Starting phenix.real_space_refine (version: dev) on Tue Dec 20 02:53:14 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6p7n_20267/12_2022/6p7n_20267.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6p7n_20267/12_2022/6p7n_20267.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6p7n_20267/12_2022/6p7n_20267.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6p7n_20267/12_2022/6p7n_20267.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6p7n_20267/12_2022/6p7n_20267.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6p7n_20267/12_2022/6p7n_20267.pdb" } resolution = 4.9 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= 0.002 sd= 0.032 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 17892 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "C ARG 187": "NH1" <-> "NH2" Residue "C ARG 203": "NH1" <-> "NH2" Residue "C ARG 206": "NH1" <-> "NH2" Residue "C ARG 217": "NH1" <-> "NH2" Residue "C GLU 219": "OE1" <-> "OE2" Residue "G ARG 187": "NH1" <-> "NH2" Residue "G ARG 203": "NH1" <-> "NH2" Residue "G ARG 206": "NH1" <-> "NH2" Residue "G ARG 217": "NH1" <-> "NH2" Residue "G GLU 219": "OE1" <-> "OE2" Residue "A GLU 29": "OE1" <-> "OE2" Residue "A GLU 41": "OE1" <-> "OE2" Residue "A ASP 64": "OD1" <-> "OD2" Residue "A ASP 136": "OD1" <-> "OD2" Residue "A ARG 174": "NH1" <-> "NH2" Residue "A GLU 191": "OE1" <-> "OE2" Residue "A TYR 214": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 223": "OE1" <-> "OE2" Residue "A ASP 297": "OD1" <-> "OD2" Residue "A ASP 360": "OD1" <-> "OD2" Residue "A ASP 384": "OD1" <-> "OD2" Residue "A ASP 407": "OD1" <-> "OD2" Residue "A GLU 433": "OE1" <-> "OE2" Residue "A ASP 450": "OD1" <-> "OD2" Residue "A PHE 486": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 495": "OD1" <-> "OD2" Residue "A GLU 683": "OE1" <-> "OE2" Residue "A ASP 691": "OD1" <-> "OD2" Residue "A TYR 705": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 709": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 730": "OE1" <-> "OE2" Residue "A ARG 737": "NH1" <-> "NH2" Residue "A GLU 743": "OE1" <-> "OE2" Residue "A ASP 832": "OD1" <-> "OD2" Residue "A TYR 840": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 867": "NH1" <-> "NH2" Residue "A ARG 883": "NH1" <-> "NH2" Residue "A PHE 884": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 887": "NH1" <-> "NH2" Residue "A ARG 1054": "NH1" <-> "NH2" Residue "A ARG 1073": "NH1" <-> "NH2" Residue "A PHE 1127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 29": "OE1" <-> "OE2" Residue "E GLU 41": "OE1" <-> "OE2" Residue "E ASP 64": "OD1" <-> "OD2" Residue "E ASP 136": "OD1" <-> "OD2" Residue "E ARG 174": "NH1" <-> "NH2" Residue "E GLU 191": "OE1" <-> "OE2" Residue "E TYR 214": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 223": "OE1" <-> "OE2" Residue "E ASP 297": "OD1" <-> "OD2" Residue "E ASP 360": "OD1" <-> "OD2" Residue "E ASP 384": "OD1" <-> "OD2" Residue "E ASP 407": "OD1" <-> "OD2" Residue "E GLU 433": "OE1" <-> "OE2" Residue "E ASP 450": "OD1" <-> "OD2" Residue "E PHE 486": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 495": "OD1" <-> "OD2" Residue "E GLU 683": "OE1" <-> "OE2" Residue "E ASP 691": "OD1" <-> "OD2" Residue "E TYR 705": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 709": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 730": "OE1" <-> "OE2" Residue "E ARG 737": "NH1" <-> "NH2" Residue "E GLU 743": "OE1" <-> "OE2" Residue "E ASP 832": "OD1" <-> "OD2" Residue "E TYR 840": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 867": "NH1" <-> "NH2" Residue "E ARG 883": "NH1" <-> "NH2" Residue "E PHE 884": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 887": "NH1" <-> "NH2" Residue "E ARG 1054": "NH1" <-> "NH2" Residue "E ARG 1073": "NH1" <-> "NH2" Residue "E PHE 1127": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/chem_data/mon_lib" Total number of atoms: 20356 Number of models: 1 Model: "" Number of chains: 10 Chain: "C" Number of atoms: 847 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 847 Classifications: {'peptide': 106} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 7, 'TRANS': 98} Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "G" Number of atoms: 847 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 847 Classifications: {'peptide': 106} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 7, 'TRANS': 98} Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "A" Number of atoms: 8796 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1070, 8796 Classifications: {'peptide': 