Starting phenix.real_space_refine on Thu Jun 12 14:38:44 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8oqa_17110/06_2025/8oqa_17110.cif Found real_map, /net/cci-nas-00/data/ceres_data/8oqa_17110/06_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_17110/06_2025/8oqa_17110.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8oqa_17110/06_2025/8oqa_17110.map" model { file = "/net/cci-nas-00/data/ceres_data/8oqa_17110/06_2025/8oqa_17110.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8oqa_17110/06_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-5710/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: 9.43, per 1000 atoms: 0.69 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: 4.78 Conformation dependent library (CDL) restraints added in 2.2 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: 1.56 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: 4.73 Time building geometry restraints manager: 5.44 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 2125 1.32 - 1.45: 4202 1.45 - 1.57: 7648 1.57 - 1.69: 1 1.69 - 1.82: 140 Bond restraints: 14116 Sorted by residual: bond pdb=" C15 RI5 B 610 " pdb=" O16 RI5 B 610 " ideal model delta sigma weight residual 1.396 1.447 -0.051 2.00e-02 2.50e+03 6.53e+00 bond pdb=" CB ILE E 341 " pdb=" CG1 ILE E 341 " ideal model delta sigma weight residual 1.530 1.487 0.043 2.00e-02 2.50e+03 4.61e+00 bond pdb=" C08 RI5 B 610 " pdb=" O20 RI5 B 610 " ideal model delta sigma weight residual 1.395 1.433 -0.038 2.00e-02 2.50e+03 3.62e+00 bond pdb=" C14 RI5 B 610 " pdb=" O16 RI5 B 610 " ideal model delta sigma weight residual 1.419 1.451 -0.032 2.00e-02 2.50e+03 2.64e+00 bond pdb=" N ABU D 601 " pdb=" CA ABU D 601 " ideal model delta sigma weight residual 1.457 1.485 -0.028 2.00e-02 2.50e+03 1.95e+00 ... (remaining 14111 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.84: 18808 1.84 - 3.67: 292 3.67 - 5.51: 58 5.51 - 7.34: 5 7.34 - 9.18: 2 Bond angle restraints: 19165 Sorted by residual: angle pdb=" N ILE E 341 " pdb=" CA ILE E 341 " pdb=" CB ILE E 341 " ideal model delta sigma weight residual 110.86 115.88 -5.02 1.60e+00 3.91e-01 9.85e+00 angle pdb=" C ILE E 341 " pdb=" CA ILE E 341 " pdb=" CB ILE E 341 " ideal model delta sigma weight residual 110.98 106.61 4.37 1.41e+00 5.03e-01 9.59e+00 angle pdb=" CA TYR C 362 " pdb=" CB TYR C 362 " pdb=" CG TYR C 362 " ideal model delta sigma weight residual 113.90 108.60 5.30 1.80e+00 3.09e-01 8.66e+00 angle pdb=" CA TYR A 362 " pdb=" CB TYR A 362 " pdb=" CG TYR A 362 " ideal model delta sigma weight residual 113.90 108.98 4.92 1.80e+00 3.09e-01 7.47e+00 angle pdb=" CB ILE E 341 " pdb=" CG1 ILE E 341 " pdb=" CD1 ILE E 341 " ideal model delta sigma weight residual 113.80 108.13 5.67 2.10e+00 2.27e-01 7.29e+00 ... (remaining 19160 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.57: 7973 17.57 - 35.14: 368 35.14 - 52.71: 54 52.71 - 70.28: 10 70.28 - 87.84: 5 Dihedral angle restraints: 8410 sinusoidal: 3485 harmonic: 4925 Sorted by residual: dihedral pdb=" CA LEU C 108 " pdb=" C LEU C 108 " pdb=" N ASP C 109 " pdb=" CA ASP C 109 " ideal model delta harmonic sigma weight residual -180.00 -159.66 -20.34 0 5.00e+00 4.00e-02 1.65e+01 dihedral pdb=" CA GLN B 251 " pdb=" C GLN B 251 " pdb=" N GLU B 252 " pdb=" CA GLU B 252 " ideal model delta harmonic sigma weight residual 180.00 162.03 17.97 0 5.00e+00 4.00e-02 1.29e+01 dihedral pdb=" CA LEU B 108 " pdb=" C LEU B 108 " pdb=" N ASP B 109 " pdb=" CA ASP B 109 " ideal model delta harmonic sigma weight residual -180.00 -162.28 -17.72 0 5.00e+00 4.00e-02 1.26e+01 ... (remaining 8407 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.149: 2187 0.149 - 0.298: 1 0.298 - 0.447: 3 0.447 - 0.597: 2 0.597 - 0.746: 4 Chirality restraints: 2197 Sorted by residual: chirality pdb=" C1 NAG B 603 " pdb=" ND2 ASN B 140 " pdb=" C2 NAG B 603 " pdb=" O5 NAG B 603 " both_signs ideal model delta sigma weight residual False -2.40 -3.15 0.75 2.00e-01 2.50e+01 1.39e+01 chirality pdb=" C1 NAG A 501 " pdb=" ND2 ASN A 140 " pdb=" C2 NAG A 501 " pdb=" O5 NAG A 501 " both_signs ideal model delta sigma weight residual False -2.40 -3.12 0.72 2.00e-01 2.50e+01 1.30e+01 chirality pdb=" C1 NAG C 602 " pdb=" ND2 ASN C 140 " pdb=" C2 NAG C 602 " pdb=" O5 NAG C 602 " both_signs ideal model delta sigma weight residual False -2.40 -3.11 0.71 2.00e-01 2.50e+01 1.26e+01 ... (remaining 2194 not shown) Planarity restraints: 2344 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN B 234 " 0.007 2.00e-02 2.50e+03 3.52e-01 1.55e+03 pdb=" CG ASN B 234 " -0.093 2.00e-02 2.50e+03 pdb=" OD1 ASN B 234 " 0.282 2.00e-02 2.50e+03 pdb=" ND2 ASN B 234 " -0.605 2.00e-02 2.50e+03 pdb=" C1 NAG B 604 " 0.408 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 234 " -0.230 2.00e-02 2.50e+03 3.05e-01 1.16e+03 pdb=" CG ASN C 234 " 0.100 2.00e-02 2.50e+03 pdb=" OD1 ASN C 234 " -0.016 2.00e-02 2.50e+03 pdb=" ND2 ASN C 234 " 0.515 2.00e-02 2.50e+03 pdb=" C1 NAG C 603 " -0.369 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 234 " 0.273 2.00e-02 2.50e+03 3.04e-01 1.15e+03 pdb=" CG ASN A 234 " -0.106 2.00e-02 2.50e+03 pdb=" OD1 ASN A 234 " -0.090 2.00e-02 2.50e+03 pdb=" ND2 ASN A 234 " -0.466 2.00e-02 2.50e+03 pdb=" C1 NAG A 502 " 0.388 2.00e-02 2.50e+03 ... (remaining 2341 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.64: 90 2.64 - 3.20: 11410 3.20 - 3.77: 19775 3.77 - 4.33: 29404 4.33 - 4.90: 48746 Nonbonded interactions: 109425 Sorted by model distance: nonbonded pdb=" CB ASN B 140 " pdb=" O5 NAG B 603 " model vdw 2.070 3.440 nonbonded pdb=" O PRO D 315 " pdb=" OG1 THR D 319 " model vdw 2.198 3.040 nonbonded pdb=" ND2 ASN D 332 " pdb=" OE1 GLN E 287 " model vdw 2.232 3.120 nonbonded pdb=" CD2 HIS C 254 " pdb=" O6 NAG C 603 " model vdw 2.252 2.608 nonbonded pdb=" O VAL B 296 " pdb=" OG SER B 299 " model vdw 2.264 3.040 ... (remaining 109420 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 80 through 372 or (resid 373 through 451 and (name N or na \ me CA or name C or name O or name CB )) or resid 452 through 479)) selection = (chain 'B' and (resid 80 through 81 or (resid 82 and (name N or name CA or name \ C or name O or name CB )) or resid 83 through 251 or (resid 252 and (name N or n \ ame CA or name C or name O or name CB )) or resid 253 through 374 or (resid 375 \ through 451 and (name N or name CA or name C or name O or name CB )) or resid 45 \ 2 through 479)) selection = (chain 'C' and (resid 80 through 81 or (resid 82 and (name N or name CA or name \ C or name O or name CB )) or resid 83 through 371 or (resid 372 through 451 and \ (name N or name CA or name C or name O or name CB )) or resid 452 through 479)) selection = (chain 'D' and (resid 80 through 81 or (resid 82 and (name N or name CA or name \ C or name O or name CB )) or resid 83 through 371 or (resid 372 through 451 and \ (name N or name CA or name C or name O or name CB )) or resid 452 through 479)) selection = (chain 'E' and (resid 80 through 251 or (resid 252 and (name N or name CA or nam \ e C or name O or name CB )) or resid 253 through 371 or (resid 372 through 451 a \ nd (name N or name CA or name C or name O or name CB )) or resid 452 through 479 \ )) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.640 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: 0.540 Check model and map are aligned: 0.090 Set scattering table: 0.110 Process input model: 36.820 Find NCS groups from input model: 0.780 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:13.