Starting phenix.real_space_refine on Sat Oct 11 10:51:12 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8oqa_17110/10_2025/8oqa_17110.cif Found real_map, /net/cci-nas-00/data/ceres_data/8oqa_17110/10_2025/8oqa_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 { model { file = "/net/cci-nas-00/data/ceres_data/8oqa_17110/10_2025/8oqa_17110.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8oqa_17110/10_2025/8oqa_17110.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8oqa_17110/10_2025/8oqa_17110.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8oqa_17110/10_2025/8oqa_17110.map" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/site-packages/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: {'ARG:plan': 3, 'ASP:plan': 2, 'GLU:plan': 2, 'GLN:plan1': 1} 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: {'ARG:plan': 3, 'GLN:plan1': 2, 'GLU:plan': 2, '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: {'ARG:plan': 3, 'GLU:plan': 2, 'GLN:plan1': 1, '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: {'ARG:plan': 2, 'GLU:plan': 2, 'GLN:plan1': 1} 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: {'ARG:plan': 3, 'ASP:plan': 2, 'GLU:plan': 1} 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: 3.82, per 1000 atoms: 0.28 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: 1.18 Conformation dependent library (CDL) restraints added in 551.8 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.49 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: 2.28 Time building geometry restraints manager: 1.55 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: 7.240 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.300 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 14.410 Find NCS groups from input model: 0.360 Set up NCS constraints: 0.030 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:6.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.350 ------------------------------------------------------------------------------- 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 : 0.005 0.348 14128 Z= 0.376 Angle : 0.906 44.237 19197 Z= 0.382 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.006 0.001 ARG C 191 TYR 0.022 0.001 TYR C 362 PHE 0.017 0.001 PHE E 290 TRP 0.017 0.001 TRP B 349 HIS 0.002 0.001 HIS E 254 Details of bonding type rmsd covalent geometry : bond 0.00276 (14116) covalent geometry : angle 0.59154 (19165) SS BOND : bond 0.00216 ( 1) SS BOND : angle 0.87749 ( 2) hydrogen bonds : bond 0.16681 ( 706) hydrogen bonds : angle 6.31232 ( 2295) Misc. bond : bond 0.34777 ( 1) link_NAG-ASN : bond 0.13333 ( 10) link_NAG-ASN : angle 17.37292 ( 30) *********************** 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 : 0.559 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: 0.7155 (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: 0.6727 time to fit residues: 259.3700 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 : 0.626 ------------------------------------------------------------------------------- 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 98 optimal weight: 2.9990 chunk 107 optimal weight: 0.0870 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 0.9990 chunk 91 optimal weight: 0.3980 chunk 149 optimal weight: 0.8980 overall best weight: 0.6762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 162 HIS A 199 ASN A 210 GLN A 287 GLN B 210 GLN B 247 GLN C 269 ASN D 251 GLN D 287 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.131484 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.109727 restraints weight = 16058.337| |-----------------------------------------------------------------------------| r_work (start): 0.3121 rms_B_bonded: 1.73 r_work: 0.3024 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.2909 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.2909 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8359 moved from start: 0.1687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 14128 Z= 0.147 Angle : 0.687 19.534 19197 Z= 0.336 Chirality : 0.052 0.941 2197 Planarity : 0.004 0.035 2334 Dihedral : 7.290 77.966 2175 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 2.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.74 % Favored : 99.26 % Rotamer: Outliers : 3.03 % Allowed : 12.26 % Favored : 84.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.32 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.84 (0.21), residues: 1630 helix: 2.00 (0.22), residues: 610 sheet: 1.24 (0.23), residues: 465 loop : 0.42 (0.25), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 308 TYR 0.021 0.002 TYR B 362 PHE 0.015 0.001 PHE E 290 TRP 0.013 0.001 TRP B 349 HIS 0.004 0.001 HIS E 126 Details of bonding type rmsd covalent geometry : bond 0.00278 (14116) covalent geometry : angle 0.59548 (19165) SS BOND : bond 0.00238 ( 1) SS BOND : angle 0.87850 ( 2) hydrogen bonds : bond 0.06696 ( 706) hydrogen bonds : angle 4.45209 ( 2295) Misc. bond : bond 0.00052 ( 1) link_NAG-ASN : bond 0.01729 ( 10) link_NAG-ASN : angle 8.67726 ( 30) *********************** 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 304 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 259 time to evaluate : 0.584 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 183 ASP cc_start: 0.7643 (OUTLIER) cc_final: 0.7281 (p0) REVERT: A 269 ASN cc_start: 0.8125 (OUTLIER) cc_final: 0.7710 (m-40) REVERT: B 82 ASP cc_start: 0.6705 (m-30) cc_final: 0.6176 (p0) REVERT: B 116 MET cc_start: 0.8356 (mtt) cc_final: 0.8020 (mtm) REVERT: B 117 ASP cc_start: 0.8229 (p0) cc_final: 0.7987 (p0) REVERT: B 197 MET cc_start: 0.8093 (ptp) cc_final: 0.7889 (ptt) REVERT: B 223 GLU cc_start: 0.8373 (pt0) cc_final: 0.7803 (pp20) REVERT: B 235 ASP cc_start: 0.7819 (OUTLIER) cc_final: 0.7159 (t0) REVERT: B 462 ILE cc_start: 0.8030 (OUTLIER) cc_final: 0.7820 (mp) REVERT: C 143 MET cc_start: 0.7913 (mmm) cc_final: 0.7660 (mmp) REVERT: D 148 ARG cc_start: 0.7338 (ptp-170) cc_final: 0.7053 (ptt180) REVERT: D 234 ASN cc_start: 0.6682 (OUTLIER) cc_final: 0.6026 (t160) REVERT: D 241 GLU cc_start: 0.7330 (mm-30) cc_final: 0.7121 (tp30) REVERT: D 287 GLN cc_start: 0.7564 (OUTLIER) cc_final: 0.6918 (mp-120) REVERT: D 304 TRP cc_start: 0.8118 (m100) cc_final: 0.7876 (m-90) REVERT: D 326 THR cc_start: 0.8478 (m) cc_final: 0.8099 (p) REVERT: D 337 ARG cc_start: 0.6622 (mtt180) cc_final: 0.5951 (mtp-110) REVERT: E 232 LYS cc_start: 0.7289 (mttt) cc_final: 0.6686 (mtpp) REVERT: E 295 MET cc_start: 0.8409 (mmm) cc_final: 0.8164 (mmp) REVERT: E 335 MET cc_start: 0.5438 (mmt) cc_final: 0.5014 (mmm) REVERT: E 477 ILE cc_start: 0.6572 (mt) cc_final: 0.6349 (mp) outliers start: 45 outliers final: 20 residues processed: 283 average time/residue: 0.6363 time to fit residues: 195.9931 Evaluate side-chains 263 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 237 time to evaluate : 0.