Starting phenix.real_space_refine on Sun Nov 17 15:23:29 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oqa_17110/11_2024/8oqa_17110.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oqa_17110/11_2024/8oqa_17110.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oqa_17110/11_2024/8oqa_17110.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oqa_17110/11_2024/8oqa_17110.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oqa_17110/11_2024/8oqa_17110.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oqa_17110/11_2024/8oqa_17110.cif" } resolution = 2.9 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= 0.000 sd= 0.001 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 75 5.16 5 Cl 2 4.86 5 C 9027 2.51 5 N 2177 2.21 5 O 2481 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 13762 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 2682 Number of conformers: 1 Conformer: "" Number of residues, atoms: 330, 2682 Classifications: {'peptide': 330} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 11, 'TRANS': 316} Chain breaks: 1 Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 56 Unresolved non-hydrogen dihedrals: 38 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ARG:plan': 3, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 33 Chain: "B" Number of atoms: 2689 Number of conformers: 1 Conformer: "" Number of residues, atoms: 330, 2689 Classifications: {'peptide': 330} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 11, 'TRANS': 316} Chain breaks: 1 Unresolved non-hydrogen bonds: 40 Unresolved non-hydrogen angles: 49 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 2, 'ARG:plan': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 34 Chain: "C" Number of atoms: 2689 Number of conformers: 1 Conformer: "" Number of residues, atoms: 330, 2689 Classifications: {'peptide': 330} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 11, 'TRANS': 316} Chain breaks: 1 Unresolved non-hydrogen bonds: 40 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ARG:plan': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 30 Chain: "D" Number of atoms: 2694 Number of conformers: 1 Conformer: "" Number of residues, atoms: 330, 2694 Classifications: {'peptide': 330} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 11, 'TRANS': 316} Chain breaks: 1 Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 41 Unresolved non-hydrogen dihedrals: 29 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 22 Chain: "E" Number of atoms: 2694 Number of conformers: 1 Conformer: "" Number of residues, atoms: 330, 2694 Classifications: {'peptide': 330} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 11, 'TRANS': 316} Chain breaks: 1 Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 28 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 3, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 25 Chain: "A" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 62 Unusual residues: {' CL': 2, 'HEX': 4, 'NAG': 2, 'OCT': 1} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 95 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 95 Unusual residues: {'ABU': 2, 'HEX': 4, 'NAG': 2, 'OCT': 1, 'RI5': 1} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 55 Unusual residues: {'ABU': 1, 'HEX': 2, 'NAG': 2, 'OCT': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 55 Unusual residues: {'ABU': 1, 'HEX': 2, 'NAG': 2, 'OCT': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 47 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 47 Unusual residues: {'ABU': 1, 'HEX': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 10.37, per 1000 atoms: 0.75 Number of scatterers: 13762 At special positions: 0 Unit cell: (93.03, 95.688, 136.222, 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) Cl 2 17.00 S 75 16.00 O 2481 8.00 N 2177 7.00 C 9027 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 198 " - pdb=" SG CYS A 212 " 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=1, symmetry=0 Links applied NAG-ASN " NAG A 501 " - " ASN A 140 " " NAG A 502 " - " ASN A 234 " " NAG B 603 " - " ASN B 140 " " NAG B 604 " - " ASN B 234 " " NAG C 602 " - " ASN C 140 " " NAG C 603 " - " ASN C 234 " " NAG D 602 " - " ASN D 140 " " NAG D 603 " - " ASN D 234 " " NAG E 503 " - " ASN E 140 " " NAG E 504 " - " ASN E 234 " Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.78 Conformation dependent library (CDL) restraints added in 1.8 seconds 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3200 Finding SS restraints... Secondary structure from input PDB file: 46 helices and 15 sheets defined 40.5% alpha, 40.