Starting phenix.real_space_refine on Sun May 25 23:17:35 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8bho_16063/05_2025/8bho_16063_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8bho_16063/05_2025/8bho_16063.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.93 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8bho_16063/05_2025/8bho_16063.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8bho_16063/05_2025/8bho_16063.map" model { file = "/net/cci-nas-00/data/ceres_data/8bho_16063/05_2025/8bho_16063_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8bho_16063/05_2025/8bho_16063_trim.cif" } resolution = 2.93 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= 0.001 sd= 0.023 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 85 5.16 5 C 8925 2.51 5 N 2275 2.21 5 O 2490 1.98 5 H 13415 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 27190 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 5399 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 5399 Classifications: {'peptide': 336} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 13, 'TRANS': 320} Chain: "B" Number of atoms: 5399 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 5399 Classifications: {'peptide': 336} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 13, 'TRANS': 320} Chain: "C" Number of atoms: 5399 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 5399 Classifications: {'peptide': 336} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 13, 'TRANS': 320} Chain: "D" Number of atoms: 5399 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 5399 Classifications: {'peptide': 336} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 13, 'TRANS': 320} Chain: "E" Number of atoms: 5399 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 5399 Classifications: {'peptide': 336} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 13, 'TRANS': 320} Chain: "A" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 39 Unusual residues: {'NAG': 1, 'QMJ': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 39 Unusual residues: {'NAG': 1, 'QMJ': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 39 Unusual residues: {'NAG': 1, 'QMJ': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 39 Unusual residues: {'NAG': 1, 'QMJ': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 39 Unusual residues: {'NAG': 1, 'QMJ': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 12.45, per 1000 atoms: 0.46 Number of scatterers: 27190 At special positions: 0 Unit cell: (92.4, 94.5, 123.9, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 85 16.00 O 2490 8.00 N 2275 7.00 C 8925 6.00 H 13415 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 142 " - pdb=" SG CYS A 156 " distance=2.03 Simple disulfide: pdb=" SG CYS B 142 " - pdb=" SG CYS B 156 " distance=2.03 Simple disulfide: pdb=" SG CYS C 142 " - pdb=" SG CYS C 156 " distance=2.03 Simple disulfide: pdb=" SG CYS D 142 " - pdb=" SG CYS D 156 " distance=2.03 Simple disulfide: pdb=" SG CYS E 142 " - pdb=" SG CYS E 156 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A 501 " - " ASN A 205 " " NAG B 501 " - " ASN B 205 " " NAG C 501 " - " ASN C 205 " " NAG D 501 " - " ASN D 205 " " NAG E 501 " - " ASN E 205 " Time building additional restraints: 7.55 Conformation dependent library (CDL) restraints added in 2.1 seconds 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3190 Finding SS restraints... Secondary structure from input PDB file: 45 helices and 15 sheets defined 39.9% alpha, 38.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.57 Creating SS restraints... Processing helix chain 'A' and resid 15 through 27 removed outlier: 3.672A pdb=" N THR A 19 " --> pdb=" O ILE A 15 " (cutoff:3.500A) Processing helix chain 'A' and resid 76 through 79 Processing helix chain 'A' and resid 177 through 181 Processing helix chain 'A' and resid 227 through 233 Processing helix chain 'A' and resid 233 through 246 Processing helix chain 'A' and resid 247 through 250 Processing helix chain 'A' and resid 254 through 280 removed outlier: 3.859A pdb=" N PHE A 261 " --> pdb=" O ALA A 257 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N SER A 279 " --> pdb=" O SER A 275 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N LEU A 280 " --> pdb=" O ALA A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 314 Processing helix chain 'A' and resid 317 through 418 removed outlier: 3.521A pdb=" N ALA A 321 " --> pdb=" O GLN A 317 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N ILE A 400 " --> pdb=" O LYS A 396 " (cutoff:3.500A) Proline residue: A 403 - end of helix Processing helix chain 'B' and resid 15 through 