 332 No H-bonds generated for 'chain 'A' and resid 330 through 332' Processing helix chain 'A' and resid 346 through 360 Processing helix chain 'B' and resid 54 through 57 No H-bonds generated for 'chain 'B' and resid 54 through 57' Processing helix chain 'B' and resid 59 through 65 Processing helix chain 'B' and resid 68 through 97 removed outlier: 3.503A pdb=" N LEU B 73 " --> pdb=" O PRO B 69 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N VAL B 89 " --> pdb=" O LEU B 85 " (cutoff:3.500A) Processing helix chain 'B' and resid 117 through 129 Processing helix chain 'B' and resid 143 through 171 Processing helix chain 'B' and resid 175 through 180 removed outlier: 3.776A pdb=" N GLU B 179 " --> pdb=" O HIS B 175 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N THR B 180 " --> pdb=" O ARG B 176 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 175 through 180' Processing helix chain 'B' and resid 266 through 269 removed outlier: 4.276A pdb=" N ASP B 269 " --> pdb=" O PRO B 266 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 266 through 269' Processing helix chain 'B' and resid 306 through 308 No H-bonds generated for 'chain 'B' and resid 306 through 308' Processing helix chain 'B' and resid 330 through 332 No H-bonds generated for 'chain 'B' and resid 330 through 332' Processing helix chain 'B' and resid 346 through 361 Processing helix chain 'C' and resid 54 through 57 No H-bonds generated for 'chain 'C' and resid 54 through 57' Processing helix chain 'C' and resid 59 through 65 Processing helix chain 'C' and resid 68 through 97 removed outlier: 3.593A pdb=" N LEU C 73 " --> pdb=" O PRO C 69 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N VAL C 89 " --> pdb=" O LEU C 85 " (cutoff:3.500A) Processing helix chain 'C' and resid 117 through 128 Processing helix chain 'C' and resid 143 through 171 Processing helix chain 'C' and resid 178 through 180 No H-bonds generated for 'chain 'C' and resid 178 through 180' Processing helix chain 'C' and resid 272 through 274 No H-bonds generated for 'chain 'C' and resid 272 through 274' Processing helix chain 'C' and resid 330 through 332 No H-bonds generated for 'chain 'C' and resid 330 through 332' Processing helix chain 'C' and resid 346 through 360 Processing helix chain 'D' and resid 54 through 57 No H-bonds generated for 'chain 'D' and resid 54 through 57' Processing helix chain 'D' and resid 59 through 65 Processing helix chain 'D' and resid 68 through 97 Processing helix chain 'D' and resid 117 through 128 Processing helix chain 'D' and resid 143 through 171 Processing helix chain 'D' and resid 175 through 180 removed outlier: 3.560A pdb=" N GLU D 179 " --> pdb=" O HIS D 175 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N THR D 180 " --> pdb=" O ARG D 176 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 175 through 180' Processing helix chain 'D' and resid 272 through 274 No H-bonds generated for 'chain 'D' and resid 272 through 274' Processing helix chain 'D' and resid 306 through 308 No H-bonds generated for 'chain 'D' and resid 306 through 308' Processing helix chain 'D' and resid 330 through 332 No H-bonds generated for 'chain 'D' and resid 330 through 332' Processing helix chain 'D' and resid 346 through 359 Processing helix chain 'E' and resid 9 through 12 No H-bonds generated for 'chain 'E' and resid 9 through 12' Processing helix chain 'E' and resid 21 through 23 No H-bonds generated for 'chain 'E' and resid 21 through 23' Processing helix chain 'E' and resid 27 through 56 removed outlier: 3.572A pdb=" N VAL E 33 " --> pdb=" O ASP E 29 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N VAL E 34 " --> pdb=" O ALA E 30 " (cutoff:3.500A) Proline