1070} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 21, 'TRANS': 1048} Chain breaks: 7 Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "E" Number of atoms: 8796 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1070, 8796 Classifications: {'peptide': 1070} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 21, 'TRANS': 1048} Chain breaks: 7 Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "B" Number of atoms: 533 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 533 Classifications: {'DNA': 1, 'RNA': 25} Modifications used: {'5*END': 1, 'rna2p_pur': 6, 'rna2p_pyr': 3, 'rna3p_pur': 8, 'rna3p_pyr': 8} Link IDs: {'rna2p': 9, 'rna3p': 16} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {' G:plan2': 1, ' G:plan': 1} Unresolved non-hydrogen planarities: 14 Chain: "F" Number of atoms: 533 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 533 Classifications: {'DNA': 1, 'RNA': 25} Modifications used: {'5*END': 1, 'rna2p_pur': 6, 'rna2p_pyr': 3, 'rna3p_pur': 8, 'rna3p_pyr': 8} Link IDs: {'rna2p': 9, 'rna3p': 16} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {' G:plan2': 1, ' G:plan': 1} Unresolved non-hydrogen planarities: 14 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 12.19, per 1000 atoms: 0.60 Number of scatterers: 20356 At special positions: 0 Unit cell: (152.1, 165.6, 167.4, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 56 16.00 P 50 15.00 Mg 4 11.99 O 4008 8.00 N 3362 7.00 C 12876 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: 9.33 Conformation dependent library (CDL) restraints added in 3.0 seconds 4632 Ramachandran restraints generated. 2316 Oldfield, 0 Emsley, 2316 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4500 Finding SS restraints... Secondary structure from input PDB file: 100 helices and 22 sheets defined 48.9% alpha, 13.3% beta 12 base pairs and 26 stacking pairs defined. Time for finding SS restraints: 6.78 Creating SS restraints... Processing helix chain 'C' and resid 128 through 148 Processing helix chain 'C' and resid 151 through 155 removed outlier: 3.552A pdb=" N ARG C 155 " --> pdb=" O TYR C 152 " (cutoff:3.500A) Processing helix chain 'C' and resid 200 through 204 Processing helix chain 'C' and resid 229 through 233 Processing helix chain 'G' and resid 129 through 148 Processing helix chain 'G' and resid 151 through 155 removed outlier: 3.553A pdb=" N ARG G 155 " --> pdb=" O TYR G 152 " (cutoff:3.500A) Processing helix chain 'G' and resid 200 through 204 Processing helix chain 'G' and resid 229 through 233 Processing helix chain 'A' and resid 3 through 7 Processing helix chain 'A' and resid 26 through 33 Processing helix chain 'A' and resid 38 through 66 removed outlier: 4.581A pdb=" N LYS A 48 " --> pdb=" O ALA A 44 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N GLY A 49 " --> pdb=" O GLU A 45 " (cutoff:3.500A) Processing helix chain 'A' and resid 73 through 82 removed outlier: 3.670A pdb=" N ARG A 82 " --> pdb=" O ILE A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 94 through 110 Processing helix chain 'A' and resid 114 through 120 removed outlier: 4.221A pdb=" N PHE A 119 " --> pdb=" O LYS A 116 " (cutoff:3.500A) Processing helix chain 'A' and resid 121 through 126 Processing helix chain 'A' and resid 127 through 132 removed outlier: 3.597A pdb=" N LEU A 132 " --> pdb=" O LEU A 128 " (cutoff:3.500A) Processing helix chain 'A' and resid 136 through 144 removed outlier: 3.968A pdb=" N LEU A 140 " --> pdb=" O ASP A 136 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N PHE A 144 " --> pdb=" O LEU A 140 " (cutoff:3.500A) Processing helix chain 'A' and resid 147 through 150 Processing helix chain 'A' and resid 151 through 159 Processing helix chain 'A' and resid 170 through 178 removed outlier: 3.762A pdb=" N GLU A 178 " --> pdb=" O ARG A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 179 through 193 Processing helix chain 'A' and resid 201 through 211 removed outlier: 4.355A pdb=" N ILE A 205 " --> pdb=" O GLU A 201 " (cutoff:3.500A) Processing helix chain 'A' and resid 216 through 221 Processing helix chain 'A' and resid 230 through 243 Processing helix chain 'A' and resid 254 through 266 Processing helix chain 'A' and resid 296 through 308 Processing helix chain 'A' and resid 312 through 327 Processing helix chain 'A' and resid 341 through 352 removed outlier: 3.709A pdb=" N SER A 345 " --> pdb=" O GLY A 341 " (cutoff:3.500A) Processing helix chain 'A' and resid 357 through 371 removed outlier: 3.974A pdb=" N ILE A 369 " --> pdb=" O GLU