27 removed outlier: 3.673A pdb=" N THR B 19 " --> pdb=" O ILE B 15 " (cutoff:3.500A) Processing helix chain 'B' and resid 76 through 79 Processing helix chain 'B' and resid 177 through 181 Processing helix chain 'B' and resid 227 through 233 Processing helix chain 'B' and resid 233 through 246 Processing helix chain 'B' and resid 247 through 250 Processing helix chain 'B' and resid 254 through 280 removed outlier: 3.858A pdb=" N PHE B 261 " --> pdb=" O ALA B 257 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N SER B 279 " --> pdb=" O SER B 275 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N LEU B 280 " --> pdb=" O ALA B 276 " (cutoff:3.500A) Processing helix chain 'B' and resid 287 through 314 Processing helix chain 'B' and resid 317 through 418 removed outlier: 3.521A pdb=" N ALA B 321 " --> pdb=" O GLN B 317 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N ILE B 400 " --> pdb=" O LYS B 396 " (cutoff:3.500A) Proline residue: B 403 - end of helix Processing helix chain 'C' and resid 15 through 27 removed outlier: 3.673A pdb=" N THR C 19 " --> pdb=" O ILE C 15 " (cutoff:3.500A) Processing helix chain 'C' and resid 76 through 79 Processing helix chain 'C' and resid 177 through 181 Processing helix chain 'C' and resid 227 through 233 Processing helix chain 'C' and resid 233 through 246 Processing helix chain 'C' and resid 247 through 250 Processing helix chain 'C' and resid 254 through 280 removed outlier: 3.859A pdb=" N PHE C 261 " --> pdb=" O ALA C 257 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N SER C 279 " --> pdb=" O SER C 275 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N LEU C 280 " --> pdb=" O ALA C 276 " (cutoff:3.500A) Processing helix chain 'C' and resid 287 through 314 Processing helix chain 'C' and resid 317 through 418 removed outlier: 3.521A pdb=" N ALA C 321 " --> pdb=" O GLN C 317 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N ILE C 400 " --> pdb=" O LYS C 396 " (cutoff:3.500A) Proline residue: C 403 - end of helix Processing helix chain 'D' and resid 15 through 27 removed outlier: 3.673A pdb=" N THR D 19 " --> pdb=" O ILE D 15 " (cutoff:3.500A) Processing helix chain 'D' and resid 76 through 79 Processing helix chain 'D' and resid 177 through 181 Processing helix chain 'D' and resid 227 through 233 Processing helix chain 'D' and resid 233 through 246 Processing helix chain 'D' and resid 247 through 250 Processing helix chain 'D' and resid 254 through 280 removed outlier: 3.859A pdb=" N PHE D 261 " --> pdb=" O ALA D 257 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N SER D 279 " --> pdb=" O SER D 275 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N LEU D 280 " --> pdb=" O ALA D 276 " (cutoff:3.500A) Processing helix chain 'D' and resid 287 through 314 Processing helix chain 'D' and resid 317 through 418 removed outlier: 3.521A pdb=" N ALA D 321 " --> pdb=" O GLN D 317 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N ILE D 400 " --> pdb=" O LYS D 396 " (cutoff:3.500A) Proline residue: D 403 - end of helix Processing helix chain 'E' and resid 15 through 27 removed outlier: 3.672A pdb=" N THR E 19 " --> pdb=" O ILE E 15 " (cutoff:3.500A) Processing helix chain 'E' and resid 76 through 79 Processing helix chain 'E' and resid 177 through 181 Processing helix chain 'E' and resid 227 through 233 Processing helix chain 'E' and resid 233 through 246 Processing helix chain 'E' and resid 247 through 250 Processing helix chain 'E' and resid 254 through 280 removed outlier: 3.858A pdb=" N PHE E 261 " --> pdb=" O ALA E 257 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N SER E 279 " --> pdb=" O SER E 275 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N LEU E 280 " --> pdb=" O ALA E 276 " (cutoff:3.500A) Processing helix chain 'E' and resid 287 through 314 Processing helix chain 'E' and resid 317 through 418 removed outlier: 3.521A pdb=" N ALA E 321 " --> pdb=" O GLN E 317 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N ILE E 400 " --> pdb=" O LYS E 396 " (cutoff:3.500A) Proline residue: E 403 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 107 through 112 removed outlier: 6.735A pdb=" N GLY A 107 " --> pdb=" O GLU A 141 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N GLU A 141 " --> pdb=" O GLY A 107 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N LYS A 109 " --> pdb=" O SER A 139 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N GLU A 62 " --> pdb=" O PRO A 55 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N THR A 64 " --> pdb=" O PHE A 53 " (cutoff:3.500A) removed outlier: 5.275A pdb=" N PHE A 53 " --> pdb=" O THR A 64 " (cutoff:3.500A) removed