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.69 Creating SS restraints... Processing helix chain 'A' and resid 80 through 84 removed outlier: 3.568A pdb=" N ASP A 83 " --> pdb=" O ARG A 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 134 Processing helix chain 'A' and resid 147 through 153 removed outlier: 3.606A pdb=" N VAL A 150 " --> pdb=" O GLY A 147 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N LYS A 151 " --> pdb=" O ARG A 148 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ILE A 153 " --> pdb=" O VAL A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 235 No H-bonds generated for 'chain 'A' and resid 233 through 235' Processing helix chain 'A' and resid 281 through 300 removed outlier: 4.346A pdb=" N PHE A 290 " --> pdb=" O LEU A 286 " (cutoff:3.500A) Proline residue: A 291 - end of helix Processing helix chain 'A' and resid 301 through 305 Processing helix chain 'A' and resid 309 through 333 Proline residue: A 315 - end of helix Processing helix chain 'A' and resid 342 through 380 Processing helix chain 'A' and resid 453 through 478 removed outlier: 4.061A pdb=" N ILE A 461 " --> pdb=" O LYS A 457 " (cutoff:3.500A) Proline residue: A 464 - end of helix removed outlier: 3.561A pdb=" N SER A 476 " --> pdb=" O LEU A 472 " (cutoff:3.500A) Processing helix chain 'B' and resid 80 through 84 removed outlier: 3.524A pdb=" N HIS B 84 " --> pdb=" O ILE B 81 " (cutoff:3.500A) Processing helix chain 'B' and resid 131 through 134 Processing helix chain 'B' and resid 147 through 152 removed outlier: 3.579A pdb=" N VAL B 150 " --> pdb=" O GLY B 147 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N LYS B 151 " --> pdb=" O ARG B 148 " (cutoff:3.500A) Processing helix chain 'B' and resid 232 through 235 Processing helix chain 'B' and resid 281 through 288 Processing helix chain 'B' and resid 288 through 300 removed outlier: 3.609A pdb=" N ALA B 292 " --> pdb=" O THR B 288 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N TRP B 300 " --> pdb=" O VAL B 296 " (cutoff:3.500A) Processing helix chain 'B' and resid 301 through 305 Processing helix chain 'B' and resid 309 through 333 Proline residue: B 315 - end of helix Processing helix chain 'B' and resid 342 through 380 Processing helix chain 'B' and resid 453 through 478 removed outlier: 4.038A pdb=" N ILE B 461 " --> pdb=" O LYS B 457 " (cutoff:3.500A) Proline residue: B 464 - end of helix Processing helix chain 'C' and resid 80 through 84 removed outlier: 3.705A pdb=" N HIS C 84 " --> pdb=" O ILE C 81 " (cutoff:3.500A) Processing helix chain 'C' and resid 131 through 134 removed outlier: 3.562A pdb=" N SER C 134 " --> pdb=" O GLU C 131 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 131 through 134' Processing helix chain 'C' and resid 147 through 153 removed outlier: 3.613A pdb=" N LYS C 151 " --> pdb=" O ARG C 148 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ILE C 153 " --> pdb=" O VAL C 150 " (cutoff:3.500A) Processing helix chain 'C' and resid 232 through 235 Processing helix chain 'C' and resid 281 through 288 Processing helix chain 'C' and resid 288 through 300 removed outlier: 3.629A pdb=" N ALA C 292 " --> pdb=" O THR C 288 " (cutoff:3.500A) Processing helix chain 'C' and resid 301 through 305 Processing helix chain 'C' and resid 309 through 333 Proline residue: C 315 - end of helix Processing helix chain 'C' and resid 342 through 380 Processing helix chain 'C' and resid 453 through 478 removed outlier: 4.107A pdb=" N ILE C 461 " --> pdb=" O LYS C 457 " (cutoff:3.500A) Proline residue: C 464 - end of helix Processing helix chain 'D' and resid 131 through 134 removed outlier: 3.515A pdb=" N SER D 134 " --> pdb=" O GLU D 131 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 131 through 134' Processing helix chain 'D' and resid 147 through 153 removed outlier: 3.764A pdb=" N LYS D 151 " --> pdb=" O ARG D 148 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ILE D 153 " --> pdb=" O VAL D 150 " (cutoff:3.500A) Processing helix chain 'D' and resid 232 through 235 Processing helix chain 'D' and resid 281 through 300 removed outlier: 4.384A pdb=" N PHE D 290 " --> pdb=" O LEU D 286 " (cutoff:3.500A) Proline residue: D 291 - end of helix removed outlier: 3.582A pdb=" N TRP D 300 " --> pdb=" O VAL D 296 " (cutoff:3.500A) Processing helix chain 'D' and resid 301 through 305 Processing helix chain 'D' and resid 309 through 333 Proline residue: D 315 - end of helix Processing helix chain 'D' and resid 342 through 380 Processing helix chain 'D' and resid 453 through 478 removed outlier: 4.199A pdb=" N ILE D 461 " --> pdb=" O LYS D 457 " (cutoff:3.500A) Proline residue: D 464 - end of helix Processing helix chain 'E' and resid 80 through 84 removed outlier: 3.701A pdb=" N HIS E 84 " --> pdb=" O ILE E 81 " (cutoff:3.500A) Processing helix chain 'E' and resid 131 through 134 Processing helix chain 'E' and resid 147 through 152 removed outlier: 3.530A pdb=" N VAL E 150 " --> pdb=" O GLY E 147 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N LYS E 151 " --> pdb=" O ARG E 148 " (cutoff:3.500A) Processing helix chain 'E' and resid 232 through 235 Processing helix chain 'E' and resid 281 through 300 removed outlier: 4.289A pdb=" N PHE E 290 " --> pdb=" O LEU E 286 " (cutoff:3.500A) Proline residue: E 291 - end of helix removed outlier: 3.540A pdb=" N TRP E 300 " --> pdb=" O VAL E 296 " (cutoff:3.500A) Processing