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 57.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.348 14128 Z= 0.376 Angle : 0.906 44.237 19197 Z= 0.382 Chirality : 0.056 0.746 2197 Planarity : 0.004 0.031 2334 Dihedral : 10.525 87.844 5207 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.86 % Favored : 99.14 % Rotamer: Outliers : 0.61 % Allowed : 3.97 % Favored : 95.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.32 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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 Details of bonding type rmsd link_NAG-ASN : bond 0.13333 ( 10) link_NAG-ASN : angle 17.37292 ( 30) hydrogen bonds : bond 0.16681 ( 706) hydrogen bonds : angle 6.31232 ( 2295) SS BOND : bond 0.00216 ( 1) SS BOND : angle 0.87749 ( 2) covalent geometry : bond 0.00276 (14116) covalent geometry : angle 0.59154 (19165) Misc. bond : bond 0.34777 ( 1) *********************** 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 : 1.614 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: 1.3532 time to fit residues: 522.7784 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 : 1.452 ------------------------------------------------------------------------------- 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 = 0.129286 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.107667 restraints weight = 16002.192| |-----------------------------------------------------------------------------| r_work (start): 0.3074 rms_B_bonded: 1.71 r_work: 0.2976 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.2861 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.2861 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8423 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 14128 Z= 0.199 Angle : 0.759 19.972 19197 Z= 0.377 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 Details of bonding type rmsd link_NAG-ASN : bond 0.01790 ( 10) link_NAG-ASN : angle 9.01951 ( 30) hydrogen bonds : bond 0.08157 ( 706) hydrogen bonds : angle 4.67875 ( 2295) SS BOND : bond 0.00557 ( 1) SS BOND : angle 1.32766 ( 2) covalent geometry : bond 0.00433 (14116) covalent geometry : angle 0.67055 (19165) Misc. bond : bond 0.00099 ( 1) *********************** 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 : 1.600 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 183 ASP cc_start: 0.7806 (OUTLIER) cc_final: 0.7468 (p0) REVERT: A 269 ASN cc_start: 0.8135 (OUTLIER) cc_final: 0.7732 (m-40) REVERT: B 82 ASP cc_start: 0.6779 (m-30) cc_final: 0.6206 (p0) REVERT: B 116 MET cc_start: 0.8394 (mtt) cc_final: 0.8039 (mtm) REVERT: B 117 ASP cc_start: 0.8249 (p0) cc_final: 0.7978 (p0) REVERT: B 223 GLU cc_start: 0.8424 (pt0) cc_final: 0.7870 (pp20) REVERT: B 462 ILE cc_start: 0.8083 (OUTLIER) cc_final: 0.7883 (mp) REVERT: C 143 MET cc_start: 0.8010 (mmm) cc_final: 0.7718 (mmp) REVERT: D 113 GLU cc_start: 0.8043 (mt-10) cc_final: 0.7826 (mp0) REVERT: D 148 ARG cc_start: 0.7434 (ptp-170) cc_final: 0.7115 (ptt180) REVERT: D 234 ASN cc_start: 0.6835 (OUTLIER) cc_final: 0.6187 (t160) REVERT: D 241 GLU cc_start: 0.7391 (mm-30) cc_final: 0.7093 (tp30) REVERT: D 287 GLN cc_start: 0.7624 (OUTLIER) cc_final: 0.6961 (mp-120) REVERT: D 326 THR cc_start: 0.8525 (m) cc_final: 0.8184 (p) REVERT: E 232 LYS cc_start: 0.7422 (mttt) cc_final: 0.6808 (mtpp) REVERT: E 295 MET cc_start: 0.8418 (mmm) cc_final: 0.8131 (mmp) outliers start: 56 outliers final: 29 residues processed: 274 average time/residue: 1.2583 time to fit residues: 376.4699 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 : 1.531 ------------------------------------------------------------------------------- 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: 3.9990 chunk 94 optimal weight: 2.9990 chunk 132 optimal weight: 4.9990 chunk 157 optimal weight: 10.0000 chunk 6 optimal weight: 6.9990 chunk 20 optimal weight: 0.8980 chunk 86 optimal weight: 4.9990 chunk 159 optimal weight: 1.9990 chunk 75 optimal weight: 0.9990 chunk 51 optimal weight: 1.9990 chunk 62 optimal weight: 5.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 210 GLN A 287 GLN B 247 GLN C 210 GLN D 287 GLN E 126 HIS E 287 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.125537 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.103050 restraints weight = 16213.676| |-----------------------------------------------------------------------------| r_work (start): 0.3052 rms_B_bonded: 1.77 r_work: 0.2952 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.2833 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.2833 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8438 moved from start: 0.1959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 14128 Z= 0.208 Angle : 0.734 18.068 19197 Z= 0.368 Chirality : 0.048 0.432 2197 Planarity : 0.005 0.043 2334 Dihedral : 7.444 77.284 2170 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 3.