outlier: 7.107A pdb=" N ASP A 66 " --> pdb=" O ASN A 51 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N TYR A 49 " --> pdb=" O PHE A 68 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N LYS A 74 " --> pdb=" O GLN A 43 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N GLN A 43 " --> pdb=" O LYS A 74 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 120 through 124 removed outlier: 3.675A pdb=" N THR A 133 " --> pdb=" O MET A 121 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N GLU A 62 " --> pdb=" O PRO A 55 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N THR A 64 " --> pdb=" O PHE A 53 " (cutoff:3.500A) removed outlier: 5.275A pdb=" N PHE A 53 " --> pdb=" O THR A 64 " (cutoff:3.500A) removed outlier: 7.107A pdb=" N ASP A 66 " --> pdb=" O ASN A 51 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N TYR A 49 " --> pdb=" O PHE A 68 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N LYS A 74 " --> pdb=" O GLN A 43 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N GLN A 43 " --> pdb=" O LYS A 74 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 102 through 104 removed outlier: 4.674A pdb=" N SER A 162 " --> pdb=" O THR A 214 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N THR A 214 " --> pdb=" O SER A 162 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N GLY A 198 " --> pdb=" O HIS A 221 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N LYS A 223 " --> pdb=" O LEU A 196 " (cutoff:3.500A) removed outlier: 5.575A pdb=" N LEU A 196 " --> pdb=" O LYS A 223 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 107 through 112 removed outlier: 6.735A pdb=" N GLY B 107 " --> pdb=" O GLU B 141 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N GLU B 141 " --> pdb=" O GLY B 107 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N LYS B 109 " --> pdb=" O SER B 139 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N GLU B 62 " --> pdb=" O PRO B 55 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N THR B 64 " --> pdb=" O PHE B 53 " (cutoff:3.500A) removed outlier: 5.275A pdb=" N PHE B 53 " --> pdb=" O THR B 64 " (cutoff:3.500A) removed outlier: 7.108A pdb=" N ASP B 66 " --> pdb=" O ASN B 51 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N TYR B 49 " --> pdb=" O PHE B 68 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N LYS B 74 " --> pdb=" O GLN B 43 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N GLN B 43 " --> pdb=" O LYS B 74 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 120 through 124 removed outlier: 3.676A pdb=" N THR B 133 " --> pdb=" O MET B 121 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N GLU B 62 " --> pdb=" O PRO B 55 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N THR B 64 " --> pdb=" O PHE B 53 " (cutoff:3.500A) removed outlier: 5.275A pdb=" N PHE B 53 " --> pdb=" O THR B 64 " (cutoff:3.500A) removed outlier: 7.108A pdb=" N ASP B 66 " --> pdb=" O ASN B 51 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N TYR B 49 " --> pdb=" O PHE B 68 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N LYS B 74 " --> pdb=" O GLN B 43 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N GLN B 43 " --> pdb=" O LYS B 74 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 102 through 104 removed outlier: 4.675A pdb=" N SER B 162 " --> pdb=" O THR B 214 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N THR B 214 " --> pdb=" O SER B 162 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N GLY B 198 " --> pdb=" O HIS B 221 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N LYS B 223 " --> pdb=" O LEU B 196 " (cutoff:3.500A) removed outlier: 5.575A pdb=" N LEU B 196 " --> pdb=" O LYS B 223 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 107 through 112 removed outlier: 6.735A pdb=" N GLY C 107 " --> pdb=" O GLU C 141 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N GLU C 141 " --> pdb=" O GLY C 107 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N LYS C 109 " --> pdb=" O SER C 139 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N GLU C 62 " --> pdb=" O PRO C 55 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N THR C 64 " --> pdb=" O PHE C 53 " (cutoff:3.500A) removed outlier: 5.275A pdb=" N PHE C 53 " --> pdb=" O THR C 64 " (cutoff:3.500A) removed outlier: 7.107A pdb=" N ASP C 66 " --> pdb=" O ASN C 51 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N TYR C 49 " --> pdb=" O PHE C 68 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N LYS C 74 " --> pdb=" O GLN C 43 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N GLN C 43 " --> pdb=" O LYS C 74 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 120 