A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 378 through 392 Processing helix chain 'A' and resid 397 through 403 Processing helix chain 'A' and resid 409 through 431 Processing helix chain 'A' and resid 433 through 437 removed outlier: 3.649A pdb=" N PHE A 436 " --> pdb=" O GLU A 433 " (cutoff:3.500A) Processing helix chain 'A' and resid 450 through 471 Processing helix chain 'A' and resid 472 through 474 No H-bonds generated for 'chain 'A' and resid 472 through 474' Processing helix chain 'A' and resid 483 through 498 removed outlier: 4.456A pdb=" N ASP A 489 " --> pdb=" O SER A 485 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N ILE A 496 " --> pdb=" O LEU A 492 " (cutoff:3.500A) Processing helix chain 'A' and resid 499 through 512 Processing helix chain 'A' and resid 686 through 697 Processing helix chain 'A' and resid 718 through 728 removed outlier: 4.083A pdb=" N PHE A 728 " --> pdb=" O PHE A 724 " (cutoff:3.500A) Processing helix chain 'A' and resid 786 through 791 removed outlier: 4.115A pdb=" N GLU A 791 " --> pdb=" O ARG A 788 " (cutoff:3.500A) Processing helix chain 'A' and resid 811 through 822 Processing helix chain 'A' and resid 872 through 886 Processing helix chain 'A' and resid 890 through 919 removed outlier: 3.609A pdb=" N GLU A 894 " --> pdb=" O TRP A 890 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N HIS A 909 " --> pdb=" O SER A 905 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N LYS A 917 " --> pdb=" O GLU A 913 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N TYR A 918 " --> pdb=" O LEU A 914 " (cutoff:3.500A) Processing helix chain 'A' and resid 939 through 955 Processing helix chain 'A' and resid 969 through 973 removed outlier: 4.244A pdb=" N GLY A 973 " --> pdb=" O ALA A 970 " (cutoff:3.500A) Processing helix chain 'A' and resid 1020 through 1029 Processing helix chain 'A' and resid 1048 through 1052 removed outlier: 3.506A pdb=" N PHE A1052 " --> pdb=" O TYR A1049 " (cutoff:3.500A) Processing helix chain 'A' and resid 1091 through 1102 Processing helix chain 'A' and resid 1111 through 1116 Processing helix chain 'A' and resid 1120 through 1135 removed outlier: 4.256A pdb=" N TYR A1124 " --> pdb=" O ASP A1120 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N SER A1125 " --> pdb=" O LYS A1121 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LEU A1135 " --> pdb=" O MET A1131 " (cutoff:3.500A) Processing helix chain 'A' and resid 1165 through 1167 No H-bonds generated for 'chain 'A' and resid 1165 through 1167' Processing helix chain 'A' and resid 1178 through 1201 removed outlier: 3.680A pdb=" N VAL A1191 " --> pdb=" O ILE A1187 " (cutoff:3.500A) Processing helix chain 'A' and resid 1205 through 1209 Processing helix chain 'A' and resid 1214 through 1225 Processing helix chain 'E' and resid 3 through 7 Processing helix chain 'E' and resid 26 through 33 Processing helix chain 'E' and resid 38 through 66 removed outlier: 4.583A pdb=" N LYS E 48 " --> pdb=" O ALA E 44 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N GLY E 49 " --> pdb=" O GLU E 45 " (cutoff:3.500A) Processing helix chain 'E' and resid 73 through 82 removed outlier: 3.671A pdb=" N ARG E 82 " --> pdb=" O ILE E 78 " (cutoff:3.500A) Processing helix chain 'E' and resid 94 through 110 Processing helix chain 'E' and resid 114 through 120 removed outlier: 4.221A pdb=" N PHE E 119 " --> pdb=" O LYS E 116 " (cutoff:3.500A) Processing helix chain 'E' and resid 121 through 126 Processing helix chain 'E' and resid 127 through 132 removed outlier: 3.597A pdb=" N LEU E 132 " --> pdb=" O LEU E 128 " (cutoff:3.500A) Processing helix chain 'E' and resid 136 through 144 removed outlier: 3.968A pdb=" N LEU E 140 " --> pdb=" O ASP E 136 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N PHE E 144 " --> pdb=" O LEU E 140 " (cutoff:3.500A) Processing helix chain 'E' and resid 147 through 150 Processing helix chain 'E' and resid 151 through 159 Processing helix chain 'E' and resid 170 through 178 removed outlier: 3.763A pdb=" N GLU E 178 " --> pdb=" O ARG E 174 " (cutoff:3.500A) Processing helix chain 'E' and resid 179 through 193 Processing helix chain 'E' and resid 201 through 211 removed outlier: 4.355A pdb=" N ILE E 205 " --> pdb=" O GLU E 201 " (cutoff:3.500A) Processing helix chain 'E' and resid 216 through 221 Processing helix chain 'E' and resid 230 through 243 Processing helix chain 'E' and resid 254 through 266 Processing helix chain 'E' and resid 296 through 308 Processing helix chain 'E' and resid 312 through 327 Processing helix