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 4.38 % Allowed : 13.27 % Favored : 82.36 % 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: 1.14 (0.20), residues: 1630 helix: 1.57 (0.22), residues: 610 sheet: 0.78 (0.23), residues: 470 loop : -0.08 (0.24), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 349 HIS 0.007 0.001 HIS C 254 PHE 0.020 0.002 PHE A 356 TYR 0.024 0.002 TYR E 362 ARG 0.003 0.001 ARG A 270 Details of bonding type rmsd link_NAG-ASN : bond 0.01586 ( 10) link_NAG-ASN : angle 8.43064 ( 30) hydrogen bonds : bond 0.08178 ( 706) hydrogen bonds : angle 4.59030 ( 2295) SS BOND : bond 0.00719 ( 1) SS BOND : angle 1.69872 ( 2) covalent geometry : bond 0.00458 (14116) covalent geometry : angle 0.65467 (19165) Misc. bond : bond 0.00138 ( 1) *********************** 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 301 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 236 time to evaluate : 1.470 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 183 ASP cc_start: 0.7832 (OUTLIER) cc_final: 0.7530 (p0) REVERT: A 235 ASP cc_start: 0.7153 (p0) cc_final: 0.6584 (t70) REVERT: A 241 GLU cc_start: 0.7394 (pm20) cc_final: 0.7136 (mp0) REVERT: A 269 ASN cc_start: 0.8156 (OUTLIER) cc_final: 0.7776 (m-40) REVERT: B 82 ASP cc_start: 0.6788 (m-30) cc_final: 0.6238 (p0) REVERT: B 108 LEU cc_start: 0.8885 (OUTLIER) cc_final: 0.8510 (mt) REVERT: B 116 MET cc_start: 0.8401 (mtt) cc_final: 0.8025 (mtm) REVERT: B 117 ASP cc_start: 0.8183 (p0) cc_final: 0.7910 (p0) REVERT: B 223 GLU cc_start: 0.8507 (pt0) cc_final: 0.7957 (pp20) REVERT: C 143 MET cc_start: 0.8000 (mmm) cc_final: 0.7710 (mmp) REVERT: C 151 LYS cc_start: 0.8487 (OUTLIER) cc_final: 0.8039 (mmpt) REVERT: C 258 LYS cc_start: 0.8365 (OUTLIER) cc_final: 0.7675 (ttpp) REVERT: D 113 GLU cc_start: 0.8034 (mt-10) cc_final: 0.7808 (mp0) REVERT: D 148 ARG cc_start: 0.7497 (ptp-170) cc_final: 0.7014 (ptt180) REVERT: D 241 GLU cc_start: 0.7421 (mm-30) cc_final: 0.7150 (tp30) REVERT: D 326 THR cc_start: 0.8569 (m) cc_final: 0.8232 (p) REVERT: E 232 LYS cc_start: 0.7507 (mttt) cc_final: 0.6869 (mtpp) REVERT: E 295 MET cc_start: 0.8431 (mmm) cc_final: 0.8061 (mmp) REVERT: E 456 ASP cc_start: 0.7446 (m-30) cc_final: 0.6873 (m-30) outliers start: 65 outliers final: 40 residues processed: 272 average time/residue: 1.2828 time to fit residues: 380.5807 Evaluate side-chains 277 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 232 time to evaluate : 1.581 ------------------------------------------------------------------------------- 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 108 LEU Chi-restraints excluded: chain B residue 142 SER Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 256 THR Chi-restraints excluded: chain B residue 263 SER Chi-restraints excluded: chain B residue 314 VAL Chi-restraints excluded: chain B residue 331 VAL Chi-restraints excluded: chain B residue 335 MET Chi-restraints excluded: chain B residue 371 VAL Chi-restraints excluded: chain C residue 82 ASP 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 258 LYS Chi-restraints excluded: chain C residue 325 SER Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain C residue 370 THR Chi-restraints excluded: chain C residue 371 VAL Chi-restraints excluded: chain D residue 151 LYS Chi-restraints excluded: chain D residue 234 ASN Chi-restraints excluded: chain D residue 256 THR Chi-restraints excluded: chain D residue 257 THR Chi-restraints excluded: chain D residue 288 THR Chi-restraints excluded: chain D residue 370 THR Chi-restraints excluded: chain D residue 371 VAL Chi-restraints excluded: chain E residue 108 LEU Chi-restraints excluded: chain E residue 114 VAL Chi-restraints excluded: chain E residue 140 ASN Chi-restraints excluded: chain E residue 244 SER Chi-restraints excluded: chain E residue 298 LEU Chi-restraints excluded: chain E residue 338 VAL Chi-restraints excluded: chain E residue 360 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 21 optimal weight: 0.8980 chunk 144 optimal weight: 3.9990 chunk 44 optimal weight: 4.9990 chunk 114 optimal weight: 1.9990 chunk 69 optimal weight: 0.6980 chunk 65 optimal weight: 2.9990 chunk 98 optimal weight: 2.9990 chunk 150 optimal weight: 1.9990 chunk 132 optimal weight: 7.9990 chunk 53 optimal weight: 1.9990 chunk 25 optimal weight: 0.1980 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 210 GLN A 251 GLN A 287 GLN B 247 GLN B 332 ASN ** E 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.127269 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.104756 restraints weight = 16095.107| |-----------------------------------------------------------------------------| r_work (start): 0.3070 rms_B_bonded: 1.76 r_work: 0.2976 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.2859 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.2859 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8410 moved from start: 0.2120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 14128 Z= 0.162 Angle : 0.662 17.341 19197 Z= 0.332 Chirality : 0.045 0.441 2197 Planarity : 0.004 0.044 2334 Dihedral : 7.144 77.145 2170 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 2.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.98 % Favored : 99.02 % Rotamer: Outliers : 4.44 % Allowed : 14.95 % Favored : 80.61 % 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: 1.25 (0.20), residues: 1630 helix: 1.82 (0.22), residues: 605 sheet: 0.95 (0.24), residues: 440 loop : -0.27 (0.23), residues: 585 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 349 HIS 0.005 0.001 HIS C 254 PHE 0.016 0.002 PHE E 356 TYR 0.023 0.002 TYR B 362 ARG 0.002 0.000 ARG E 308 Details of bonding type rmsd link_NAG-ASN : bond 0.01599 ( 10) link_NAG-ASN : angle 7.60698 ( 30) hydrogen bonds : bond 0.07145 ( 706) hydrogen bonds : angle 4.37605 ( 2295) SS BOND : bond 0.00488 ( 1) SS BOND : angle 1.16871 ( 2) covalent geometry : bond 0.00341 (14116) covalent geometry : angle 0.58985 (19165) Misc. bond : bond 0.00118 ( 1) *********************** 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 305 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 239 time to evaluate : 1.717 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 140 ASN cc_start: 0.5784 (OUTLIER) cc_final: 0.5380 (t0) REVERT: A 183 ASP cc_start: 0.7795 (OUTLIER) cc_final: 0.7496 (p0) REVERT: A 232 LYS cc_start: 0.8315 (mmpt) cc_final: 0.8087 (mmmt) REVERT: A 235 ASP cc_start: 0.7125 (p0) cc_final: 0.6492 (t70) REVERT: A 241 GLU cc_start: 0.7367 (pm20) cc_final: 0.7143 (mp0) REVERT: A 269 ASN cc_start: 0.8132 (OUTLIER) cc_final: 0.7718 (m-40) REVERT: B 82 ASP cc_start: 0.6829 (m-30) cc_final: 0.6295 (p0) REVERT: B 108 LEU cc_start: 0.8840 (OUTLIER) cc_final: 0.8497 (mt) REVERT: B 116 MET cc_start: 0.8355 (mtt) cc_final: 0.7997 (mtm) REVERT: B 117 ASP cc_start: 0.8101 (p0) cc_final: 0.7847 (p0) REVERT: B 131 GLU cc_start: 0.7674 (tp30) cc_final: 0.7400 (tp30) REVERT: B 223 GLU cc_start: 0.8496 (pt0) cc_final: 0.7944 (pp20) REVERT: B 457 LYS cc_start: 0.7389 (OUTLIER) cc_final: 0.6851 (pttt) REVERT: C 143 MET cc_start: 0.7923 (mmm) cc_final: 0.7668 (mmp) REVERT: C 151 LYS cc_start: 0.8432 (OUTLIER) cc_final: 0.8065 (mmpt) REVERT: C 235 ASP cc_start: 0.7264 (m-30) cc_final: 0.6834 (t0) REVERT: D 148 ARG cc_start: 0.7452 (ptp-170) cc_final: 0.6975 (ptt180) REVERT: D 241 GLU cc_start: 0.7424 (mm-30) cc_final: 0.7125 (tp30) REVERT: D 287 GLN cc_start: 0.7694 (OUTLIER) cc_final: 0.6895 (mp10) REVERT: D 326 THR cc_start: 0.8533 (m) cc_final: 0.8186 (p) REVERT: D 457 LYS cc_start: 0.7057 (tttp) cc_final: 0.6203 (ttmm) REVERT: E 232 LYS cc_start: 0.7482 (mttt) cc_final: 0.6872 (mtpp) REVERT: E 295 MET cc_start: 0.8436 (mmm) cc_final: 0.8120 (mmp) outliers start: 66 outliers final: 36 residues processed: 279 average time/residue: 1.6748 time to fit residues: 509.8261 Evaluate side-chains 276 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 233 time to evaluate : 1.439 ------------------------------------------------------------------------------- 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 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 264 SER Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain A residue 326 THR Chi-restraints excluded: chain A residue 344 VAL Chi-restraints excluded: chain A residue 461 ILE Chi-restraints excluded: chain A residue 469 LEU Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 142 SER Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 256 THR Chi-restraints excluded: chain B residue 263 SER Chi-restraints excluded: chain B residue 331 VAL Chi-restraints excluded: chain B residue 360 LEU Chi-restraints excluded: chain B residue 371 VAL 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 207 LEU Chi-restraints excluded: chain C residue 234 ASN Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain C residue 370 THR Chi-restraints excluded: chain D residue 151 LYS Chi-restraints excluded: chain D residue 249 LEU Chi-restraints excluded: chain D residue 256 THR Chi-restraints excluded: chain D residue 257 THR Chi-restraints excluded: chain D residue 287 GLN Chi-restraints excluded: chain D residue 288 THR Chi-restraints excluded: chain D residue 371 VAL Chi-restraints excluded: chain E residue 108 LEU Chi-restraints excluded: chain E residue 114 VAL Chi-restraints excluded: chain E residue 140 ASN Chi-restraints excluded: chain E residue 244 SER Chi-restraints excluded: chain E residue 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: 2.9990 chunk 155 optimal weight: 0.8980 chunk 87 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 chunk 111 optimal weight: 0.2980 chunk 39 optimal weight: 0.8980 chunk 0 optimal weight: 8.9990 chunk 43 optimal weight: 0.5980 chunk 17 optimal weight: 0.9990 chunk 90 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 ** E 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.130220 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.108332 restraints weight = 16175.414| |-----------------------------------------------------------------------------| r_work (start): 0.3124 rms_B_bonded: 1.66 r_work: 0.3029 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.2913 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.2913 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8373 moved from start: 0.2330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 14128 Z= 0.132 Angle : 0.606 13.293 19197 Z= 0.301 Chirality : 0.044 0.409 2197 Planarity : 0.004 0.043 2334 Dihedral : 6.825 75.812 2170 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 2.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.04 % Favored : 98.96 % Rotamer: Outliers : 4.18 % Allowed : 15.42 % Favored : 80.40 % 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: 1.49 (0.21), residues: 1630 helix: 2.08 (0.22), residues: 605 sheet: 1.04 (0.24), residues: 440 loop : -0.17 (0.23), residues: 585 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 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 0.004 0.000 ARG E 308 Details of bonding type rmsd link_NAG-ASN : bond 0.01541 ( 10) link_NAG-ASN : angle 7.29277 ( 30) hydrogen bonds : bond 0.05959 ( 706) hydrogen bonds : angle 4.11560 ( 2295) SS BOND : bond 0.00313 ( 1) SS BOND : angle 0.78610 ( 2) covalent geometry : bond 0.00261 (14116) covalent geometry : angle 0.53387 (19165) Misc. bond : bond 0.00074 ( 1) *********************** 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 309 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 247 time to evaluate : 1.664 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 235 ASP cc_start: 0.7107 (p0) cc_final: 0.6420 (t70) REVERT: A 269 ASN cc_start: 0.8043 (OUTLIER) cc_final: 0.7517 (m-40) REVERT: B 82 ASP cc_start: 0.6795 (m-30) cc_final: 0.6286 (p0) REVERT: B 108 LEU cc_start: 0.8754 (OUTLIER) cc_final: 0.8446 (mt) REVERT: B 116 MET cc_start: 0.8339 (mtt) cc_final: 0.7973 (mtm) REVERT: B 223 GLU cc_start: 0.8454 (pt0) cc_final: 0.7872 (pp20) REVERT: B 457 LYS cc_start: 0.7278 (OUTLIER) cc_final: 0.6748 (pttt) REVERT: C 151 LYS cc_start: 0.8384 (OUTLIER) cc_final: 0.8044 (mmpt) REVERT: C 235 ASP cc_start: 0.7191 (m-30) cc_final: 0.6815 (t0) REVERT: C 258 LYS cc_start: 0.8347 (OUTLIER) cc_final: 0.8120 (tttp) REVERT: D 148 ARG cc_start: 0.7421 (ptp-170) cc_final: 0.6980 (ptt180) REVERT: D 326 THR cc_start: 0.8435 (m) cc_final: 0.8071 (p) REVERT: D 457 LYS cc_start: 0.6935 (tttp) cc_final: 0.6151 (mttm) REVERT: E 197 MET cc_start: 0.8122 (ptm) cc_final: 0.7874 (ptt) REVERT: E 232 LYS cc_start: 0.7435 (mttt) cc_final: 0.6812 (mtpp) REVERT: E 295 MET cc_start: 0.8433 (mmm) cc_final: 0.8151 (mmp) outliers start: 62 outliers final: 34 residues processed: 283 average time/residue: 1.3089 time to fit residues: 404.5175 Evaluate side-chains 273 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 234 time to evaluate : 1.592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 234 ASN Chi-restraints excluded: chain A residue 246 SER Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain A residue 326 THR Chi-restraints excluded: chain A residue 334 SER Chi-restraints excluded: chain A residue 469 LEU Chi-restraints excluded: chain B residue 108 LEU 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 331 VAL Chi-restraints excluded: chain B residue 457 LYS Chi-restraints excluded: chain C residue 82 ASP Chi-restraints excluded: chain C residue 102 ASP Chi-restraints excluded: chain C residue 122 LEU Chi-restraints excluded: chain C residue 140 ASN Chi-restraints excluded: chain C residue 151 LYS Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 234 ASN Chi-restraints excluded: chain C residue 258 LYS Chi-restraints