residue: E 35 - end of helix removed outlier: 3.614A pdb=" N LEU E 39 " --> pdb=" O PRO E 35 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N PHE E 44 " --> pdb=" O LEU E 40 " (cutoff:3.500A) Proline residue: E 45 - end of helix removed outlier: 4.132A pdb=" N SER E 56 " --> pdb=" O GLY E 52 " (cutoff:3.500A) Processing helix chain 'E' and resid 59 through 61 No H-bonds generated for 'chain 'E' and resid 59 through 61' Processing helix chain 'E' and resid 71 through 97 removed outlier: 4.014A pdb=" N GLY E 97 " --> pdb=" O ILE E 93 " (cutoff:3.500A) Processing helix chain 'E' and resid 104 through 106 No H-bonds generated for 'chain 'E' and resid 104 through 106' Processing helix chain 'E' and resid 108 through 129 Processing helix chain 'E' and resid 133 through 159 removed outlier: 3.528A pdb=" N ILE E 141 " --> pdb=" O ALA E 138 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ALA E 146 " --> pdb=" O TRP E 143 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N PHE E 147 " --> pdb=" O THR E 144 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N THR E 149 " --> pdb=" O ALA E 146 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LYS E 150 " --> pdb=" O PHE E 147 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N VAL E 155 " --> pdb=" O ILE E 152 " (cutoff:3.500A) Processing helix chain 'E' and resid 167 through 193 Processing helix chain 'E' and resid 208 through 211 No H-bonds generated for 'chain 'E' and resid 208 through 211' Processing helix chain 'E' and resid 224 through 229 Processing helix chain 'E' and resid 231 through 242 removed outlier: 3.690A pdb=" N ALA E 235 " --> pdb=" O TRP E 232 " (cutoff:3.500A) Processing helix chain 'E' and resid 255 through 257 No H-bonds generated for 'chain 'E' and resid 255 through 257' Processing helix chain 'E' and resid 259 through 276 Processing helix chain 'E' and resid 284 through 327 removed outlier: 5.310A pdb=" N ARG E 297 " --> pdb=" O HIS E 293 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N ARG E 298 " --> pdb=" O ALA E 294 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N LEU E 301 " --> pdb=" O ARG E 297 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N PHE E 314 " --> pdb=" O ASP E 310 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ALA E 315 " --> pdb=" O LEU E 311 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N GLY E 316 " --> pdb=" O LEU E 312 " (cutoff:3.500A) Proline residue: E 317 - end of helix Processing helix chain 'E' and resid 348 through 351 No H-bonds generated for 'chain 'E' and resid 348 through 351' Processing helix chain 'E' and resid 355 through 400 removed outlier: 3.765A pdb=" N GLN E 374 " --> pdb=" O ARG E 370 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N THR E 393 " --> pdb=" O GLY E 389 " (cutoff:3.500A) Processing helix chain 'E' and resid 414 through 455 removed outlier: 3.614A pdb=" N VAL E 421 " --> pdb=" O ILE E 417 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N THR E 425 " --> pdb=" O VAL E 421 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ASN E 426 " --> pdb=" O ALA E 422 " (cutoff:3.500A) Proline residue: E 436 - end of helix removed outlier: 3.799A pdb=" N TRP E 439 " --> pdb=" O CYS E 435 " (cutoff:3.500A) Proline residue: E 442 - end of helix removed outlier: 3.676A pdb=" N TYR E 454 " --> pdb=" O ILE E 450 " (cutoff:3.500A) Processing helix chain 'E' and resid 459 through 502 removed outlier: 3.731A pdb=" N VAL E 466 " --> pdb=" O ILE E 462 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ILE E 467 " --> pdb=" O GLY E 463 " (cutoff:3.500A) Proline residue: E 472 - end of helix removed outlier: 3.507A pdb=" N GLU E 501 " --> pdb=" O LYS E 497 " (cutoff:3.500A) Processing