Starting phenix.real_space_refine on Sat Mar 23 17:29:53 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6p7n_20267/03_2024/6p7n_20267.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6p7n_20267/03_2024/6p7n_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_20267/03_2024/6p7n_20267.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6p7n_20267/03_2024/6p7n_20267.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6p7n_20267/03_2024/6p7n_20267.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6p7n_20267/03_2024/6p7n_20267.pdb" } resolution = 4.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 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 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. 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-5265/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: 10.99, per 1000 atoms: 0.54 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: 7.92 Conformation dependent library (CDL) restraints added in 3.2 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: 6.22 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: 8.23 Time building geometry restraints manager: 8.64 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: 12230 31.28 - 62.57: 382 62.57 - 93.85: 42 93.85 - 125.13: 0 125.13 - 156.41: 2 Dihedral angle restraints: 12656 sinusoidal: 5686 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 12653 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. 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: 4.150 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.240 Construct map_model_manager: 0.010 Extract box with map and model: 9.260 Check model and map are aligned: 0.300 Set scattering table: 0.200 Process input model: 59.310 Find NCS groups from input model: 0.970 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 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: 77.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6012 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 : 15.216 156.413 8156 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.57 % Favored : 94.43 % Rotamer: Outliers : 1.33 % Allowed : 3.84 % Favored : 94.83 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A1193 HIS 0.006 0.001 HIS E 909 PHE 0.013 0.001 PHE E 946 TYR 0.011 0.001 TYR C 188 ARG 0.006 0.000 ARG C 187 *********************** 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 : 1.055 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 317 SER cc_start: 0.9347 (OUTLIER) cc_final: 0.8712 (p) REVERT: A 701 MET cc_start: 0.9055 (ttm) cc_final: 0.8792 (tpp) REVERT: A 796 LEU cc_start: 0.9855 (tp) cc_final: 0.9629 (pp) outliers start: 13 outliers final: 3 residues processed: 78 average time/residue: 0.2822 time to fit residues: 30.0018 Evaluate side-chains 38 residues out of total 968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 34 time to evaluate : 1.042 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.019 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0240 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 Evaluate side-chains 27 residues out of total 100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 26 time to evaluate : 0.100 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 176 GLU cc_start: 0.8927 (mm-30) cc_final: 0.8618 (pm20) REVERT: C 224 MET cc_start: 0.7124 (mtp) cc_final: 0.6570 (mtm) outliers start: 1 outliers final: 0 residues processed: 27 average time/residue: 0.1552 time to fit residues: 4.5359 Evaluate side-chains 16 residues out of total 100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 16 time to evaluate : 0.108 ------------------------------------------------------------------------------- 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: 0.6053 moved from start: 0.1676 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= 0.116 Angle : 0.494 10.131 28310 Z= 0.256 Chirality : 0.040 0.214 3096 Planarity : 0.003 0.061 3434 Dihedral : 11.214 169.621 3288 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % 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: -1.47 (0.17), residues: 2316 helix: 0.24 (0.16), residues: 1040 sheet: -2.09 (0.31), residues: 252 loop : -1.95 (0.19), residues: 1024 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A1193 HIS 0.004 0.001 HIS C 190 PHE 0.011 0.001 PHE A 724 TYR 0.010 0.001 TYR E1095 ARG 0.006 0.000 ARG G 217 *********************** 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 43 residues out of total 968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 43 time to evaluate : 1.012 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 