excluded: chain C residue 310 VAL 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 236 SER 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 96 optimal weight: 3.9990 chunk 133 optimal weight: 0.0050 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: 0.9980 chunk 122 optimal weight: 0.6980 chunk 13 optimal weight: 7.9990 chunk 48 optimal weight: 3.9990 chunk 143 optimal weight: 6.9990 overall best weight: 1.9398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 210 GLN A 287 GLN B 210 GLN E 251 GLN E 287 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.125269 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.103269 restraints weight = 16271.981| |-----------------------------------------------------------------------------| r_work (start): 0.3055 rms_B_bonded: 1.67 r_work: 0.2959 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.2842 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.2842 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8445 moved from start: 0.2362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 14128 Z= 0.213 Angle : 0.742 14.514 19197 Z= 0.373 Chirality : 0.049 0.452 2197 Planarity : 0.005 0.047 2334 Dihedral : 7.550 75.041 2170 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 3.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 4.31 % Allowed : 15.42 % Favored : 80.27 % 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: 1.03 (0.20), residues: 1630 helix: 1.62 (0.22), residues: 605 sheet: 0.76 (0.23), residues: 465 loop : -0.34 (0.23), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 349 HIS 0.007 0.001 HIS C 254 PHE 0.022 0.002 PHE A 356 TYR 0.026 0.002 TYR E 362 ARG 0.004 0.001 ARG D 125 Details of bonding type rmsd link_NAG-ASN : bond 0.01161 ( 10) link_NAG-ASN : angle 7.97401 ( 30) hydrogen bonds : bond 0.08055 ( 706) hydrogen bonds : angle 4.48673 ( 2295) SS BOND : bond 0.00750 ( 1) SS BOND : angle 1.76836 ( 2) covalent geometry : bond 0.00487 (14116) covalent geometry : angle 0.67172 (19165) Misc. bond : bond 0.00121 ( 1) *********************** 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 295 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 231 time to evaluate : 1.533 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 235 ASP cc_start: 0.7318 (p0) cc_final: 0.6635 (t70) REVERT: A 269 ASN cc_start: 0.8141 (OUTLIER) cc_final: 0.7763 (m-40) REVERT: B 82 ASP cc_start: 0.6801 (m-30) cc_final: 0.6319 (p0) REVERT: B 108 LEU cc_start: 0.8901 (OUTLIER) cc_final: 0.8533 (mt) REVERT: B 116 MET cc_start: 0.8396 (mtt) cc_final: 0.8139 (mtm) REVERT: B 131 GLU cc_start: 0.7714 (tp30) cc_final: 0.7441 (tp30) REVERT: B 223 GLU cc_start: 0.8455 (pt0) cc_final: 0.7931 (pp20) REVERT: C 151 LYS cc_start: 0.8451 (OUTLIER) cc_final: 0.8030 (mmpt) REVERT: C 235 ASP cc_start: 0.7396 (m-30) cc_final: 0.6965 (t0) REVERT: D 148 ARG cc_start: 0.7489 (ptp-170) cc_final: 0.6937 (ptt180) REVERT: D 183 ASP cc_start: 0.6481 (p0) cc_final: 0.6078 (p0) REVERT: D 326 THR cc_start: 0.8550 (m) cc_final: 0.8224 (p) REVERT: D 457 LYS cc_start: 0.7085 (tttp) cc_final: 0.6236 (mttm) REVERT: E 116 MET cc_start: 0.8216 (mtm) cc_final: 0.7822 (mtp) REVERT: E 232 LYS cc_start: 0.7594 (mttt) cc_final: 0.7007 (mtpp) REVERT: E 295 MET cc_start: 0.8426 (mmm) cc_final: 0.8028 (mmp) REVERT: E 456 ASP cc_start: 0.7467 (m-30) cc_final: 0.6872 (m-30) outliers start: 64 outliers final: 46 residues processed: 270 average time/residue: 1.4079 time to fit residues: 415.8888 Evaluate side-chains 275 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 226 time to evaluate : 2.006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 234 ASN Chi-restraints excluded: chain A residue 246 SER Chi-restraints excluded: chain A residue 264 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 264 SER 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 B residue 371 VAL 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 140 ASN Chi-restraints excluded: chain C residue 151 LYS Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 234 ASN Chi-restraints excluded: chain C residue 325 SER Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain C residue 370 THR Chi-restraints excluded: chain C residue 371 VAL Chi-restraints excluded: chain D residue 102 ASP Chi-restraints excluded: chain D residue 151 LYS Chi-restraints excluded: chain D residue 161 VAL Chi-restraints excluded: chain D residue 180 VAL Chi-restraints excluded: chain D residue 236 SER Chi-restraints excluded: chain D residue 249 LEU Chi-restraints excluded: chain D residue 256 THR Chi-restraints excluded: chain D residue 257 THR Chi-restraints excluded: chain D residue 288 THR Chi-restraints excluded: chain D residue 358 SER 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 318 ILE Chi-restraints excluded: chain E residue 338 VAL 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: 0.2980 chunk 59 optimal weight: 0.9980 chunk 22 optimal weight: 4.9990 chunk 34 optimal weight: 2.9990 chunk 136 optimal weight: 1.9990 chunk 139 optimal weight: 1.9990 chunk 83 optimal weight: 3.9990 chunk 65 optimal weight: 1.9990 chunk 135 optimal weight: 0.9990 chunk 160 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.126184 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.104341 restraints weight = 16391.570| |-----------------------------------------------------------------------------| r_work (start): 0.3068 rms_B_bonded: 1.66 r_work: 0.2977 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.2860 rms_B_bonded: 3.45 restraints_weight: 0.2500 r_work (final): 0.2860 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8428 moved from start: 0.2367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 14128 Z= 0.177 Angle : 0.918 59.197 19197 Z= 0.482 Chirality : 0.047 0.445 2197 Planarity : 0.005 0.045 2334 Dihedral : 7.461 75.034 2170 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 3.