helix chain 'E' and resid 506 through 511 Processing helix chain 'E' and resid 515 through 564 removed outlier: 3.593A pdb=" N SER E 520 " --> pdb=" O SER E 516 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ARG E 521 " --> pdb=" O ILE E 517 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N VAL E 522 " --> pdb=" O PHE E 518 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N SER E 532 " --> pdb=" O LYS E 528 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ILE E 550 " --> pdb=" O MET E 546 " (cutoff:3.500A) Proline residue: E 551 - end of helix Processing helix chain 'E' and resid 573 through 590 removed outlier: 3.766A pdb=" N ALA E 578 " --> pdb=" O SER E 574 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N SER E 581 " --> pdb=" O PHE E 577 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N THR E 588 " --> pdb=" O HIS E 584 " (cutoff:3.500A) Proline residue: E 589 - end of helix Processing helix chain 'E' and resid 593 through 615 removed outlier: 3.563A pdb=" N SER E 615 " --> pdb=" O SER E 611 " (cutoff:3.500A) Processing helix chain 'E' and resid 720 through 725 Processing helix chain 'E' and resid 784 through 789 Processing helix chain 'E' and resid 796 through 806 removed outlier: 3.585A pdb=" N MET E 801 " --> pdb=" O GLN E 797 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N VAL E 802 " --> pdb=" O ARG E 798 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ALA E 805 " --> pdb=" O MET E 801 " (cutoff:3.500A) Processing helix chain 'E' and resid 809 through 812 No H-bonds generated for 'chain 'E' and resid 809 through 812' Processing helix chain 'E' and resid 818 through 820 No H-bonds generated for 'chain 'E' and resid 818 through 820' Processing helix chain 'E' and resid 832 through 845 removed outlier: 3.615A pdb=" N LEU E 844 " --> pdb=" O VAL E 840 " (cutoff:3.500A) Processing helix chain 'E' and resid 863 through 879 removed outlier: 3.528A pdb=" N HIS E 867 " --> pdb=" O HIS E 863 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LEU E 868 " --> pdb=" O LEU E 864 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N MET E 869 " --> pdb=" O SER E 865 " (cutoff:3.500A) Processing helix chain 'E' and resid 914 through 918 Processing helix chain 'E' and resid 988 through 992 Processing helix chain 'E' and resid 997 through 1007 removed outlier: 3.614A pdb=" N CYS E1001 " --> pdb=" O PRO E 997 " (cutoff:3.500A) Processing helix chain 'E' and resid 1011 through 1041 removed outlier: 3.597A pdb=" N ASP E1031 " --> pdb=" O LEU E1027 " (cutoff:3.500A) Processing helix chain 'E' and resid 1067 through 1105 Processing helix chain 'E' and resid 1110 through 1115 Processing helix chain 'E' and resid 1120 through 1134 removed outlier: 5.015A pdb=" N ASP E1128 " --> pdb=" O ARG E1124 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N CYS E1129 " --> pdb=" O PHE E1125 " (cutoff:3.500A) Processing helix chain 'E' and resid 1136 through 1160 removed outlier: 4.111A pdb=" N GLU E1141 " --> pdb=" O PRO E1137 " (cutoff:3.500A) Processing helix chain 'E' and resid 1164 through 1209 removed outlier: 3.731A pdb=" N LEU E1169 " --> pdb=" O LEU E1165 " (cutoff:3.500A) Proline residue: E1170 - end of helix removed outlier: 3.687A pdb=" N VAL E1174 " --> pdb=" O PRO E1170 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N ARG E1183 " --> pdb=" O GLN E1179 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N VAL E1184 " --> pdb=" O LYS E1180 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ASP E1188 " --> pdb=" O VAL E1184 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N GLN E1197 " --> pdb=" O ASP E1193 " (cutoff:3.500A) Proline residue: E1199 - end of helix Processing helix chain 'E' and resid 