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 326 THR Chi-restraints excluded: chain A residue 469 LEU Chi-restraints excluded: chain B residue 235 ASP Chi-restraints excluded: chain B residue 256 THR Chi-restraints excluded: chain B residue 462 ILE 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 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 338 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 105 optimal weight: 6.9990 chunk 53 optimal weight: 0.9980 chunk 73 optimal weight: 3.9990 chunk 83 optimal weight: 1.9990 chunk 152 optimal weight: 5.9990 chunk 120 optimal weight: 1.9990 chunk 47 optimal weight: 0.7980 chunk 158 optimal weight: 3.9990 chunk 63 optimal weight: 0.6980 chunk 129 optimal weight: 2.9990 chunk 5 optimal weight: 0.7980 overall best weight: 1.0582 ------------------------------------------------------------------------------- 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 251 GLN D 287 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.128542 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.105853 restraints weight = 16263.322| |-----------------------------------------------------------------------------| r_work (start): 0.3088 rms_B_bonded: 1.79 r_work: 0.2994 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.2877 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.2877 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8389 moved from start: 0.1848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 14128 Z= 0.157 Angle : 0.671 18.783 19197 Z= 0.330 Chirality : 0.045 0.408 2197 Planarity : 0.004 0.039 2334 Dihedral : 6.867 76.392 2168 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 2.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.04 % Favored : 98.96 % Rotamer: Outliers : 3.64 % Allowed : 13.80 % Favored : 82.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.32 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.64 (0.21), residues: 1630 helix: 1.96 (0.22), residues: 610 sheet: 1.01 (0.23), residues: 470 loop : 0.27 (0.24), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 308 TYR 0.021 0.002 TYR B 362 PHE 0.016 0.002 PHE A 356 TRP 0.012 0.001 TRP B 349 HIS 0.006 0.001 HIS C 254 Details of bonding type rmsd covalent geometry : bond 0.00322 (14116) covalent geometry : angle 0.57960 (19165) SS BOND : bond 0.00416 ( 1) SS BOND : angle 1.12881 ( 2) hydrogen bonds : bond 0.06897 ( 706) hydrogen bonds : angle 4.30992 ( 2295) Misc. bond : bond 0.00091 ( 1) link_NAG-ASN : bond 0.01546 ( 10) link_NAG-ASN : angle 8.56617 ( 30) *********************** 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 291 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 237 time to evaluate : 0.546 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 183 ASP cc_start: 0.7735 (OUTLIER) cc_final: 0.7410 (p0) REVERT: A 235 ASP cc_start: 0.7044 (p0) cc_final: 0.6482 (t70) REVERT: A 269 ASN cc_start: 0.8114 (OUTLIER) cc_final: 0.7701 (m-40) REVERT: A 334 SER cc_start: 0.4327 (OUTLIER) cc_final: 0.4119 (p) REVERT: B 82 ASP cc_start: 0.6711 (m-30) cc_final: 0.6165 (p0) REVERT: B 108 LEU cc_start: 0.8842 (OUTLIER) cc_final: 0.8488 (mt) REVERT: B 116 MET cc_start: 0.8376 (mtt) cc_final: 0.8020 (mtm) REVERT: B 117 ASP cc_start: 0.8140 (p0) cc_final: 0.7913 (p0) REVERT: B 223 GLU cc_start: 0.8422 (pt0) cc_final: 0.7834 (pp20) REVERT: B 457 LYS cc_start: 0.7329 (OUTLIER) cc_final: 0.6773 (pttt) REVERT: C 108 LEU cc_start: 0.8848 (OUTLIER) cc_final: 0.8366 (tt) REVERT: C 143 MET cc_start: 0.7916 (mmm) cc_final: 0.7684 (mmp) REVERT: D 148 ARG cc_start: 0.7394 (ptp-170) cc_final: 0.7050 (ptt180) REVERT: D 241 GLU cc_start: 0.7386 (mm-30) cc_final: 0.7166 (tp30) REVERT: D 304 TRP cc_start: 0.8133 (m100) cc_final: 0.7886 (m-90) REVERT: D 326 THR cc_start: 0.8514 (m) cc_final: 0.8122 (p) REVERT: D 337 ARG cc_start: 0.6685 (mtt180) cc_final: 0.5948 (mtp-110) REVERT: E 232 LYS cc_start: 0.7335 (mttt) cc_final: 0.6732 (mtpp) REVERT: E 295 MET cc_start: 0.8402 (mmm) cc_final: 0.8083 (mmp) outliers start: 54 outliers final: 33 residues processed: 265 average time/residue: 0.6403 time to fit residues: 184.8657 Evaluate side-chains 272 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 233 time to evaluate : 0.548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 155 VAL Chi-restraints excluded: chain B residue 235 ASP Chi-restraints excluded: chain B residue 256 THR Chi-restraints excluded: chain B residue 331 VAL Chi-restraints excluded: chain B residue 371 VAL Chi-restraints excluded: chain B residue 457 LYS Chi-restraints excluded: chain C residue 82 ASP Chi-restraints excluded: chain C residue 102 ASP Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 234 ASN 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 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 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 223 GLU Chi-restraints excluded: chain E residue 244 SER Chi-restraints excluded: chain E residue 298 LEU Chi-restraints excluded: chain E residue 338 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 98 optimal weight: 3.9990 chunk 72 optimal weight: 5.9990 chunk 131 optimal weight: 3.9990 chunk 54 optimal weight: 0.6980 chunk 39 optimal weight: 2.9990 chunk 103 optimal weight: 4.9990 chunk 157 optimal weight: 20.0000 chunk 97 optimal weight: 2.9990 chunk 44 optimal weight: 0.7980 chunk 87 optimal weight: 0.9980 chunk 55 optimal weight: 1.