chain 'E' and resid 341 through 352 removed outlier: 3.709A pdb=" N SER E 345 " --> pdb=" O GLY E 341 " (cutoff:3.500A) Processing helix chain 'E' and resid 357 through 371 removed outlier: 3.974A pdb=" N ILE E 369 " --> pdb=" O GLU E 365 " (cutoff:3.500A) Processing helix chain 'E' and resid 378 through 392 Processing helix chain 'E' and resid 397 through 403 Processing helix chain 'E' and resid 409 through 431 Processing helix chain 'E' and resid 433 through 437 removed outlier: 3.650A pdb=" N PHE E 436 " --> pdb=" O GLU E 433 " (cutoff:3.500A) Processing helix chain 'E' and resid 450 through 471 Processing helix chain 'E' and resid 472 through 474 No H-bonds generated for 'chain 'E' and resid 472 through 474' Processing helix chain 'E' and resid 483 through 498 removed outlier: 4.456A pdb=" N ASP E 489 " --> pdb=" O SER E 485 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N ILE E 496 " --> pdb=" O LEU E 492 " (cutoff:3.500A) Processing helix chain 'E' and resid 499 through 512 Processing helix chain 'E' and resid 686 through 697 Processing helix chain 'E' and resid 718 through 728 removed outlier: 4.082A pdb=" N PHE E 728 " --> pdb=" O PHE E 724 " (cutoff:3.500A) Processing helix chain 'E' and resid 786 through 791 removed outlier: 4.115A pdb=" N GLU E 791 " --> pdb=" O ARG E 788 " (cutoff:3.500A) Processing helix chain 'E' and resid 811 through 822 Processing helix chain 'E' and resid 872 through 886 Processing helix chain 'E' and resid 890 through 919 removed outlier: 3.608A pdb=" N GLU E 894 " --> pdb=" O TRP E 890 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N HIS E 909 " --> pdb=" O SER E 905 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N LYS E 917 " --> pdb=" O GLU E 913 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N TYR E 918 " --> pdb=" O LEU E 914 " (cutoff:3.500A) Processing helix chain 'E' and resid 939 through 955 Processing helix chain 'E' and resid 969 through 973 removed outlier: 4.243A pdb=" N GLY E 973 " --> pdb=" O ALA E 970 " (cutoff:3.500A) Processing helix chain 'E' and resid 1020 through 1029 Processing helix chain 'E' and resid 1048 through 1052 removed outlier: 3.506A pdb=" N PHE E1052 " --> pdb=" O TYR E1049 " (cutoff:3.500A) Processing helix chain 'E' and resid 1091 through 1102 Processing helix chain 'E' and resid 1111 through 1116 Processing helix chain 'E' and resid 1120 through 1135 removed outlier: 4.257A pdb=" N TYR E1124 " --> pdb=" O ASP E1120 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N SER E1125 " --> pdb=" O LYS E1121 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LEU E1135 " --> pdb=" O MET E1131 " (cutoff:3.500A) Processing helix chain 'E' and resid 1165 through 1167 No H-bonds generated for 'chain 'E' and resid 1165 through 1167' Processing helix chain 'E' and resid 1178 through 1201 removed outlier: 3.679A pdb=" N VAL E1191 " --> pdb=" O ILE E1187 " (cutoff:3.500A) Processing helix chain 'E' and resid 1205 through 1209 Processing helix chain 'E' and resid 1214 through 1225 Processing sheet with id=AA1, first strand: chain 'C' and resid 206 through 207 removed outlier: 6.894A pdb=" N CYS C 195 " --> pdb=" O CYS C 185 " (cutoff:3.500A) removed outlier: 4.945A pdb=" N CYS C 185 " --> pdb=" O CYS C 195 " (cutoff:3.500A) removed outlier: 5.896A pdb=" N TYR C 197 " --> pdb=" O GLY C 183 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N ASN C 157 " --> pdb=" O VAL C 213 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N ARG C 222 " --> pdb=" O ILE C 214 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 206 through 207 removed outlier: 6.894A pdb=" N CYS C 195 " --> pdb=" O CYS C 185 " (cutoff:3.500A) removed outlier: 4.945A pdb=" N CYS C 185 " --> pdb=" O CYS C 195 " (cutoff:3.500A) removed outlier: 5.896A pdb=" N TYR C 197 " --> pdb=" O GLY C 183 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'G' and resid 206 through 207 removed outlier: 6.893A pdb=" N CYS G 195 " --> pdb=" O CYS G 185 " (cutoff:3.500A) removed outlier: 4.945A pdb=" N CYS G 185 " --> pdb=" O CYS G 195 " (cutoff:3.500A) removed outlier: 5.896A pdb=" N TYR G 197 " --> pdb=" O GLY G 183 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N ASN G 157 " --> pdb=" O VAL G 213 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N ARG G 222 " --> pdb=" O ILE G 214 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'G' and resid 206 through 207 removed outlier: 6.893A pdb=" N CYS G 195 " --> pdb=" O CYS G 185 " (cutoff:3.500A) removed outlier: 4.945A pdb=" N CYS G 185 " --> pdb=" O CYS