Starting phenix.real_space_refine on Sun Jan 19 16:57:21 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8oqa_17110/01_2025/8oqa_17110.cif Found real_map, /net/cci-nas-00/data/ceres_data/8oqa_17110/01_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8oqa_17110/01_2025/8oqa_17110.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8oqa_17110/01_2025/8oqa_17110.map" model { file = "/net/cci-nas-00/data/ceres_data/8oqa_17110/01_2025/8oqa_17110.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8oqa_17110/01_2025/8oqa_17110.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 75 5.16 5 Cl 2 4.86 5 C 9027 2.51 5 N 2177 2.21 5 O 2481 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 13762 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 2682 Number of conformers: 1 Conformer: "" Number of residues, atoms: 330, 2682 Classifications: {'peptide': 330} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 11, 'TRANS': 316} Chain breaks: 1 Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 56 Unresolved non-hydrogen dihedrals: 38 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ARG:plan': 3, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 33 Chain: "B" Number of atoms: 2689 Number of conformers: 1 Conformer: "" Number of residues, atoms: 330, 2689 Classifications: {'peptide': 330} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 11, 'TRANS': 316} Chain breaks: 1 Unresolved non-hydrogen bonds: 40 Unresolved non-hydrogen angles: 49 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 2, 'ARG:plan': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 34 Chain: "C" Number of atoms: 2689 Number of conformers: 1 Conformer: "" Number of residues, atoms: 330, 2689 Classifications: {'peptide': 330} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 11, 'TRANS': 316} Chain breaks: 1 Unresolved non-hydrogen bonds: 40 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ARG:plan': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 30 Chain: "D" Number of atoms: 2694 Number of conformers: 1 Conformer: "" Number of residues, atoms: 330, 2694 Classifications: {'peptide': 330} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 11, 'TRANS': 316} Chain breaks: 1 Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 41 Unresolved non-hydrogen dihedrals: 29 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 22 Chain: "E" Number of atoms: 2694 Number of conformers: 1 Conformer: "" Number of residues, atoms: 330, 2694 Classifications: {'peptide': 330} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 11, 'TRANS': 316} Chain breaks: 1 Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 28 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 3, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 25 Chain: "A" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 62 Unusual residues: {' CL': 2, 'HEX': 4, 'NAG': 2, 'OCT': 1} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 95 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 95 Unusual residues: {'ABU': 2, 'HEX': 4, 'NAG': 2, 'OCT': 1, 'RI5': 1} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 55 Unusual residues: {'ABU': 1, 'HEX': 2, 'NAG': 2, 'OCT': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 55 Unusual residues: {'ABU': 1, 'HEX': 2, 'NAG': 2, 'OCT': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 47 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 47 Unusual residues: {'ABU': 1, 'HEX': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 9.64, per 1000 atoms: 0.70 Number of scatterers: 13762 At special positions: 0 Unit cell: (93.03, 95.688, 136.222, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Cl 2 17.00 S 75 16.00 O 2481 8.00 N 2177 7.00 C 9027 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 198 " - pdb=" SG CYS A 212 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Links applied NAG-ASN " NAG A 501 " - " ASN A 140 " " NAG A 502 " - " ASN A 234 " " NAG B 603 " - " ASN B 140 " " NAG B 604 " - " ASN B 234 " " NAG C 602 " - " ASN C 140 " " NAG C 603 " - " ASN C 234 " " NAG D 602 " - " ASN D 140 " " NAG D 603 " - " ASN D 234 " " NAG E 503 " - " ASN E 140 " " NAG E 504 " - " ASN E 234 " Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.36 Conformation dependent library (CDL) restraints added in 1.7 seconds 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3200 Finding SS restraints... Secondary structure from input PDB file: 46 helices and 15 sheets defined 40.5% alpha, 40.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.43 Creating SS restraints... Processing helix chain 'A' and resid 80 through 84 removed outlier: 3.568A pdb=" N ASP A 83 " --> pdb=" O ARG A 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 134 Processing helix chain 'A' and resid 147 through 153 removed outlier: 3.606A pdb=" N VAL A 150 " --> pdb=" O GLY A 147 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N LYS A 151 " --> pdb=" O ARG A 148 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ILE A 153 " --> pdb=" O VAL A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 235 No H-bonds generated for 'chain 'A' and resid 233 through 235' Processing helix chain 'A' and resid 281 through 300 removed outlier: 4.346A pdb=" N PHE A 290 " --> pdb=" O LEU A 286 " (cutoff:3.500A) Proline residue: A 291 - end of helix Processing helix chain 'A' and resid 301 through 305 Processing helix chain 'A' and resid 309 through 333 Proline residue: A 315 - end of helix Processing helix chain 'A' and resid 342 through 380 Processing helix chain 'A' and resid 453 through 478 removed outlier: 4.061A pdb=" N ILE A 461 " --> pdb=" O LYS A 457 " (cutoff:3.500A) Proline residue: A 464 - end of helix removed outlier: 3.561A pdb=" N SER A 476 " --> pdb=" O LEU A 472 " (cutoff:3.500A) Processing helix chain 'B' and resid 80 through 84 removed outlier: 3.524A pdb=" N HIS B 84 " --> pdb=" O ILE B 81 " (cutoff:3.500A) Processing helix chain 'B' and resid 131 through 134 Processing helix chain 'B' and resid 147 through 152 removed outlier: 3.579A pdb=" N VAL B 150 " --> pdb=" O GLY B 147 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N LYS B 151 " --> pdb=" O ARG B 148 " (cutoff:3.500A) Processing helix chain 'B' and resid 232 through 235 Processing helix chain 'B' and resid 281 through 288 Processing helix chain 'B' and resid 288 through 300 removed outlier: 3.609A pdb=" N ALA B 292 " --> pdb=" O THR B 288 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N TRP B 300 " --> pdb=" O VAL B 296 " (cutoff:3.500A) Processing helix chain 'B' and resid 301 through 305 Processing helix chain 'B' and resid 309 through 333 Proline residue: B 315 - end of helix Processing helix chain 'B' and resid 342 through 380 Processing helix chain 'B' and resid 453 through 478 removed outlier: 4.038A pdb=" N ILE B 461 " --> pdb=" O LYS B 457 " (cutoff:3.500A) Proline residue: B 464 - end of helix Processing helix chain 'C' and resid 80 through 84 removed outlier: 3.705A pdb=" N HIS C 84 " --> pdb=" O ILE C 81 " (cutoff:3.500A) Processing helix chain 'C' and resid 131 through 134 removed outlier: 3.562A pdb=" N SER C 134 " --> pdb=" O GLU C 131 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 131 through 134' Processing helix chain 'C' and resid 147 through 153 removed outlier: 3.613A pdb=" N LYS C 151 " --> pdb=" O ARG C 148 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ILE C 153 " --> pdb=" O VAL C 150 " (cutoff:3.500A) Processing helix chain 'C' and resid 232 through 235 Processing helix chain 'C' and resid 281 through 288 Processing helix chain 'C' and resid 288 through 300 removed outlier: 3.629A pdb=" N ALA C 292 " --> pdb=" O THR C 288 " (cutoff:3.500A) Processing helix chain 'C' and resid 301 through 305 Processing helix chain 'C' and resid 309 through 333 Proline residue: C 315 - end of helix Processing helix chain 'C' and resid 342 through 380 Processing helix chain 'C' and resid 453 through 478 removed