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 210 GLN A 251 GLN A 287 GLN B 210 GLN B 247 GLN B 332 ASN E 287 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.126383 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.103776 restraints weight = 16230.057| |-----------------------------------------------------------------------------| r_work (start): 0.3065 rms_B_bonded: 1.77 r_work: 0.2970 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.2854 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.2854 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8426 moved from start: 0.2063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 14128 Z= 0.183 Angle : 0.688 16.710 19197 Z= 0.347 Chirality : 0.046 0.450 2197 Planarity : 0.005 0.044 2334 Dihedral : 7.186 75.400 2168 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 3.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 4.58 % Allowed : 13.54 % Favored : 81.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.32 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.33 (0.20), residues: 1630 helix: 1.81 (0.22), residues: 605 sheet: 0.85 (0.23), residues: 465 loop : -0.03 (0.24), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 308 TYR 0.024 0.002 TYR E 362 PHE 0.019 0.002 PHE A 356 TRP 0.012 0.001 TRP B 349 HIS 0.007 0.001 HIS C 254 Details of bonding type rmsd covalent geometry : bond 0.00399 (14116) covalent geometry : angle 0.61699 (19165) SS BOND : bond 0.00678 ( 1) SS BOND : angle 1.52744 ( 2) hydrogen bonds : bond 0.07596 ( 706) hydrogen bonds : angle 4.42292 ( 2295) Misc. bond : bond 0.00088 ( 1) link_NAG-ASN : bond 0.01683 ( 10) link_NAG-ASN : angle 7.73052 ( 30) *********************** REFINEMENT MACRO_CYCLE 4 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 309 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 241 time to evaluate : 0.482 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 183 ASP cc_start: 0.7797 (OUTLIER) cc_final: 0.7500 (p0) REVERT: A 235 ASP cc_start: 0.7182 (p0) cc_final: 0.6542 (t70) REVERT: A 241 GLU cc_start: 0.7383 (pm20) cc_final: 0.7145 (mp0) REVERT: A 269 ASN cc_start: 0.8143 (OUTLIER) cc_final: 0.7745 (m-40) REVERT: A 334 SER cc_start: 0.4407 (OUTLIER) cc_final: 0.4201 (p) REVERT: B 82 ASP cc_start: 0.6805 (m-30) cc_final: 0.6271 (p0) REVERT: B 108 LEU cc_start: 0.8871 (OUTLIER) cc_final: 0.8503 (mt) REVERT: B 116 MET cc_start: 0.8373 (mtt) cc_final: 0.8003 (mtm) REVERT: B 117 ASP cc_start: 0.8138 (p0) cc_final: 0.7893 (p0) REVERT: B 131 GLU cc_start: 0.7727 (tp30) cc_final: 0.7395 (tp30) REVERT: B 223 GLU cc_start: 0.8486 (pt0) cc_final: 0.7897 (pp20) REVERT: C 108 LEU cc_start: 0.8885 (OUTLIER) cc_final: 0.8445 (tt) REVERT: C 143 MET cc_start: 0.7895 (mmm) cc_final: 0.7640 (mmp) REVERT: C 235 ASP cc_start: 0.7286 (m-30) cc_final: 0.6879 (t0) REVERT: C 258 LYS cc_start: 0.8386 (OUTLIER) cc_final: 0.8173 (tttp) REVERT: D 148 ARG cc_start: 0.7480 (ptp-170) cc_final: 0.6989 (ptt180) REVERT: D 304 TRP cc_start: 0.8149 (m100) cc_final: 0.7885 (m-90) REVERT: D 326 THR cc_start: 0.8565 (m) cc_final: 0.8192 (p) REVERT: D 337 ARG cc_start: 0.6706 (mtt180) cc_final: 0.5936 (mtp-110) REVERT: D 457 LYS cc_start: 0.7050 (tttp) cc_final: 0.6237 (ttmm) REVERT: E 116 MET cc_start: 0.8190 (mtm) cc_final: 0.7798 (mtp) REVERT: E 232 LYS cc_start: 0.7520 (mttt) cc_final: 0.6918 (mtpp) REVERT: E 295 MET cc_start: 0.8406 (mmm) cc_final: 0.8021 (mmp) outliers start: 68 outliers final: 40 residues processed: 279 average time/residue: 0.6165 time to fit residues: 187.4000 Evaluate side-chains 280 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 234 time to evaluate : 0.548 ------------------------------------------------------------------------------- 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 344 VAL 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 155 VAL Chi-restraints excluded: chain B residue 256 THR Chi-restraints excluded: chain B residue 263 SER Chi-restraints excluded: chain B residue 301 VAL Chi-restraints excluded: chain B residue 331 VAL 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 108 LEU Chi-restraints excluded: chain C residue 122 LEU 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 102 ASP Chi-restraints excluded: chain D residue 151 LYS Chi-restraints excluded: chain D residue 173 THR 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 108 optimal weight: 5.9990 chunk 137 optimal weight: 0.0020 chunk 93 optimal weight: 2.9990 chunk 83 optimal weight: 0.2980 chunk 110 optimal weight: 0.7980 chunk 105 optimal weight: 5.9990 chunk 63 optimal weight: 6.9990 chunk 15 optimal weight: 3.9990 chunk 117 optimal weight: 1.9990 chunk 84 optimal weight: 3.9990 chunk 102 optimal weight: 0.9990 overall best weight: 0.8192 ------------------------------------------------------------------------------- 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 210 GLN D 287 GLN ** E 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.132313 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.110723 restraints weight = 16078.198| |-----------------------------------------------------------------------------| r_work (start): 0.3111 rms_B_bonded: 1.67 r_work: 0.3014 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.2899 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.2899 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8391 moved from start: 0.2245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 14128 Z= 0.141 Angle : 0.638 15.444 19197 Z= 0.315 Chirality : 0.047 0.764 2197 Planarity : 0.004 0.042 2334 Dihedral : 6.990 75.107 2168 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 2.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.92 % Favored : 99.08 % Rotamer: Outliers : 3.91 % Allowed : 15.08 % Favored : 81.