TYR cc_start: 0.9541 (t80) cc_final: 0.9284 (t80) REVERT: A 452 VAL cc_start: 0.9416 (m) cc_final: 0.9214 (p) REVERT: A 555 LEU cc_start: 0.9787 (tp) cc_final: 0.9502 (pp) REVERT: A 701 MET cc_start: 0.8962 (ttm) cc_final: 0.8732 (tpp) REVERT: A 722 MET cc_start: 0.8642 (mtm) cc_final: 0.8353 (mtt) REVERT: A 796 LEU cc_start: 0.9850 (tp) cc_final: 0.9579 (pp) REVERT: A 949 MET cc_start: 0.9781 (mmp) cc_final: 0.9524 (mtm) REVERT: A 1035 MET cc_start: 0.8963 (ppp) cc_final: 0.8612 (ppp) REVERT: A 1128 MET cc_start: 0.9183 (tpp) cc_final: 0.8876 (tpp) outliers start: 0 outliers final: 0 residues processed: 43 average time/residue: 0.2578 time to fit residues: 15.7342 Evaluate side-chains 36 residues out of total 968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 36 time to evaluate : 0.974 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.014 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0181 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 Evaluate side-chains 19 residues out of total 100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 19 time to evaluate : 0.081 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 176 GLU cc_start: 0.8957 (mm-30) cc_final: 0.8747 (pm20) REVERT: C 209 TYR cc_start: 0.9244 (m-80) cc_final: 0.8830 (m-80) REVERT: C 224 MET cc_start: 0.7206 (mtp) cc_final: 0.6845 (mtm) outliers start: 0 outliers final: 0 residues processed: 19 average time/residue: 0.1316 time to fit residues: 2.7818 Evaluate side-chains 13 residues out of total 100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 13 time to evaluate : 0.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 120 optimal weight: 1.9990 chunk 67 optimal weight: 7.9990 chunk 179 optimal weight: 30.0000 chunk 147 optimal weight: 20.0000 chunk 59 optimal weight: 9.9990 chunk 216 optimal weight: 10.0000 chunk 233 optimal weight: 20.0000 chunk 192 optimal weight: 30.0000 chunk 214 optimal weight: 8.9990 chunk 73 optimal weight: 40.0000 chunk 173 optimal weight: 20.0000 overall best weight: 7.7992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 268 GLN A 306 ASN Total number of N/Q/H flips: 2 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6067 moved from start: 0.1825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.240 20860 Z= 0.471 Angle : 1.033 40.043 28310 Z= 0.513 Chirality : 0.060 0.693 3096 Planarity : 0.009 0.093 3434 Dihedral : 11.258 170.015 3288 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 12.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 0.19 % Allowed : 2.75 % Favored : 97.06 % 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: -1.66 (0.17), residues: 2316 helix: -0.11 (0.16), residues: 1052 sheet: -2.11 (0.30), residues: 252 loop : -1.85 (0.19), residues: 1012 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP E 355 HIS 0.097 0.011 HIS C 233 PHE 0.106 0.004 PHE A 81 TYR 0.146 0.007 TYR A 840 ARG 0.050 0.002 ARG G 203 *********************** REFINEMENT MACRO_CYCLE 3 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 40 residues out of total 968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 39 time to evaluate : 1.031 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 TYR cc_start: 0.9537 (t80) cc_final: 0.9332 (t80) REVERT: A 81 PHE cc_start: 0.6959 (t80) cc_final: 0.6669 (t80) REVERT: A 555 LEU cc_start: 0.9723 (tp) cc_final: 0.9511 (pp) REVERT: A 701 MET cc_start: 0.9001 (ttm) cc_final: 0.8760 (tpp) REVERT: A 722 MET cc_start: 0.8631 (mtm) cc_final: 0.8363 (mtt) REVERT: A 796 LEU cc_start: 0.9816 (tp) cc_final: 0.9559 (pp) REVERT: A 949 MET cc_start: 0.9784 (mmp) cc_final: 0.9530 (mtm) REVERT: A 1035 MET cc_start: 0.8975 (ppp) cc_final: 0.8632 (ppp) REVERT: A 1128 MET cc_start: 0.9191 (tpp) cc_final: 0.8902 (tpp) outliers start: 1 outliers final: 0 residues processed: 40 average time/residue: 0.2518 time to fit residues: 14.4291 Evaluate side-chains 35 residues out of total 968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 35 time to evaluate : 0.980 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 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0205 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 Evaluate side-chains 17 residues out of total 100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 16 time to evaluate : 0.107 Fit side-chains revert: symmetry clash REVERT: C 209 TYR cc_start: 0.9270 (m-80) cc_final: 0.8856 (m-80) REVERT: C 224 MET cc_start: 0.7236 (mtp) cc_final: 0.6898 (mtm) outliers start: 1 outliers final: 0 residues processed: 17 average time/residue: 0.1497 time to fit residues: 2.8263 Evaluate side-chains 11 residues out of total 100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 11 time to evaluate : 0.