1211 through 1216 Processing helix chain 'E' and resid 1220 through 1272 removed outlier: 3.874A pdb=" N GLY E1256 " --> pdb=" O MET E1252 " (cutoff:3.500A) Processing helix chain 'E' and resid 1279 through 1286 removed outlier: 3.679A pdb=" N LEU E1283 " --> pdb=" O GLY E1279 " (cutoff:3.500A) Processing helix chain 'E' and resid 1291 through 1320 removed outlier: 3.576A pdb=" N ALA E1311 " --> pdb=" O ILE E1307 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N VAL E1312 " --> pdb=" O GLN E1308 " (cutoff:3.500A) Processing helix chain 'E' and resid 1383 through 1392 removed outlier: 3.877A pdb=" N SER E1387 " --> pdb=" O SER E1383 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N PHE E1388 " --> pdb=" O GLY E1384 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU E1390 " --> pdb=" O SER E1386 " (cutoff:3.500A) Processing helix chain 'E' and resid 1415 through 1420 Processing helix chain 'E' and resid 1450 through 1458 removed outlier: 3.553A pdb=" N GLU E1456 " --> pdb=" O TRP E1452 " (cutoff:3.500A) Processing helix chain 'E' and resid 1461 through 1466 removed outlier: 3.629A pdb=" N LYS E1465 " --> pdb=" O LYS E1461 " (cutoff:3.500A) Processing helix chain 'E' and resid 1470 through 1472 No H-bonds generated for 'chain 'E' and resid 1470 through 1472' Processing helix chain 'E' and resid 1484 through 1497 removed outlier: 4.412A pdb=" N ARG E1487 " --> pdb=" O GLN E1484 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ALA E1495 " --> pdb=" O LEU E1492 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N PHE E1496 " --> pdb=" O ALA E1493 " (cutoff:3.500A) Processing helix chain 'E' and resid 1513 through 1528 removed outlier: 3.501A pdb=" N GLU E1517 " --> pdb=" O ASP E1513 " (cutoff:3.500A) Processing helix chain 'E' and resid 1540 through 1544 Processing helix chain 'E' and resid 1565 through 1569 Processing helix chain 'E' and resid 1571 through 1577 Processing sheet with id= A, first strand: chain 'A' and resid 181 through 183 Processing sheet with id= B, first strand: chain 'A' and resid 309 through 311 removed outlier: 6.706A pdb=" N ALA A 187 " --> pdb=" O LEU A 310 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 234 through 238 removed outlier: 4.143A pdb=" N MET A 217 " --> pdb=" O ILE A 238 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLY A 289 " --> pdb=" O THR A 298 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 313 through 315 Processing sheet with id= E, first strand: chain 'B' and resid 181 through 183 Processing sheet with id= F, first strand: chain 'B' and resid 309 through 311 removed outlier: 6.895A pdb=" N ALA B 187 " --> pdb=" O LEU B 310 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 234 through 238 removed outlier: 4.108A pdb=" N MET B 217 " --> pdb=" O ILE B 238 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 313 through 315 Processing sheet with id= I, first strand: chain 'B' and resid 319 through 321 Processing sheet with id= J, first strand: chain 'C' and resid 181 through 183 Processing sheet with id= K, first strand: chain 'C' and resid 309 through 311 removed outlier: 6.636A pdb=" N ALA C 187 " --> pdb=" O LEU C 310 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'C' and resid 234 through 238 removed outlier: 4.332A pdb=" N MET C 217 " --> pdb=" O ILE C 238 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'C' and resid 313 through 315 Processing sheet with id= N, first strand: chain 'D' and resid 181 through 183 Processing sheet with id= O, first strand: chain 'D' and resid 309 through 311 removed outlier: 6.769A pdb=" N ALA D 187 " --> pdb=" O LEU D 310 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'D' and resid 234 through 238 removed