helix chain 'E' and resid 301 through 305 Processing helix chain 'E' and resid 309 through 333 Proline residue: E 315 - end of helix Processing helix chain 'E' and resid 342 through 380 Processing helix chain 'E' and resid 453 through 478 removed outlier: 4.329A pdb=" N ILE E 461 " --> pdb=" O LYS E 457 " (cutoff:3.500A) Proline residue: E 464 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 143 through 145 removed outlier: 4.479A pdb=" N LEU A 178 " --> pdb=" O PHE A 145 " (cutoff:3.500A) removed outlier: 7.088A pdb=" N ASP A 117 " --> pdb=" O SER A 110 " (cutoff:3.500A) removed outlier: 7.113A pdb=" N SER A 110 " --> pdb=" O ASP A 117 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N THR A 119 " --> pdb=" O LEU A 108 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N LEU A 108 " --> pdb=" O THR A 119 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N THR A 121 " --> pdb=" O GLU A 106 " (cutoff:3.500A) removed outlier: 5.098A pdb=" N LYS A 129 " --> pdb=" O PRO A 98 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 163 through 168 removed outlier: 7.060A pdb=" N THR A 195 " --> pdb=" O LYS A 164 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N SER A 166 " --> pdb=" O THR A 193 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N THR A 193 " --> pdb=" O SER A 166 " (cutoff:3.500A) removed outlier: 4.954A pdb=" N ILE A 168 " --> pdb=" O ARG A 191 " (cutoff:3.500A) removed outlier: 7.842A pdb=" N ARG A 191 " --> pdb=" O ILE A 168 " (cutoff:3.500A) removed outlier: 7.088A pdb=" N ASP A 117 " --> pdb=" O SER A 110 " (cutoff:3.500A) removed outlier: 7.113A pdb=" N SER A 110 " --> pdb=" O ASP A 117 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N THR A 119 " --> pdb=" O LEU A 108 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N LEU A 108 " --> pdb=" O THR A 119 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N THR A 121 " --> pdb=" O GLU A 106 " (cutoff:3.500A) removed outlier: 5.098A pdb=" N LYS A 129 " --> pdb=" O PRO A 98 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 158 through 161 removed outlier: 4.662A pdb=" N GLU A 215 " --> pdb=" O VAL A 161 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N SER A 218 " --> pdb=" O ASN A 269 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N ASN A 269 " --> pdb=" O SER A 218 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N THR A 276 " --> pdb=" O GLU A 252 " (cutoff:3.500A) removed outlier: 5.598A pdb=" N GLU A 252 " --> pdb=" O THR A 276 " (cutoff:3.500A) removed outlier: 7.280A pdb=" N ARG A 278 " --> pdb=" O ILE A 250 " (cutoff:3.500A) removed outlier: 5.622A pdb=" N ILE A 250 " --> pdb=" O ARG A 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 143 through 145 removed outlier: 4.644A pdb=" N LEU B 178 " --> pdb=" O PHE B 145 " (cutoff:3.500A) removed outlier: 7.076A pdb=" N ASP B 117 " --> pdb=" O SER B 110 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N SER B 110 " --> pdb=" O ASP B 117 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N THR B 119 " --> pdb=" O LEU B 108 " (cutoff:3.500A) removed outlier: 4.732A pdb=" N LEU B 108 " --> pdb=" O THR B 119 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N THR B 121 " --> pdb=" O GLU B 106 " (cutoff:3.500A) removed outlier: 5.099A pdb=" N LYS B 129 " --> pdb=" O PRO B 98 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 163 through 168 removed outlier: 6.922A pdb=" N THR B 195 " --> pdb=" O LYS B 164 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N SER B 166 " --> pdb=" O THR B 193 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N THR B 193 " --> pdb=" O SER B 166 " (cutoff:3.500A) removed outlier: 5.017A pdb=" N ILE B 168 " --> pdb=" O ARG B 191 " (cutoff:3.500A) removed outlier: 7.818A pdb=" N ARG B 191 " --> pdb=" O ILE B 168 " (cutoff:3.500A) removed outlier: 7.076A pdb=" N ASP B 117 " --> pdb=" O SER B 110 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N SER B 110 " --> pdb=" O ASP B 117 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N THR B 119 " --> pdb=" O LEU B 108 " (cutoff:3.500A) removed outlier: 4.732A pdb=" N LEU B 108 " --> pdb=" O THR B 119 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N THR B 121 " --> pdb=" O GLU B 106 " (cutoff:3.500A) removed outlier: 5.099A pdb=" N LYS B 129 " --> pdb=" O PRO B 98 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 158 through 161 removed outlier: 4.771A pdb=" N GLU B 215 " --> pdb=" O VAL B 161 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N SER B 218 " --> pdb=" O ASN B 269 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N ASN B 269 " --> pdb=" O SER B 218 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N THR B 276 " --> pdb=" O GLU B 252 " (cutoff:3.500A) removed outlier: 5.414A pdb=" N GLU B 252 " --> pdb=" O THR B 276 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N ARG B 278 " --> pdb=" O ILE B 250 " (cutoff:3.500A) removed outlier: 5.523A pdb=" N ILE B 250 " --> pdb=" O ARG B 278 