through 124 removed outlier: 3.676A pdb=" N THR C 133 " --> pdb=" O MET C 121 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N GLU C 62 " --> pdb=" O PRO C 55 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N THR C 64 " --> pdb=" O PHE C 53 " (cutoff:3.500A) removed outlier: 5.275A pdb=" N PHE C 53 " --> pdb=" O THR C 64 " (cutoff:3.500A) removed outlier: 7.107A pdb=" N ASP C 66 " --> pdb=" O ASN C 51 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N TYR C 49 " --> pdb=" O PHE C 68 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N LYS C 74 " --> pdb=" O GLN C 43 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N GLN C 43 " --> pdb=" O LYS C 74 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 102 through 104 removed outlier: 4.675A pdb=" N SER C 162 " --> pdb=" O THR C 214 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N THR C 214 " --> pdb=" O SER C 162 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N GLY C 198 " --> pdb=" O HIS C 221 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N LYS C 223 " --> pdb=" O LEU C 196 " (cutoff:3.500A) removed outlier: 5.575A pdb=" N LEU C 196 " --> pdb=" O LYS C 223 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 107 through 112 removed outlier: 6.735A pdb=" N GLY D 107 " --> pdb=" O GLU D 141 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N GLU D 141 " --> pdb=" O GLY D 107 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N LYS D 109 " --> pdb=" O SER D 139 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N GLU D 62 " --> pdb=" O PRO D 55 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N THR D 64 " --> pdb=" O PHE D 53 " (cutoff:3.500A) removed outlier: 5.275A pdb=" N PHE D 53 " --> pdb=" O THR D 64 " (cutoff:3.500A) removed outlier: 7.107A pdb=" N ASP D 66 " --> pdb=" O ASN D 51 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N TYR D 49 " --> pdb=" O PHE D 68 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N LYS D 74 " --> pdb=" O GLN D 43 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N GLN D 43 " --> pdb=" O LYS D 74 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 120 through 124 removed outlier: 3.676A pdb=" N THR D 133 " --> pdb=" O MET D 121 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N GLU D 62 " --> pdb=" O PRO D 55 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N THR D 64 " --> pdb=" O PHE D 53 " (cutoff:3.500A) removed outlier: 5.275A pdb=" N PHE D 53 " --> pdb=" O THR D 64 " (cutoff:3.500A) removed outlier: 7.107A pdb=" N ASP D 66 " --> pdb=" O ASN D 51 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N TYR D 49 " --> pdb=" O PHE D 68 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N LYS D 74 " --> pdb=" O GLN D 43 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N GLN D 43 " --> pdb=" O LYS D 74 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 102 through 104 removed outlier: 4.675A pdb=" N SER D 162 " --> pdb=" O THR D 214 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N THR D 214 " --> pdb=" O SER D 162 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N GLY D 198 " --> pdb=" O HIS D 221 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N LYS D 223 " --> pdb=" O LEU D 196 " (cutoff:3.500A) removed outlier: 5.574A pdb=" N LEU D 196 " --> pdb=" O LYS D 223 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 107 through 112 removed outlier: 6.734A pdb=" N GLY E 107 " --> pdb=" O GLU E 141 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N GLU E 141 " --> pdb=" O GLY E 107 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N LYS E 109 " --> pdb=" O SER E 139 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N GLU E 62 " --> pdb=" O PRO E 55 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N THR E 64 " --> pdb=" O PHE E 53 " (cutoff:3.500A) removed outlier: 5.275A pdb=" N PHE E 53 " --> pdb=" O THR E 64 " (cutoff:3.500A) removed outlier: 7.107A pdb=" N ASP E 66 " --> pdb=" O ASN E 51 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N TYR E 49 " --> pdb=" O PHE E 68 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N LYS E 74 " --> pdb=" O GLN E 43 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N GLN E 43 " --> pdb=" O LYS E 74 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 120 through 124 removed outlier: 3.676A pdb=" N THR E 133 " --> pdb=" O MET E 121 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N GLU E 62 " --> pdb=" O PRO E 55 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N THR E 64 " --> pdb=" O PHE E 53 " (cutoff:3.500A) removed outlier: 5.275A pdb=" N PHE E 53 " --> pdb=" O THR E 64 " (cutoff:3.500A) removed outlier: 7.107A