outlier: 4.107A pdb=" N ILE C 461 " --> pdb=" O LYS C 457 " (cutoff:3.500A) Proline residue: C 464 - end of helix Processing helix chain 'D' and resid 131 through 134 removed outlier: 3.515A pdb=" N SER D 134 " --> pdb=" O GLU D 131 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 131 through 134' Processing helix chain 'D' and resid 147 through 153 removed outlier: 3.764A pdb=" N LYS D 151 " --> pdb=" O ARG D 148 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ILE D 153 " --> pdb=" O VAL D 150 " (cutoff:3.500A) Processing helix chain 'D' and resid 232 through 235 Processing helix chain 'D' and resid 281 through 300 removed outlier: 4.384A pdb=" N PHE D 290 " --> pdb=" O LEU D 286 " (cutoff:3.500A) Proline residue: D 291 - end of helix removed outlier: 3.582A pdb=" N TRP D 300 " --> pdb=" O VAL D 296 " (cutoff:3.500A) Processing helix chain 'D' and resid 301 through 305 Processing helix chain 'D' and resid 309 through 333 Proline residue: D 315 - end of helix Processing helix chain 'D' and resid 342 through 380 Processing helix chain 'D' and resid 453 through 478 removed outlier: 4.199A pdb=" N ILE D 461 " --> pdb=" O LYS D 457 " (cutoff:3.500A) Proline residue: D 464 - end of helix Processing helix chain 'E' and resid 80 through 84 removed outlier: 3.701A pdb=" N HIS E 84 " --> pdb=" O ILE E 81 " (cutoff:3.500A) Processing helix chain 'E' and resid 131 through 134 Processing helix chain 'E' and resid 147 through 152 removed outlier: 3.530A pdb=" N VAL E 150 " --> pdb=" O GLY E 147 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N LYS E 151 " --> pdb=" O ARG E 148 " (cutoff:3.500A) Processing helix chain 'E' and resid 232 through 235 Processing helix chain 'E' and resid 281 through 300 removed outlier: 4.289A pdb=" N PHE E 290 " --> pdb=" O LEU E 286 " (cutoff:3.500A) Proline residue: E 291 - end of helix removed outlier: 3.540A pdb=" N TRP E 300 " --> pdb=" O VAL E 296 " (cutoff:3.500A) Processing helix chain 'E' and resid 301 through 305 Processing helix chain 'E' and resid 309 through 333 Proline residue: E 315 - end of helix Processing helix chain 'E' and resid 342 through 380 Processing helix chain 'E' and resid 453 through 478 removed outlier: 4.329A pdb=" N ILE E 461 " --> pdb=" O LYS E 457 " (cutoff:3.500A) Proline residue: E 464 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 143 through 145 removed outlier: 4.479A pdb=" N LEU A 178 " --> pdb=" O PHE A 145 " (cutoff:3.500A) removed outlier: 7.088A pdb=" N ASP A 117 " --> pdb=" O SER A 110 " (cutoff:3.500A) removed outlier: 7.113A pdb=" N SER A 110 " --> pdb=" O ASP A 117 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N THR A 119 " --> pdb=" O LEU A 108 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N LEU A 108 " --> pdb=" O THR A 119 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N THR A 121 " --> pdb=" O GLU A 106 " (cutoff:3.500A) removed outlier: 5.098A pdb=" N LYS A 129 " --> pdb=" O PRO A 98 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 163 through 168 removed outlier: 7.060A pdb=" N THR A 195 " --> pdb=" O LYS A 164 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N SER A 166 " --> pdb=" O THR A 193 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N THR A 193 " --> pdb=" O SER A 166 " (cutoff:3.500A) removed outlier: 4.954A pdb=" N ILE A 168 " --> pdb=" O ARG A 191 " (cutoff:3.500A) removed outlier: 7.842A pdb=" N ARG A 191 " --> pdb=" O ILE A 168 " (cutoff:3.500A) removed outlier: 7.088A pdb=" N ASP A 117 " --> pdb=" O SER A 110 " (cutoff:3.500A) removed outlier: 7.113A pdb=" N SER A 110 " --> pdb=" O ASP A 117 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N THR A 119 " --> pdb=" O LEU A 108 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N LEU A 108 " --> pdb=" O THR A 119 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N THR A 121 " --> pdb=" O GLU A 106 " (cutoff:3.500A) removed outlier: 5.098A pdb=" N LYS A 129 " --> pdb=" O PRO A 98 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 158 through 161 removed outlier: 4.662A pdb=" N GLU A 215 " --> pdb=" O VAL A 161 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N SER A 218 " --> pdb=" O ASN A 269 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N ASN A 269 " --> pdb=" O SER A 218 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N THR A 276 " --> pdb=" O GLU A 252 " (cutoff:3.500A) removed outlier: 5.598A pdb=" N GLU A 252 " --> pdb=" O THR A 276 " (cutoff:3.500A) removed outlier: 7.280A pdb=" N ARG A 278 " --> pdb=" O ILE A 250 " (cutoff:3.500A) removed outlier: 5.622A pdb=" N ILE A 250 " --> pdb=" O ARG A 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 143 through 145 removed outlier: 4.644A pdb=" N LEU B 178 " --> pdb=" O PHE B 145 " (cutoff:3.500A) removed outlier: 7.076A pdb=" N ASP B 117 " --> pdb=" O SER B 110 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N SER B 110 " --> pdb=" O ASP B 117 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N THR B 119 " --> pdb=" O LEU B 108 " (cutoff:3.500A) removed outlier: 4.732A pdb=" N LEU B 108 " --> pdb=" O THR B 119 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N THR B 121 " --> pdb=" O GLU B 106 " (cutoff:3.500A) removed outlier: 5.099A pdb=" N LYS B 129 " --> pdb=" O PRO B 98 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 163 through 168 removed outlier: 6.922A pdb=" N THR B 195 " --> pdb=" O LYS B 164 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N SER B 166 " --> pdb=" O THR B 193 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N THR B 193 " --> pdb=" O SER B 166 " (cutoff:3.500A) removed outlier: 5.017A pdb=" N ILE B 168 " --> pdb=" O ARG B 191 " (cutoff:3.500A) removed outlier: 7.818A pdb=" N ARG B 191 " --> pdb=" O ILE B 168 " (cutoff:3.500A) removed outlier: 7.076A pdb=" N ASP B 117 " --> pdb=" O SER B 110 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N SER B 110 " --> pdb=" O ASP B 117 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N THR B 119 " --> pdb=" O LEU B 108 " (cutoff:3.500A) removed outlier: 4.732A pdb=" N LEU B 108 " --> pdb=" O THR B 119 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N THR B 121 " --> pdb=" O GLU B 106 " (cutoff:3.500A) removed outlier: 5.099A pdb=" N LYS B 129 " --> pdb=" O PRO B 98 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 158 through 161 removed outlier: 4.771A pdb=" N GLU B 215 " --> pdb=" O VAL B 161 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N SER B 218 " --> pdb=" O ASN B 269 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N ASN B 269 " --> pdb=" O SER B 218 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N THR B 276 " --> pdb=" O GLU B 252 " (cutoff:3.500A) removed outlier: 5.414A pdb=" N GLU B 252 " --> pdb=" O THR B 276 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N ARG B 278 " --> pdb=" O ILE B 250 " (cutoff:3.500A) removed outlier: 5.523A pdb=" N ILE B 250 " --> pdb=" O ARG B 278 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 143 through 145 removed outlier: 4.460A pdb=" N LEU C 178 " --> pdb=" O PHE C 145 " (cutoff:3.500A) removed outlier: 7.051A pdb=" N ASP C 117 " --> pdb=" O SER C 110 " (cutoff:3.500A) removed outlier: 7.055A pdb=" N SER C 110 " --> pdb=" O ASP C 117 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N THR C 119 " --> pdb=" O LEU C 108 " (cutoff:3.500A) removed outlier: 4.810A pdb=" N LEU C 108 " --> pdb=" O THR C 119 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N THR C 121 " --> pdb=" O GLU C 106 " (cutoff:3.500A) removed outlier: 5.106A pdb=" N LYS C 129 " --> pdb=" O PRO C 98 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 163 through 168 removed outlier: 6.976A pdb=" N THR C 195 " --> pdb=" O LYS C 164 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N SER C 166 " --> pdb=" O THR C 193 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N THR C 193 " --> pdb=" O SER C 166 " (cutoff:3.500A) removed outlier: 4.949A pdb=" N ILE C 168 " --> pdb=" O ARG C 191 " (cutoff:3.500A) removed outlier: 7.820A pdb=" N ARG C 191 " --> pdb=" O ILE C 168 " (cutoff:3.500A) removed outlier: 7.051A pdb=" N ASP C 117 " --> pdb=" O SER C 110 " (cutoff:3.500A) removed outlier: 7.055A pdb=" N SER C 110 " --> pdb=" O ASP C 117 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N THR C 119 " --> pdb=" O LEU C 108 " (cutoff:3.500A) removed outlier: 4.810A pdb=" N LEU C 108 " --> pdb=" O THR C 119 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N THR C 121 " --> pdb=" O GLU C 106 " (cutoff:3.500A) removed outlier: 5.106A pdb=" N LYS C 129 " --> pdb=" O PRO C 98 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 158 through 161 removed outlier: 4.669A pdb=" N GLU C 215 " --> pdb=" O VAL C 161 " (cutoff:3.500A) removed outlier: 4.982A pdb=" N SER C 218 " --> pdb=" O ASN C 269 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N ASN C 269 " --> pdb=" O SER C 218 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N THR C 276 " --> pdb=" O GLU C 252 " (cutoff:3.500A) removed outlier: 5.416A pdb=" N GLU C 252 " --> pdb=" O THR C 276 " (cutoff:3.500A) removed outlier: 7.185A pdb=" N ARG C 278 " --> pdb=" O ILE C 250 " (cutoff:3.500A) removed outlier: 5.551A pdb=" N ILE C 250 " --> pdb=" O ARG C 278 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 143 through 145 removed outlier: 4.497A pdb=" N LEU D 178 " --> pdb=" O PHE D 145 " (cutoff:3.500A) removed outlier: 7.073A pdb=" N ASP D 117 " --> pdb=" O SER D 110 " (cutoff:3.500A) removed outlier: 7.062A pdb=" N SER D 110 " --> pdb=" O ASP D 117 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N THR D 119 " --> pdb=" O LEU D 108 " (cutoff:3.500A) removed outlier: 4.770A pdb=" N LEU D 108 " --> pdb=" O THR D 119 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N THR D 121 " --> pdb=" O GLU D 106 " (cutoff:3.500A) removed outlier: 5.221A pdb=" N LYS D 129 " --> pdb=" O PRO D 98 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 163 through 168 removed outlier: 6.972A pdb=" N THR D 195 " --> pdb=" O LYS D 164 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N SER D 166 " --> pdb=" O THR D 193 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N THR D 193 " --> pdb=" O SER D 166 " (cutoff:3.500A) removed outlier: 4.944A pdb=" N ILE D 168 " --> pdb=" O ARG D 191 " (cutoff:3.500A) removed outlier: 7.766A pdb=" N ARG D 191 " --> pdb=" O ILE D 168 " (cutoff:3.500A) removed outlier: 7.073A pdb=" N ASP D 117 " --> pdb=" O SER D 110 " (cutoff:3.500A) removed outlier: 7.062A pdb=" N SER D 110 " --> pdb=" O ASP D 117 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N THR D 119 " --> pdb=" O LEU D 108 " (cutoff:3.500A) removed outlier: 4.770A pdb=" N LEU D 108 " --> pdb=" O THR D 119 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N THR D 121 " --> pdb=" O GLU D 106 " (cutoff:3.500A) removed outlier: 5.221A pdb=" N LYS D 129 " --> pdb=" O PRO D 98 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 158 through 161 removed outlier: 4.725A pdb=" N GLU D 215 " --> pdb=" O VAL D 161 " (cutoff:3.500A) removed outlier: 4.777A pdb=" N SER D 218 " --> pdb=" O ASN D 269 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N ASN D 269 " --> pdb=" O SER D 218 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N THR D 276 " --> pdb=" O GLU D 252 " (cutoff:3.500A) removed outlier: 5.495A pdb=" N GLU D 252 " --> pdb=" O THR D 276 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N ARG D 278 " --> pdb=" O ILE D 250 " (cutoff:3.500A) removed outlier: 5.477A pdb=" N ILE D 250 " --> pdb=" O ARG D 278 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 143 through 144 removed outlier: 7.062A pdb=" N ASP E 117 " --> pdb=" O SER E 110 " (cutoff:3.500A) removed outlier: 7.066A pdb=" N SER E 110 " --> pdb=" O ASP E 117 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N THR E 119 " --> pdb=" O LEU E 108 " (cutoff:3.500A) removed outlier: 4.732A pdb=" N LEU E 108 " --> pdb=" O THR E 119 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N THR E 121 " --> pdb=" O GLU E 106 " (cutoff:3.500A) removed outlier: 5.202A pdb=" N LYS E 129 " --> pdb=" O PRO E 98 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 163 through 168 removed outlier: 6.808A pdb=" N SER E 163 " --> pdb=" O MET E 197 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N MET E 197 " --> pdb=" O SER E 163 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ARG E 165 " --> pdb=" O THR E 195 " (cutoff:3.500A) removed outlier: 7.062A pdb=" N ASP E 117 " --> pdb=" O SER E 110 " (cutoff:3.500A) removed outlier: 7.066A pdb=" N SER E 110 " --> pdb=" O ASP E 117 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N THR E 119 " --> pdb=" O LEU E 108 " (cutoff:3.500A) removed outlier: 4.732A pdb=" N LEU E 108 " --> pdb=" O THR E 119 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N THR E 121 " --> pdb=" O GLU E 106 " (cutoff:3.500A) removed outlier: 5.202A pdb=" N LYS E 129 " --> pdb=" O PRO E 98 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 158 through 161 removed outlier: 4.743A pdb=" N GLU E 215 " --> pdb=" O VAL E 161 " (cutoff:3.500A) removed outlier: 4.961A pdb=" N SER E 218 " --> pdb=" O ASN E 269 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N ASN E 269 " --> pdb=" O SER E 218 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N THR E 276 " --> pdb=" O GLU E 252 " (cutoff:3.500A) removed outlier: 5.361A pdb=" N GLU E 252 " --> pdb=" O THR E 276 " (cutoff:3.500A) removed outlier: 7.096A pdb=" N ARG E 278 " --> pdb=" O ILE E 250 " (cutoff:3.500A) removed outlier: 5.516A pdb=" N ILE E 250 " --> pdb=" O ARG E 278 " (cutoff:3.500A) 801 hydrogen bonds defined for protein. 2295 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.55 Time building geometry restraints manager: 3.82 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: 6.340 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.530 Check model and map are aligned: 0.090 Set scattering table: 0.110 Process input model: 33.130 Find NCS groups from input model: 0.750 Set up NCS constraints: 0.060 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:13.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 14116 Z= 0.177 Angle : 0.592 9.179 19165 Z= 0.306 Chirality : 0.056 0.746 2197 Planarity : 0.004 0.031 2334 Dihedral : 10.525 87.844 5207 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.86 % Favored : 99.14 % Rotamer: Outliers : 0.61 % Allowed : 3.97 % Favored : 95.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.32 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.11 (0.21), residues: 1630 helix: 2.15 (0.22), residues: 575 sheet: 1.44 (0.24), residues: 455 loop : 0.75 (0.24), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 349 HIS 0.002 0.001 HIS E 254 PHE 0.017 0.001 PHE E 290 TYR 0.022 0.001 TYR C 362 ARG 0.006 0.001 ARG C 191 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 358 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 349 time to evaluate : 1.459 Fit side-chains revert: symmetry clash REVERT: A 143 MET cc_start: 0.7357 (mmm) cc_final: 0.7109 (mmt) REVERT: B 82 ASP cc_start: 0.6502 (m-30) cc_final: 0.6152 (p0) REVERT: B 83 ASP cc_start: 0.7157 (m-30) cc_final: 0.6918 (m-30) REVERT: B 116 MET cc_start: 0.8120 (mtt) cc_final: 0.7861 (mtm) REVERT: B 117 ASP cc_start: 0.7805 (p0) cc_final: 0.7514 (p0) REVERT: B 223 GLU cc_start: 0.7577 (pt0) cc_final: 0.7304 (pp20) REVERT: B 258 LYS cc_start: 0.8000 (tttt) cc_final: 0.7755 (ttpt) REVERT: C 143 MET cc_start: 0.7568 (mmm) cc_final: 0.7156 (mmp) REVERT: D 304 TRP cc_start: 0.8146 (m100) cc_final: 0.7926 (m-90) REVERT: D 326 THR cc_start: 0.8469 (m) cc_final: 0.8156 (p) REVERT: D 337 ARG cc_start: 0.6283 (mtt180) cc_final: 0.5930 (mtp-110) REVERT: E 102 ASP cc_start: 0.7733 (t0) cc_final: 0.7382 (t0) REVERT: E 232 LYS cc_start: 0.7543 (mttt) cc_final: 0.7038 (mtpp) REVERT: E 295 MET cc_start: 0.8136 (mmm) cc_final: 0.7390 (mmt) outliers start: 9 