G 195 " (cutoff:3.500A) removed outlier: 5.896A pdb=" N TYR G 197 " --> pdb=" O GLY G 183 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 545 through 549 removed outlier: 4.866A pdb=" N TYR A 553 " --> pdb=" O ILE A 704 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N TYR A 794 " --> pdb=" O ALA A 21 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ARG A 737 " --> pdb=" O ALA A 801 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 545 through 549 removed outlier: 4.866A pdb=" N TYR A 553 " --> pdb=" O ILE A 704 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N TYR A 794 " --> pdb=" O ALA A 21 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 337 through 339 Processing sheet with id=AA8, first strand: chain 'A' and resid 765 through 766 Processing sheet with id=AA9, first strand: chain 'A' and resid 850 through 855 removed outlier: 6.464A pdb=" N VAL A 843 " --> pdb=" O VAL A 851 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N GLN A 853 " --> pdb=" O ILE A 841 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N ILE A 841 " --> pdb=" O GLN A 853 " (cutoff:3.500A) removed outlier: 4.666A pdb=" N GLU A 925 " --> pdb=" O ILE A 831 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N ILE A 922 " --> pdb=" O PHE A 994 " (cutoff:3.500A) removed outlier: 7.669A pdb=" N ILE A 996 " --> pdb=" O ILE A 922 " (cutoff:3.500A) removed outlier: 6.107A pdb=" N LEU A 924 " --> pdb=" O ILE A 996 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 858 through 863 removed outlier: 3.503A pdb=" N ILE A 868 " --> pdb=" O ASN A 861 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 1033 through 1037 removed outlier: 3.793A pdb=" N LEU A1065 " --> pdb=" O PHE A1045 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 1070 through 1073 Processing sheet with id=AB4, first strand: chain 'A' and resid 1151 through 1155 removed outlier: 4.724A pdb=" N TYR A1162 " --> pdb=" O SER A1152 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 545 through 549 removed outlier: 4.866A pdb=" N TYR E 553 " --> pdb=" O ILE E 704 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N TYR E 794 " --> pdb=" O ALA E 21 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ARG E 737 " --> pdb=" O ALA E 801 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 545 through 549 removed outlier: 4.866A pdb=" N TYR E 553 " --> pdb=" O ILE E 704 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N TYR E 794 " --> pdb=" O ALA E 21 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 337 through 339 Processing sheet with id=AB8, first strand: chain 'E' and resid 765 through 766 Processing sheet with id=AB9, first strand: chain 'E' and resid 850 through 855 removed outlier: 6.465A pdb=" N VAL E 843 " --> pdb=" O VAL E 851 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N GLN E 853 " --> pdb=" O ILE E 841 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N ILE E 841 " --> pdb=" O GLN E 853 " (cutoff:3.500A) removed outlier: 4.666A pdb=" N GLU E 925 " --> pdb=" O ILE E 831 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N ILE E 922 " --> pdb=" O PHE E 994 " (cutoff:3.500A) removed outlier: 7.667A pdb=" N ILE E 996 " --> pdb=" O ILE E 922 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N LEU E 924 " --> pdb=" O ILE E 996 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 858 through 863 removed outlier: 3.504A pdb=" N ILE E 868 " --> pdb=" O ASN E 861 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 1033 through 1037 removed outlier: 3.793A pdb=" N LEU E1065 " --> pdb=" O PHE E1045 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 1070 through 1073 Processing sheet with id=AC4, first strand: chain 'E' and resid 1151 through 1155 removed outlier: 4.724A pdb=" N TYR E1162 " --> pdb=" O SER E1152 " (cutoff:3.500A) 909 hydrogen bonds defined for protein. 2499 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 28 hydrogen bonds 48 hydrogen bond angles 0 basepair planarities 12 basepair parallelities 26 stacking parallelities Total time for adding SS restraints: 8.51 Time building geometry restraints manager: 9.89 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: 6240 1.34 - 1.46: 3449 1.46 - 1.57: 10977 1.57 - 1.69: 100 1.69 - 1.81: 94 Bond restraints: 20860 Sorted by residual: bond pdb=" CB GLU E 443 " pdb=" CG GLU E 443 " ideal model delta sigma weight residual 1.520 1.549 -0.029 3.00e-02 1.11e+03 9.29e-01 bond pdb=" CB GLU A 443 " pdb=" CG GLU A 443 " ideal model delta sigma weight residual 1.520 1.549 -0.029 3.00e-02 1.11e+03 