pdb=" N ASP E 66 " --> pdb=" O ASN E 51 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N TYR E 49 " --> pdb=" O PHE E 68 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N LYS E 74 " --> pdb=" O GLN E 43 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N GLN E 43 " --> pdb=" O LYS E 74 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 102 through 104 removed outlier: 4.674A pdb=" N SER E 162 " --> pdb=" O THR E 214 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N THR E 214 " --> pdb=" O SER E 162 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N GLY E 198 " --> pdb=" O HIS E 221 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N LYS E 223 " --> pdb=" O LEU E 196 " (cutoff:3.500A) removed outlier: 5.575A pdb=" N LEU E 196 " --> pdb=" O LYS E 223 " (cutoff:3.500A) 800 hydrogen bonds defined for protein. 2355 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 10.83 Time building geometry restraints manager: 8.91 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 13415 1.03 - 1.23: 10 1.23 - 1.42: 6105 1.42 - 1.61: 7885 1.61 - 1.81: 150 Bond restraints: 27565 Sorted by residual: bond pdb=" N ASN D 14 " pdb=" H ASN D 14 " ideal model delta sigma weight residual 0.860 0.960 -0.100 2.00e-02 2.50e+03 2.52e+01 bond pdb=" N ASN A 14 " pdb=" H ASN A 14 " ideal model delta sigma weight residual 0.860 0.960 -0.100 2.00e-02 2.50e+03 2.51e+01 bond pdb=" N ASN E 14 " pdb=" H ASN E 14 " ideal model delta sigma weight residual 0.860 0.960 -0.100 2.00e-02 2.50e+03 2.50e+01 bond pdb=" N ASN B 14 " pdb=" H ASN B 14 " ideal model delta sigma weight residual 0.860 0.960 -0.100 2.00e-02 2.50e+03 2.48e+01 bond pdb=" N ASN C 14 " pdb=" H ASN C 14 " ideal model delta sigma weight residual 0.860 0.959 -0.099 2.00e-02 2.50e+03 2.46e+01 ... (remaining 27560 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.72: 49291 1.72 - 3.44: 190 3.44 - 5.16: 39 5.16 - 6.87: 5 6.87 - 8.59: 15 Bond angle restraints: 49540 Sorted by residual: angle pdb=" C MET C 115 " pdb=" N THR C 116 " pdb=" CA THR C 116 " ideal model delta sigma weight residual 121.70 127.39 -5.69 1.80e+00 3.09e-01 9.98e+00 angle pdb=" C MET A 115 " pdb=" N THR A 116 " pdb=" CA THR A 116 " ideal model delta sigma weight residual 121.70 127.37 -5.67 1.80e+00 3.09e-01 9.93e+00 angle pdb=" C MET D 115 " pdb=" N THR D 116 " pdb=" CA THR D 116 " ideal model delta sigma weight residual 121.70 127.37 -5.67 1.80e+00 3.09e-01 9.92e+00 angle pdb=" C MET B 115 " pdb=" N THR B 116 " pdb=" CA THR B 116 " ideal model delta sigma weight residual 121.70 127.34 -5.64 1.80e+00 3.09e-01 9.83e+00 angle pdb=" C MET E 115 " pdb=" N THR E 116 " pdb=" CA THR E 116 " ideal model delta sigma weight residual 121.70 127.34 -5.64 1.80e+00 3.09e-01 9.82e+00 ... (remaining 49535 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.62: 12611 14.62 - 29.25: 374 29.25 - 43.87: 130 43.87 - 58.49: 105 58.49 - 73.12: 15 Dihedral angle restraints: 13235 sinusoidal: 7105 harmonic: 6130 Sorted by residual: dihedral pdb=" CB LYS D 315 " pdb=" CG LYS D 315 " pdb=" CD LYS D 315 " pdb=" CE LYS D 315 " ideal model delta sinusoidal sigma weight residual 60.00 100.65 -40.65 3 1.50e+01 4.44e-03 7.25e+00 dihedral pdb=" CB LYS B 315 " pdb=" CG LYS B 315 " pdb=" CD LYS B 315 " pdb=" CE LYS B 315 " ideal model delta sinusoidal sigma weight residual 60.00 100.64 -40.64 3 1.50e+01 4.44e-03 7.25e+00 dihedral pdb=" CB LYS C 315 " pdb=" CG LYS C 315 " pdb=" CD LYS C 315 " pdb=" CE LYS C 315 " ideal model delta sinusoidal sigma weight residual 60.00 100.64 -40.64 3 1.50e+01 4.44e-03 7.25e+00 ... (remaining 13232 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 1889 0.055 - 0.111: 256 0.111 - 0.166: 15 0.166 - 0.221: 0 0.221 - 0.277: 5 Chirality restraints: 2165 Sorted by residual: chirality pdb=" C13 QMJ D 502 " pdb=" C14 QMJ D 502 " pdb=" C4 QMJ D 502 " pdb=" N2 QMJ D 502 " both_signs ideal model delta sigma weight residual False -2.58 -2.31 -0.28 2.00e-01 2.50e+01 1.91e+00 chirality pdb=" C13 QMJ C 502 " pdb=" C14 QMJ C 502 " pdb=" C4 QMJ C 502 " pdb=" N2 QMJ C 502 " both_signs ideal model delta sigma weight residual False -2.58 -2.31 -0.28 2.00e-01 2.50e+01 1.90e+00 chirality pdb=" C13 QMJ A 502 " pdb=" C14 QMJ A 502 " pdb=" C4 QMJ A 502 " pdb=" N2 QMJ A 502 " both_signs ideal model delta sigma weight residual False -2.58 -2.31 -0.27 2.00e-01 2.50e+01 1.87e+00 ... (remaining 2162 not shown) Planarity restraints: 4000 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C11 QMJ A 502 " 0.378 2.00e-02 2.50e+03 3.01e-01 1.36e+03 pdb=" C12 QMJ A 502 " -0.032 2.00e-02 2.50e+03 pdb=" C13 QMJ A 502 " -0.348 2.00e-02 2.50e+03 pdb=" C16 QMJ A 502 " 