outliers final: 6 residues processed: 356 average time/residue: 1.3929 time to fit residues: 537.5834 Evaluate side-chains 265 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 259 time to evaluate : 1.525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain B residue 234 ASN Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain D residue 319 THR Chi-restraints excluded: chain E residue 234 ASN Chi-restraints excluded: chain E residue 338 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 139 optimal weight: 0.0970 chunk 125 optimal weight: 4.9990 chunk 69 optimal weight: 5.9990 chunk 42 optimal weight: 6.9990 chunk 84 optimal weight: 2.9990 chunk 66 optimal weight: 5.9990 chunk 129 optimal weight: 7.9990 chunk 50 optimal weight: 4.9990 chunk 78 optimal weight: 0.9990 chunk 96 optimal weight: 2.9990 chunk 149 optimal weight: 0.8980 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 199 ASN A 210 GLN A 287 GLN B 210 GLN B 247 GLN ** C 254 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 269 ASN D 251 GLN D 287 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.129287 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.107687 restraints weight = 16002.152| |-----------------------------------------------------------------------------| r_work (start): 0.3070 rms_B_bonded: 1.71 r_work: 0.2972 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.2857 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.2857 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8421 moved from start: 0.1674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 14116 Z= 0.280 Angle : 0.671 9.494 19165 Z= 0.358 Chirality : 0.054 0.990 2197 Planarity : 0.005 0.039 2334 Dihedral : 7.574 76.945 2175 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 3.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.98 % Favored : 99.02 % Rotamer: Outliers : 3.77 % Allowed : 11.99 % Favored : 84.24 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.32 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.46 (0.20), residues: 1630 helix: 1.71 (0.22), residues: 610 sheet: 1.04 (0.23), residues: 465 loop : 0.19 (0.24), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 349 HIS 0.005 0.001 HIS E 126 PHE 0.019 0.002 PHE A 356 TYR 0.023 0.002 TYR E 362 ARG 0.003 0.000 ARG A 270 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 241 time to evaluate : 1.485 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 183 ASP cc_start: 0.7810 (OUTLIER) cc_final: 0.7468 (p0) REVERT: A 269 ASN cc_start: 0.8135 (OUTLIER) cc_final: 0.7735 (m-40) REVERT: B 82 ASP cc_start: 0.6775 (m-30) cc_final: 0.6201 (p0) REVERT: B 116 MET cc_start: 0.8392 (mtt) cc_final: 0.8036 (mtm) REVERT: B 117 ASP cc_start: 0.8250 (p0) cc_final: 0.7980 (p0) REVERT: B 223 GLU cc_start: 0.8426 (pt0) cc_final: 0.7868 (pp20) REVERT: B 462 ILE cc_start: 0.8075 (OUTLIER) cc_final: 0.7875 (mp) REVERT: C 143 MET cc_start: 0.8010 (mmm) cc_final: 0.7720 (mmp) REVERT: D 113 GLU cc_start: 0.8043 (mt-10) cc_final: 0.7828 (mp0) REVERT: D 148 ARG cc_start: 0.7433 (ptp-170) cc_final: 0.7112 (ptt180) REVERT: D 234 ASN cc_start: 0.6837 (OUTLIER) cc_final: 0.6185 (t160) REVERT: D 241 GLU cc_start: 0.7390 (mm-30) cc_final: 0.7093 (tp30) REVERT: D 287 GLN cc_start: 0.7625 (OUTLIER) cc_final: 0.6959 (mp-120) REVERT: D 326 THR cc_start: 0.8522 (m) cc_final: 0.8179 (p) REVERT: E 232 LYS cc_start: 0.7419 (mttt) cc_final: 0.6803 (mtpp) REVERT: E 295 MET cc_start: 0.8414 (mmm) cc_final: 0.8127 (mmp) outliers start: 56 outliers final: 29 residues processed: 274 average time/residue: 1.3420 time to fit residues: 401.5958 Evaluate side-chains 267 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 233 time to evaluate : 1.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 174 ASP Chi-restraints excluded: chain A residue 183 ASP Chi-restraints excluded: chain A residue 234 ASN Chi-restraints excluded: chain A residue 246 SER Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 326 THR Chi-restraints excluded: chain A residue 334 SER Chi-restraints excluded: chain A residue 469 LEU Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 235 ASP Chi-restraints excluded: chain B residue 256 THR Chi-restraints excluded: chain B residue 371 VAL Chi-restraints excluded: chain 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 325 SER Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain C residue 370 THR Chi-restraints excluded: chain C residue 371 VAL Chi-restraints excluded: chain D residue 151 LYS Chi-restraints excluded: chain D residue 234 ASN Chi-restraints excluded: chain D residue 256 THR Chi-restraints excluded: chain D residue 287 GLN Chi-restraints excluded: chain D residue 288 THR Chi-restraints excluded: chain D residue 371 VAL Chi-restraints excluded: chain E residue 108 LEU Chi-restraints excluded: chain E residue 114 VAL Chi-restraints excluded: chain E residue 244 SER Chi-restraints excluded: chain E residue 338 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 18 optimal weight: 0.5980 chunk 94 optimal weight: 2.9990 chunk 132 optimal weight: 5.9990 chunk 157 optimal weight: 9.9990 chunk 6 optimal weight: 6.9990 chunk 20 optimal weight: 0.6980 chunk 86 optimal weight: 4.9990 chunk 159 optimal weight: 0.9980 chunk 75 optimal weight: 0.8980 chunk 51 optimal weight: 0.3980 chunk 62 optimal weight: 5.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 247 GLN C 210 GLN D 287 GLN E 287 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.129507 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.106901 restraints weight = 16134.280| |-----------------------------------------------------------------------------| r_work (start): 0.3101 rms_B_bonded: 1.78 r_work: 0.3006 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.2890 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.2890 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8380 moved from start: 0.1921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 14116 Z= 0.178 Angle : 0.559 8.108 19165 Z= 0.298 Chirality : 0.044 0.421 2197 Planarity : 0.004 0.040 2334 Dihedral : 6.871 77.065 2170 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 2.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.92 % Favored : 99.08 % Rotamer: Outliers : 2.96 % Allowed : 14.14 % Favored : 82.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.32 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.62 (0.21), residues: 1630 helix: 1.95 (0.22), residues: 610 sheet: 1.18 (0.24), residues: 435 loop : 0.14 (0.23), residues: 585 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 349 HIS 0.004 0.001 HIS C 254 PHE 0.017 0.001 PHE E 356 TYR 0.021 0.002 TYR B 362 ARG 0.003 0.000 ARG E 308 *********************** 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 292 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 248 time to evaluate : 1.716 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 183 ASP cc_start: 0.7751 (OUTLIER) cc_final: 0.7432 (p0) REVERT: A 235 ASP cc_start: 0.6992 (p0) cc_final: 0.6423 (t70) REVERT: A 269 ASN cc_start: 0.8069 (OUTLIER) cc_final: 0.7642 (m-40) REVERT: B 82 ASP cc_start: 0.6762 (m-30) cc_final: 0.6216 (p0) REVERT: B 108 LEU cc_start: 0.8818 (OUTLIER) cc_final: 0.8481 (mt) REVERT: B 116 MET cc_start: 0.8351 (mtt) cc_final: 0.8058 (mtm) REVERT: B 117 ASP cc_start: 0.8141 (p0) cc_final: 0.7918 (p0) REVERT: B 223 GLU cc_start: 0.8470 (pt0) cc_final: 0.7881 (pp20) REVERT: C 108 LEU cc_start: 0.8846 (OUTLIER) cc_final: 0.8392 (tt) REVERT: C 143 MET cc_start: 0.7904 (mmm) cc_final: 0.7687 (mmp) REVERT: D 148 ARG cc_start: 0.7416 (ptp-170) cc_final: 0.7050 (ptt180) REVERT: D 241 GLU cc_start: 0.7386 (mm-30) cc_final: 0.7149 (tp30) REVERT: D 304 TRP cc_start: 0.8129 (m100) cc_final: 0.7867 (m-90) REVERT: D 326 THR cc_start: 0.8486 (m) cc_final: 0.8095 (p) REVERT: E 197 MET cc_start: 0.8082 (ptm) cc_final: 0.7816 (ptt) REVERT: E 232 LYS cc_start: 0.7322 (mttt) cc_final: 