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.32 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.49 (0.21), residues: 1630 helix: 2.03 (0.22), residues: 605 sheet: 1.03 (0.24), residues: 440 loop : -0.09 (0.23), residues: 585 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 308 TYR 0.021 0.002 TYR B 362 PHE 0.017 0.001 PHE E 356 TRP 0.013 0.001 TRP C 349 HIS 0.004 0.001 HIS C 254 Details of bonding type rmsd covalent geometry : bond 0.00281 (14116) covalent geometry : angle 0.55977 (19165) SS BOND : bond 0.00368 ( 1) SS BOND : angle 0.87718 ( 2) hydrogen bonds : bond 0.06350 ( 706) hydrogen bonds : angle 4.19229 ( 2295) Misc. bond : bond 0.00088 ( 1) link_NAG-ASN : bond 0.01578 ( 10) link_NAG-ASN : angle 7.76262 ( 30) *********************** REFINEMENT MACRO_CYCLE 5 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 299 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 241 time to evaluate : 0.560 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 235 ASP cc_start: 0.7112 (p0) cc_final: 0.6480 (t70) REVERT: A 269 ASN cc_start: 0.8090 (OUTLIER) cc_final: 0.7588 (m-40) REVERT: B 82 ASP cc_start: 0.6777 (m-30) cc_final: 0.6257 (p0) REVERT: B 108 LEU cc_start: 0.8773 (OUTLIER) cc_final: 0.8466 (mt) REVERT: B 116 MET cc_start: 0.8344 (mtt) cc_final: 0.8007 (mtm) REVERT: B 131 GLU cc_start: 0.7637 (tp30) cc_final: 0.7355 (tp30) REVERT: B 223 GLU cc_start: 0.8468 (pt0) cc_final: 0.7870 (pp20) REVERT: C 108 LEU cc_start: 0.8868 (OUTLIER) cc_final: 0.8357 (tt) REVERT: C 143 MET cc_start: 0.7733 (mmm) cc_final: 0.7531 (mmp) REVERT: C 151 LYS cc_start: 0.8410 (OUTLIER) cc_final: 0.8071 (mmpt) REVERT: C 235 ASP cc_start: 0.7227 (m-30) cc_final: 0.6852 (t0) REVERT: D 148 ARG cc_start: 0.7433 (ptp-170) cc_final: 0.6987 (ptt180) REVERT: D 304 TRP cc_start: 0.8124 (m100) cc_final: 0.7877 (m-90) REVERT: D 326 THR cc_start: 0.8513 (m) cc_final: 0.8121 (p) REVERT: D 337 ARG cc_start: 0.6684 (mtt180) cc_final: 0.5906 (mtp-110) REVERT: D 457 LYS cc_start: 0.7056 (tttp) cc_final: 0.6231 (mttm) REVERT: E 197 MET cc_start: 0.8115 (ptm) cc_final: 0.7836 (ptt) REVERT: E 232 LYS cc_start: 0.7474 (mttt) cc_final: 0.6911 (mtpp) REVERT: E 295 MET cc_start: 0.8417 (mmm) cc_final: 0.8156 (mmp) outliers start: 58 outliers final: 34 residues processed: 275 average time/residue: 0.6433 time to fit residues: 192.2900 Evaluate side-chains 265 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 227 time to evaluate : 0.540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 234 ASN Chi-restraints excluded: chain A residue 246 SER Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain A residue 326 THR Chi-restraints excluded: chain A residue 344 VAL Chi-restraints excluded: chain A residue 469 LEU Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 207 LEU Chi-restraints excluded: chain B residue 256 THR Chi-restraints excluded: chain B residue 263 SER Chi-restraints excluded: chain B residue 331 VAL Chi-restraints excluded: chain C residue 82 ASP Chi-restraints excluded: chain C residue 102 ASP Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain C residue 140 ASN Chi-restraints excluded: chain C residue 151 LYS 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 338 VAL Chi-restraints excluded: chain C residue 370 THR Chi-restraints excluded: chain D residue 102 ASP Chi-restraints excluded: chain D residue 151 LYS Chi-restraints excluded: chain D residue 173 THR Chi-restraints excluded: chain D residue 249 LEU Chi-restraints excluded: chain D residue 256 THR Chi-restraints excluded: chain D residue 257 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 140 ASN Chi-restraints excluded: chain E residue 244 SER Chi-restraints excluded: chain E residue 318 ILE Chi-restraints excluded: chain E residue 338 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 85 optimal weight: 0.8980 chunk 80 optimal weight: 0.0970 chunk 112 optimal weight: 4.9990 chunk 118 optimal weight: 0.7980 chunk 11 optimal weight: 4.9990 chunk 35 optimal weight: 0.7980 chunk 138 optimal weight: 1.9990 chunk 39 optimal weight: 0.5980 chunk 32 optimal weight: 5.9990 chunk 26 optimal weight: 1.9990 chunk 91 optimal weight: 0.0010 overall best weight: 0.4584 ------------------------------------------------------------------------------- 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 210 GLN D 287 GLN E 251 GLN E 287 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.131880 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.110077 restraints weight = 16188.640| |-----------------------------------------------------------------------------| r_work (start): 0.3135 rms_B_bonded: 1.66 r_work: 0.3045 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.2929 rms_B_bonded: 3.47 restraints_weight: 0.2500 r_work (final): 0.2929 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8349 moved from start: 0.2397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 14128 Z= 0.124 Angle : 0.619 16.142 19197 Z= 0.302 Chirality : 0.045 0.529 2197 Planarity : 0.004 0.040 2334 Dihedral : 6.645 74.525 2168 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 2.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer: Outliers : 3.10 % Allowed : 15.89 % Favored : 81.01 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.32 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.71 (0.21), residues: 1630 helix: 2.18 (0.22), residues: 605 sheet: 1.21 (0.24), residues: 455 loop : -0.03 (0.24), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 308 TYR 0.020 0.001 TYR B 362 PHE 0.017 0.001 PHE E 356 TRP 0.013 0.001 TRP D 349 HIS 0.003 0.001 HIS C 254 Details of bonding type rmsd covalent geometry : bond 0.00234 (14116) covalent geometry : angle 0.53246 (19165) SS BOND : bond 0.00255 ( 1) SS BOND : angle 0.66167 ( 2) hydrogen bonds : bond 0.05589 ( 706) hydrogen bonds : angle 4.03425 ( 2295) Misc. bond : bond 0.00061 ( 1) link_NAG-ASN : bond 0.01385 ( 10) link_NAG-ASN : angle 7.99894 ( 30) *********************** REFINEMENT MACRO_CYCLE 6 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 286 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 240 time to evaluate : 0.542 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 235 ASP cc_start: 0.7073 (p0) cc_final: 0.6379 (t70) REVERT: A 269 ASN cc_start: 0.7970 (OUTLIER) cc_final: 0.7492 (m-40) REVERT: B 82 ASP cc_start: 0.6779 (m-30) cc_final: 0.6281 (p0) REVERT: B 108 LEU cc_start: 0.8711 (OUTLIER) cc_final: 0.8431 (mt) REVERT: B 116 MET cc_start: 0.8329 (mtt) cc_final: 0.8040 (mtm) REVERT: B 131 GLU cc_start: 0.7640 (tp30) cc_final: 0.7367 (tp30) REVERT: C 151 LYS cc_start: 0.8386 (OUTLIER) cc_final: 0.8056 (mmpt) REVERT: C 235 ASP cc_start: 0.7156 (m-30) cc_final: 0.6810 (t0) REVERT: D 148 ARG cc_start: 0.7381 (ptp-170) cc_final: 0.6944 (ptt180) REVERT: D 304 TRP cc_start: 0.8111 (m100) cc_final: 0.7873 (m-90) REVERT: D 326 THR cc_start: 0.8448 (m) cc_final: 0.8038 (p) REVERT: D 337 ARG cc_start: 0.6705 (mtt180) cc_final: 0.5868 (mtp-110) REVERT: D 457 LYS cc_start: 0.6898 (tttp) cc_final: 0.6149 (mttm) REVERT: E 197 MET cc_start: 0.8088 (ptm) cc_final: 0.7830 (ptt) REVERT: E 232 LYS cc_start: 0.7417 (mttt) cc_final: 0.6805 (mtpp) REVERT: E 295 MET cc_start: 0.8390 (mmm) cc_final: 0.8012 (mmp) outliers start: 46 outliers final: 29 residues processed: 267 average time/residue: 0.6379 time to fit residues: 185.2217 Evaluate side-chains 264 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 232 time to evaluate : 0.