0.374 2.00e-02 2.50e+03 pdb=" N2 QMJ A 502 " 0.003 2.00e-02 2.50e+03 pdb=" O2 QMJ A 502 " -0.375 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C11 QMJ E 502 " 0.378 2.00e-02 2.50e+03 3.01e-01 1.36e+03 pdb=" C12 QMJ E 502 " -0.032 2.00e-02 2.50e+03 pdb=" C13 QMJ E 502 " -0.348 2.00e-02 2.50e+03 pdb=" C16 QMJ E 502 " 0.374 2.00e-02 2.50e+03 pdb=" N2 QMJ E 502 " 0.003 2.00e-02 2.50e+03 pdb=" O2 QMJ E 502 " -0.375 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C11 QMJ C 502 " -0.378 2.00e-02 2.50e+03 3.01e-01 1.36e+03 pdb=" C12 QMJ C 502 " 0.031 2.00e-02 2.50e+03 pdb=" C13 QMJ C 502 " 0.348 2.00e-02 2.50e+03 pdb=" C16 QMJ C 502 " -0.374 2.00e-02 2.50e+03 pdb=" N2 QMJ C 502 " -0.003 2.00e-02 2.50e+03 pdb=" O2 QMJ C 502 " 0.375 2.00e-02 2.50e+03 ... (remaining 3997 not shown) Histogram of nonbonded interaction distances: 1.73 - 2.31: 5486 2.31 - 2.88: 62144 2.88 - 3.45: 67787 3.45 - 4.03: 97104 4.03 - 4.60: 146582 Nonbonded interactions: 379103 Sorted by model distance: nonbonded pdb=" H ASN D 167 " pdb=" O GLU D 212 " model vdw 1.735 2.450 nonbonded pdb=" H ASN B 167 " pdb=" O GLU B 212 " model vdw 1.735 2.450 nonbonded pdb=" H ASN C 167 " pdb=" O GLU C 212 " model vdw 1.735 2.450 nonbonded pdb=" H ASN E 167 " pdb=" O GLU E 212 " model vdw 1.735 2.450 nonbonded pdb=" H ASN A 167 " pdb=" O GLU A 212 " model vdw 1.735 2.450 ... (remaining 379098 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.12 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.830 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.480 Extract box with map and model: 1.030 Check model and map are aligned: 0.180 Set scattering table: 0.240 Process input model: 57.040 Find NCS groups from input model: 0.390 Set up NCS constraints: 0.110 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:12.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 73.650 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8078 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 0.035 14160 Z= 0.081 Angle : 0.446 8.592 19290 Z= 0.193 Chirality : 0.039 0.277 2165 Planarity : 0.014 0.301 2395 Dihedral : 7.455 73.117 5225 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 2.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.90 % Favored : 99.10 % Rotamer: Outliers : 0.00 % Allowed : 0.67 % Favored : 99.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.31 % 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: 2.52 (0.22), residues: 1670 helix: 3.34 (0.21), residues: 575 sheet: 0.79 (0.27), residues: 435 loop : 0.89 (0.26), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP C 73 HIS 0.002 0.000 HIS E 195 PHE 0.004 0.000 PHE C 149 TYR 0.004 0.001 TYR C 285 ARG 0.001 0.000 ARG E 34 Details of bonding type rmsd link_NAG-ASN : bond 0.00031 ( 5) link_NAG-ASN : angle 1.37233 ( 15) hydrogen bonds : bond 0.23740 ( 710) hydrogen bonds : angle 7.59655 ( 2355) SS BOND : bond 0.00050 ( 5) SS BOND : angle 0.22623 ( 10) covalent geometry : bond 0.00170 (14150) covalent geometry : angle 0.44487 (19265) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 160 time to evaluate : 2.113 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 MET cc_start: 0.8782 (ttm) cc_final: 0.8433 (ttm) REVERT: B 48 MET cc_start: 0.8877 (ttm) cc_final: 0.8649 (mtp) REVERT: B 289 MET cc_start: 0.8636 (ttp) cc_final: 0.8315 (ttp) REVERT: D 289 MET cc_start: 0.8606 (ttp) cc_final: 0.8395 (ttp) REVERT: E 289 MET cc_start: 0.8619 (ttp) cc_final: 0.8387 (ttp) outliers start: 0 outliers final: 0 residues processed: 160 average time/residue: 2.9833 time to fit residues: 521.3409 Evaluate side-chains 106 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 106 time to evaluate : 2.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 139 optimal weight: 6.9990 chunk 125 optimal weight: 2.9990 chunk 69 optimal weight: 2.9990 chunk 42 optimal weight: 3.9990 chunk 84 optimal weight: 2.9990 chunk 66 optimal weight: 4.9990 chunk 129 optimal weight: 0.8980 chunk 50 optimal weight: 2.9990 chunk 78 optimal weight: 2.9990 chunk 96 optimal weight: 2.9990 chunk 149 optimal weight: 3.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 GLN B 71 GLN B 85 GLN C 71 GLN D 71 GLN D 85 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.076300 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.063081 restraints weight = 97100.257| |-----------------------------------------------------------------------------| r_work (start): 0.3085 rms_B_bonded: 2.99 r_work: 0.2976 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.2976 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 moved from start: 0.2755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.049 14160 Z= 0.291 Angle : 0.604 6.205 19290 Z= 0.325 Chirality : 0.043 0.144 2165 Planarity : 0.006 0.087 2395 Dihedral : 5.662 62.529 2090 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 3.