0.6716 (mtpp) REVERT: E 295 MET cc_start: 0.8413 (mmm) cc_final: 0.8085 (mmp) outliers start: 44 outliers final: 25 residues processed: 274 average time/residue: 1.3421 time to fit residues: 401.5843 Evaluate side-chains 266 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 237 time to evaluate : 1.829 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 LEU 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 344 VAL Chi-restraints excluded: chain A residue 469 LEU Chi-restraints excluded: chain B residue 108 LEU 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 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 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 338 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 21 optimal weight: 0.9980 chunk 144 optimal weight: 2.9990 chunk 44 optimal weight: 0.9980 chunk 114 optimal weight: 1.9990 chunk 69 optimal weight: 2.9990 chunk 65 optimal weight: 3.9990 chunk 98 optimal weight: 3.9990 chunk 150 optimal weight: 0.0870 chunk 132 optimal weight: 9.9990 chunk 53 optimal weight: 0.9980 chunk 25 optimal weight: 0.0010 overall best weight: 0.6164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 199 ASN A 210 GLN A 287 GLN B 210 GLN B 247 GLN B 332 ASN ** E 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.131322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.108654 restraints weight = 16050.699| |-----------------------------------------------------------------------------| r_work (start): 0.3121 rms_B_bonded: 1.77 r_work: 0.3028 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.2911 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.2911 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8358 moved from start: 0.2182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 14116 Z= 0.163 Angle : 0.525 8.984 19165 Z= 0.280 Chirality : 0.043 0.419 2197 Planarity : 0.004 0.041 2334 Dihedral : 6.585 75.941 2170 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 2.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.80 % Favored : 99.20 % Rotamer: Outliers : 4.24 % Allowed : 14.14 % Favored : 81.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.32 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.72 (0.21), residues: 1630 helix: 2.12 (0.22), residues: 610 sheet: 1.23 (0.24), residues: 435 loop : 0.08 (0.24), residues: 585 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 349 HIS 0.004 0.001 HIS C 254 PHE 0.017 0.001 PHE E 356 TYR 0.023 0.002 TYR B 362 ARG 0.004 0.000 ARG E 308 *********************** 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 314 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 251 time to evaluate : 1.548 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 235 ASP cc_start: 0.6994 (p0) cc_final: 0.6279 (t70) REVERT: A 269 ASN cc_start: 0.8040 (OUTLIER) cc_final: 0.7518 (m-40) REVERT: B 82 ASP cc_start: 0.6785 (m-30) cc_final: 0.6242 (p0) REVERT: B 108 LEU cc_start: 0.8734 (OUTLIER) cc_final: 0.8430 (mt) REVERT: B 116 MET cc_start: 0.8340 (mtt) cc_final: 0.8005 (mtm) REVERT: B 457 LYS cc_start: 0.7295 (OUTLIER) cc_final: 0.6727 (pttt) REVERT: C 151 LYS cc_start: 0.8399 (OUTLIER) cc_final: 0.8055 (mmpt) REVERT: C 181 GLN cc_start: 0.8805 (OUTLIER) cc_final: 0.8598 (mt0) REVERT: C 235 ASP cc_start: 0.7199 (m-30) cc_final: 0.6854 (t0) REVERT: C 258 LYS cc_start: 0.8345 (OUTLIER) cc_final: 0.8132 (tttp) REVERT: D 148 ARG cc_start: 0.7392 (ptp-170) cc_final: 0.6964 (ptt180) REVERT: D 234 ASN cc_start: 0.6702 (OUTLIER) cc_final: 0.6427 (p0) REVERT: D 241 GLU cc_start: 0.7375 (mm-30) cc_final: 0.7146 (tp30) REVERT: D 287 GLN cc_start: 0.7664 (OUTLIER) cc_final: 0.6846 (mp10) REVERT: D 326 THR cc_start: 0.8478 (m) cc_final: 0.8112 (p) REVERT: D 337 ARG cc_start: 0.6723 (mtt180) cc_final: 0.5940 (mtp-110) REVERT: D 457 LYS cc_start: 0.6911 (tttp) cc_final: 0.6161 (ttmm) REVERT: E 197 MET cc_start: 0.8054 (ptm) cc_final: 0.7794 (ptt) REVERT: E 232 LYS cc_start: 0.7363 (mttt) cc_final: 0.6795 (mtpp) REVERT: E 295 MET cc_start: 0.8413 (mmm) cc_final: 0.8056 (mmp) outliers start: 63 outliers final: 30 residues processed: 289 average time/residue: 1.3091 time to fit residues: 413.6372 Evaluate side-chains 267 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 229 time to evaluate : 1.696 ------------------------------------------------------------------------------- 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 A residue 326 THR Chi-restraints excluded: chain A residue 469 LEU Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 235 ASP Chi-restraints excluded: chain B residue 256 THR Chi-restraints excluded: chain B residue 263 SER Chi-restraints excluded: chain B residue 360 LEU Chi-restraints excluded: chain B residue 457 LYS 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 122 LEU Chi-restraints excluded: chain C residue 151 LYS Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 181 GLN 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 338 VAL Chi-restraints excluded: chain C residue 370 THR Chi-restraints excluded: chain D residue 102 ASP Chi-restraints excluded: chain D residue 113 GLU 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 287 GLN 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 140 optimal weight: 3.9990 chunk 101 optimal weight: 0.2980 chunk 155 optimal weight: 0.0060 chunk 87 optimal weight: 0.8980 chunk 8 optimal weight: 2.9990 chunk 111 optimal weight: 0.3980 chunk 39 optimal weight: 2.9990 chunk 0 optimal weight: 7.9990 chunk 43 optimal weight: 0.5980 chunk 17 optimal weight: 0.7980 chunk 90 optimal weight: 1.9990 overall best weight: 0.4196 ------------------------------------------------------------------------------- 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 B 247 GLN C 210 GLN D 287 GLN E 287 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.132757 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.110071 restraints weight = 16169.999| |-----------------------------------------------------------------------------| r_work (start): 0.3139 rms_B_bonded: 1.77 r_work: 0.3049 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.2933 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.2933 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8330 moved from start: 0.2421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 14116 Z= 0.148 Angle : 0.519 9.218 19165 Z= 0.273 Chirality : 0.049 1.008 2197 Planarity : 0.004 0.040 2334 Dihedral : 6.653 74.592 2168 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 2.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.92 % Favored : 99.08 % Rotamer: Outliers : 3.37 % Allowed : 15.56 % Favored : 81.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.32 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.87 (0.21), residues: 1630 helix: 2.23 (0.22), residues: 610 sheet: 1.29 (0.24), residues: 455 loop : 0.16 (0.25), residues: 565 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 349 HIS 0.003 0.001 HIS C 254 PHE 0.019 0.001 PHE E 356 TYR 0.019 0.001 TYR B 362 ARG 0.004 0.000 ARG E 308 *********************** 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 292 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 242 time to evaluate : 1.665 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 235 ASP cc_start: 0.6970 (p0) cc_final: 0.6211 (t70) REVERT: A 269 ASN cc_start: 0.7958 (OUTLIER) cc_final: 0.7441 (m-40) REVERT: B 82 ASP cc_start: 0.6760 (m-30) cc_final: 0.6232 (p0) REVERT: B 108 LEU cc_start: 0.8671 (OUTLIER) cc_final: 0.8403 (mt) REVERT: B 116 MET cc_start: 0.8286 (mtt) cc_final: 0.7996 (mtm) REVERT: B 197 MET cc_start: 0.8170 (ptt) cc_final: 0.7861 (ppp) REVERT: B 457 LYS cc_start: 0.7139 (OUTLIER) cc_final: 0.6577 (pttt) REVERT: C 151 LYS cc_start: 0.8356 (OUTLIER) cc_final: 0.8034 (mmpt) REVERT: C 181 GLN cc_start: 0.8792 (OUTLIER) cc_final: 0.8584 (mt0) REVERT: C 235 ASP cc_start: 0.7175 (m-30) cc_final: 0.6833 (t0) REVERT: D 148 ARG cc_start: 0.7328 (ptp-170) cc_final: 0.6911 (ptt180) REVERT: D 234 ASN cc_start: 0.6648 (OUTLIER) cc_final: 0.6214 (t0) REVERT: D 241 GLU cc_start: 0.7345 (mm-30) cc_final: 0.7123 (tp30) REVERT: D 326 THR cc_start: 0.8379 (m) cc_final: 0.8009 (p) REVERT: D 337 ARG cc_start: 0.6728 (mtt180) cc_final: 0.5905 (mtp-110) REVERT: D 457 LYS cc_start: 0.6833 (tttp) cc_final: 0.6151 (ttmm) REVERT: E 197 MET cc_start: 0.8026 (ptm) cc_final: 0.7817 (ptt) REVERT: E 232 LYS cc_start: 0.7312 (mttt) cc_final: 0.6708 (mtpp) REVERT: E 295 MET cc_start: 0.8370 (mmm) cc_final: 0.8066 (mmp) outliers start: 50 outliers final: 24 residues processed: 269 average time/residue: 1.2959 time to fit residues: 380.8548 Evaluate side-chains 257 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 227 time to evaluate : 1.