outlier: 4.135A pdb=" N MET D 217 " --> pdb=" O ILE D 238 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N THR D 214 " --> pdb=" O GLU D 288 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N GLY D 289 " --> pdb=" O THR D 298 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'D' and resid 313 through 315 Processing sheet with id= R, first strand: chain 'D' and resid 319 through 321 Processing sheet with id= S, first strand: chain 'E' and resid 679 through 681 Processing sheet with id= T, first strand: chain 'E' and resid 709 through 713 removed outlier: 6.815A pdb=" N TRP E 899 " --> pdb=" O MET E 710 " (cutoff:3.500A) removed outlier: 7.530A pdb=" N VAL E 712 " --> pdb=" O TRP E 899 " (cutoff:3.500A) removed outlier: 5.895A pdb=" N ILE E 901 " --> pdb=" O VAL E 712 " (cutoff:3.500A) No H-bonds generated for sheet with id= T Processing sheet with id= U, first strand: chain 'E' and resid 850 through 854 removed outlier: 5.367A pdb=" N THR E 883 " --> pdb=" O VAL E 851 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N LEU E 853 " --> pdb=" O THR E 883 " (cutoff:3.500A) removed outlier: 5.777A pdb=" N VAL E 885 " --> pdb=" O LEU E 853 " (cutoff:3.500A) No H-bonds generated for sheet with id= U Processing sheet with id= V, first strand: chain 'E' and resid 1374 through 1376 removed outlier: 5.633A pdb=" N VAL E1533 " --> pdb=" O ILE E1375 " (cutoff:3.500A) No H-bonds generated for sheet with id= V Processing sheet with id= W, first strand: chain 'E' and resid 1422 through 1424 removed outlier: 6.792A pdb=" N ILE E1502 " --> pdb=" O SER E1423 " (cutoff:3.500A) No H-bonds generated for sheet with id= W Processing sheet with id= X, first strand: chain 'E' and resid 685 through 687 removed outlier: 3.752A pdb=" N SER E 734 " --> pdb=" O PHE E 685 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N THR E 687 " --> pdb=" O LYS E 732 " (cutoff:3.500A) removed outlier: 4.781A pdb=" N LYS E 732 " --> pdb=" O THR E 687 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'E' and resid 1549 through 1553 removed outlier: 5.007A pdb=" N LYS E1553 " --> pdb=" O ILE E1557 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N ILE E1557 " --> pdb=" O LYS E1553 " (cutoff:3.500A) 1004 hydrogen bonds defined for protein. 2847 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: 7.74 Time building geometry restraints manager: 10.02 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 3536 1.32 - 1.45: 5521 1.45 - 1.57: 12437 1.57 - 1.69: 61 1.69 - 1.81: 170 Bond restraints: 21725 Sorted by residual: bond pdb=" C16 BJX E1602 " pdb=" N1 BJX E1602 " ideal model delta sigma weight residual 1.344 1.461 -0.117 2.00e-02 2.50e+03 3.43e+01 bond pdb=" N BJX E1602 " pdb=" C6 BJX E1602 " ideal model delta sigma weight residual 1.412 1.515 -0.103 2.00e-02 2.50e+03 2.67e+01 bond pdb=" C21 BJX E1602 " pdb=" O1 BJX E1602 " ideal model delta sigma weight residual 1.347 1.422 -0.075 2.00e-02 2.50e+03 1.40e+01 bond pdb=" C5 BJX E1602 " pdb=" N1 BJX E1602 " ideal model delta sigma weight residual 1.446 1.515 -0.069 2.00e-02 2.50e+03 1.19e+01 bond pdb=" C5 BJX E1602 " pdb=" C7 BJX E1602 " ideal model delta sigma weight residual 1.518 1.585 -0.067 2.00e-02 2.50e+03 1.11e+01 ... (remaining 21720 not shown) Histogram of bond angle deviations from ideal: 92.67 - 102.13: 91 102.13 - 111.59: 10982 111.59 - 121.04: 12685 121.04 - 130.50: 5697 130.50 - 139.96: 138 Bond angle restraints: 29593 Sorted by residual: angle pdb=" C16 BJX E1602 " pdb=" N1 BJX E1602 " pdb=" C5 BJX E1602 " ideal model delta sigma weight residual 123.13 133.78 -10.65 3.00e+00 1.11e-01 1.26e+01 angle pdb=" C LEU B 270 " pdb=" N ALA B 271 " pdb=" CA ALA B 271 " ideal model delta sigma weight residual 