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 143 through 145 removed outlier: 4.460A pdb=" N LEU C 178 " --> pdb=" O PHE C 145 " (cutoff:3.500A) removed outlier: 7.051A pdb=" N ASP C 117 " --> pdb=" O SER C 110 " (cutoff:3.500A) removed outlier: 7.055A pdb=" N SER C 110 " --> pdb=" O ASP C 117 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N THR C 119 " --> pdb=" O LEU C 108 " (cutoff:3.500A) removed outlier: 4.810A pdb=" N LEU C 108 " --> pdb=" O THR C 119 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N THR C 121 " --> pdb=" O GLU C 106 " (cutoff:3.500A) removed outlier: 5.106A pdb=" N LYS C 129 " --> pdb=" O PRO C 98 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 163 through 168 removed outlier: 6.976A pdb=" N THR C 195 " --> pdb=" O LYS C 164 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N SER C 166 " --> pdb=" O THR C 193 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N THR C 193 " --> pdb=" O SER C 166 " (cutoff:3.500A) removed outlier: 4.949A pdb=" N ILE C 168 " --> pdb=" O ARG C 191 " (cutoff:3.500A) removed outlier: 7.820A pdb=" N ARG C 191 " --> pdb=" O ILE C 168 " (cutoff:3.500A) removed outlier: 7.051A pdb=" N ASP C 117 " --> pdb=" O SER C 110 " (cutoff:3.500A) removed outlier: 7.055A pdb=" N SER C 110 " --> pdb=" O ASP C 117 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N THR C 119 " --> pdb=" O LEU C 108 " (cutoff:3.500A) removed outlier: 4.810A pdb=" N LEU C 108 " --> pdb=" O THR C 119 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N THR C 121 " --> pdb=" O GLU C 106 " (cutoff:3.500A) removed outlier: 5.106A pdb=" N LYS C 129 " --> pdb=" O PRO C 98 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 158 through 161 removed outlier: 4.669A pdb=" N GLU C 215 " --> pdb=" O VAL C 161 " (cutoff:3.500A) removed outlier: 4.982A pdb=" N SER C 218 " --> pdb=" O ASN C 269 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N ASN C 269 " --> pdb=" O SER C 218 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N THR C 276 " --> pdb=" O GLU C 252 " (cutoff:3.500A) removed outlier: 5.416A pdb=" N GLU C 252 " --> pdb=" O THR C 276 " (cutoff:3.500A) removed outlier: 7.185A pdb=" N ARG C 278 " --> pdb=" O ILE C 250 " (cutoff:3.500A) removed outlier: 5.551A pdb=" N ILE C 250 " --> pdb=" O ARG C 278 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 143 through 145 removed outlier: 4.497A pdb=" N LEU D 178 " --> pdb=" O PHE D 145 " (cutoff:3.500A) removed outlier: 7.073A pdb=" N ASP D 117 " --> pdb=" O SER D 110 " (cutoff:3.500A) removed outlier: 7.062A pdb=" N SER D 110 " --> pdb=" O ASP D 117 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N THR D 119 " --> pdb=" O LEU D 108 " (cutoff:3.500A) removed outlier: 4.770A pdb=" N LEU D 108 " --> pdb=" O THR D 119 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N THR D 121 " --> pdb=" O GLU D 106 " (cutoff:3.500A) removed outlier: 5.221A pdb=" N LYS D 129 " --> pdb=" O PRO D 98 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 163 through 168 removed outlier: 6.972A pdb=" N THR D 195 " --> pdb=" O LYS D 164 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N SER D 166 " --> pdb=" O THR D 193 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N THR D 193 " --> pdb=" O SER D 166 " (cutoff:3.500A) removed outlier: 4.944A pdb=" N ILE D 168 " --> pdb=" O ARG D 191 " (cutoff:3.500A) removed outlier: 7.766A pdb=" N ARG D 191 " --> pdb=" O ILE D 168 " (cutoff:3.500A) removed outlier: 7.073A pdb=" N ASP D 117 " --> pdb=" O SER D 110 " (cutoff:3.500A) removed outlier: 7.062A pdb=" N SER D 110 " --> pdb=" O ASP D 117 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N THR D 119 " --> pdb=" O LEU D 108 " (cutoff:3.500A) removed outlier: 4.770A pdb=" N LEU D 108 " --> pdb=" O THR D 119 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N THR D 121 " --> pdb=" O GLU D 106 " (cutoff:3.500A) removed outlier: 5.221A pdb=" N LYS D 129 " --> pdb=" O PRO D 98 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 158 through 161 removed outlier: 4.725A pdb=" N GLU D 215 " --> pdb=" O VAL D 161 " (cutoff:3.500A) removed outlier: 4.777A pdb=" N SER D 218 " --> pdb=" O ASN D 269 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N ASN D 269 " --> pdb=" O SER D 218 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N THR D 276 " --> pdb=" O GLU D 252 " (cutoff:3.500A) removed outlier: 5.495A pdb=" N GLU D 252 " --> pdb=" O THR D 276 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N ARG D 278 " --> pdb=" O ILE D 250 " (cutoff:3.500A) removed outlier: 5.477A pdb=" N ILE D 250 " --> pdb=" O ARG D 278 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 143 through 144 removed outlier: 7.062A pdb=" N ASP E 117 " --> pdb=" O SER E 110 " (cutoff:3.500A) removed outlier: 7.066A pdb=" N SER E 110 " --> pdb=" O ASP E 117 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N THR E 119 " --> pdb=" O LEU E 108 " (cutoff:3.500A) removed outlier: 4.732A pdb=" N LEU E 108 " --> pdb=" O THR E 119 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N