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 234 ASN Chi-restraints excluded: chain A residue 246 SER Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain A residue 326 THR Chi-restraints excluded: chain A residue 335 MET Chi-restraints excluded: chain A residue 469 LEU Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 207 LEU Chi-restraints excluded: chain B residue 256 THR Chi-restraints excluded: chain B residue 301 VAL Chi-restraints excluded: chain C residue 82 ASP Chi-restraints excluded: chain C residue 102 ASP Chi-restraints excluded: chain C residue 140 ASN Chi-restraints excluded: chain C residue 151 LYS Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 234 ASN 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 D residue 102 ASP Chi-restraints excluded: chain D residue 151 LYS Chi-restraints excluded: chain D residue 173 THR Chi-restraints excluded: chain D residue 256 THR Chi-restraints excluded: chain D residue 257 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 318 ILE Chi-restraints excluded: chain E residue 338 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 36 optimal weight: 1.9990 chunk 133 optimal weight: 0.0980 chunk 102 optimal weight: 4.9990 chunk 2 optimal weight: 0.7980 chunk 35 optimal weight: 1.9990 chunk 125 optimal weight: 0.2980 chunk 137 optimal weight: 0.0470 chunk 51 optimal weight: 0.7980 chunk 146 optimal weight: 4.9990 chunk 128 optimal weight: 1.9990 chunk 114 optimal weight: 0.7980 overall best weight: 0.4078 ------------------------------------------------------------------------------- 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 210 GLN C 210 GLN E 251 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.133612 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.111618 restraints weight = 16246.026| |-----------------------------------------------------------------------------| r_work (start): 0.3157 rms_B_bonded: 1.67 r_work: 0.3066 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.2951 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.2951 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8320 moved from start: 0.2616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 14128 Z= 0.115 Angle : 0.574 12.821 19197 Z= 0.282 Chirality : 0.043 0.409 2197 Planarity : 0.004 0.040 2334 Dihedral : 6.473 73.750 2168 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 2.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 3.03 % Allowed : 16.43 % Favored : 80.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.32 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.83 (0.21), residues: 1630 helix: 2.24 (0.22), residues: 610 sheet: 1.26 (0.24), residues: 455 loop : 0.08 (0.24), residues: 565 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 308 TYR 0.017 0.001 TYR B 362 PHE 0.016 0.001 PHE E 356 TRP 0.012 0.001 TRP C 349 HIS 0.003 0.001 HIS C 254 Details of bonding type rmsd covalent geometry : bond 0.00221 (14116) covalent geometry : angle 0.50221 (19165) SS BOND : bond 0.00248 ( 1) SS BOND : angle 0.59852 ( 2) hydrogen bonds : bond 0.04950 ( 706) hydrogen bonds : angle 3.86351 ( 2295) Misc. bond : bond 0.00053 ( 1) link_NAG-ASN : bond 0.01632 ( 10) link_NAG-ASN : angle 7.02859 ( 30) *********************** REFINEMENT MACRO_CYCLE 7 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 284 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 239 time to evaluate : 0.553 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 235 ASP cc_start: 0.7024 (p0) cc_final: 0.6293 (t70) REVERT: A 269 ASN cc_start: 0.7908 (OUTLIER) cc_final: 0.7369 (m-40) REVERT: A 324 MET cc_start: 0.8764 (tpt) cc_final: 0.8459 (tpt) REVERT: B 82 ASP cc_start: 0.6783 (m-30) cc_final: 0.6264 (p0) REVERT: B 108 LEU cc_start: 0.8671 (OUTLIER) cc_final: 0.8405 (mt) REVERT: B 116 MET cc_start: 0.8265 (mtt) cc_final: 0.7976 (mtm) REVERT: B 131 GLU cc_start: 0.7610 (tp30) cc_final: 0.7297 (tp30) REVERT: B 197 MET cc_start: 0.8180 (ptt) cc_final: 0.7871 (ppp) REVERT: B 223 GLU cc_start: 0.8370 (pt0) cc_final: 0.7816 (pp20) REVERT: C 151 LYS cc_start: 0.8343 (OUTLIER) cc_final: 0.8040 (mmpt) REVERT: C 235 ASP cc_start: 0.7122 (m-30) cc_final: 0.6740 (t0) REVERT: D 148 ARG cc_start: 0.7340 (ptp-170) cc_final: 0.6893 (ptt180) REVERT: D 287 GLN cc_start: 0.7456 (OUTLIER) cc_final: 0.6413 (mp10) REVERT: D 304 TRP cc_start: 0.8078 (m100) cc_final: 0.7853 (m-90) REVERT: D 326 THR cc_start: 0.8450 (m) cc_final: 0.8055 (p) REVERT: D 337 ARG cc_start: 0.6795 (mtt180) cc_final: 0.5996 (mtp-110) REVERT: D 457 LYS cc_start: 0.6793 (tttp) cc_final: 0.6125 (mttm) REVERT: E 197 MET cc_start: 0.8001 (ptm) cc_final: 0.7790 (ptt) REVERT: E 232 LYS cc_start: 0.7392 (mttt) cc_final: 0.6807 (mtpp) REVERT: E 295 MET cc_start: 0.8395 (mmm) cc_final: 0.8054 (mmp) outliers start: 45 outliers final: 22 residues processed: 266 average time/residue: 0.6463 time to fit residues: 186.9700 Evaluate side-chains 255 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 229 time to evaluate : 0.523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 234 ASN Chi-restraints excluded: chain A residue 246 SER Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain B residue 108 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 301 VAL Chi-restraints excluded: chain B residue 360 LEU Chi-restraints excluded: chain C residue 102 ASP Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 140 ASN Chi-restraints excluded: chain C residue 151 LYS Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 234 ASN Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain C residue 370 THR Chi-restraints excluded: chain D residue 151 LYS Chi-restraints excluded: chain D residue 256 THR Chi-restraints excluded: chain D residue 257 THR Chi-restraints excluded: chain D residue 287 GLN 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 318 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 155 optimal weight: 3.9990 chunk 149 optimal weight: 0.9980 chunk 146 optimal weight: 4.9990 chunk 77 optimal weight: 0.6980 chunk 15 optimal weight: 3.9990 chunk 76 optimal weight: 0.5980 chunk 58 optimal weight: 3.9990 chunk 59 optimal weight: 4.9990 chunk 109 optimal weight: 3.9990 chunk 23 optimal weight: 0.6980 chunk 89 optimal weight: 0.0980 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 210 GLN D 287 GLN E 251 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.132712 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.110791 restraints weight = 16184.419| |-----------------------------------------------------------------------------| r_work (start): 0.3146 rms_B_bonded: 1.65 r_work: 0.3049 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.2931 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.2931 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.2607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 14128 Z= 0.121 Angle : 0.580 12.754 19197 Z= 0.289 Chirality : 0.044 0.407 2197 Planarity : 0.004 0.042 2334 Dihedral : 7.428 110.508 2167 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 2.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.04 % Favored : 98.96 % Rotamer: Outliers : 2.69 % Allowed : 17.31 % Favored : 80.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.32 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.82 (0.21), residues: 1630 helix: 2.23 (0.22), residues: 610 sheet: 1.19 (0.24), residues: 460 loop : 0.14 (0.25), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 308 TYR 0.021 0.001 TYR B 362 PHE 0.019 0.001 PHE E 356 TRP 0.011 0.001 TRP D 349 HIS 0.004 0.001 HIS C 254 Details of bonding type rmsd covalent geometry : bond 0.00242 (14116) covalent geometry : angle 0.52182 (19165) SS BOND : bond 0.00305 ( 1) SS BOND : angle 0.75785 ( 2) hydrogen bonds : bond 0.05225 ( 706) hydrogen bonds : angle 3.89282 ( 2295) Misc. bond : bond 0.00051 ( 1) link_NAG-ASN : bond 0.01321 ( 10) link_NAG-ASN : angle 6.41987 ( 30) *********************** REFINEMENT MACRO_CYCLE 8 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 271 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 231 time to evaluate : 0.554 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 235 ASP cc_start: 0.7095 (p0) cc_final: 0.6342 (t70) REVERT: A 269 ASN cc_start: 0.7982 (OUTLIER) cc_final: 0.7493 (m-40) REVERT: A 295 MET cc_start: 0.8559 (mmp) cc_final: 0.8214 (mmp) REVERT: B 82 ASP cc_start: 0.6755 (m-30) cc_final: 0.6248 (p0) REVERT: B 108 LEU cc_start: 0.8699 (OUTLIER) cc_final: 0.8408 (mt) REVERT: B 116 MET cc_start: 0.8277 (mtt) cc_final: 0.7997 (mtm) REVERT: B 131 GLU cc_start: 0.7636 (tp30) cc_final: 0.7349 (tp30) REVERT: B 197 MET cc_start: 0.8261 (ptt) cc_final: 0.7845 (ppp) REVERT: B 223 GLU cc_start: 0.8387 (pt0) cc_final: 0.7851 (pp20) REVERT: B 247 GLN cc_start: 0.7890 (mp10) cc_final: 0.7685 (mp10) REVERT: C 131 GLU cc_start: 0.8177 (mm-30) cc_final: 0.7383 (tm-30) REVERT: C 151 LYS cc_start: 0.8365 (OUTLIER) cc_final: 0.8066 (mmpt) REVERT: C 200 MET cc_start: 0.8509 (mtp) cc_final: 0.8012 (mtp) REVERT: C 235 ASP cc_start: 0.7193 (m-30) cc_final: 0.6789 (t0) REVERT: C 477 ILE cc_start: 0.8199 (OUTLIER) cc_final: 0.7890 (mt) REVERT: D 148 ARG cc_start: 0.7368 (ptp-170) cc_final: 0.6914 (ptt180) REVERT: D 304 TRP cc_start: 0.8104 (m100) cc_final: 0.7872 (m-90) REVERT: D 326 THR cc_start: 0.8477 (m) cc_final: 0.8069 (p) REVERT: D 337 ARG cc_start: 0.6791 (mtt180) cc_final: 0.5916 (mtp-110) REVERT: D 457 LYS cc_start: 0.6847 (tttp) cc_final: 0.6180 (mttm) REVERT: E 197 MET cc_start: 0.8036 (ptm) cc_final: 0.7828 (ptt) REVERT: E 232 LYS cc_start: 0.7440 (mttt) cc_final: 0.6853 (mtpp) REVERT: E 295 MET cc_start: 0.8412 (mmm) cc_final: 0.8093 (mmp) outliers start: 40 outliers final: 28 residues processed: 254 average time/residue: 0.6330 time to fit residues: 174.8342 Evaluate side-chains 260 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 228 time to evaluate : 0.580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 234 ASN Chi-restraints excluded: chain A residue 246 SER Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain A residue 326 THR Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 207 LEU Chi-restraints excluded: chain B residue 256 THR Chi-restraints excluded: chain B residue 263 SER Chi-restraints excluded: chain B residue 301 VAL Chi-restraints excluded: chain B residue 360 LEU Chi-restraints excluded: chain C residue 102 ASP Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 140 ASN Chi-restraints excluded: chain C residue 151 LYS Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 234 ASN 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 477 ILE Chi-restraints excluded: chain D residue 102 ASP Chi-restraints excluded: chain D residue 151 LYS Chi-restraints excluded: chain D residue 173 THR Chi-restraints excluded: chain D residue 256 THR Chi-restraints excluded: chain D residue 257 THR Chi-restraints excluded: chain D residue 287 GLN 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 318 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 122 optimal weight: 0.9990 chunk 130 optimal weight: 3.9990 chunk 2 optimal weight: 0.7980 chunk 118 optimal weight: 0.9990 chunk 57 optimal weight: 4.9990 chunk 9 optimal weight: 6.9990 chunk 102 optimal weight: 4.9990 chunk 54 optimal weight: 0.6980 chunk 140 optimal weight: 3.9990 chunk 65 optimal weight: 2.9990 chunk 115 optimal weight: 0.9990 overall best weight: 0.8986 ------------------------------------------------------------------------------- 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 210 GLN E 251 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.130359 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.108277 restraints weight = 16143.084| |-----------------------------------------------------------------------------| r_work (start): 0.3121 rms_B_bonded: 1.65 r_work: 0.3033 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.2919 rms_B_bonded: 3.45 restraints_weight: 0.2500 r_work (final): 0.2919 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8358 moved from start: 0.2566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 14128 Z= 0.136 Angle : 0.593 12.674 19197 Z= 0.299 Chirality : 0.044 0.414 2197 Planarity : 0.004 0.042 2334 Dihedral : 7.980 124.252 2167 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 2.