120.97 113.73 7.24 2.84e+00 1.24e-01 6.49e+00 angle pdb=" N ILE E 60 " pdb=" CA ILE E 60 " pdb=" C ILE E 60 " ideal model delta sigma weight residual 112.98 109.86 3.12 1.25e+00 6.40e-01 6.23e+00 angle pdb=" C8 65I E1610 " pdb=" C7 65I E1610 " pdb=" O6 65I E1610 " ideal model delta sigma weight residual 104.59 111.85 -7.26 3.00e+00 1.11e-01 5.85e+00 angle pdb=" C8 65I E1606 " pdb=" C7 65I E1606 " pdb=" O6 65I E1606 " ideal model delta sigma weight residual 104.59 111.82 -7.23 3.00e+00 1.11e-01 5.81e+00 ... (remaining 29588 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.34: 12432 32.34 - 64.68: 282 64.68 - 97.01: 35 97.01 - 129.35: 10 129.35 - 161.69: 2 Dihedral angle restraints: 12761 sinusoidal: 4660 harmonic: 8101 Sorted by residual: dihedral pdb=" O BJX E1602 " pdb=" C16 BJX E1602 " pdb=" C17 BJX E1602 " pdb=" C18 BJX E1602 " ideal model delta sinusoidal sigma weight residual 10.31 -151.38 161.69 1 3.00e+01 1.11e-03 2.08e+01 dihedral pdb=" C 65I E1606 " pdb=" C1 65I E1606 " pdb=" C2 65I E1606 " pdb=" C3 65I E1606 " ideal model delta sinusoidal sigma weight residual 179.71 47.84 131.87 1 3.00e+01 1.11e-03 1.78e+01 dihedral pdb=" C 65I E1610 " pdb=" C1 65I E1610 " pdb=" C2 65I E1610 " pdb=" C3 65I E1610 " ideal model delta sinusoidal sigma weight residual 179.71 51.95 127.76 1 3.00e+01 1.11e-03 1.72e+01 ... (remaining 12758 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 2954 0.055 - 0.110: 513 0.110 - 0.166: 55 0.166 - 0.221: 0 0.221 - 0.276: 2 Chirality restraints: 3524 Sorted by residual: chirality pdb=" C1 NAG F 1 " pdb=" ND2 ASN E 10 " pdb=" C2 NAG F 1 " pdb=" O5 NAG F 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.12 -0.28 2.00e-01 2.50e+01 1.91e+00 chirality pdb=" C5 BJX E1602 " pdb=" C7 BJX E1602 " pdb=" C8 BJX E1602 " pdb=" N1 BJX E1602 " both_signs ideal model delta sigma weight residual False 2.44 2.66 -0.23 2.00e-01 2.50e+01 1.27e+00 chirality pdb=" CA VAL E 34 " pdb=" N VAL E 34 " pdb=" C VAL E 34 " pdb=" CB VAL E 34 " both_signs ideal model delta sigma weight residual False 2.44 2.30 0.15 2.00e-01 2.50e+01 5.31e-01 ... (remaining 3521 not shown) Planarity restraints: 3637 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR E 588 " -0.025 5.00e-02 4.00e+02 3.78e-02 2.28e+00 pdb=" N PRO E 589 " 0.065 5.00e-02 4.00e+02 pdb=" CA PRO E 589 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO E 589 " -0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY E 316 " -0.023 5.00e-02 4.00e+02 3.48e-02 1.94e+00 pdb=" N PRO E 317 " 0.060 5.00e-02 4.00e+02 pdb=" CA PRO E 317 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO E 317 " -0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER D 225 " -0.022 5.00e-02 4.00e+02 3.30e-02 1.74e+00 pdb=" N PRO D 226 " 0.057 5.00e-02 4.00e+02 pdb=" CA PRO D 226 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO D 226 " -0.019 5.00e-02 4.00e+02 ... (remaining 3634 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.82: 6191 2.82 - 3.40: 23578 3.40 - 3.98: 38806 3.98 - 4.56: 55393 4.56 - 5.14: 80789 Nonbonded interactions: 204757 Sorted by model distance: nonbonded pdb=" O SER E 541 " pdb=" OG SER E1083 " model vdw 2.235 2.440 nonbonded pdb=" O CYS B 110 " pdb=" OG1 THR B 139 " model vdw 2.242 2.440 nonbonded pdb=" OE1 GLN E 219 " pdb=" NE1 TRP E 232 " model vdw 2.260 2.520 nonbonded pdb=" OD2 ASP B 58 " pdb=" NH1 ARG C 206 " model vdw 2.271 2.520 nonbonded pdb=" O THR E 726 " pdb=" NH2 ARG E 767 " model vdw 2.276 2.520 ... (remaining 204752 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 30 through 53 or (resid 54 and (name N or name CA or name \ C or name O or name CB )) or resid 55 or (resid 56 and (name N or name CA or nam \ e C or name O or name CB )) or