THR E 121 " --> pdb=" O GLU E 106 " (cutoff:3.500A) removed outlier: 5.202A pdb=" N LYS E 129 " --> pdb=" O PRO E 98 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 163 through 168 removed outlier: 6.808A pdb=" N SER E 163 " --> pdb=" O MET E 197 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N MET E 197 " --> pdb=" O SER E 163 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ARG E 165 " --> pdb=" O THR E 195 " (cutoff:3.500A) removed outlier: 7.062A pdb=" N ASP E 117 " --> pdb=" O SER E 110 " (cutoff:3.500A) removed outlier: 7.066A pdb=" N SER E 110 " --> pdb=" O ASP E 117 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N THR E 119 " --> pdb=" O LEU E 108 " (cutoff:3.500A) removed outlier: 4.732A pdb=" N LEU E 108 " --> pdb=" O THR E 119 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N THR E 121 " --> pdb=" O GLU E 106 " (cutoff:3.500A) removed outlier: 5.202A pdb=" N LYS E 129 " --> pdb=" O PRO E 98 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 158 through 161 removed outlier: 4.743A pdb=" N GLU E 215 " --> pdb=" O VAL E 161 " (cutoff:3.500A) removed outlier: 4.961A pdb=" N SER E 218 " --> pdb=" O ASN E 269 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N ASN E 269 " --> pdb=" O SER E 218 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N THR E 276 " --> pdb=" O GLU E 252 " (cutoff:3.500A) removed outlier: 5.361A pdb=" N GLU E 252 " --> pdb=" O THR E 276 " (cutoff:3.500A) removed outlier: 7.096A pdb=" N ARG E 278 " --> pdb=" O ILE E 250 " (cutoff:3.500A) removed outlier: 5.516A pdb=" N ILE E 250 " --> pdb=" O ARG E 278 " (cutoff:3.500A) 801 hydrogen bonds defined for protein. 2295 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: 4.66 Time building geometry restraints manager: 4.12 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 2125 1.32 - 1.45: 4202 1.45 - 1.57: 7648 1.57 - 1.69: 1 1.69 - 1.82: 140 Bond restraints: 14116 Sorted by residual: bond pdb=" C15 RI5 B 610 " pdb=" O16 RI5 B 610 " ideal model delta sigma weight residual 1.396 1.447 -0.051 2.00e-02 2.50e+03 6.53e+00 bond pdb=" CB ILE E 341 " pdb=" CG1 ILE E 341 " ideal model delta sigma weight residual 1.530 1.487 0.043 2.00e-02 2.50e+03 4.61e+00 bond pdb=" C08 RI5 B 610 " pdb=" O20 RI5 B 610 " ideal model delta sigma weight residual 1.395 1.433 -0.038 2.00e-02 2.50e+03 3.62e+00 bond pdb=" C14 RI5 B 610 " pdb=" O16 RI5 B 610 " ideal model delta sigma weight residual 1.419 1.451 -0.032 2.00e-02 2.50e+03 2.64e+00 bond pdb=" N ABU D 601 " pdb=" CA ABU D 601 " ideal model delta sigma weight residual 1.457 1.485 -0.028 2.00e-02 2.50e+03 1.95e+00 ... (remaining 14111 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.84: 18808 1.84 - 3.67: 292 3.67 - 5.51: 58 5.51 - 7.34: 5 7.34 - 9.18: 2 Bond angle restraints: 19165 Sorted by residual: angle pdb=" N ILE E 341 " pdb=" CA ILE E 341 " pdb=" CB ILE E 341 " ideal model delta sigma weight residual 110.86 115.88 -5.02 1.60e+00 3.91e-01 9.85e+00 angle pdb=" C ILE E 341 " pdb=" CA ILE E 341 " pdb=" CB ILE E 341 " ideal model delta sigma weight residual 110.98 106.61 4.37 1.41e+00 5.03e-01 9.59e+00 angle pdb=" CA TYR C 362 " pdb=" CB TYR C 362 " pdb=" CG TYR C 362 " ideal model delta sigma weight residual 113.90 108.60 5.30 1.80e+00 3.09e-01 8.66e+00 angle pdb=" CA TYR A 362 " pdb=" CB TYR A 362 " pdb=" CG TYR A 362 " ideal model delta sigma weight residual 113.90 108.98 4.92 1.80e+00 3.09e-01 7.47e+00 angle pdb=" CB ILE E 341 " pdb=" CG1 ILE E 341 " pdb=" CD1 ILE E 341 " ideal model delta sigma weight residual 113.80 108.13 5.67 2.10e+00 2.27e-01 7.29e+00 ... (remaining 19160 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.57: 7973 17.57 - 35.14: 368 35.14 - 52.71: 54 52.71 - 70.28: 10 70.28 - 87.84: 5 Dihedral angle restraints: 8410 sinusoidal: 3485 harmonic: 4925 Sorted by residual: dihedral pdb=" CA LEU C 108 " pdb=" C LEU C 108 " pdb=" N ASP C 109 " pdb=" CA ASP C 109 " ideal model delta harmonic sigma weight residual -180.00 -159.66 -20.34 0 5.00e+00 4.00e-02 1.65e+01 dihedral pdb=" CA GLN B 251 " pdb=" C GLN B 251 " pdb=" N GLU B 252 " pdb=" CA GLU B 252 " ideal model delta harmonic sigma weight residual 180.00 162.03 17.97 0 5.00e+00 4.00e-02 1.29e+01 dihedral pdb=" CA LEU B 108 " pdb=" C LEU B 108 " pdb=" N ASP B 109 " pdb=" CA ASP B 109 " ideal model delta harmonic sigma weight residual -180.00 -162.28 -17.72 0 5.00e+00 4.00e-02 1.26e+01 ... (remaining 8407 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.149: 2187 0.149 - 0.298: 1 0.298 - 0.447: 3 0.447 - 0.597: 2 0.597 - 0.746: 4 Chirality restraints: 2197 Sorted by residual: chirality pdb=" C1 NAG B 603 " pdb=" ND2 ASN B 140 " pdb=" C2 NAG B 603 " pdb=" O5 NAG B 603 " both_signs ideal model delta sigma weight residual False -2.40 -3.15 0.75 2.00e-01 2.50e+01 1.39e+01 chirality pdb=" C1 NAG A 501 " pdb=" ND2 ASN A 140 " pdb=" C2 NAG A 501 " pdb=" O5 NAG A 501 " both_signs ideal model delta sigma weight residual False -2.40 -3.12 0.72 2.00e-01 2.50e+01 1.30e+01 