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.29 % Favored : 98.71 % Rotamer: Outliers : 2.83 % Allowed : 17.44 % Favored : 79.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.32 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.67 (0.21), residues: 1630 helix: 2.16 (0.22), residues: 610 sheet: 1.11 (0.24), residues: 440 loop : 0.02 (0.24), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 308 TYR 0.019 0.002 TYR B 362 PHE 0.018 0.002 PHE E 356 TRP 0.010 0.001 TRP D 349 HIS 0.005 0.001 HIS C 254 Details of bonding type rmsd covalent geometry : bond 0.00285 (14116) covalent geometry : angle 0.54283 (19165) SS BOND : bond 0.00395 ( 1) SS BOND : angle 0.95329 ( 2) hydrogen bonds : bond 0.05746 ( 706) hydrogen bonds : angle 3.98369 ( 2295) Misc. bond : bond 0.00065 ( 1) link_NAG-ASN : bond 0.01177 ( 10) link_NAG-ASN : angle 6.03960 ( 30) *********************** REFINEMENT MACRO_CYCLE 9 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 269 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 227 time to evaluate : 0.541 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 235 ASP cc_start: 0.7156 (p0) cc_final: 0.6422 (t70) REVERT: A 269 ASN cc_start: 0.8023 (OUTLIER) cc_final: 0.7545 (m-40) REVERT: B 82 ASP cc_start: 0.6762 (m-30) cc_final: 0.6263 (p0) REVERT: B 108 LEU cc_start: 0.8765 (OUTLIER) cc_final: 0.8461 (mt) REVERT: B 116 MET cc_start: 0.8269 (mtt) cc_final: 0.7996 (mtm) REVERT: B 131 GLU cc_start: 0.7684 (tp30) cc_final: 0.7377 (tp30) REVERT: B 197 MET cc_start: 0.8213 (ptt) cc_final: 0.7756 (ppp) REVERT: B 247 GLN cc_start: 0.7880 (mp10) cc_final: 0.7669 (mp10) REVERT: B 457 LYS cc_start: 0.7187 (OUTLIER) cc_final: 0.6618 (pttt) REVERT: C 131 GLU cc_start: 0.8200 (mm-30) cc_final: 0.7410 (mm-30) REVERT: C 151 LYS cc_start: 0.8348 (OUTLIER) cc_final: 0.8029 (mmpt) REVERT: C 235 ASP cc_start: 0.7149 (m-30) cc_final: 0.6772 (t0) REVERT: C 477 ILE cc_start: 0.8208 (OUTLIER) cc_final: 0.7896 (mt) REVERT: D 148 ARG cc_start: 0.7409 (ptp-170) cc_final: 0.6936 (ptt180) REVERT: D 304 TRP cc_start: 0.8113 (m100) cc_final: 0.7868 (m-90) REVERT: D 326 THR cc_start: 0.8501 (m) cc_final: 0.8074 (p) REVERT: D 337 ARG cc_start: 0.6784 (mtt180) cc_final: 0.5894 (mtp-110) REVERT: D 457 LYS cc_start: 0.6906 (tttp) cc_final: 0.6214 (mttm) REVERT: E 197 MET cc_start: 0.8012 (ptm) cc_final: 0.7772 (ptt) REVERT: E 232 LYS cc_start: 0.7452 (mttt) cc_final: 0.6855 (mtpp) REVERT: E 295 MET cc_start: 0.8399 (mmm) cc_final: 0.8039 (mmp) outliers start: 42 outliers final: 30 residues processed: 254 average time/residue: 0.6327 time to fit residues: 174.8707 Evaluate side-chains 259 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 224 time to evaluate : 0.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 234 ASN Chi-restraints excluded: chain A residue 246 SER Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain A residue 326 THR Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 207 LEU Chi-restraints excluded: chain B residue 256 THR Chi-restraints excluded: chain B residue 263 SER Chi-restraints excluded: chain B residue 301 VAL Chi-restraints excluded: chain B residue 360 LEU Chi-restraints excluded: chain B residue 457 LYS Chi-restraints excluded: chain C residue 102 ASP Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 122 LEU Chi-restraints excluded: chain C residue 140 ASN Chi-restraints excluded: chain C residue 151 LYS Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 234 ASN 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 477 ILE Chi-restraints excluded: chain D residue 151 LYS Chi-restraints excluded: chain D residue 173 THR Chi-restraints excluded: chain D residue 249 LEU 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 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 251 GLN Chi-restraints excluded: chain E residue 318 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 52 optimal weight: 3.9990 chunk 73 optimal weight: 1.9990 chunk 25 optimal weight: 0.6980 chunk 89 optimal weight: 2.9990 chunk 45 optimal weight: 3.9990 chunk 95 optimal weight: 2.9990 chunk 93 optimal weight: 1.9990 chunk 143 optimal weight: 2.9990 chunk 113 optimal weight: 1.9990 chunk 53 optimal weight: 0.6980 chunk 1 optimal weight: 0.9980 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 162 HIS A 210 GLN A 287 GLN B 210 GLN C 332 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.130398 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.108301 restraints weight = 16152.559| |-----------------------------------------------------------------------------| r_work (start): 0.3114 rms_B_bonded: 1.65 r_work: 0.3022 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.2907 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.2907 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8371 moved from start: 0.2563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.207 14128 Z= 0.207 Angle : 0.941 59.171 19197 Z= 0.487 Chirality : 0.046 0.414 2197 Planarity : 0.004 0.057 2334 Dihedral : 8.002 120.700 2167 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 2.