resid 57 through 69 or (resid 70 and (name N or n \ ame CA or name C or name O or name CB )) or resid 71 through 72 or (resid 73 and \ (name N or name CA or name C or name O or name CB )) or resid 74 through 98 or \ (resid 99 through 101 and (name N or name CA or name C or name O or name CB )) o \ r resid 102 through 105 or (resid 106 and (name N or name CA or name C or name O \ or name CB )) or resid 107 through 322 or (resid 323 and (name N or name CA or \ name C or name O or name CB )) or resid 324 or (resid 325 and (name N or name CA \ or name C or name O or name CB )) or resid 326 through 331 or (resid 332 and (n \ ame N or name CA or name C or name O or name CB )) or resid 333 through 347 or ( \ resid 348 and (name N or name CA or name C or name O or name CB )) or resid 349 \ through 360)) selection = (chain 'B' and ((resid 30 through 33 and (name N or name CA or name C or name O \ or name CB )) or resid 34 through 36 or (resid 37 and (name N or name CA or name \ C or name O or name CB )) or resid 38 through 46 or (resid 47 and (name N or na \ me CA or name C or name O or name CB )) or resid 48 through 53 or (resid 54 and \ (name N or name CA or name C or name O or name CB )) or resid 55 or (resid 56 an \ d (name N or name CA or name C or name O or name CB )) or resid 57 through 69 or \ (resid 70 and (name N or name CA or name C or name O or name CB )) or resid 71 \ through 72 or (resid 73 and (name N or name CA or name C or name O or name CB )) \ or resid 74 through 87 or (resid 88 and (name N or name CA or name C or name O \ or name CB )) or resid 89 through 98 or (resid 99 through 101 and (name N or nam \ e CA or name C or name O or name CB )) or resid 102 through 105 or (resid 106 an \ d (name N or name CA or name C or name O or name CB )) or resid 107 through 125 \ or (resid 126 and (name N or name CA or name C or name O or name CB )) or resid \ 127 through 331 or (resid 332 and (name N or name CA or name C or name O or name \ CB )) or resid 333 through 338 or (resid 339 and (name N or name CA or name C o \ r name O or name CB )) or resid 340 through 343 or (resid 344 and (name N or nam \ e CA or name C or name O or name CB )) or resid 345 through 347 or (resid 348 an \ d (name N or name CA or name C or name O or name CB )) or resid 349 through 352 \ or (resid 353 through 360 and (name N or name CA or name C or name O or name CB \ )))) selection = (chain 'C' and ((resid 30 through 33 and (name N or name CA or name C or name O \ or name CB )) or resid 34 through 36 or (resid 37 and (name N or name CA or name \ C or name O or name CB )) or resid 38 through 46 or (resid 47 and (name N or na \ me CA or name C or name O or name CB )) or resid 48 through 72 or (resid 73 and \ (name N or name CA or name C or name O or name CB )) or resid 74 through 87 or ( \ resid 88 and (name N or name CA or name C or name O or name CB )) or resid 89 th \ rough 125 or (resid 126 and (name N or name CA or name C or name O or name CB )) \ or resid 127 through 322 or (resid 323 and (name N or name CA or name C or name \ O or name CB )) or resid 324 or (resid 325 and (name N or name CA or name C or \ name O or name CB )) or resid 326 through 331 or (resid 332 and (name N or name \ CA or name C or name O or name CB )) or resid 333 through 338 or (resid 339 and \ (name N or name CA or name C or name O or name CB )) or resid 340 through 343 or \ (resid 344 and (name N or name CA or name C or name O or name CB )) or resid 34 \ 5 through 347 or (resid 348 and (name N or name CA or name C or name O or name C \ B )) or resid 349 through 351 or (resid 352 through 360 and (name N or name CA o \ r name C or name O or name CB )))) selection = (chain 'D' and ((resid 30 