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 0.81 % Allowed : 4.70 % Favored : 94.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.31 % 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: 1.79 (0.21), residues: 1670 helix: 3.16 (0.21), residues: 580 sheet: 0.17 (0.25), residues: 460 loop : 0.16 (0.24), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 174 HIS 0.005 0.001 HIS B 221 PHE 0.012 0.002 PHE E 229 TYR 0.012 0.001 TYR D 163 ARG 0.007 0.001 ARG C 190 Details of bonding type rmsd link_NAG-ASN : bond 0.00203 ( 5) link_NAG-ASN : angle 1.16631 ( 15) hydrogen bonds : bond 0.05120 ( 710) hydrogen bonds : angle 5.00456 ( 2355) SS BOND : bond 0.00471 ( 5) SS BOND : angle 0.42071 ( 10) covalent geometry : bond 0.00659 (14150) covalent geometry : angle 0.60329 (19265) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 108 time to evaluate : 2.231 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 239 MET cc_start: 0.9039 (mmm) cc_final: 0.8770 (mmm) REVERT: A 245 GLN cc_start: 0.8554 (OUTLIER) cc_final: 0.8186 (mp10) REVERT: A 301 PHE cc_start: 0.8580 (t80) cc_final: 0.8361 (t80) REVERT: D 397 MET cc_start: 0.8454 (OUTLIER) cc_final: 0.8214 (ttt) REVERT: E 397 MET cc_start: 0.8276 (OUTLIER) cc_final: 0.7914 (ttp) outliers start: 12 outliers final: 1 residues processed: 110 average time/residue: 2.5942 time to fit residues: 314.7461 Evaluate side-chains 93 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 89 time to evaluate : 2.030 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 245 GLN Chi-restraints excluded: chain D residue 397 MET Chi-restraints excluded: chain E residue 167 ASN Chi-restraints excluded: chain E residue 397 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 62 optimal weight: 2.9990 chunk 128 optimal weight: 2.9990 chunk 108 optimal weight: 2.9990 chunk 154 optimal weight: 0.7980 chunk 14 optimal weight: 1.9990 chunk 106 optimal weight: 0.8980 chunk 42 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 116 optimal weight: 2.9990 chunk 19 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.077009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.063547 restraints weight = 96108.919| |-----------------------------------------------------------------------------| r_work (start): 0.3104 rms_B_bonded: 3.05 r_work: 0.2983 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.2983 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8134 moved from start: 0.3207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 14160 Z= 0.178 Angle : 0.495 5.915 19290 Z= 0.262 Chirality : 0.040 0.141 2165 Planarity : 0.005 0.074 2395 Dihedral : 3.970 32.473 2090 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 2.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 0.81 % Allowed : 6.04 % Favored : 93.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.31 % 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: 1.65 (0.21), residues: 1670 helix: 3.30 (0.21), residues: 550 sheet: 0.01 (0.24), residues: 455 loop : 0.05 (0.23), residues: 665 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 114 HIS 0.002 0.000 HIS B 221 PHE 0.011 0.001 PHE C 229 TYR 0.009 0.001 TYR A 417 ARG 0.008 0.000 ARG E 190 Details of bonding type rmsd link_NAG-ASN : bond 0.00135 ( 5) link_NAG-ASN : angle 1.17380 ( 15) hydrogen bonds : bond 0.04473 ( 710) hydrogen bonds : angle 4.58130 ( 2355) SS BOND : bond 0.00412 ( 5) SS BOND : angle 0.72651 ( 10) covalent geometry : bond 0.00387 (14150) covalent geometry : angle 0.49357 (19265) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 102 time to evaluate : 2.226 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 239 MET cc_start: 0.9049 (mmm) cc_final: 0.8846 (mmm) REVERT: A 245 GLN cc_start: 0.8524 (OUTLIER) cc_final: 0.8007 (mp10) REVERT: A 301 PHE cc_start: 0.8635 (t80) cc_final: 0.8388 (t80) REVERT: B 84 MET cc_start: 0.6686 (ttt) cc_final: 0.6417 (ttm) REVERT: C 306 GLU cc_start: 0.8833 (OUTLIER) cc_final: 0.8528 (tm-30) REVERT: D 216 MET cc_start: 0.9189 (mmm) cc_final: 0.8957 (mmm) REVERT: D 397 MET cc_start: 0.8503 (OUTLIER) cc_final: 0.8244 (ttt) REVERT: E 397 MET cc_start: 0.8421 (OUTLIER) cc_final: 0.7991 (ttp) outliers start: 12 outliers final: 0 residues processed: 103 average time/residue: 2.6668 time to fit residues: 303.1382 Evaluate side-chains 97 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 93 time to evaluate : 2.086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 