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.29 % Favored : 98.71 % Rotamer: Outliers : 2.90 % Allowed : 17.58 % Favored : 79.53 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.32 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.65 (0.21), residues: 1630 helix: 2.15 (0.22), residues: 610 sheet: 1.11 (0.24), residues: 440 loop : 0.01 (0.24), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 308 TYR 0.019 0.002 TYR E 362 PHE 0.018 0.002 PHE E 356 TRP 0.010 0.001 TRP D 349 HIS 0.005 0.001 HIS C 254 Details of bonding type rmsd covalent geometry : bond 0.00388 (14116) covalent geometry : angle 0.84945 (19165) SS BOND : bond 0.00454 ( 1) SS BOND : angle 1.01969 ( 2) hydrogen bonds : bond 0.05813 ( 706) hydrogen bonds : angle 3.98586 ( 2295) Misc. bond : bond 0.00056 ( 1) link_NAG-ASN : bond 0.06663 ( 10) link_NAG-ASN : angle 10.26789 ( 30) ********************** REFINEMENT MACRO_CYCLE 10 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 268 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 225 time to evaluate : 0.506 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 235 ASP cc_start: 0.7193 (p0) cc_final: 0.6450 (t70) REVERT: A 269 ASN cc_start: 0.8024 (OUTLIER) cc_final: 0.7555 (m-40) REVERT: B 82 ASP cc_start: 0.6762 (m-30) cc_final: 0.6259 (p0) REVERT: B 108 LEU cc_start: 0.8768 (OUTLIER) cc_final: 0.8468 (mt) REVERT: B 116 MET cc_start: 0.8284 (mtt) cc_final: 0.8010 (mtm) REVERT: B 131 GLU cc_start: 0.7687 (tp30) cc_final: 0.7387 (tp30) REVERT: B 197 MET cc_start: 0.8229 (ptt) cc_final: 0.7781 (ppp) REVERT: B 247 GLN cc_start: 0.7902 (mp10) cc_final: 0.7694 (mp10) REVERT: B 457 LYS cc_start: 0.7209 (OUTLIER) cc_final: 0.6651 (pttt) REVERT: C 131 GLU cc_start: 0.8210 (mm-30) cc_final: 0.7395 (tm-30) REVERT: C 151 LYS cc_start: 0.8362 (OUTLIER) cc_final: 0.8048 (mmpt) REVERT: C 235 ASP cc_start: 0.7153 (m-30) cc_final: 0.6790 (t0) REVERT: C 477 ILE cc_start: 0.8228 (OUTLIER) cc_final: 0.7912 (mt) REVERT: D 148 ARG cc_start: 0.7442 (ptp-170) cc_final: 0.6976 (ptt180) REVERT: D 287 GLN cc_start: 0.7498 (OUTLIER) cc_final: 0.6514 (mp10) REVERT: D 304 TRP cc_start: 0.8125 (m100) cc_final: 0.7886 (m-90) REVERT: D 326 THR cc_start: 0.8516 (m) cc_final: 0.8100 (p) REVERT: D 337 ARG cc_start: 0.6778 (mtt180) cc_final: 0.5895 (mtp-110) REVERT: D 457 LYS cc_start: 0.6921 (tttp) cc_final: 0.6238 (mttm) REVERT: E 197 MET cc_start: 0.8026 (ptm) cc_final: 0.7793 (ptt) REVERT: E 232 LYS cc_start: 0.7472 (mttt) cc_final: 0.6877 (mtpp) REVERT: E 241 GLU cc_start: 0.6831 (OUTLIER) cc_final: 0.6508 (mp0) REVERT: E 295 MET cc_start: 0.8411 (mmm) cc_final: 0.8044 (mmp) outliers start: 43 outliers final: 30 residues processed: 248 average time/residue: 0.6299 time to fit residues: 169.9522 Evaluate side-chains 260 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 223 time to evaluate : 0.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 234 ASN Chi-restraints excluded: chain A residue 241 GLU Chi-restraints excluded: chain A residue 246 SER Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain A residue 326 THR Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 207 LEU Chi-restraints excluded: chain B residue 256 THR Chi-restraints excluded: chain B residue 263 SER Chi-restraints excluded: chain B residue 301 VAL Chi-restraints excluded: chain B residue 360 LEU Chi-restraints excluded: chain B residue 457 LYS Chi-restraints excluded: chain C residue 102 ASP Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 122 LEU Chi-restraints excluded: chain C residue 140 ASN Chi-restraints excluded: chain C residue 151 LYS Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 234 ASN 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 477 ILE Chi-restraints excluded: chain D residue 151 LYS Chi-restraints excluded: chain D residue 173 THR Chi-restraints excluded: chain D residue 249 LEU Chi-restraints excluded: chain D residue 256 THR Chi-restraints excluded: chain D residue 257 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 140 ASN Chi-restraints excluded: chain E residue 241 GLU Chi-restraints excluded: chain E residue 318 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 99 optimal weight: 4.9990 chunk 84 optimal weight: 0.7980 chunk 56 optimal weight: 0.8980 chunk 20 optimal weight: 3.9990 chunk 55 optimal weight: 0.7980 chunk 52 optimal weight: 2.9990 chunk 12 optimal weight: 0.9980 chunk 150 optimal weight: 0.9990 chunk 151 optimal weight: 0.9990 chunk 123 optimal weight: 5.9990 chunk 137 optimal weight: 5.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- 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 210 GLN C 332 ASN ** E 251 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.130160 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.108106 restraints weight = 16217.642| |-----------------------------------------------------------------------------| r_work (start): 0.3114 rms_B_bonded: 1.65 r_work: 0.3022 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.2907 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.2907 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8369 moved from start: 0.2570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.207 14128 Z= 0.207 Angle : 0.941 59.171 19197 Z= 0.487 Chirality : 0.046 0.414 2197 Planarity : 0.004 0.057 2334 Dihedral : 8.002 120.700 2167 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 2.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.29 % Favored : 98.71 % Rotamer: Outliers : 2.56 % Allowed : 18.05 % Favored : 79.39 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.32 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.65 (0.21), residues: 1630 helix: 2.15 (0.22), residues: 610 sheet: 1.11 (0.24), residues: 440 loop : 0.01 (0.24), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 308 TYR 0.019 0.002 TYR E 362 PHE 0.018 0.002 PHE E 356 TRP 0.010 0.001 TRP D 349 HIS 0.005 0.001 HIS C 254 Details of bonding type rmsd covalent geometry : bond 0.00388 (14116) covalent geometry : angle 0.84945 (19165) SS BOND : bond 0.00454 ( 1) SS BOND : angle 1.01969 ( 2) hydrogen bonds : bond 0.05813 ( 706) hydrogen bonds : angle 3.98586 ( 2295) Misc. bond : bond 0.00056 ( 1) link_NAG-ASN : bond 0.06663 ( 10) link_NAG-ASN : angle 10.26789 ( 30) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5034.78 seconds wall clock time: 86 minutes 35.54 seconds (5195.54 seconds total)