chirality pdb=" C1 NAG C 602 " pdb=" ND2 ASN C 140 " pdb=" C2 NAG C 602 " pdb=" O5 NAG C 602 " both_signs ideal model delta sigma weight residual False -2.40 -3.11 0.71 2.00e-01 2.50e+01 1.26e+01 ... (remaining 2194 not shown) Planarity restraints: 2344 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN B 234 " 0.007 2.00e-02 2.50e+03 3.52e-01 1.55e+03 pdb=" CG ASN B 234 " -0.093 2.00e-02 2.50e+03 pdb=" OD1 ASN B 234 " 0.282 2.00e-02 2.50e+03 pdb=" ND2 ASN B 234 " -0.605 2.00e-02 2.50e+03 pdb=" C1 NAG B 604 " 0.408 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 234 " -0.230 2.00e-02 2.50e+03 3.05e-01 1.16e+03 pdb=" CG ASN C 234 " 0.100 2.00e-02 2.50e+03 pdb=" OD1 ASN C 234 " -0.016 2.00e-02 2.50e+03 pdb=" ND2 ASN C 234 " 0.515 2.00e-02 2.50e+03 pdb=" C1 NAG C 603 " -0.369 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 234 " 0.273 2.00e-02 2.50e+03 3.04e-01 1.15e+03 pdb=" CG ASN A 234 " -0.106 2.00e-02 2.50e+03 pdb=" OD1 ASN A 234 " -0.090 2.00e-02 2.50e+03 pdb=" ND2 ASN A 234 " -0.466 2.00e-02 2.50e+03 pdb=" C1 NAG A 502 " 0.388 2.00e-02 2.50e+03 ... (remaining 2341 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.64: 90 2.64 - 3.20: 11410 3.20 - 3.77: 19775 3.77 - 4.33: 29404 4.33 - 4.90: 48746 Nonbonded interactions: 109425 Sorted by model distance: nonbonded pdb=" CB ASN B 140 " pdb=" O5 NAG B 603 " model vdw 2.070 3.440 nonbonded pdb=" O PRO D 315 " pdb=" OG1 THR D 319 " model vdw 2.198 3.040 nonbonded pdb=" ND2 ASN D 332 " pdb=" OE1 GLN E 287 " model vdw 2.232 3.120 nonbonded pdb=" CD2 HIS C 254 " pdb=" O6 NAG C 603 " model vdw 2.252 2.608 nonbonded pdb=" O VAL B 296 " pdb=" OG SER B 299 " model vdw 2.264 3.040 ... (remaining 109420 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 80 through 372 or (resid 373 through 451 and (name N or na \ me CA or name C or name O or name CB )) or resid 452 through 479)) selection = (chain 'B' and (resid 80 through 81 or (resid 82 and (name N or name CA or name \ C or name O or name CB )) or resid 83 through 251 or (resid 252 and (name N or n \ ame CA or name C or name O or name CB )) or resid 253 through 374 or (resid 375 \ through 451 and (name N or name CA or name C or name O or name CB )) or resid 45 \ 2 through 479)) selection = (chain 'C' and (resid 80 through 81 or (resid 82 and (name N or name CA or name \ C or name O or name CB )) or resid 83 through 371 or (resid 372 through 451 and \ (name N or name CA or name C or name O or name CB )) or resid 452 through 479)) selection = (chain 'D' and (resid 80 through 81 or (resid 82 and (name N or name CA or name \ C or name O or name CB )) or resid 83 through 371 or (resid 372 through 451 and \ (name N or name CA or name C or name O or name CB )) or resid 452 through 479)) selection = (chain 'E' and (resid 80 through 251 or (resid 252 and (name N or name CA or nam \ e C or name O or name CB )) or resid 253 through 371 or (resid 372 through 451 a \ nd (name N or name CA or name C or name O or name CB )) or resid 452 through 479 \ )) } 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: 5.310 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: 0.010 Extract box with map and model: 0.650 Check model and map are aligned: 0.100 Set scattering table: 0.150 Process input model: 35.390 Find NCS groups from input model: 1.070 Set up NCS constraints: 0.050 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:14.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 56.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 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 : 0.003 0.051 14116 Z= 0.177 Angle : 0.592 9.179 19165 Z= 0.306 Chirality : 0.056 0.746 2197 Planarity : 0.004 0.031 2334 Dihedral : 10.525 87.844 5207 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.86 % Favored : 99.14 % Rotamer: Outliers : 0.61 % Allowed : 3.97 % Favored : 95.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.32 % 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: 2.11 (0.21), residues: 1630 helix: 2.15 (0.22), residues: 575 sheet: 1.44 (0.24), residues: 455 loop : 0.75 (0.24), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 349 HIS 0.002 0.001 HIS E 254 PHE 0.017 0.001 PHE E 290 TYR 0.022 0.001 TYR C 362 ARG 0.006 0.001 ARG C 191 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 358 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 349 time to evaluate : 1.665 Fit side-chains revert: symmetry clash REVERT: A 143 MET cc_start: 0.7357 (mmm) cc_final: 0.7109 (mmt) REVERT: B 82 ASP cc_start: 0.6502 (m-30) cc_final: 0.6152 (p0) REVERT: B 83 ASP cc_start: 0.7157 (m-30) cc_final: 0.6918 (m-30) REVERT: B 116 MET cc_start: 0.8120 (mtt) cc_final: 0.7861 (mtm) REVERT: B 117 ASP cc_start: 0.7805 (p0) cc_final: 0.7514 (p0) REVERT: B 223 GLU cc_start: 0.7577 (pt0) cc_final: 0.7304 (pp20) REVERT: B 258 LYS cc_start: 0.8000 (tttt) cc_final: 0.7755 (ttpt) REVERT: C 143 MET cc_start: 0.7568 (mmm) cc_final: 0.7156 (mmp) REVERT: D 304 TRP cc_start: 0.8146 (m100) cc_final: 0.7926 (m-90) REVERT: D 