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer: Outliers : 3.84 % Allowed : 16.30 % Favored : 79.87 % 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: 1.02 (0.20), residues: 1630 helix: 1.64 (0.22), residues: 605 sheet: 0.74 (0.23), residues: 465 loop : -0.37 (0.23), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 349 HIS 0.006 0.001 HIS C 254 PHE 0.020 0.002 PHE A 356 TYR 0.023 0.002 TYR E 362 ARG 0.003 0.000 ARG E 308 Details of bonding type rmsd link_NAG-ASN : bond 0.01319 ( 10) link_NAG-ASN : angle 9.35964 ( 30) hydrogen bonds : bond 0.07633 ( 706) hydrogen bonds : angle 4.44508 ( 2295) SS BOND : bond 0.00535 ( 1) SS BOND : angle 1.31721 ( 2) covalent geometry : bond 0.00376 (14116) covalent geometry : angle 0.84081 (19165) Misc. bond : bond 0.00136 ( 1) *********************** 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 282 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 225 time to evaluate : 1.539 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 235 ASP cc_start: 0.7307 (p0) cc_final: 0.6606 (t70) REVERT: A 269 ASN cc_start: 0.8129 (OUTLIER) cc_final: 0.7736 (m-40) REVERT: B 82 ASP cc_start: 0.6821 (m-30) cc_final: 0.6342 (p0) REVERT: B 108 LEU cc_start: 0.8868 (OUTLIER) cc_final: 0.8502 (mt) REVERT: B 116 MET cc_start: 0.8368 (mtt) cc_final: 0.8041 (mtm) REVERT: B 131 GLU cc_start: 0.7678 (tp30) cc_final: 0.7392 (tp30) REVERT: B 223 GLU cc_start: 0.8437 (pt0) cc_final: 0.7959 (pp20) REVERT: C 235 ASP cc_start: 0.7365 (m-30) cc_final: 0.6941 (t0) REVERT: D 148 ARG cc_start: 0.7488 (ptp-170) cc_final: 0.6946 (ptt180) REVERT: D 183 ASP cc_start: 0.6443 (p0) cc_final: 0.6080 (p0) REVERT: D 326 THR cc_start: 0.8538 (m) cc_final: 0.8185 (p) REVERT: D 457 LYS cc_start: 0.7076 (tttp) cc_final: 0.6237 (mttm) REVERT: E 232 LYS cc_start: 0.7583 (mttt) cc_final: 0.6950 (mtpp) REVERT: E 295 MET cc_start: 0.8401 (mmm) cc_final: 0.7993 (mmp) REVERT: E 456 ASP cc_start: 0.7508 (m-30) cc_final: 0.6913 (m-30) outliers start: 57 outliers final: 44 residues processed: 258 average time/residue: 1.2683 time to fit residues: 357.8719 Evaluate side-chains 270 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 224 time to evaluate : 1.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 234 ASN Chi-restraints excluded: chain A residue 246 SER Chi-restraints excluded: chain A residue 264 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 264 SER Chi-restraints excluded: chain B residue 314 VAL Chi-restraints excluded: chain B residue 331 VAL Chi-restraints excluded: chain B residue 335 MET Chi-restraints excluded: chain B residue 360 LEU Chi-restraints excluded: chain B residue 371 VAL 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 140 ASN Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 234 ASN Chi-restraints excluded: chain C residue 325 SER Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain C residue 370 THR Chi-restraints excluded: chain C residue 371 VAL Chi-restraints excluded: chain D residue 102 ASP Chi-restraints excluded: chain D residue 151 LYS Chi-restraints excluded: chain D residue 161 VAL Chi-restraints excluded: chain D residue 180 VAL Chi-restraints excluded: chain D residue 249 LEU Chi-restraints excluded: chain D residue 256 THR Chi-restraints excluded: chain D residue 257 THR Chi-restraints excluded: chain D residue 288 THR Chi-restraints excluded: chain D residue 358 SER 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 318 ILE Chi-restraints excluded: chain E residue 338 VAL Chi-restraints excluded: chain E residue 360 LEU 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: 0.9980 chunk 97 optimal weight: 2.9990 chunk 134 optimal weight: 3.9990 chunk 76 optimal weight: 2.9990 chunk 48 optimal weight: 3.9990 chunk 82 optimal weight: 2.9990 chunk 2 optimal weight: 0.6980 chunk 34 optimal weight: 3.9990 chunk 17 optimal weight: 2.9990 overall best weight: 1.6984 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.125510 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.103229 restraints weight = 16425.146| |-----------------------------------------------------------------------------| r_work (start): 0.3052 rms_B_bonded: 1.74 r_work: 0.2956 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.2836 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.2836 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8427 moved from start: 0.2417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 14128 Z= 0.195 Angle : 0.722 15.178 19197 Z= 0.361 Chirality : 0.048 0.441 2197 Planarity : 0.005 0.046 2334 Dihedral : 7.612 74.450 2170 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 3.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 3.77 % Allowed : 16.50 % Favored : 79.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.32 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.93 (0.20), residues: 1630 helix: 1.60 (0.22), residues: 605 sheet: 0.61 (0.23), residues: 470 loop : -0.38 (0.23), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 349 HIS 0.006 0.001 HIS C 254 PHE 0.020 0.002 PHE A 356 TYR 0.025 0.002 TYR E 362 ARG 0.003 0.001 ARG A 270 Details of bonding type rmsd link_NAG-ASN : bond 0.01150 ( 10) link_NAG-ASN : angle 7.61565 ( 30) hydrogen bonds : bond 0.07748 ( 706) hydrogen bonds : angle 4.44476 ( 2295) SS BOND : bond 0.00720 ( 1) SS BOND : angle 1.47941 ( 2) covalent geometry : bond 0.00438 (14116) covalent geometry : angle 0.65654 (19165) Misc. bond : bond 0.00143 ( 1) *********************** 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 281 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 225 time to evaluate : 3.044 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 235 ASP cc_start: 0.7323 (p0) cc_final: 0.6582 (t70) REVERT: A 269 ASN cc_start: 0.8137 (OUTLIER) cc_final: 0.7735 (m-40) REVERT: B 82 ASP cc_start: 0.6819 (m-30) cc_final: 0.6330 (p0) REVERT: B 108 LEU cc_start: 0.8879 (OUTLIER) cc_final: 0.8509 (mt) REVERT: B 116 MET cc_start: 0.8339 (mtt) cc_final: 0.8046 (mtm) REVERT: B 131 GLU cc_start: 0.7705 (tp30) cc_final: 0.7381 (tp30) REVERT: B 223 GLU cc_start: 0.8443 (pt0) cc_final: 0.7891 (pp20) REVERT: C 151 LYS cc_start: 0.8465 (OUTLIER) cc_final: 0.8045 (mmpt) REVERT: C 235 ASP cc_start: 0.7423 (m-30) cc_final: 0.6930 (t0) REVERT: D 148 ARG cc_start: 0.7490 (ptp-170) cc_final: 0.6923 (ptt180) REVERT: D 183 ASP cc_start: 0.6437 (p0) cc_final: 0.6021 (p0) REVERT: D 326 THR cc_start: 0.8547 (m) cc_final: 0.8188 (p) REVERT: D 457 LYS cc_start: 0.7050 (tttp) cc_final: 0.6200 (mttm) REVERT: E 232 LYS cc_start: 0.7621 (mttt) cc_final: 0.7025 (mtpp) REVERT: E 295 MET cc_start: 0.8401 (mmm) cc_final: 0.8000 (mmp) REVERT: E 456 ASP cc_start: 0.7461 (m-30) cc_final: 0.6833 (m-30) outliers start: 56 outliers final: 43 residues processed: 260 average time/residue: 1.5841 time to fit residues: 453.6331 Evaluate side-chains 272 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 226 time to evaluate : 1.696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 234 ASN Chi-restraints excluded: chain A residue 246 SER Chi-restraints excluded: chain A residue 264 