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 ASN 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 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 235 ASP Chi-restraints excluded: chain B residue 256 THR Chi-restraints excluded: chain B residue 263 SER 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 151 LYS Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 181 GLN 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 287 GLN Chi-restraints excluded: chain D residue 288 THR Chi-restraints excluded: chain E residue 108 LEU Chi-restraints excluded: chain E residue 114 VAL Chi-restraints excluded: chain E residue 140 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 96 optimal weight: 0.0770 chunk 133 optimal weight: 0.8980 chunk 47 optimal weight: 3.9990 chunk 28 optimal weight: 4.9990 chunk 147 optimal weight: 3.9990 chunk 62 optimal weight: 6.9990 chunk 104 optimal weight: 3.9990 chunk 122 optimal weight: 0.7980 chunk 13 optimal weight: 10.0000 chunk 48 optimal weight: 3.9990 chunk 143 optimal weight: 6.9990 overall best weight: 1.9542 ------------------------------------------------------------------------------- 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 251 GLN A 287 GLN B 210 GLN B 247 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.125417 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.103516 restraints weight = 16368.917| |-----------------------------------------------------------------------------| r_work (start): 0.3083 rms_B_bonded: 1.67 r_work: 0.2988 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.2872 rms_B_bonded: 3.46 restraints_weight: 0.2500 r_work (final): 0.2872 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8440 moved from start: 0.2321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 14116 Z= 0.318 Angle : 0.664 9.909 19165 Z= 0.355 Chirality : 0.049 0.457 2197 Planarity : 0.005 0.044 2334 Dihedral : 7.479 73.308 2167 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 2.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 4.11 % Allowed : 15.56 % Favored : 80.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.32 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.19 (0.20), residues: 1630 helix: 1.74 (0.22), residues: 605 sheet: 0.78 (0.23), residues: 470 loop : -0.16 (0.24), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 304 HIS 0.008 0.002 HIS C 254 PHE 0.022 0.002 PHE A 356 TYR 0.027 0.002 TYR E 362 ARG 0.004 0.001 ARG E 308 *********************** 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 296 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 235 time to evaluate : 1.478 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 235 ASP cc_start: 0.7336 (p0) cc_final: 0.6614 (t70) REVERT: A 241 GLU cc_start: 0.7351 (pm20) cc_final: 0.7135 (mp0) REVERT: A 269 ASN cc_start: 0.8132 (OUTLIER) cc_final: 0.7746 (m-40) REVERT: B 82 ASP cc_start: 0.6771 (m-30) cc_final: 0.6269 (p0) REVERT: B 108 LEU cc_start: 0.8915 (OUTLIER) cc_final: 0.8535 (mt) REVERT: B 116 MET cc_start: 0.8337 (mtt) cc_final: 0.8050 (mtm) REVERT: B 131 GLU cc_start: 0.7739 (tp30) cc_final: 0.7415 (tp30) REVERT: B 223 GLU cc_start: 0.8437 (pt0) cc_final: 0.7905 (pp20) REVERT: C 151 LYS cc_start: 0.8446 (OUTLIER) cc_final: 0.8041 (mmpt) REVERT: C 235 ASP cc_start: 0.7376 (m-30) cc_final: 0.6972 (t0) REVERT: D 148 ARG cc_start: 0.7483 (ptp-170) cc_final: 0.6965 (ptt180) REVERT: D 234 ASN cc_start: 0.6791 (OUTLIER) cc_final: 0.6324 (t0) REVERT: D 326 THR cc_start: 0.8558 (m) cc_final: 0.8257 (p) REVERT: D 457 LYS cc_start: 0.7011 (tttp) cc_final: 0.6147 (mttm) REVERT: E 116 MET cc_start: 0.8228 (mtm) cc_final: 0.7838 (mtp) REVERT: E 232 LYS cc_start: 0.7572 (mttt) cc_final: 0.7007 (mtpp) REVERT: E 295 MET cc_start: 0.8374 (mmm) cc_final: 0.7988 (mmp) outliers start: 61 outliers final: 35 residues processed: 268 average time/residue: 1.3205 time to fit residues: 385.4514 Evaluate side-chains 266 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 227 time to evaluate : 1.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 140 ASN 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 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 263 SER Chi-restraints excluded: chain B residue 301 VAL Chi-restraints excluded: chain B residue 331 VAL Chi-restraints excluded: chain B residue 360 LEU Chi-restraints excluded: chain B residue 371 VAL Chi-restraints excluded: chain C residue 102 ASP Chi-restraints excluded: chain C residue 122 LEU 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 234 ASN Chi-restraints excluded: chain D residue 256 THR Chi-restraints excluded: chain D residue 257 THR Chi-restraints excluded: chain D residue 288 THR Chi-restraints excluded: chain D residue 370 THR Chi-restraints excluded: chain D residue 371 VAL Chi-restraints excluded: chain E residue 108 LEU Chi-restraints excluded: chain E residue 114 VAL Chi-restraints excluded: chain E residue 140 ASN Chi-restraints excluded: chain E residue 244 SER Chi-restraints excluded: chain E residue 360 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 125 optimal weight: 0.8980 chunk 59 optimal weight: 0.7980 chunk 22 optimal weight: 4.9990 chunk 34 optimal weight: 3.9990 chunk 136 optimal weight: 1.9990 chunk 139 optimal weight: 0.0870 chunk 83 optimal weight: 5.9990 chunk 65 optimal weight: 0.9990 chunk 135 optimal weight: 0.2980 chunk 160 optimal weight: 3.9990 chunk 20 optimal weight: 2.9990 overall best weight: 0.6160 ------------------------------------------------------------------------------- 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 B 247 GLN D 287 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.130076 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.108201 restraints weight = 16406.810| |-----------------------------------------------------------------------------| r_work (start): 0.3122 rms_B_bonded: 1.67 r_work: 0.3027 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.2913 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.2913 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8372 moved from start: 0.2446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 14116 Z= 0.165 Angle : 0.526 10.166 19165 Z= 0.280 Chirality : 0.044 0.417 2197 Planarity : 0.004 0.042 2334 Dihedral : 7.064 79.061 2167 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 2.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % Rotamer: Outliers : 2.96 % Allowed : 16.90 % Favored : 80.