through 33 and (name N or name CA or name C or name O \ or name CB )) or resid 34 through 36 or (resid 37 and (name N or name CA or name \ C or name O or name CB )) or resid 38 through 46 or (resid 47 and (name N or na \ me CA or name C or name O or name CB )) or resid 48 through 53 or (resid 54 and \ (name N or name CA or name C or name O or name CB )) or resid 55 or (resid 56 an \ d (name N or name CA or name C or name O or name CB )) or resid 57 through 69 or \ (resid 70 and (name N or name CA or name C or name O or name CB )) or resid 71 \ through 87 or (resid 88 and (name N or name CA or name C or name O or name CB )) \ or resid 89 through 98 or (resid 99 through 101 and (name N or name CA or name \ C or name O or name CB )) or resid 102 through 105 or (resid 106 and (name N or \ name CA or name C or name O or name CB )) or resid 107 through 125 or (resid 126 \ and (name N or name CA or name C or name O or name CB )) or resid 127 through 3 \ 22 or (resid 323 and (name N or name CA or name C or name O or name CB )) or res \ id 324 or (resid 325 and (name N or name CA or name C or name O or name CB )) or \ resid 326 through 338 or (resid 339 and (name N or name CA or name C or name O \ or name CB )) or resid 340 through 360)) } 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: 6 Type Number sf(0) Gaussians K 2 8.98 5 P 32 5.49 5 S 109 5.16 5 C 13777 2.51 5 N 3588 2.21 5 O 3778 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.120 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: 0.030 Extract box with map and model: 2.760 Check model and map are aligned: 0.300 Process input model: 58.470 Find NCS groups from input model: 1.040 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Set scattering table: 0.180 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 65.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8073 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 : 0.004 0.117 21725 Z= 0.243 Angle : 0.516 10.647 29593 Z= 0.247 Chirality : 0.042 0.276 3524 Planarity : 0.003 0.038 3636 Dihedral : 14.591 161.688 7480 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer Outliers : 2.39 % 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: -0.22 (0.16), residues: 2770 helix: 1.06 (0.14), residues: 1318 sheet: -1.56 (0.31), residues: 291 loop : -1.13 (0.19), residues: 1161 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5540 Ramachandran restraints generated. 2770 Oldfield, 0 Emsley, 2770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5540 Ramachandran restraints generated. 2770 Oldfield, 0 Emsley, 2770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 635 residues out of total 2432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 588 time to evaluate : 2.262 Fit side-chains revert: symmetry clash outliers start: 47 outliers final: 24 residues processed: 620 average time/residue: 0.2616 time to fit residues: 252.2681 Evaluate side-chains 533 residues out of total 2432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4893/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-4893/modules/cctbx_project/iotbx/cli_parser.py", line 865, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4893/modules/phenix/phenix/programs/real_space_refine.py", line 192, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4893/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4893/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-4893/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 318, in caller self.log.flush() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4893/modules/cctbx_project/libtbx/utils.py", line 1570, in flush if (flush is not None): flush() IOError: [Errno 28] No space left on device