9.26e-01 bond pdb=" CA ASP C 137 " pdb=" C ASP C 137 " ideal model delta sigma weight residual 1.522 1.509 0.013 1.40e-02 5.10e+03 7.97e-01 bond pdb=" CA ASP G 137 " pdb=" C ASP G 137 " ideal model delta sigma weight residual 1.522 1.509 0.012 1.40e-02 5.10e+03 7.52e-01 bond pdb=" CG LEU A1130 " pdb=" CD2 LEU A1130 " ideal model delta sigma weight residual 1.521 1.493 0.028 3.30e-02 9.18e+02 7.10e-01 ... (remaining 20855 not shown) Histogram of bond angle deviations from ideal: 100.32 - 107.06: 632 107.06 - 113.80: 11314 113.80 - 120.54: 8583 120.54 - 127.28: 7565 127.28 - 134.02: 216 Bond angle restraints: 28310 Sorted by residual: angle pdb=" N LEU C 138 " pdb=" CA LEU C 138 " pdb=" C LEU C 138 " ideal model delta sigma weight residual 111.36 107.38 3.98 1.09e+00 8.42e-01 1.33e+01 angle pdb=" N LEU G 138 " pdb=" CA LEU G 138 " pdb=" C LEU G 138 " ideal model delta sigma weight residual 111.36 107.39 3.97 1.09e+00 8.42e-01 1.33e+01 angle pdb=" CA LEU C 138 " pdb=" CB LEU C 138 " pdb=" CG LEU C 138 " ideal model delta sigma weight residual 116.30 128.71 -12.41 3.50e+00 8.16e-02 1.26e+01 angle pdb=" CA LEU G 138 " pdb=" CB LEU G 138 " pdb=" CG LEU G 138 " ideal model delta sigma weight residual 116.30 128.66 -12.36 3.50e+00 8.16e-02 1.25e+01 angle pdb=" C LEU A 497 " pdb=" N LEU A 498 " pdb=" CA LEU A 498 " ideal model delta sigma weight residual 122.31 116.41 5.90 2.00e+00 2.50e-01 8.71e+00 ... (remaining 28305 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.28: 12162 31.28 - 62.57: 334 62.57 - 93.85: 22 93.85 - 125.13: 0 125.13 - 156.41: 2 Dihedral angle restraints: 12520 sinusoidal: 5550 harmonic: 6970 Sorted by residual: dihedral pdb=" O4' U B 14 " pdb=" C1' U B 14 " pdb=" N1 U B 14 " pdb=" C2 U B 14 " ideal model delta sinusoidal sigma weight residual 232.00 75.59 156.41 1 1.70e+01 3.46e-03 6.37e+01 dihedral pdb=" O4' U F 14 " pdb=" C1' U F 14 " pdb=" N1 U F 14 " pdb=" C2 U F 14 " ideal model delta sinusoidal sigma weight residual 232.00 75.67 156.33 1 1.70e+01 3.46e-03 6.36e+01 dihedral pdb=" CA ALA E 195 " pdb=" C ALA E 195 " pdb=" N ILE E 196 " pdb=" CA ILE E 196 " ideal model delta harmonic sigma weight residual 180.00 157.44 22.56 0 5.00e+00 4.00e-02 2.04e+01 ... (remaining 12517 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 2246 0.039 - 0.078: 632 0.078 - 0.117: 182 0.117 - 0.156: 31 0.156 - 0.195: 5 Chirality restraints: 3096 Sorted by residual: chirality pdb=" C1' C B 9 " pdb=" O4' C B 9 " pdb=" C2' C B 9 " pdb=" N1 C B 9 " both_signs ideal model delta sigma weight residual False 2.47 2.27 0.20 2.00e-01 2.50e+01 9.55e-01 chirality pdb=" C1' C F 9 " pdb=" O4' C F 9 " pdb=" C2' C F 9 " pdb=" N1 C F 9 " both_signs ideal model delta sigma weight residual False 2.47 2.28 0.19 2.00e-01 2.50e+01 9.10e-01 chirality pdb=" CB THR G 140 " pdb=" CA THR G 140 " pdb=" OG1 THR G 140 " pdb=" CG2 THR G 140 " both_signs ideal model delta sigma weight residual False 2.55 2.37 0.18 2.00e-01 2.50e+01 8.43e-01 ... (remaining 3093 not shown) Planarity restraints: 3434 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE G 136 " -0.017 2.00e-02 2.50e+03 3.31e-02 1.10e+01 pdb=" C ILE G 136 " 0.057 2.00e-02 2.50e+03 pdb=" O ILE G 136 " -0.021 2.00e-02 2.50e+03 pdb=" N ASP G 137 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE C 136 " 0.017 2.00e-02 2.50e+03 3.30e-02 1.09e+01 pdb=" C ILE C 136 " -0.057 2.00e-02 2.50e+03 pdb=" O ILE C 136 " 0.021 2.00e-02 2.50e+03 pdb=" N ASP C 137 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE E 176 " -0.015 2.00e-02 2.50e+03 2.97e-02 8.84e+00 pdb=" C ILE E 176 " 0.051 2.00e-02 2.50e+03 pdb=" O ILE E 176 " -0.019 2.00e-02 2.50e+03 pdb=" N ASN E 177 " -0.017 2.00e-02 2.50e+03 ... (remaining 3431 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 594 2.70 - 3.25: 20158 3.25 - 3.80: 31076 3.80 - 4.35: 43031 4.35 - 4.90: 70067 Nonbonded interactions: 164926 Sorted by model distance: nonbonded pdb=" O SER A 68 " pdb=" OG SER A 68 " model vdw 2.152 2.440 nonbonded pdb=" O SER E 68 " pdb=" OG SER E 68 " model vdw 2.152 2.440 nonbonded pdb=" OP2 A B 17 " pdb="MG MG A1301 " model vdw 2.195 2.170 nonbonded pdb=" OP2 A F 17 " pdb="MG MG E1301 " model vdw 2.202 2.170 nonbonded pdb=" OE1 GLU C 184 " pdb=" O5' A B 1 " model vdw 2.209 2.440 ... (remaining 164921 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' selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'F' } ncs_group { reference = chain 'C' selection = chain 'G' } Set up NCS constraints Number of NCS constrained groups: 3 pdb_interpretation.ncs_group { reference = chain 'A' selection = chain 'E' } pdb_interpretation.ncs_group { reference = chain 'B' selection = chain 'F' } pdb_interpretation.ncs_group { reference = chain 'C' selection = chain 'G' } Set refine NCS operators NCS operators will be refined. Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 50 5.49 5 Mg 4 5.21 5 S 56 5.16 5 C 12876 2.51 5 N 3362 2.21 5 O 4008 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: 2.530 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.260 Construct map_model_manager: 0.020 Extract box with map and model: 10.650 Check model and map are aligned: 0.310 Convert atoms to be neutral: 0.190 Process input model: 62.530 Find NCS groups from input model: 1.160 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Set scattering table: 0.010 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.010 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 80.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5814 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 : 0.002 0.029 20860 Z= 0.119 Angle : 0.533 12.414 28310 Z= 0.298 Chirality : 0.040 0.195 3096 Planarity : 0.004 0.042 3434 Dihedral : 14.456 156.413 8020 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.57 % Favored : 94.43 % Rotamer Outliers : 1.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.30 (0.15), residues: 2316 helix: -1.44 (0.14), residues: 1052 sheet: -3.27 (0.29), residues: 212 loop : -2.70 (0.16), residues: 1052 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4632 Ramachandran restraints generated. 2316 Oldfield, 0 Emsley, 2316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4632 Ramachandran restraints generated. 2316 Oldfield, 0 Emsley, 2316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 66 time to evaluate : 1.070 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 3 residues processed: 78 average time/residue: 0.2444 time to fit residues: 25.8217 Evaluate side-chains 36 residues out of total 968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 33 time to evaluate : 1.027 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0722 time to fit residues: 1.8967 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.017 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0210 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.016 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0070 Evaluate side-chains 27 residues out of total 100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 26 time to evaluate : 0.105 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 27 average time/residue: 0.1472 time to fit residues: 4.3195 Evaluate side-chains 15 residues out of total 100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 15 time to evaluate : 0.100 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.1311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 200 optimal weight: 5.9990 chunk 180 optimal weight: 2.9990 chunk 100 optimal weight: 0.5980 chunk 61 optimal weight: 0.5980 chunk 121 optimal weight: 0.7980 chunk 96 optimal weight: 1.9990 chunk 186 optimal weight: 2.9990 chunk 72 optimal weight: 6.9990 chunk 113 optimal weight: 0.0870 chunk 138 optimal weight: 0.9980 chunk 216 optimal weight: 10.0000 overall best weight: 0.6158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 33 ASN A 67 HIS A 268 GLN A 420 GLN A 793 GLN A 797 HIS Total number of N/Q/H flips: 6 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 142 GLN ** C 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5863 moved from start: 0.1681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.033 20860 Z= 0.122 Angle : 0.504 10.328 28310 Z= 0.261 Chirality : 0.040 0.216 3096 Planarity : 0.003 0.052 3434 Dihedral : 8.155 168.971 3152 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer Outliers : 0.09 % 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: -1.48 (0.17), residues: 2316 helix: 0.25 (0.16), residues: 1040 sheet: -2.11 (0.30), residues: 252 loop : -1.98 (0.19), residues: 1024 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4630 Ramachandran restraints generated. 2315 Oldfield, 0 Emsley, 2315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4630 Ramachandran restraints generated. 