245 GLN Chi-restraints excluded: chain C residue 306 GLU Chi-restraints excluded: chain D residue 397 MET Chi-restraints excluded: chain E residue 397 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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-5687/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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-5687/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 64.1742 > 50: distance: 59 - 67: 20.171 distance: 67 - 68: 10.898 distance: 67 - 73: 25.532 distance: 68 - 69: 24.450 distance: 68 - 71: 10.159 distance: 68 - 74: 3.204 distance: 69 - 70: 7.788 distance: 69 - 81: 18.208 distance: 71 - 72: 37.520 distance: 71 - 75: 42.195 distance: 71 - 76: 51.335 distance: 72 - 73: 36.621 distance: 72 - 77: 32.908 distance: 72 - 78: 23.485 distance: 73 - 79: 13.798 distance: 73 - 80: 26.590 distance: 81 - 82: 13.465 distance: 81 - 89: 12.601 distance: 82 - 83: 19.824 distance: 82 - 85: 14.837 distance: 82 - 90: 17.896 distance: 83 - 84: 14.095 distance: 83 - 98: 11.481 distance: 85 - 86: 17.415 distance: 85 - 91: 18.098 distance: 85 - 92: 32.997 distance: 86 - 87: 23.315 distance: 86 - 93: 17.399 distance: 86 - 94: 8.805 distance: 87 - 88: 14.754 distance: 88 - 95: 21.916 distance: 88 - 96: 14.886 distance: 88 - 97: 9.735 distance: 98 - 99: 10.914 distance: 98 - 106: 13.040 distance: 99 - 102: 23.786 distance: 99 - 107: 9.924 distance: 100 - 101: 18.978 distance: 100 - 110: 6.170 distance: 102 - 103: 12.525 distance: 102 - 108: 8.143 distance: 102 - 109: 9.579 distance: 103 - 104: 13.427 distance: 103 - 105: 8.031 distance: 110 - 111: 13.468 distance: 110 - 118: 24.530 distance: 111 - 112: 3.235 distance: 111 - 114: 19.067 distance: 111 - 119: 26.980 distance: 112 - 113: 4.400 distance: 112 - 129: 12.756 distance: 114 - 115: 10.867 distance: 114 - 120: 29.438 distance: 114 - 121: 18.100 distance: 115 - 116: 17.175 distance: 115 - 117: 21.239 distance: 115 - 122: 19.378 distance: 116 - 123: 28.647 distance: 116 - 124: 24.796 distance: 116 - 125: 19.826 distance: 117 - 126: 9.105 distance: 117 - 127: 24.555 distance: 117 - 128: 20.088 distance: 129 - 130: 17.058 distance: 129 - 138: 12.119 distance: 130 - 131: 7.581 distance: 130 - 133: 17.974 distance: 130 - 139: 17.276 distance: 131 - 132: 10.899 distance: 131 - 144: 34.101 distance: 133 - 134: 15.964 distance: 133 - 140: 15.422 distance: 133 - 141: 33.230 distance: 134 - 135: 10.478 distance: 134 - 142: 14.164 distance: 134 - 143: 4.967 distance: 135 - 136: 17.212 distance: 135 - 137: 19.688 distance: 144 - 145: 11.944 distance: 144 - 152: 20.422 distance: 145 - 146: 11.782 distance: 145 - 148: 21.309 distance: 145 - 153: 21.209 distance: 146 - 147: 19.331 distance: 146 - 156: 25.968 distance: 148 - 149: 20.699 distance: 148 - 154: 21.184 distance: 148 - 155: 4.975 distance: 149 - 150: 26.620 distance: 149 - 151: 10.297 distance: 156 - 157: 7.463 distance: 156 - 167: 35.509 distance: 157 - 158: 14.246 distance: 157 - 160: 25.274 distance: 157 - 168: 28.139 distance: 158 - 159: 38.174 distance: 160 - 161: 37.998 distance: 160 - 169: 22.378 distance: 160 - 170: 13.610 distance: 161 - 162: 24.863 distance: 161 - 163: 39.002 distance: 162 - 164: 30.463 distance: 162 - 171: 14.687 distance: 163 - 165: 18.793 distance: 163 - 172: 20.213 distance: 164 - 166: 16.381 distance: 164 - 173: 15.929 distance: 165 - 166: 8.966 distance: 165 - 174: 16.530 distance: 166 - 175: 9.701 distance: 176 - 177: 29.803 distance: 176 - 182: 32.836 distance: 177 - 178: 20.148 distance: 177 - 180: 15.736 distance: 177 - 183: 15.384 distance: 178 - 179: 31.874 distance: 178 - 190: 36.112 distance: 180 - 181: 6.686 distance: 180 - 184: 21.742 distance: 180 - 185: 16.125 distance: 181 - 182: 15.818 distance: 181 - 186: 38.572 distance: 181 - 187: 19.854 distance: 182 - 188: 23.254 distance: 182 - 189: 33.869 distance: 190 - 191: 3.057 distance: 190 - 198: 25.957 distance: 191 - 192: 36.912 distance: 191 - 194: 21.993 distance: 191 - 199: 19.704 distance: 192 - 193: 6.746 distance: 192 - 207: 3.772 distance: 194 - 195: 22.172 distance: 194 - 200: 13.456 distance: 194 - 201: 3.838 distance: 195 - 196: 5.967 distance: 195 - 202: 22.186 distance: 195 - 203: 34.072 distance: 196 - 197: 11.624 distance: 197 - 204: 19.875 distance: 197 - 205: 15.154 distance: 197 - 206: 14.673 distance: 207 - 208: 30.894 distance: 208 - 209: 20.507 distance: 208 - 211: 4.780 distance: 208 - 216: 7.990 distance: 209 - 210: 20.089 distance: 209 - 219: 25.860 distance: 211 - 212: 6.789 distance: 211 - 217: 22.929 distance: 211 - 218: 9.133 distance: 212 - 213: 8.620 distance: 212 - 214: 27.245