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 213 optimal weight: 0.8980 chunk 162 optimal weight: 0.8980 chunk 112 optimal weight: 30.0000 chunk 23 optimal weight: 0.7980 chunk 103 optimal weight: 0.0970 chunk 145 optimal weight: 0.3980 chunk 217 optimal weight: 0.1980 chunk 230 optimal weight: 0.0050 chunk 113 optimal weight: 3.9990 chunk 205 optimal weight: 20.0000 chunk 61 optimal weight: 9.9990 overall best weight: 0.2992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 ASN A 268 GLN A 311 ASN Total number of N/Q/H flips: 3 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 Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6057 moved from start: 0.2057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.134 20860 Z= 0.336 Angle : 1.009 26.515 28310 Z= 0.513 Chirality : 0.059 0.640 3096 Planarity : 0.011 0.149 3434 Dihedral : 11.473 169.672 3288 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 12.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer: Outliers : 0.47 % Allowed : 3.80 % Favored : 95.73 % Cbeta Deviations : 0.09 % 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: -2.19 (0.16), residues: 2316 helix: -0.75 (0.15), residues: 1056 sheet: -2.41 (0.27), residues: 278 loop : -1.82 (0.19), residues: 982 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.003 TRP A 355 HIS 0.086 0.011 HIS C 233 PHE 0.056 0.003 PHE A 220 TYR 0.102 0.006 TYR A 840 ARG 0.048 0.002 ARG C 203 *********************** REFINEMENT MACRO_CYCLE 4 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 42 residues out of total 968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 40 time to evaluate : 1.042 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 TYR cc_start: 0.9162 (t80) cc_final: 0.8805 (t80) REVERT: A 456 MET cc_start: 0.8552 (mmt) cc_final: 0.8282 (mmm) REVERT: A 701 MET cc_start: 0.8965 (ttm) cc_final: 0.8730 (tpp) REVERT: A 722 MET cc_start: 0.8640 (mtm) cc_final: 0.8392 (mtt) REVERT: A 796 LEU cc_start: 0.9804 (tp) cc_final: 0.9512 (pp) REVERT: A 1035 MET cc_start: 0.8972 (ppp) cc_final: 0.8654 (ppp) REVERT: A 1128 MET cc_start: 0.9188 (tpp) cc_final: 0.8897 (tpp) REVERT: A 1131 MET cc_start: 0.9642 (mmp) cc_final: 0.9437 (mmp) outliers start: 2 outliers final: 0 residues processed: 42 average time/residue: 0.2295 time to fit residues: 14.3338 Evaluate side-chains 35 residues out of total 968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 35 time to evaluate : 1.051 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.018 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0232 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.020 Evaluate side-chains 19 residues out of total 100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 16 time to evaluate : 0.107 Fit side-chains revert: symmetry clash REVERT: C 209 TYR cc_start: 0.9280 (m-80) cc_final: 0.8881 (m-80) REVERT: C 224 MET cc_start: 0.7139 (mtp) cc_final: 0.6763 (mtm) outliers start: 3 outliers final: 0 residues processed: 19 average time/residue: 0.1179 time to fit residues: 2.5284 Evaluate side-chains 12 residues out of total 100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 12 time to evaluate : 0.100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 191 optimal weight: 10.0000 chunk 130 optimal weight: 4.9990 chunk 3 optimal weight: 40.0000 chunk 171 optimal weight: 5.9990 chunk 94 optimal weight: 0.9980 chunk 196 optimal weight: 1.9990 chunk 159 optimal weight: 7.9990 chunk 0 optimal weight: 30.0000 chunk 117 optimal weight: 0.0060 chunk 206 optimal weight: 9.9990 chunk 58 optimal weight: 50.0000 overall best weight: 2.8002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 268 GLN ** A 822 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 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 ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6059 moved from start: 0.2122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.134 20860 Z= 0.336 Angle : 1.009 26.515 28310 Z= 0.513 Chirality : 0.059 0.640 3096 Planarity : 0.011 0.149 3434 Dihedral : 11.473 169.672 3288 Min Nonbonded Distance : 1.681 Molprobity Statistics. All-atom Clashscore : 17.