326 THR cc_start: 0.8469 (m) cc_final: 0.8156 (p) REVERT: D 337 ARG cc_start: 0.6283 (mtt180) cc_final: 0.5930 (mtp-110) REVERT: E 102 ASP cc_start: 0.7733 (t0) cc_final: 0.7382 (t0) REVERT: E 232 LYS cc_start: 0.7543 (mttt) cc_final: 0.7038 (mtpp) REVERT: E 295 MET cc_start: 0.8136 (mmm) cc_final: 0.7390 (mmt) outliers start: 9 outliers final: 6 residues processed: 356 average time/residue: 1.4108 time to fit residues: 545.3575 Evaluate side-chains 265 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 259 time to evaluate : 1.719 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain B residue 234 ASN Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain D residue 319 THR Chi-restraints excluded: chain E residue 234 ASN Chi-restraints excluded: chain E residue 338 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 139 optimal weight: 0.0970 chunk 125 optimal weight: 4.9990 chunk 69 optimal weight: 5.9990 chunk 42 optimal weight: 6.9990 chunk 84 optimal weight: 2.9990 chunk 66 optimal weight: 5.9990 chunk 129 optimal weight: 7.9990 chunk 50 optimal weight: 4.9990 chunk 78 optimal weight: 0.9990 chunk 96 optimal weight: 2.9990 chunk 149 optimal weight: 0.8980 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 199 ASN A 210 GLN A 287 GLN B 210 GLN B 247 GLN ** C 254 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 269 ASN D 251 GLN D 287 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8266 moved from start: 0.1674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 14116 Z= 0.280 Angle : 0.671 9.494 19165 Z= 0.358 Chirality : 0.054 0.990 2197 Planarity : 0.005 0.039 2334 Dihedral : 7.574 76.945 2175 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 3.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.98 % Favored : 99.02 % Rotamer: Outliers : 3.77 % Allowed : 11.99 % Favored : 84.24 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.32 % 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: 1.46 (0.20), residues: 1630 helix: 1.71 (0.22), residues: 610 sheet: 1.04 (0.23), residues: 465 loop : 0.19 (0.24), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 349 HIS 0.005 0.001 HIS E 126 PHE 0.019 0.002 PHE A 356 TYR 0.023 0.002 TYR E 362 ARG 0.003 0.000 ARG A 270 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 241 time to evaluate : 1.616 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 183 ASP cc_start: 0.7526 (OUTLIER) cc_final: 0.7275 (p0) REVERT: A 269 ASN cc_start: 0.7877 (OUTLIER) cc_final: 0.7449 (m-40) REVERT: B 82 ASP cc_start: 0.6633 (m-30) cc_final: 0.6225 (p0) REVERT: B 116 MET cc_start: 0.8109 (mtt) cc_final: 0.7870 (mtm) REVERT: B 117 ASP cc_start: 0.7838 (p0) cc_final: 0.7552 (p0) REVERT: B 223 GLU cc_start: 0.7663 (pt0) cc_final: 0.7421 (pp20) REVERT: C 143 MET cc_start: 0.7441 (mmm) cc_final: 0.7038 (mmp) REVERT: D 113 GLU cc_start: 0.7728 (mt-10) cc_final: 0.7485 (mp0) REVERT: D 234 ASN cc_start: 0.6092 (OUTLIER) cc_final: 0.5823 (t160) REVERT: D 241 GLU cc_start: 0.6867 (mm-30) cc_final: 0.6521 (tp30) REVERT: D 287 GLN cc_start: 0.7378 (OUTLIER) cc_final: 0.6752 (mp-120) REVERT: D 326 THR cc_start: 0.8466 (m) cc_final: 0.8222 (p) REVERT: E 232 LYS cc_start: 0.7371 (mttt) cc_final: 0.6947 (mtpp) REVERT: E 295 MET cc_start: 0.8106 (mmm) cc_final: 0.7776 (mmp) outliers start: 56 outliers final: 29 residues processed: 274 average time/residue: 1.3631 time to fit residues: 407.7081 Evaluate side-chains 267 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 234 time to evaluate : 1.730 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 174 ASP Chi-restraints excluded: chain A residue 183 ASP Chi-restraints excluded: chain A residue 234 ASN Chi-restraints excluded: chain A residue 246 SER Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 326 THR Chi-restraints excluded: chain A residue 334 SER Chi-restraints excluded: chain A residue 469 LEU Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 235 ASP Chi-restraints excluded: chain B residue 256 THR Chi-restraints excluded: chain B residue 371 VAL Chi-restraints excluded: chain C residue 82 ASP Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 207 LEU Chi-restraints excluded: chain C residue 241 GLU Chi-restraints excluded: chain C residue 325 SER Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain C residue 370 THR Chi-restraints excluded: chain C residue 371 VAL Chi-restraints excluded: chain D residue 151 LYS Chi-restraints excluded: chain D residue 234 ASN Chi-restraints excluded: chain D residue 256 THR Chi-restraints excluded: chain D residue 287 GLN Chi-restraints excluded: chain D residue 288 THR Chi-restraints excluded: chain D residue 371 VAL Chi-restraints excluded: chain E residue 108 LEU Chi-restraints excluded: chain E residue 114 VAL Chi-restraints excluded: chain E residue 244 SER Chi-restraints excluded: chain E residue 338 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 83 optimal weight: 7.9990 chunk 46 optimal weight: 4.9990 chunk 124 optimal weight: 6.9990 chunk 102 optimal weight: 4.9990 chunk 41 optimal weight: 1.9990 chunk 150 optimal weight: 1.9990 chunk 162 optimal weight: 1.9990 chunk 133 optimal weight: 3.9990 chunk 148 optimal weight: 4.9990 chunk 51 optimal weight: 0.9990 chunk 120 optimal weight: 0.8980 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 210 GLN A 287 GLN B 247 GLN C 210 GLN D 287 GLN E 287 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8276 moved from start: 0.1935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 14116 Z= 0.271 Angle : 0.634 8.596 19165 Z= 0.341 Chirality : 0.047 0.429 2197 Planarity : 0.005 0.043 2334 Dihedral : 7.363 77.226 2170 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 2.