SER Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain A residue 326 THR Chi-restraints excluded: chain A residue 461 ILE Chi-restraints excluded: chain A residue 469 LEU Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 207 LEU Chi-restraints excluded: chain B residue 256 THR Chi-restraints excluded: chain B residue 263 SER Chi-restraints excluded: chain B residue 264 SER 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 B residue 371 VAL 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 140 ASN Chi-restraints excluded: chain C residue 151 LYS Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 234 ASN Chi-restraints excluded: chain C residue 325 SER Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain C residue 370 THR Chi-restraints excluded: chain C residue 371 VAL Chi-restraints excluded: chain D residue 102 ASP Chi-restraints excluded: chain D residue 151 LYS Chi-restraints excluded: chain D residue 180 VAL Chi-restraints excluded: chain D residue 249 LEU Chi-restraints excluded: chain D residue 256 THR Chi-restraints excluded: chain D residue 257 THR Chi-restraints excluded: chain D residue 288 THR Chi-restraints excluded: chain D residue 358 SER 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 318 ILE Chi-restraints excluded: chain E residue 338 VAL Chi-restraints excluded: chain E residue 360 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 116 optimal weight: 5.9990 chunk 136 optimal weight: 0.8980 chunk 80 optimal weight: 0.7980 chunk 77 optimal weight: 4.9990 chunk 59 optimal weight: 3.9990 chunk 133 optimal weight: 0.9980 chunk 107 optimal weight: 2.9990 chunk 20 optimal weight: 0.9980 chunk 31 optimal weight: 1.9990 chunk 120 optimal weight: 1.9990 chunk 42 optimal weight: 6.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.127673 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.105342 restraints weight = 16285.058| |-----------------------------------------------------------------------------| r_work (start): 0.3078 rms_B_bonded: 1.73 r_work: 0.2984 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.2866 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.2866 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8401 moved from start: 0.2487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 14128 Z= 0.158 Angle : 0.658 12.857 19197 Z= 0.331 Chirality : 0.045 0.421 2197 Planarity : 0.004 0.044 2334 Dihedral : 7.227 73.697 2170 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 3.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.29 % Favored : 98.71 % Rotamer: Outliers : 3.03 % Allowed : 17.51 % Favored : 79.46 % 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: 1.12 (0.21), residues: 1630 helix: 1.81 (0.22), residues: 605 sheet: 0.82 (0.24), residues: 445 loop : -0.41 (0.23), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP C 349 HIS 0.005 0.001 HIS C 254 PHE 0.019 0.002 PHE E 356 TYR 0.022 0.002 TYR E 362 ARG 0.003 0.000 ARG E 308 Details of bonding type rmsd link_NAG-ASN : bond 0.01368 ( 10) link_NAG-ASN : angle 6.84968 ( 30) hydrogen bonds : bond 0.06853 ( 706) hydrogen bonds : angle 4.28755 ( 2295) SS BOND : bond 0.00500 ( 1) SS BOND : angle 1.07847 ( 2) covalent geometry : bond 0.00336 (14116) covalent geometry : angle 0.59990 (19165) Misc. bond : bond 0.00115 ( 1) *********************** 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 : 2.108 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 235 ASP cc_start: 0.7215 (p0) cc_final: 0.6521 (t70) REVERT: A 269 ASN cc_start: 0.8085 (OUTLIER) cc_final: 0.7659 (m-40) REVERT: B 82 ASP cc_start: 0.6775 (m-30) cc_final: 0.6296 (p0) REVERT: B 108 LEU cc_start: 0.8829 (OUTLIER) cc_final: 0.8496 (mt) REVERT: B 116 MET cc_start: 0.8323 (mtt) cc_final: 0.7997 (mtm) REVERT: B 131 GLU cc_start: 0.7625 (tp30) cc_final: 0.7328 (tp30) REVERT: B 223 GLU cc_start: 0.8490 (pt0) cc_final: 0.7926 (pp20) REVERT: B 249 LEU cc_start: 0.7970 (OUTLIER) cc_final: 0.7760 (tp) REVERT: C 131 GLU cc_start: 0.8232 (mm-30) cc_final: 0.7839 (mm-30) REVERT: C 151 LYS cc_start: 0.8445 (OUTLIER) cc_final: 0.8084 (mmpt) REVERT: C 235 ASP cc_start: 0.7368 (m-30) cc_final: 0.6872 (t0) REVERT: D 148 ARG cc_start: 0.7462 (ptp-170) cc_final: 0.6902 (ptt180) REVERT: D 183 ASP cc_start: 0.6401 (p0) cc_final: 0.6059 (p0) REVERT: D 326 THR cc_start: 0.8457 (m) cc_final: 0.8088 (p) REVERT: D 457 LYS cc_start: 0.7022 (tttp) cc_final: 0.6181 (mttm) REVERT: E 197 MET cc_start: 0.8178 (ptm) cc_final: 0.7905 (ptt) REVERT: E 232 LYS cc_start: 0.7580 (mttt) cc_final: 0.6953 (mtpp) REVERT: E 295 MET cc_start: 0.8407 (mmm) cc_final: 0.8043 (mmp) outliers start: 45 outliers final: 38 residues processed: 254 average time/residue: 1.6687 time to fit residues: 464.6031 Evaluate side-chains 264 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 222 time to evaluate : 1.526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 234 ASN Chi-restraints excluded: chain A residue 246 SER Chi-restraints excluded: chain A residue 264 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 249 LEU Chi-restraints excluded: chain B residue 256 THR Chi-restraints excluded: chain B residue 263 SER Chi-restraints excluded: chain B residue 264 SER Chi-restraints excluded: chain B residue 331 VAL Chi-restraints excluded: chain B residue 360 LEU 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 140 ASN Chi-restraints excluded: chain C residue 151 LYS Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 234 ASN Chi-restraints excluded: chain C residue 325 SER Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain C residue 370 THR Chi-restraints excluded: chain D residue 102 ASP Chi-restraints excluded: chain D residue 151 LYS Chi-restraints excluded: chain D residue 180 VAL Chi-restraints excluded: chain D residue 249 LEU Chi-restraints excluded: chain D residue 256 THR Chi-restraints excluded: chain D residue 257 THR Chi-restraints excluded: chain D residue 288 THR Chi-restraints excluded: chain D residue 358 SER 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 318 ILE Chi-restraints excluded: chain E residue 338 VAL Chi-restraints excluded: chain E residue 360 LEU 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: 2.9990 chunk 96 optimal weight: 0.3980 chunk 61 optimal weight: 1.9990 chunk 160 optimal weight: 4.9990 chunk 112 optimal weight: 4.9990 chunk 40 optimal weight: 0.6980 chunk 95 optimal weight: 7.9990 chunk 60 optimal weight: 0.6980 chunk 55 optimal weight: 1.9990 chunk 80 optimal weight: 4.