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.32 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.55 (0.21), residues: 1630 helix: 2.09 (0.22), residues: 605 sheet: 1.11 (0.24), residues: 435 loop : -0.11 (0.23), residues: 590 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 349 HIS 0.004 0.001 HIS C 254 PHE 0.018 0.001 PHE E 356 TYR 0.018 0.001 TYR E 362 ARG 0.004 0.000 ARG E 308 *********************** 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 276 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 232 time to evaluate : 1.476 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 235 ASP cc_start: 0.7119 (p0) cc_final: 0.6413 (t70) REVERT: A 269 ASN cc_start: 0.7995 (OUTLIER) cc_final: 0.7512 (m-40) REVERT: A 324 MET cc_start: 0.8847 (tpp) cc_final: 0.8632 (tpt) REVERT: B 82 ASP cc_start: 0.6760 (m-30) cc_final: 0.6277 (p0) REVERT: B 108 LEU cc_start: 0.8744 (OUTLIER) cc_final: 0.8420 (mt) REVERT: B 109 ASP cc_start: 0.7659 (m-30) cc_final: 0.7444 (m-30) REVERT: B 116 MET cc_start: 0.8301 (mtt) cc_final: 0.7965 (mtm) REVERT: B 131 GLU cc_start: 0.7661 (tp30) cc_final: 0.7359 (tp30) REVERT: B 197 MET cc_start: 0.8211 (ptt) cc_final: 0.7806 (ppp) REVERT: B 223 GLU cc_start: 0.8463 (pt0) cc_final: 0.7920 (pp20) REVERT: C 131 GLU cc_start: 0.8178 (mm-30) cc_final: 0.7803 (mm-30) REVERT: C 151 LYS cc_start: 0.8383 (OUTLIER) cc_final: 0.8066 (mmpt) REVERT: C 235 ASP cc_start: 0.7247 (m-30) cc_final: 0.6863 (t0) REVERT: D 148 ARG cc_start: 0.7441 (ptp-170) cc_final: 0.6969 (ptt180) REVERT: D 234 ASN cc_start: 0.6680 (OUTLIER) cc_final: 0.6207 (t0) REVERT: D 326 THR cc_start: 0.8412 (m) cc_final: 0.8047 (p) REVERT: D 457 LYS cc_start: 0.6918 (tttp) cc_final: 0.6163 (mttm) REVERT: E 197 MET cc_start: 0.8105 (ptm) cc_final: 0.7840 (ptt) REVERT: E 232 LYS cc_start: 0.7463 (mttt) cc_final: 0.6856 (mtpp) REVERT: E 295 MET cc_start: 0.8394 (mmm) cc_final: 0.8005 (mmp) outliers start: 44 outliers final: 28 residues processed: 254 average time/residue: 1.3271 time to fit residues: 368.0727 Evaluate side-chains 263 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 231 time to evaluate : 1.506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 ASN 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 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 301 VAL Chi-restraints excluded: chain B residue 331 VAL Chi-restraints excluded: chain B residue 360 LEU Chi-restraints excluded: chain C residue 102 ASP 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 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 173 THR 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 57 optimal weight: 0.7980 chunk 160 optimal weight: 3.9990 chunk 85 optimal weight: 2.9990 chunk 97 optimal weight: 3.9990 chunk 134 optimal weight: 1.9990 chunk 76 optimal weight: 1.9990 chunk 48 optimal weight: 2.9990 chunk 82 optimal weight: 4.9990 chunk 2 optimal weight: 0.9980 chunk 34 optimal weight: 2.9990 chunk 17 optimal weight: 3.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- 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 D 287 GLN E 251 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.125939 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.104233 restraints weight = 16347.899| |-----------------------------------------------------------------------------| r_work (start): 0.3063 rms_B_bonded: 1.65 r_work: 0.2968 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.2853 rms_B_bonded: 3.42 restraints_weight: 0.2500 r_work (final): 0.2853 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8434 moved from start: 0.2408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 14116 Z= 0.288 Angle : 0.633 8.179 19165 Z= 0.338 Chirality : 0.047 0.447 2197 Planarity : 0.005 0.045 2334 Dihedral : 7.337 72.973 2167 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 3.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 3.57 % Allowed : 16.84 % Favored : 79.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.32 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.18 (0.20), residues: 1630 helix: 1.76 (0.22), residues: 605 sheet: 0.79 (0.23), residues: 465 loop : -0.21 (0.24), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 304 HIS 0.007 0.002 HIS C 254 PHE 0.021 0.002 PHE A 356 TYR 0.024 0.002 TYR E 362 ARG 0.004 0.001 ARG E 308 *********************** 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 285 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 232 time to evaluate : 1.464 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 235 ASP cc_start: 0.7354 (p0) cc_final: 0.6691 (t70) REVERT: A 269 ASN cc_start: 0.8114 (OUTLIER) cc_final: 0.7724 (m-40) REVERT: B 82 ASP cc_start: 0.6764 (m-30) cc_final: 0.6312 (p0) REVERT: B 108 LEU cc_start: 0.8881 (OUTLIER) cc_final: 0.8497 (mt) REVERT: B 116 MET cc_start: 0.8316 (mtt) cc_final: 0.7986 (mtm) REVERT: B 131 GLU cc_start: 0.7711 (tp30) cc_final: 0.7376 (tp30) REVERT: B 223 GLU cc_start: 0.8439 (pt0) cc_final: 0.7917 (pp20) REVERT: C 151 LYS cc_start: 0.8438 (OUTLIER) cc_final: 0.8031 (mmpt) REVERT: C 235 ASP cc_start: 0.7375 (m-30) cc_final: 0.6937 (t0) REVERT: D 148 ARG cc_start: 0.7508 (ptp-170) cc_final: 0.6961 (ptt180) REVERT: D 234 ASN cc_start: 0.6647 (OUTLIER) cc_final: 0.6174 (t0) REVERT: D 326 THR cc_start: 0.8546 (m) cc_final: 0.8245 (p) REVERT: D 457 LYS cc_start: 0.7031 (tttp) cc_final: 0.6207 (mttm) REVERT: E 232 LYS cc_start: 0.7597 (mttt) cc_final: 0.7034 (mtpp) REVERT: E 295 MET cc_start: 0.8397 (mmm) cc_final: 0.7999 (mmp) outliers start: 53 outliers final: 36 residues processed: 265 average time/residue: 1.3280 time to fit residues: 383.1306 Evaluate side-chains 264 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 224 time to evaluate : 1.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 ASN 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 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 301 VAL Chi-restraints excluded: chain B residue 331 VAL Chi-restraints excluded: chain B residue 335 MET Chi-restraints excluded: chain B residue 360 LEU Chi-restraints excluded: chain C residue 102 ASP Chi-restraints excluded: chain C residue 122 LEU 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 325 SER Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain C residue 370 THR Chi-restraints excluded: chain C residue 371 VAL Chi-restraints excluded: chain D residue 151 LYS Chi-restraints excluded: chain D residue 161 VAL Chi-restraints excluded: chain D residue 173 THR Chi-restraints excluded: chain D residue 234 ASN 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 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 338 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 116 optimal weight: 4.9990 chunk 136 optimal weight: 0.8980 chunk 80 optimal weight: 0.6980 chunk 77 optimal weight: 0.8980 chunk 59 optimal weight: 0.9990 chunk 133 optimal weight: 0.0670 chunk 107 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 31 optimal weight: 3.9990 chunk 120 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 overall best weight: 0.7120 ------------------------------------------------------------------------------- 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 = 0.3388 r_free = 0.3388 target = 0.128978 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.107279 restraints weight = 16196.075| |-----------------------------------------------------------------------------| r_work (start): 0.3104 rms_B_bonded: 1.64 r_work: 0.3014 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.2898 rms_B_bonded: 3.45 restraints_weight: 0.2500 r_work (final): 0.2898 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8380 moved from start: 0.2483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 14116 Z= 0.171 Angle : 0.538 7.851 19165 Z= 0.289 Chirality : 0.043 0.413 2197 Planarity : 0.004 0.042 2334 Dihedral : 6.889 73.110 2167 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 2.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer: Outliers : 3.03 % Allowed : 17.71 % Favored : 79.