2315 Oldfield, 0 Emsley, 2315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 43 time to evaluate : 1.160 Fit side-chains 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: 44 average time/residue: 0.2435 time to fit residues: 15.5198 Evaluate side-chains 33 residues out of total 968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 33 time to evaluate : 1.051 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.4879 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.024 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0306 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.021 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0099 Evaluate side-chains 19 residues out of total 100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 19 time to evaluate : 0.129 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 19 average time/residue: 0.1360 time to fit residues: 2.9027 Evaluate side-chains 11 residues out of total 100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 11 time to evaluate : 0.103 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.1353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/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-4807/modules/cctbx_project/iotbx/cli_parser.py", line 864, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/phenix/phenix/programs/real_space_refine.py", line 191, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/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-4807/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 675, in refine_xyz self.minimization_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 770, in minimization_ncs ncs_groups = ncs_groups) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/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-4807/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 400, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/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-4807/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 133, in refine refine_sites = True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/mmtbx/refinement/minimization_ncs_constraints.py", line 434, in __init__ ignore_line_search_failed_maxfev=True)) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/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-4807/modules/cctbx_project/mmtbx/refinement/minimization_ncs_constraints.py", line 459, in compute_functional_and_gradients x=self.x) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/mmtbx/refinement/minimization_ncs_constraints.py", line 248, in target_and_gradients grad = g_data) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/mmtbx/refinement/minimization_ncs_constraints.py", line 112, in restraints_target_and_grads compute_gradients = True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/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-4807/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-4807/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: 51.2601 > 50: distance: 0 - 1: 4.280 distance: 0 - 2: 9.353 distance: 4 - 5: 10.131 distance: 4 - 7: 10.949 distance: 5 - 6: 8.935 distance: 5 - 11: 3.861 distance: 7 - 8: 8.026 distance: 8 - 9: 7.036 distance: 8 - 10: 24.723 distance: 11 - 12: 10.980 distance: 12 - 13: 11.253 distance: 12 - 15: 11.169 distance: 13 - 14: 23.050 distance: 13 - 16: 12.493 distance: 16 - 17: 17.305 distance: 17 - 18: 21.545 distance: 17 - 20: 18.340 distance: 18 - 19: 6.992 distance: 18 - 24: 42.223 distance: 20 - 21: 7.469 distance: 20 - 22: 7.885 distance: 21 - 23: 15.699 distance: 24 - 25: 22.512 distance: 25 - 26: 27.078 distance: 25 - 28: 19.480 distance: 26 - 27: 17.411 distance: 26 - 35: 19.132 distance: 28 - 29: 20.677 distance: 29 - 30: 23.320 distance: 29 - 31: 17.603 distance: 30 - 32: 11.748 distance: 31 - 33: 13.023 distance: 32 - 34: 14.508 distance: 33 - 34: 31.118 distance: 35 - 36: 20.345 distance: 36 - 37: 22.613 distance: 36 - 39: 27.757 distance: 37 - 38: 19.878 distance: 37 - 43: 13.559 distance: 39 - 40: 7.456 distance: 40 - 41: 39.015 distance: 43 - 44: 6.740 distance: 44 - 45: 18.461 distance: 44 - 47: 21.158 distance: 45 - 46: 38.429 distance: 45 - 52: 28.226 distance: 47 - 48: 17.671 distance: 48 - 49: 6.301 distance: 49 - 50: 17.688 distance: 50 - 51: 47.514 distance: 52 - 53: 11.019 distance: 53 - 54: 8.464 distance: 53 - 56: 19.316 distance: 54 - 55: 7.067 distance: 54 - 62: 4.363 distance: 56 - 57: 4.355 distance: 57 - 58: 19.338 distance: 57 - 59: 28.009 distance: 58 - 60: 7.802 distance: 59 - 61: 24.836 distance: 60 - 61: 29.461 distance: 62 - 63: 3.162 distance: 63 - 64: 4.167 distance: 64 - 65: 3.230 distance: 64 - 71: 3.332 distance: 66 - 67: 6.027 distance: 67 - 68: 24.090 distance: 68 - 69: 10.760 distance: 68 - 70: 21.332 distance: 71 - 72: 3.579 distance: 72 - 73: 3.219 distance: 75 - 76: 4.462