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- 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 = 0.3368 r_free = 0.3368 target = 0.127369 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.105633 restraints weight = 16223.891| |-----------------------------------------------------------------------------| r_work (start): 0.3083 rms_B_bonded: 1.63 r_work: 0.2993 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.2877 rms_B_bonded: 3.43 restraints_weight: 0.2500 r_work (final): 0.2877 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8405 moved from start: 0.2549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 14128 Z= 0.158 Angle : 0.638 12.789 19197 Z= 0.326 Chirality : 0.045 0.422 2197 Planarity : 0.004 0.045 2334 Dihedral : 7.159 73.183 2170 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 3.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 3.23 % Allowed : 17.58 % Favored : 79.19 % 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: 1.15 (0.20), residues: 1630 helix: 1.81 (0.22), residues: 605 sheet: 0.85 (0.24), residues: 440 loop : -0.37 (0.23), residues: 585 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP C 349 HIS 0.005 0.001 HIS C 254 PHE 0.018 0.002 PHE E 356 TYR 0.023 0.002 TYR B 362 ARG 0.003 0.000 ARG B 242 Details of bonding type rmsd link_NAG-ASN : bond 0.01125 ( 10) link_NAG-ASN : angle 5.97207 ( 30) hydrogen bonds : bond 0.06869 ( 706) hydrogen bonds : angle 4.27643 ( 2295) SS BOND : bond 0.00495 ( 1) SS BOND : angle 1.13035 ( 2) covalent geometry : bond 0.00340 (14116) covalent geometry : angle 0.59350 (19165) Misc. bond : bond 0.00109 ( 1) ********************** 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 274 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 226 time to evaluate : 1.466 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 235 ASP cc_start: 0.7235 (p0) cc_final: 0.6580 (t70) REVERT: A 269 ASN cc_start: 0.8076 (OUTLIER) cc_final: 0.7651 (m-40) REVERT: B 82 ASP cc_start: 0.6794 (m-30) cc_final: 0.6331 (p0) REVERT: B 108 LEU cc_start: 0.8830 (OUTLIER) cc_final: 0.8476 (mt) REVERT: B 116 MET cc_start: 0.8309 (mtt) cc_final: 0.7971 (mtm) REVERT: B 131 GLU cc_start: 0.7632 (tp30) cc_final: 0.7318 (tp30) REVERT: B 223 GLU cc_start: 0.8456 (pt0) cc_final: 0.7916 (pp20) REVERT: B 249 LEU cc_start: 0.7968 (OUTLIER) cc_final: 0.7734 (tp) REVERT: C 151 LYS cc_start: 0.8434 (OUTLIER) cc_final: 0.8052 (mmpt) REVERT: C 235 ASP cc_start: 0.7352 (m-30) cc_final: 0.6844 (t0) REVERT: D 148 ARG cc_start: 0.7484 (ptp-170) cc_final: 0.6920 (ptt180) REVERT: D 183 ASP cc_start: 0.6566 (p0) cc_final: 0.6220 (p0) REVERT: D 326 THR cc_start: 0.8523 (m) cc_final: 0.8167 (p) REVERT: D 457 LYS cc_start: 0.7048 (tttp) cc_final: 0.6218 (mttm) REVERT: E 116 MET cc_start: 0.8233 (mtm) cc_final: 0.7814 (mtp) REVERT: E 197 MET cc_start: 0.8191 (ptm) cc_final: 0.7907 (ptt) REVERT: E 232 LYS cc_start: 0.7565 (mttt) cc_final: 0.6938 (mtpp) REVERT: E 295 MET cc_start: 0.8409 (mmm) cc_final: 0.8035 (mmp) outliers start: 48 outliers final: 37 residues processed: 253 average time/residue: 1.2478 time to fit residues: 344.9370 Evaluate side-chains 267 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 226 time to evaluate : 1.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 234 ASN Chi-restraints excluded: chain A residue 246 SER Chi-restraints excluded: chain A residue 264 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 249 LEU Chi-restraints excluded: chain B residue 256 THR Chi-restraints excluded: chain B residue 263 SER Chi-restraints excluded: chain B residue 264 SER 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 140 ASN Chi-restraints excluded: chain C residue 151 LYS Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 234 ASN Chi-restraints excluded: chain C residue 325 SER Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain C residue 370 THR Chi-restraints excluded: chain D residue 102 ASP Chi-restraints excluded: chain D residue 151 LYS Chi-restraints excluded: chain D residue 180 VAL Chi-restraints excluded: chain D residue 249 LEU Chi-restraints excluded: chain D residue 256 THR Chi-restraints excluded: chain D residue 257 THR Chi-restraints excluded: chain D residue 288 THR Chi-restraints excluded: chain D residue 358 SER 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 318 ILE 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: 4.9990 chunk 112 optimal weight: 0.9980 chunk 154 optimal weight: 1.9990 chunk 129 optimal weight: 4.9990 chunk 49 optimal weight: 3.9990 chunk 52 optimal weight: 2.9990 chunk 0 optimal weight: 8.9990 chunk 38 optimal weight: 0.0050 chunk 12 optimal weight: 0.6980 chunk 44 optimal weight: 4.9990 chunk 45 optimal weight: 2.9990 overall best weight: 1.3398 ------------------------------------------------------------------------------- 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 = 0.3359 r_free = 0.3359 target = 0.126774 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.104845 restraints weight = 16256.214| |-----------------------------------------------------------------------------| r_work (start): 0.3084 rms_B_bonded: 1.65 r_work: 0.2993 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.2877 rms_B_bonded: 3.45 restraints_weight: 0.2500 r_work (final): 0.2877 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8418 moved from start: 0.2557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 14128 Z= 0.168 Angle : 0.649 12.714 19197 Z= 0.332 Chirality : 0.045 0.423 2197 Planarity : 0.004 0.045 2334 Dihedral : 7.125 72.862 2170 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 2.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 3.10 % Allowed : 17.85 % Favored : 79.06 % 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: 1.04 (0.21), residues: 1630 helix: 1.74 (0.22), residues: 605 sheet: 0.62 (0.23), residues: 470 loop : -0.34 (0.24), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP C 349 HIS 0.006 0.001 HIS C 254 PHE 0.018 0.002 PHE A 356 TYR 0.023 0.002 TYR E 362 ARG 0.003 0.000 ARG E 308 Details of bonding type rmsd link_NAG-ASN : bond 0.01092 ( 10) link_NAG-ASN : angle 5.95021 ( 30) hydrogen bonds : bond 0.07162 ( 706) hydrogen bonds : angle 4.33047 ( 2295) SS BOND : bond 0.00536 ( 1) SS BOND : angle 1.20915 ( 2) covalent geometry : bond 0.00367 (14116) covalent geometry : angle 0.60497 (19165) Misc. bond : bond 0.00113 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10441.35 seconds wall clock time: 182 minutes 54.64 seconds (10974.64 seconds total)