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.32 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.45 (0.21), residues: 1630 helix: 2.02 (0.22), residues: 605 sheet: 1.12 (0.24), residues: 430 loop : -0.23 (0.23), residues: 595 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 349 HIS 0.004 0.001 HIS C 254 PHE 0.018 0.001 PHE E 356 TYR 0.019 0.002 TYR B 362 ARG 0.004 0.000 ARG E 308 *********************** 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 273 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 228 time to evaluate : 1.551 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 235 ASP cc_start: 0.7205 (p0) cc_final: 0.6508 (t70) REVERT: A 269 ASN cc_start: 0.8026 (OUTLIER) cc_final: 0.7556 (m-40) REVERT: B 82 ASP cc_start: 0.6745 (m-30) cc_final: 0.6281 (p0) REVERT: B 108 LEU cc_start: 0.8787 (OUTLIER) cc_final: 0.8469 (mt) REVERT: B 116 MET cc_start: 0.8277 (mtt) cc_final: 0.7944 (mtm) REVERT: B 131 GLU cc_start: 0.7637 (tp30) cc_final: 0.7351 (tp30) REVERT: B 197 MET cc_start: 0.8143 (ptt) cc_final: 0.7735 (ppp) REVERT: B 223 GLU cc_start: 0.8473 (pt0) cc_final: 0.7932 (pp20) REVERT: C 131 GLU cc_start: 0.8210 (mm-30) cc_final: 0.7407 (tm-30) REVERT: C 151 LYS cc_start: 0.8390 (OUTLIER) cc_final: 0.8038 (mmpt) REVERT: C 235 ASP cc_start: 0.7266 (m-30) cc_final: 0.6853 (t0) REVERT: C 477 ILE cc_start: 0.8202 (OUTLIER) cc_final: 0.7872 (mt) REVERT: D 148 ARG cc_start: 0.7477 (ptp-170) cc_final: 0.6927 (ptt180) REVERT: D 234 ASN cc_start: 0.6656 (OUTLIER) cc_final: 0.6179 (t0) REVERT: D 326 THR cc_start: 0.8438 (m) cc_final: 0.8081 (p) REVERT: D 457 LYS cc_start: 0.6975 (tttp) cc_final: 0.6198 (mttm) REVERT: E 197 MET cc_start: 0.8127 (ptm) cc_final: 0.7880 (ptt) REVERT: E 232 LYS cc_start: 0.7500 (mttt) cc_final: 0.6888 (mtpp) REVERT: E 295 MET cc_start: 0.8385 (mmm) cc_final: 0.7978 (mmp) outliers start: 45 outliers final: 30 residues processed: 255 average time/residue: 1.3236 time to fit residues: 368.5967 Evaluate side-chains 261 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 226 time to evaluate : 1.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 ASN 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 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 301 VAL Chi-restraints excluded: chain B residue 331 VAL Chi-restraints excluded: chain B residue 360 LEU Chi-restraints excluded: chain C residue 102 ASP 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 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 234 ASN 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 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 338 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 129 optimal weight: 4.9990 chunk 136 optimal weight: 1.9990 chunk 96 optimal weight: 0.6980 chunk 61 optimal weight: 0.9990 chunk 160 optimal weight: 3.9990 chunk 112 optimal weight: 5.9990 chunk 40 optimal weight: 0.6980 chunk 95 optimal weight: 3.9990 chunk 60 optimal weight: 0.8980 chunk 55 optimal weight: 1.9990 chunk 80 optimal weight: 0.0770 overall best weight: 0.6740 ------------------------------------------------------------------------------- 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 = 0.3405 r_free = 0.3405 target = 0.130371 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.108585 restraints weight = 16233.640| |-----------------------------------------------------------------------------| r_work (start): 0.3121 rms_B_bonded: 1.64 r_work: 0.3032 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.2917 rms_B_bonded: 3.45 restraints_weight: 0.2500 r_work (final): 0.2917 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8360 moved from start: 0.2598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 14116 Z= 0.164 Angle : 0.524 8.221 19165 Z= 0.279 Chirality : 0.043 0.400 2197 Planarity : 0.004 0.041 2334 Dihedral : 6.550 73.005 2167 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 2.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 2.76 % Allowed : 18.25 % Favored : 78.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.32 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.55 (0.21), residues: 1630 helix: 2.16 (0.22), residues: 605 sheet: 1.00 (0.24), residues: 440 loop : -0.11 (0.24), residues: 585 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 349 HIS 0.004 0.001 HIS C 254 PHE 0.018 0.001 PHE E 356 TYR 0.020 0.002 TYR B 362 ARG 0.005 0.000 ARG E 308 ********************** 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 266 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 225 time to evaluate : 1.604 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 235 ASP cc_start: 0.7181 (p0) cc_final: 0.6452 (t70) REVERT: A 269 ASN cc_start: 0.8016 (OUTLIER) cc_final: 0.7526 (m-40) REVERT: B 82 ASP cc_start: 0.6763 (m-30) cc_final: 0.6311 (p0) REVERT: B 108 LEU cc_start: 0.8755 (OUTLIER) cc_final: 0.8433 (mt) REVERT: B 116 MET cc_start: 0.8240 (mtt) cc_final: 0.7903 (mtm) REVERT: B 131 GLU cc_start: 0.7605 (tp30) cc_final: 0.7336 (tp30) REVERT: B 197 MET cc_start: 0.8148 (ptt) cc_final: 0.7758 (ppp) REVERT: B 223 GLU cc_start: 0.8448 (pt0) cc_final: 0.7895 (pp20) REVERT: C 131 GLU cc_start: 0.8187 (mm-30) cc_final: 0.7378 (tm-30) REVERT: C 151 LYS cc_start: 0.8367 (OUTLIER) cc_final: 0.8041 (mmpt) REVERT: C 235 ASP cc_start: 0.7251 (m-30) cc_final: 0.6784 (t0) REVERT: D 148 ARG cc_start: 0.7425 (ptp-170) cc_final: 0.6908 (ptt180) REVERT: D 326 THR cc_start: 0.8465 (m) cc_final: 0.8079 (p) REVERT: D 457 LYS cc_start: 0.6920 (tttp) cc_final: 0.6187 (mttm) REVERT: E 116 MET cc_start: 0.8172 (mtm) cc_final: 0.7766 (mtp) REVERT: E 197 MET cc_start: 0.8111 (ptm) cc_final: 0.7859 (ptt) REVERT: E 232 LYS cc_start: 0.7468 (mttt) cc_final: 0.6861 (mtpp) REVERT: E 295 MET cc_start: 0.8381 (mmm) cc_final: 0.8044 (mmp) outliers start: 41 outliers final: 32 residues processed: 249 average time/residue: 1.3006 time to fit residues: 354.6745 Evaluate side-chains 258 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 223 time to evaluate : 1.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 ASN 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 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 331 VAL Chi-restraints excluded: chain B residue 360 LEU Chi-restraints excluded: chain C residue 102 ASP Chi-restraints excluded: chain C residue 122 LEU 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 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 234 ASN 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 338 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 116 optimal weight: 2.9990 chunk 112 optimal weight: 3.9990 chunk 154 optimal weight: 2.9990 chunk 129 optimal weight: 3.9990 chunk 49 optimal weight: 3.9990 chunk 52 optimal weight: 3.9990 chunk 0 optimal weight: 8.9990 chunk 38 optimal weight: 2.9990 chunk 12 optimal weight: 0.7980 chunk 44 optimal weight: 5.9990 chunk 45 optimal weight: 0.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- 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 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 251 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.129842 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.108072 restraints weight = 16378.521| |-----------------------------------------------------------------------------| r_work (start): 0.3118 rms_B_bonded: 1.65 r_work: 0.3024 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.2910 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.2910 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8372 moved from start: 0.2597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.126 14116 Z= 0.260 Angle : 0.851 59.083 19165 Z= 0.479 Chirality : 0.048 0.916 2197 Planarity : 0.004 0.041 2334 Dihedral : 6.562 73.004 2167 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 3.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 3.03 % Allowed : 18.05 % Favored : 78.92 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.32 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.53 (0.21), residues: 1630 helix: 2.15 (0.22), residues: 605 sheet: 0.95 (0.24), residues: 445 loop : -0.09 (0.24), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 349 HIS 0.005 0.001 HIS C 254 PHE 0.017 0.002 PHE E 356 TYR 0.019 0.002 TYR E 362 ARG 0.004 0.000 ARG E 308 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9791.39 seconds wall clock time: 175 minutes 37.45 seconds (10537.45 seconds total)