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer: Outliers : 0.00 % Allowed : 0.09 % Favored : 99.91 % Cbeta Deviations : 0.09 % 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: -2.19 (0.16), residues: 2316 helix: -0.75 (0.15), residues: 1056 sheet: -2.41 (0.27), residues: 278 loop : -1.82 (0.19), residues: 982 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.003 TRP A 355 HIS 0.086 0.011 HIS G 233 PHE 0.056 0.003 PHE A 220 TYR 0.102 0.006 TYR A 840 ARG 0.048 0.002 ARG G 203 *********************** REFINEMENT MACRO_CYCLE 5 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 38 residues out of total 968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 38 time to evaluate : 1.058 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 TYR cc_start: 0.9162 (t80) cc_final: 0.8805 (t80) REVERT: A 456 MET cc_start: 0.8574 (mmt) cc_final: 0.8301 (mmm) REVERT: A 701 MET cc_start: 0.8965 (ttm) cc_final: 0.8734 (tpp) REVERT: A 722 MET cc_start: 0.8639 (mtm) cc_final: 0.8391 (mtt) REVERT: A 796 LEU cc_start: 0.9766 (tp) cc_final: 0.9512 (pp) REVERT: A 1035 MET cc_start: 0.8971 (ppp) cc_final: 0.8654 (ppp) REVERT: A 1128 MET cc_start: 0.9197 (tpp) cc_final: 0.8906 (tpp) outliers start: 0 outliers final: 0 residues processed: 38 average time/residue: 0.2352 time to fit residues: 13.1250 Evaluate side-chains 36 residues out of total 968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 36 time to evaluate : 0.951 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.015 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0197 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.015 Evaluate side-chains 14 residues out of total 100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 14 time to evaluate : 0.093 Fit side-chains REVERT: C 209 TYR cc_start: 0.9282 (m-80) cc_final: 0.8880 (m-80) REVERT: C 224 MET cc_start: 0.7157 (mtp) cc_final: 0.6749 (mtm) outliers start: 0 outliers final: 0 residues processed: 14 average time/residue: 0.1324 time to fit residues: 2.0950 Evaluate side-chains 10 residues out of total 100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 10 time to evaluate : 0.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/iotbx/cli_parser.py", line 944, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/programs/real_space_refine.py", line 189, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 798, in minimization_ncs ncs_groups = ncs_groups) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 400, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 133, in refine refine_sites = True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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-5265/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/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-5265/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-5265/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-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 68.6023 > 50: distance: 1 - 2: 8.155 distance: 2 - 3: 11.366 distance: 2 - 4: 12.872 distance: 3 - 5: 27.310 distance: 4 - 6: 25.008 distance: 5 - 7: 15.361 distance: 6 - 7: 13.451 distance: 8 - 9: 12.508 distance: 9 - 10: 25.076 distance: 9 - 12: 20.272 distance: 10 - 11: 4.579 distance: 10 - 17: 30.730 distance: 12 - 13: 17.841 distance: 13 - 14: 39.424 distance: 14 - 15: 22.591 distance: 15 - 16: 42.751 distance: 17 - 18: 31.821 distance: 18 - 19: 30.399 distance: 18 - 21: 32.319 distance: 19 - 20: 23.821 distance: 19 - 26: 26.550 distance: 21 - 22: 22.981 distance: 22 - 23: 6.506 distance: 23 - 24: 47.830 distance: 24 - 25: 46.902 distance: 26 - 27: 22.778 distance: 27 - 28: 13.825 distance: 27 - 30: 24.761 distance: 28 - 29: 4.269 distance: 28 - 34: 16.467 distance: 30 - 31: 4.327 distance: 30 - 32: 67.586 distance: 31 - 33: 12.512 distance: 34 - 35: 11.478 distance: 35 - 36: 23.038 distance: 36 - 37: 24.673 distance: 36 - 38: 22.816 distance: 38 - 39: 41.731 distance: 39 - 40: 24.402 distance: 39 - 42: 37.673 distance: 40 - 41: 31.257 distance: 40 - 44: 45.865 distance: 42 - 43: 52.442 distance: 44 - 45: 14.580 distance: 45 - 46: 28.650 distance: 45 - 48: 33.630 distance: 46 - 47: 21.977 distance: 46 - 55: 19.246 distance: 48 - 49: 16.934 distance: 49 - 50: 24.226 distance: 49 - 51: 22.806 distance: 50 - 52: 19.935 distance: 51 - 53: 12.667 distance: 52 - 54: 20.381 distance: 53 - 54: 22.485 distance: 55 - 56: 3.554 distance: 56 - 57: 28.272 distance: 56 - 59: 65.774 distance: 57 - 58: 20.664 distance: 57 - 61: 25.763 distance: 61 - 62: 14.914 distance: 62 - 65: 26.948 distance: 63 - 64: 7.042 distance: 63 - 69: 18.768 distance: 65 - 66: 9.614 distance: 66 - 67: 37.652 distance: 66 - 68: 41.316 distance: 69 - 70: 11.359 distance: 70 - 71: 10.888 distance: 70 - 73: 9.510 distance: 71 - 72: 3.394 distance: 71 - 78: 7.234 distance: 73 - 74: 7.725 distance: 78 - 79: 7.804 distance: 79 - 80: 8.467 distance: 79 - 82: 6.584 distance: 80 - 81: 5.869