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 4.31 % Allowed : 13.40 % Favored : 82.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.32 % 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: 1.21 (0.20), residues: 1630 helix: 1.65 (0.22), residues: 610 sheet: 0.81 (0.23), residues: 470 loop : -0.04 (0.24), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 349 HIS 0.007 0.001 HIS C 254 PHE 0.019 0.002 PHE A 356 TYR 0.023 0.002 TYR E 362 ARG 0.003 0.000 ARG A 270 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 233 time to evaluate : 1.648 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 183 ASP cc_start: 0.7536 (OUTLIER) cc_final: 0.7295 (p0) REVERT: A 235 ASP cc_start: 0.6825 (p0) cc_final: 0.6526 (t70) REVERT: A 269 ASN cc_start: 0.7865 (OUTLIER) cc_final: 0.7457 (m-40) REVERT: B 82 ASP cc_start: 0.6674 (m-30) cc_final: 0.6302 (p0) REVERT: B 108 LEU cc_start: 0.8825 (OUTLIER) cc_final: 0.8477 (mt) REVERT: B 116 MET cc_start: 0.8130 (mtt) cc_final: 0.7871 (mtm) REVERT: B 117 ASP cc_start: 0.7770 (p0) cc_final: 0.7493 (p0) REVERT: B 223 GLU cc_start: 0.7697 (pt0) cc_final: 0.7469 (pp20) REVERT: C 143 MET cc_start: 0.7415 (mmm) cc_final: 0.7030 (mmp) REVERT: C 258 LYS cc_start: 0.8223 (OUTLIER) cc_final: 0.7437 (ttpp) REVERT: D 113 GLU cc_start: 0.7721 (mt-10) cc_final: 0.7469 (mp0) REVERT: D 241 GLU cc_start: 0.6810 (mm-30) cc_final: 0.6494 (tp30) REVERT: D 326 THR cc_start: 0.8501 (m) cc_final: 0.8254 (p) REVERT: E 232 LYS cc_start: 0.7425 (mttt) cc_final: 0.7015 (mtpp) REVERT: E 295 MET cc_start: 0.8103 (mmm) cc_final: 0.7661 (mmp) REVERT: E 456 ASP cc_start: 0.7332 (m-30) cc_final: 0.6734 (m-30) outliers start: 64 outliers final: 41 residues processed: 268 average time/residue: 1.3664 time to fit residues: 399.2636 Evaluate side-chains 274 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 229 time to evaluate : 1.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 174 ASP Chi-restraints excluded: chain A residue 183 ASP Chi-restraints excluded: chain A residue 234 ASN Chi-restraints excluded: chain A residue 246 SER Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 326 THR Chi-restraints excluded: chain A residue 334 SER Chi-restraints excluded: chain A residue 461 ILE Chi-restraints excluded: chain A residue 469 LEU Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 142 SER Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 256 THR Chi-restraints excluded: chain B residue 263 SER Chi-restraints excluded: chain B residue 314 VAL Chi-restraints excluded: chain B residue 331 VAL Chi-restraints excluded: chain B residue 335 MET Chi-restraints excluded: chain B residue 371 VAL Chi-restraints excluded: chain B residue 462 ILE Chi-restraints excluded: chain C residue 82 ASP Chi-restraints excluded: chain C residue 102 ASP Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 207 LEU Chi-restraints excluded: chain C residue 234 ASN Chi-restraints excluded: chain C residue 258 LYS Chi-restraints excluded: chain C residue 325 SER Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain C residue 370 THR Chi-restraints excluded: chain C residue 371 VAL Chi-restraints excluded: chain D residue 151 LYS Chi-restraints excluded: chain D residue 234 ASN Chi-restraints excluded: chain D residue 256 THR Chi-restraints excluded: chain D residue 257 THR Chi-restraints excluded: chain D residue 288 THR Chi-restraints excluded: chain D residue 370 THR Chi-restraints excluded: chain D residue 371 VAL Chi-restraints excluded: chain E residue 108 LEU Chi-restraints excluded: chain E residue 114 VAL Chi-restraints excluded: chain E residue 140 ASN Chi-restraints excluded: chain E residue 244 SER Chi-restraints excluded: chain E residue 338 VAL Chi-restraints excluded: chain E residue 360 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 148 optimal weight: 3.9990 chunk 112 optimal weight: 4.9990 chunk 77 optimal weight: 2.9990 chunk 16 optimal weight: 0.0010 chunk 71 optimal weight: 0.6980 chunk 100 optimal weight: 0.1980 chunk 150 optimal weight: 1.9990 chunk 159 optimal weight: 2.9990 chunk 78 optimal weight: 0.3980 chunk 142 optimal weight: 1.9990 chunk 42 optimal weight: 3.9990 overall best weight: 0.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_failure.pdb'. Return code: -15 Dumping stderr: