Starting phenix.real_space_refine on Sat May 17 05:07:05 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ed1_47930/05_2025/9ed1_47930.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ed1_47930/05_2025/9ed1_47930.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9ed1_47930/05_2025/9ed1_47930.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ed1_47930/05_2025/9ed1_47930.map" model { file = "/net/cci-nas-00/data/ceres_data/9ed1_47930/05_2025/9ed1_47930.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ed1_47930/05_2025/9ed1_47930.cif" } resolution = 3.5 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= 1.000 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: 6 Type Number sf(0) Gaussians Ca 12 9.91 5 K 5 8.98 5 S 108 5.16 5 C 9892 2.51 5 N 2740 2.21 5 O 2692 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 15449 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 2781 Number of conformers: 1 Conformer: "" Number of residues, atoms: 360, 2781 Classifications: {'peptide': 360} Incomplete info: {'truncation_to_alanine': 25} Link IDs: {'PTRANS': 7, 'TRANS': 352} Chain breaks: 1 Unresolved non-hydrogen bonds: 79 Unresolved non-hydrogen angles: 100 Unresolved non-hydrogen dihedrals: 61 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 1, 'ASN:plan1': 3, 'ASP:plan': 3, 'GLU:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 50 Chain: "B" Number of atoms: 2781 Number of conformers: 1 Conformer: "" Number of residues, atoms: 360, 2781 Classifications: {'peptide': 360} Incomplete info: {'truncation_to_alanine': 25} Link IDs: {'PTRANS': 7, 'TRANS': 352} Chain breaks: 1 Unresolved non-hydrogen bonds: 79 Unresolved non-hydrogen angles: 100 Unresolved non-hydrogen dihedrals: 61 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 1, 'ASN:plan1': 3, 'ASP:plan': 3, 'GLU:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 50 Chain: "C" Number of atoms: 2781 Number of conformers: 1 Conformer: "" Number of residues, atoms: 360, 2781 Classifications: {'peptide': 360} Incomplete info: {'truncation_to_alanine': 25} Link IDs: {'PTRANS': 7, 'TRANS': 352} Chain breaks: 1 Unresolved non-hydrogen bonds: 79 Unresolved non-hydrogen angles: 100 Unresolved non-hydrogen dihedrals: 61 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 1, 'ASN:plan1': 3, 'ASP:plan': 3, 'GLU:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 50 Chain: "D" Number of atoms: 2781 Number of conformers: 1 Conformer: "" Number of residues, atoms: 360, 2781 Classifications: {'peptide': 360} Incomplete info: {'truncation_to_alanine': 25} Link IDs: {'PTRANS': 7, 'TRANS': 352} Chain breaks: 1 Unresolved non-hydrogen bonds: 79 Unresolved non-hydrogen angles: 100 Unresolved non-hydrogen dihedrals: 61 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 1, 'ASN:plan1': 3, 'ASP:plan': 3, 'GLU:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 50 Chain: "E" Number of atoms: 1077 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 1077 Classifications: {'peptide': 145} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 2, 'TRANS': 142} Unresolved non-hydrogen bonds: 66 Unresolved non-hydrogen angles: 82 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 6, 'ARG:plan': 2, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 50 Chain: "F" Number of atoms: 1077 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 1077 Classifications: {'peptide': 145} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 2, 'TRANS': 142} Unresolved non-hydrogen bonds: 66 Unresolved non-hydrogen angles: 82 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 6, 'ARG:plan': 2, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 50 Chain: "G" Number of atoms: 1077 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 1077 Classifications: {'peptide': 145} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 2, 'TRANS': 142} Unresolved non-hydrogen bonds: 66 Unresolved non-hydrogen angles: 82 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 6, 'ARG:plan': 2, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 50 Chain: "H" Number of atoms: 1077 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 1077 Classifications: {'peptide': 145} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 2, 'TRANS': 142} Unresolved non-hydrogen bonds: 66 Unresolved non-hydrogen angles: 82 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 6, 'ARG:plan': 2, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 50 Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' K': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' K': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' CA': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "F" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' CA': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "G" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' CA': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "H" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' CA': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 9.90, per 1000 atoms: 0.64 Number of scatterers: 15449 At special positions: 0 Unit cell: (138.46, 138.46, 107.5, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Ca 12 19.99 K 5 19.00 S 108 16.00 O 2692 8.00 N 2740 7.00 C 9892 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.91 Conformation dependent library (CDL) restraints added in 1.9 seconds 3992 Ramachandran restraints generated. 1996 Oldfield, 0 Emsley, 1996 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3752 Finding SS restraints... Secondary structure from input PDB file: 108 helices and 0 sheets defined 71.9% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.41 Creating SS restraints... Processing helix chain 'A' and resid 14 through 19 removed outlier: 3.509A pdb=" N LEU A 19 " --> pdb=" O ARG A 15 " (cutoff:3.500A) Processing helix chain 'A' and resid 30 through 38 removed outlier: 3.597A pdb=" N GLY A 36 " --> pdb=" O LEU A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 39 through 46 removed outlier: 3.577A pdb=" N HIS A 43 " --> pdb=" O LEU A 39 " (cutoff:3.500A) Processing helix chain 'A' and resid 57 through 92 removed outlier: 3.853A pdb=" N VAL A 61 " --> pdb=" O TYR A 57 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N LYS A 62 " --> pdb=" O LEU A 58 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N CYS A 63 " --> pdb=" O PHE A 59 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N SER A 66 " --> pdb=" O LYS A 62 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LEU A 75 " --> pdb=" O LEU A 71 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N VAL A 77 " --> pdb=" O LEU A 73 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N ALA A 78 " --> pdb=" O CYS A 74 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N GLU A 83 " --> pdb=" O PHE A 79 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N VAL A 84 " --> pdb=" O HIS A 80 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N GLN A 85 " --> pdb=" O ALA A 81 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N LEU A 86 " --> pdb=" O LYS A 82 " (cutoff:3.500A) Processing helix chain 'A' and resid 95 through 100 removed outlier: 4.105A pdb=" N ALA A 99 " --> pdb=" O ASP A 95 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LEU A 100 " --> pdb=" O TRP A 96 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 95 through 100' Processing helix chain 'A' and resid 103 through 115 removed outlier: 4.123A pdb=" N VAL A 109 " --> pdb=" O ALA A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 149 through 155 Processing helix chain 'A' and resid 156 through 160 removed outlier: 3.547A pdb=" N LEU A 160 " --> pdb=" O LEU A 157 " (cutoff:3.500A) Processing helix chain 'A' and resid 161 through 169 removed outlier: 4.622A pdb=" N ARG A 165 " --> pdb=" O TYR A 161 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU A 169 " --> pdb=" O ARG A 165 " (cutoff:3.500A) Processing helix chain 'A' and resid 176 through 184 removed outlier: 3.543A pdb=" N SER A 181 " --> pdb=" O ALA A 177 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N ILE A 182 " --> pdb=" O SER A 178 " (cutoff:3.500A) Processing helix chain 'A' and resid 191 through 203 removed outlier: 3.633A pdb=" N VAL A 195 " --> pdb=" O ARG A 191 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ALA A 196 " --> pdb=" O HIS A 192 " (cutoff:3.500A) Processing helix chain 'A' and resid 203 through 223 removed outlier: 4.127A pdb=" N LEU A 207 " --> pdb=" O HIS A 203 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N TRP A 216 " --> pdb=" O THR A 212 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N LEU A 217 " --> pdb=" O LEU A 213 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N THR A 218 " --> pdb=" O GLY A 214 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N THR A 219 " --> pdb=" O LEU A 215 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N ALA A 220 " --> pdb=" O TRP A 216 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N TRP A 221 " --> pdb=" O LEU A 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 223 through 228 Processing helix chain 'A' and resid 236 through 241 Processing helix chain 'A' and resid 242 through 249 removed outlier: 3.873A pdb=" N ILE A 246 " --> pdb=" O TRP A 242 " (cutoff:3.500A) Processing helix chain 'A' and resid 262 through 289 removed outlier: 4.280A pdb=" N VAL A 266 " --> pdb=" O TRP A 262 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N CYS A 267 " --> pdb=" O GLY A 263 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N LEU A 268 " --> pdb=" O LYS A 264 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N GLY A 271 " --> pdb=" O CYS A 267 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N VAL A 272 " --> pdb=" O LEU A 268 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N MET A 273 " --> pdb=" O CYS A 269 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N LEU A 289 " --> pdb=" O VAL A 285 " (cutoff:3.500A) Processing helix chain 'A' and resid 292 through 332 removed outlier: 3.854A pdb=" N VAL A 298 " --> pdb=" O ALA A 294 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ILE A 305 " --> pdb=" O PHE A 301 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N GLN A 306 " --> pdb=" O MET A 302 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N ALA A 316 " --> pdb=" O LYS A 312 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N ARG A 317 " --> pdb=" O GLU A 313 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N VAL A 318 " --> pdb=" O SER A 314 " (cutoff:3.500A) removed outlier: 4.709A pdb=" N LEU A 319 " --> pdb=" O ALA A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 336 through 369 removed outlier: 3.811A pdb=" N ARG A 342 " --> pdb=" O ARG A 338 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N LYS A 343 " --> pdb=" O ARG A 339 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LEU A 344 " --> pdb=" O HIS A 340 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N LEU A 345 " --> pdb=" O GLN A 341 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N ALA A 346 " --> pdb=" O ARG A 342 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ASN A 349 " --> pdb=" O LEU A 345 " (cutoff:3.500A) Processing helix chain 'A' and resid 372 through 385 Processing helix chain 'B' and resid 31 through 50 removed outlier: 3.713A pdb=" N GLY B 36 " --> pdb=" O LEU B 32 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N ILE B 37 " --> pdb=" O ALA B 33 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N MET B 40 " --> pdb=" O GLY B 36 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N VAL B 41 " --> pdb=" O ILE B 37 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N LEU B 42 " --> pdb=" O GLY B 38 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N HIS B 43 " --> pdb=" O LEU B 39 " (cutoff:3.500A) Processing helix chain 'B' and resid 57 through 71 removed outlier: 3.664A pdb=" N VAL B 61 " --> pdb=" O TYR B 57 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N LYS B 62 " --> pdb=" O LEU B 58 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N CYS B 63 " --> pdb=" O PHE B 59 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N SER B 66 " --> pdb=" O LYS B 62 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N THR B 69 " --> pdb=" O ILE B 65 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N PHE B 70 " --> pdb=" O SER B 66 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LEU B 71 " --> pdb=" O ILE B 67 " (cutoff:3.500A) Processing helix chain 'B' and resid 72 through 91 removed outlier: 3.842A pdb=" N VAL B 77 " --> pdb=" O LEU B 73 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N ALA B 78 " --> pdb=" O CYS B 74 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N VAL B 84 " --> pdb=" O HIS B 80 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N GLN B 85 " --> pdb=" O ALA B 81 " (cutoff:3.500A) Processing helix chain 'B' and resid 95 through 100 removed outlier: 4.096A pdb=" N ALA B 99 " --> pdb=" O ASP B 95 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N LEU B 100 " --> pdb=" O TRP B 96 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 95 through 100' Processing helix chain 'B' and resid 103 through 115 removed outlier: 3.853A pdb=" N VAL B 109 " --> pdb=" O ALA B 105 " (cutoff:3.500A) Processing helix chain 'B' and resid 149 through 155 removed outlier: 3.737A pdb=" N LEU B 154 " --> pdb=" O ALA B 150 " (cutoff:3.500A) Processing helix chain 'B' and resid 156 through 160 removed outlier: 3.551A pdb=" N LEU B 160 " --> pdb=" O LEU B 157 " (cutoff:3.500A) Processing helix chain 'B' and resid 161 through 171 removed outlier: 4.595A pdb=" N ARG B 165 " --> pdb=" O TYR B 161 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LEU B 169 " --> pdb=" O ARG B 165 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ARG B 170 " --> pdb=" O ALA B 166 " (cutoff:3.500A) Processing helix chain 'B' and resid 190 through 203 removed outlier: 3.535A pdb=" N PHE B 194 " --> pdb=" O PHE B 190 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N VAL B 195 " --> pdb=" O ARG B 191 " (cutoff:3.500A) Processing helix chain 'B' and resid 203 through 223 removed outlier: 4.183A pdb=" N LEU B 207 " --> pdb=" O HIS B 203 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N TRP B 216 " --> pdb=" O THR B 212 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N LEU B 217 " --> pdb=" O LEU B 213 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N THR B 218 " --> pdb=" O GLY B 214 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N THR B 219 " --> pdb=" O LEU B 215 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N ALA B 220 " --> pdb=" O TRP B 216 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N TRP B 221 " --> pdb=" O LEU B 217 " (cutoff:3.500A) Processing helix chain 'B' and resid 223 through 228 Processing helix chain 'B' and resid 236 through 241 Processing helix chain 'B' and resid 242 through 249 removed outlier: 3.920A pdb=" N ILE B 246 " --> pdb=" O TRP B 242 " (cutoff:3.500A) Processing helix chain 'B' and resid 262 through 289 removed outlier: 4.259A pdb=" N VAL B 266 " --> pdb=" O TRP B 262 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N CYS B 267 " --> pdb=" O GLY B 263 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N LEU B 268 " --> pdb=" O LYS B 264 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N GLY B 271 " --> pdb=" O CYS B 267 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N VAL B 272 " --> pdb=" O LEU B 268 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N ALA B 283 " --> pdb=" O ALA B 279 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N VAL B 284 " --> pdb=" O LEU B 280 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N LEU B 289 " --> pdb=" O VAL B 285 " (cutoff:3.500A) Processing helix chain 'B' and resid 292 through 315 removed outlier: 3.877A pdb=" N HIS B 297 " --> pdb=" O LYS B 293 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N VAL B 298 " --> pdb=" O ALA B 294 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ASP B 304 " --> pdb=" O ASN B 300 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N ILE B 305 " --> pdb=" O PHE B 301 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N GLN B 306 " --> pdb=" O MET B 302 " (cutoff:3.500A) Processing helix chain 'B' and resid 315 through 332 removed outlier: 4.547A pdb=" N LEU B 319 " --> pdb=" O ALA B 315 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N GLN B 320 " --> pdb=" O ALA B 316 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N GLU B 321 " --> pdb=" O ARG B 317 " (cutoff:3.500A) Processing helix chain 'B' and resid 336 through 369 removed outlier: 4.202A pdb=" N ARG B 342 " --> pdb=" O ARG B 338 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N LYS B 343 " --> pdb=" O ARG B 339 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LEU B 344 " --> pdb=" O HIS B 340 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N LEU B 345 " --> pdb=" O GLN B 341 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N ALA B 346 " --> pdb=" O ARG B 342 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ASN B 349 " --> pdb=" O LEU B 345 " (cutoff:3.500A) Processing helix chain 'B' and resid 371 through 385 removed outlier: 4.221A pdb=" N HIS B 375 " --> pdb=" O ILE B 371 " (cutoff:3.500A) Processing helix chain 'C' and resid 31 through 36 removed outlier: 3.629A pdb=" N GLY C 36 " --> pdb=" O LEU C 32 " (cutoff:3.500A) Processing helix chain 'C' and resid 36 through 50 removed outlier: 3.907A pdb=" N VAL C 41 " --> pdb=" O ILE C 37 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N LEU C 42 " --> pdb=" O GLY C 38 " (cutoff:3.500A) Processing helix chain 'C' and resid 59 through 91 removed outlier: 3.645A pdb=" N LEU C 75 " --> pdb=" O LEU C 71 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N VAL C 77 " --> pdb=" O LEU C 73 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N ALA C 78 " --> pdb=" O CYS C 74 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N PHE C 87 " --> pdb=" O GLU C 83 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N MET C 88 " --> pdb=" O VAL C 84 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N THR C 89 " --> pdb=" O GLN C 85 " (cutoff:3.500A) Processing helix chain 'C' and resid 95 through 100 removed outlier: 4.080A pdb=" N ALA C 99 " --> pdb=" O ASP C 95 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N LEU C 100 " --> pdb=" O TRP C 96 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 95 through 100' Processing helix chain 'C' and resid 103 through 115 removed outlier: 3.849A pdb=" N VAL C 109 " --> pdb=" O ALA C 105 " (cutoff:3.500A) Processing helix chain 'C' and resid 148 through 155 removed outlier: 3.864A pdb=" N LEU C 154 " --> pdb=" O ALA C 150 " (cutoff:3.500A) Processing helix chain 'C' and resid 156 through 161 removed outlier: 3.598A pdb=" N ARG C 159 " --> pdb=" O MET C 156 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LEU C 160 " --> pdb=" O LEU C 157 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N TYR C 161 " --> pdb=" O LEU C 158 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 156 through 161' Processing helix chain 'C' and resid 162 through 171 Processing helix chain 'C' and resid 176 through 184 removed outlier: 4.450A pdb=" N ILE C 182 " --> pdb=" O SER C 178 " (cutoff:3.500A) Processing helix chain 'C' and resid 191 through 203 removed outlier: 3.514A pdb=" N VAL C 195 " --> pdb=" O ARG C 191 " (cutoff:3.500A) Processing helix chain 'C' and resid 203 through 223 removed outlier: 3.984A pdb=" N LEU C 207 " --> pdb=" O HIS C 203 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N TRP C 216 " --> pdb=" O THR C 212 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N LEU C 217 " --> pdb=" O LEU C 213 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N THR C 218 " --> pdb=" O GLY C 214 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N THR C 219 " --> pdb=" O LEU C 215 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N ALA C 220 " --> pdb=" O TRP C 216 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N TRP C 221 " --> pdb=" O LEU C 217 " (cutoff:3.500A) Processing helix chain 'C' and resid 223 through 228 Processing helix chain 'C' and resid 236 through 241 Processing helix chain 'C' and resid 242 through 249 removed outlier: 3.935A pdb=" N ILE C 246 " --> pdb=" O TRP C 242 " (cutoff:3.500A) Processing helix chain 'C' and resid 260 through 264 Processing helix chain 'C' and resid 265 through 289 removed outlier: 3.597A pdb=" N GLY C 271 " --> pdb=" O CYS C 267 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N ALA C 283 " --> pdb=" O ALA C 279 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N VAL C 284 " --> pdb=" O LEU C 280 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N LEU C 289 " --> pdb=" O VAL C 285 " (cutoff:3.500A) Processing helix chain 'C' and resid 292 through 303 Processing helix chain 'C' and resid 303 through 332 removed outlier: 3.718A pdb=" N TYR C 307 " --> pdb=" O MET C 303 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N VAL C 318 " --> pdb=" O SER C 314 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N LEU C 319 " --> pdb=" O ALA C 315 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N GLN C 320 " --> pdb=" O ALA C 316 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N GLU C 321 " --> pdb=" O ARG C 317 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N TYR C 326 " --> pdb=" O ALA C 322 " (cutoff:3.500A) Processing helix chain 'C' and resid 336 through 369 removed outlier: 4.420A pdb=" N ARG C 342 " --> pdb=" O ARG C 338 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N LYS C 343 " --> pdb=" O ARG C 339 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N LEU C 345 " --> pdb=" O GLN C 341 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ASN C 349 " --> pdb=" O LEU C 345 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N VAL C 369 " --> pdb=" O VAL C 365 " (cutoff:3.500A) Processing helix chain 'C' and resid 372 through 385 removed outlier: 3.776A pdb=" N MET C 376 " --> pdb=" O SER C 372 " (cutoff:3.500A) Processing helix chain 'D' and resid 27 through 50 removed outlier: 3.898A pdb=" N LEU D 32 " --> pdb=" O TRP D 28 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N ALA D 33 " --> pdb=" O ALA D 29 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLY D 36 " --> pdb=" O LEU D 32 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N MET D 40 " --> pdb=" O GLY D 36 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N VAL D 41 " --> pdb=" O ILE D 37 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N LEU D 42 " --> pdb=" O GLY D 38 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N HIS D 43 " --> pdb=" O LEU D 39 " (cutoff:3.500A) Processing helix chain 'D' and resid 57 through 71 removed outlier: 3.680A pdb=" N VAL D 61 " --> pdb=" O TYR D 57 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N LYS D 62 " --> pdb=" O LEU D 58 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N CYS D 63 " --> pdb=" O PHE D 59 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N SER D 66 " --> pdb=" O LYS D 62 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N THR D 69 " --> pdb=" O ILE D 65 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N PHE D 70 " --> pdb=" O SER D 66 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LEU D 71 " --> pdb=" O ILE D 67 " (cutoff:3.500A) Processing helix chain 'D' and resid 72 through 91 removed outlier: 3.723A pdb=" N VAL D 77 " --> pdb=" O LEU D 73 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N ALA D 78 " --> pdb=" O CYS D 74 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N GLU D 83 " --> pdb=" O PHE D 79 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N VAL D 84 " --> pdb=" O HIS D 80 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N GLN D 85 " --> pdb=" O ALA D 81 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N LEU D 86 " --> pdb=" O LYS D 82 " (cutoff:3.500A) Processing helix chain 'D' and resid 95 through 100 removed outlier: 4.045A pdb=" N ALA D 99 " --> pdb=" O ASP D 95 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LEU D 100 " --> pdb=" O TRP D 96 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 95 through 100' Processing helix chain 'D' and resid 103 through 115 removed outlier: 3.622A pdb=" N ILE D 108 " --> pdb=" O GLN D 104 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N VAL D 109 " --> pdb=" O ALA D 105 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LEU D 110 " --> pdb=" O ALA D 106 " (cutoff:3.500A) Processing helix chain 'D' and resid 149 through 155 removed outlier: 3.701A pdb=" N LEU D 154 " --> pdb=" O ALA D 150 " (cutoff:3.500A) Processing helix chain 'D' and resid 156 through 161 removed outlier: 3.528A pdb=" N LEU D 160 " --> pdb=" O LEU D 157 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N TYR D 161 " --> pdb=" O LEU D 158 " (cutoff:3.500A) Processing helix chain 'D' and resid 162 through 170 Processing helix chain 'D' and resid 176 through 184 removed outlier: 3.582A pdb=" N SER D 181 " --> pdb=" O ALA D 177 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N ILE D 182 " --> pdb=" O SER D 178 " (cutoff:3.500A) Processing helix chain 'D' and resid 191 through 203 Processing helix chain 'D' and resid 203 through 219 removed outlier: 4.007A pdb=" N LEU D 207 " --> pdb=" O HIS D 203 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N TRP D 216 " --> pdb=" O THR D 212 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N LEU D 217 " --> pdb=" O LEU D 213 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N THR D 218 " --> pdb=" O GLY D 214 " (cutoff:3.500A) Processing helix chain 'D' and resid 223 through 228 removed outlier: 3.527A pdb=" N ARG D 228 " --> pdb=" O SER D 224 " (cutoff:3.500A) Processing helix chain 'D' and resid 236 through 241 Processing helix chain 'D' and resid 242 through 249 removed outlier: 3.890A pdb=" N ILE D 246 " --> pdb=" O TRP D 242 " (cutoff:3.500A) Processing helix chain 'D' and resid 265 through 286 removed outlier: 3.769A pdb=" N GLY D 271 " --> pdb=" O CYS D 267 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N VAL D 272 " --> pdb=" O LEU D 268 " (cutoff:3.500A) Processing helix chain 'D' and resid 292 through 315 removed outlier: 3.829A pdb=" N HIS D 297 " --> pdb=" O LYS D 293 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N VAL D 298 " --> pdb=" O ALA D 294 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N ILE D 305 " --> pdb=" O PHE D 301 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N GLN D 306 " --> pdb=" O MET D 302 " (cutoff:3.500A) Processing helix chain 'D' and resid 318 through 332 Processing helix chain 'D' and resid 336 through 368 removed outlier: 3.783A pdb=" N ARG D 342 " --> pdb=" O ARG D 338 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N LYS D 343 " --> pdb=" O ARG D 339 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LEU D 344 " --> pdb=" O HIS D 340 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N LEU D 345 " --> pdb=" O GLN D 341 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N ALA D 346 " --> pdb=" O ARG D 342 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ASN D 349 " --> pdb=" O LEU D 345 " (cutoff:3.500A) Processing helix chain 'D' and resid 369 through 371 No H-bonds generated for 'chain 'D' and resid 369 through 371' Processing helix chain 'D' and resid 372 through 383 removed outlier: 3.591A pdb=" N MET D 376 " --> pdb=" O SER D 372 " (cutoff:3.500A) Processing helix chain 'E' and resid 7 through 20 removed outlier: 3.570A pdb=" N LEU E 18 " --> pdb=" O GLU E 14 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N PHE E 19 " --> pdb=" O ALA E 15 " (cutoff:3.500A) Processing helix chain 'E' and resid 28 through 39 Processing helix chain 'E' and resid 44 through 51 Processing helix chain 'E' and resid 65 through 76 removed outlier: 3.630A pdb=" N THR E 70 " --> pdb=" O PRO E 66 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N MET E 71 " --> pdb=" O GLU E 67 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ARG E 74 " --> pdb=" O THR E 70 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N MET E 76 " --> pdb=" O MET E 72 " (cutoff:3.500A) Processing helix chain 'E' and resid 101 through 112 removed outlier: 3.862A pdb=" N THR E 110 " --> pdb=" O ARG E 106 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LEU E 112 " --> pdb=" O VAL E 108 " (cutoff:3.500A) Processing helix chain 'E' and resid 117 through 129 Processing helix chain 'E' and resid 137 through 147 Processing helix chain 'F' and resid 5 through 17 Processing helix chain 'F' and resid 28 through 39 removed outlier: 3.533A pdb=" N GLY F 33 " --> pdb=" O THR F 29 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N THR F 34 " --> pdb=" O LYS F 30 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N VAL F 35 " --> pdb=" O GLU F 31 " (cutoff:3.500A) Processing helix chain 'F' and resid 44 through 56 removed outlier: 3.909A pdb=" N VAL F 55 " --> pdb=" O MET F 51 " (cutoff:3.500A) Processing helix chain 'F' and resid 65 through 76 removed outlier: 3.707A pdb=" N THR F 70 " --> pdb=" O PRO F 66 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N MET F 71 " --> pdb=" O GLU F 67 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ARG F 74 " --> pdb=" O THR F 70 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N MET F 76 " --> pdb=" O MET F 72 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 87 Processing helix chain 'F' and resid 101 through 112 removed outlier: 3.777A pdb=" N THR F 110 " --> pdb=" O ARG F 106 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LEU F 112 " --> pdb=" O VAL F 108 " (cutoff:3.500A) Processing helix chain 'F' and resid 117 through 129 Processing helix chain 'F' and resid 137 through 147 Processing helix chain 'G' and resid 5 through 21 removed outlier: 3.578A pdb=" N LEU G 18 " --> pdb=" O GLU G 14 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N PHE G 19 " --> pdb=" O ALA G 15 " (cutoff:3.500A) Processing helix chain 'G' and resid 28 through 39 removed outlier: 3.519A pdb=" N GLY G 33 " --> pdb=" O THR G 29 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N THR G 34 " --> pdb=" O LYS G 30 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N VAL G 35 " --> pdb=" O GLU G 31 " (cutoff:3.500A) Processing helix chain 'G' and resid 44 through 54 removed outlier: 3.611A pdb=" N GLU G 54 " --> pdb=" O ASP G 50 " (cutoff:3.500A) Processing helix chain 'G' and resid 64 through 73 removed outlier: 3.693A pdb=" N THR G 70 " --> pdb=" O PRO G 66 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N MET G 71 " --> pdb=" O GLU G 67 " (cutoff:3.500A) Processing helix chain 'G' and resid 82 through 87 Processing helix chain 'G' and resid 101 through 112 removed outlier: 3.507A pdb=" N LEU G 105 " --> pdb=" O SER G 101 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N THR G 110 " --> pdb=" O ARG G 106 " (cutoff:3.500A) Processing helix chain 'G' and resid 117 through 129 Processing helix chain 'G' and resid 137 through 147 Processing helix chain 'H' and resid 5 through 17 Processing helix chain 'H' and resid 30 through 39 removed outlier: 3.651A pdb=" N THR H 34 " --> pdb=" O LYS H 30 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N VAL H 35 " --> pdb=" O GLU H 31 " (cutoff:3.500A) Processing helix chain 'H' and resid 44 through 56 removed outlier: 3.827A pdb=" N ILE H 52 " --> pdb=" O LEU H 48 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N VAL H 55 " --> pdb=" O MET H 51 " (cutoff:3.500A) Processing helix chain 'H' and resid 65 through 76 removed outlier: 3.724A pdb=" N THR H 70 " --> pdb=" O PRO H 66 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N MET H 71 " --> pdb=" O GLU H 67 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N ARG H 74 " --> pdb=" O THR H 70 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LYS H 75 " --> pdb=" O MET H 71 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N MET H 76 " --> pdb=" O MET H 72 " (cutoff:3.500A) Processing helix chain 'H' and resid 82 through 87 Processing helix chain 'H' and resid 101 through 112 removed outlier: 3.846A pdb=" N THR H 110 " --> pdb=" O ARG H 106 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LEU H 112 " --> pdb=" O VAL H 108 " (cutoff:3.500A) Processing helix chain 'H' and resid 117 through 129 Processing helix chain 'H' and resid 137 through 146 787 hydrogen bonds defined for protein. 2346 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: 4.22 Time building geometry restraints manager: 4.58 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 5074 1.34 - 1.46: 3397 1.46 - 1.58: 7053 1.58 - 1.69: 0 1.69 - 1.81: 188 Bond restraints: 15712 Sorted by residual: bond pdb=" N PRO A 119 " pdb=" CA PRO A 119 " ideal model delta sigma weight residual 1.469 1.480 -0.012 1.28e-02 6.10e+03 8.28e-01 bond pdb=" N PRO B 119 " pdb=" CA PRO B 119 " ideal model delta sigma weight residual 1.469 1.480 -0.012 1.28e-02 6.10e+03 8.08e-01 bond pdb=" CA ASP F 131 " pdb=" CB ASP F 131 " ideal model delta sigma weight residual 1.530 1.544 -0.014 1.69e-02 3.50e+03 6.93e-01 bond pdb=" CA ILE C 244 " pdb=" C ILE C 244 " ideal model delta sigma weight residual 1.523 1.530 -0.007 9.20e-03 1.18e+04 5.91e-01 bond pdb=" N SER C 334 " pdb=" CA SER C 334 " ideal model delta sigma weight residual 1.457 1.467 -0.010 1.29e-02 6.01e+03 5.72e-01 ... (remaining 15707 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.68: 20983 1.68 - 3.36: 223 3.36 - 5.05: 26 5.05 - 6.73: 17 6.73 - 8.41: 3 Bond angle restraints: 21252 Sorted by residual: angle pdb=" N ILE B 182 " pdb=" CA ILE B 182 " pdb=" C ILE B 182 " ideal model delta sigma weight residual 113.43 107.00 6.43 1.09e+00 8.42e-01 3.48e+01 angle pdb=" N ILE H 85 " pdb=" CA ILE H 85 " pdb=" C ILE H 85 " ideal model delta sigma weight residual 112.96 108.27 4.69 1.00e+00 1.00e+00 2.20e+01 angle pdb=" N MET A 46 " pdb=" CA MET A 46 " pdb=" C MET A 46 " ideal model delta sigma weight residual 113.88 108.79 5.09 1.23e+00 6.61e-01 1.71e+01 angle pdb=" N SER B 181 " pdb=" CA SER B 181 " pdb=" C SER B 181 " ideal model delta sigma weight residual 113.97 109.20 4.77 1.28e+00 6.10e-01 1.39e+01 angle pdb=" N ASN A 186 " pdb=" CA ASN A 186 " pdb=" C ASN A 186 " ideal model delta sigma weight residual 114.39 109.08 5.31 1.45e+00 4.76e-01 1.34e+01 ... (remaining 21247 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.00: 8543 18.00 - 36.00: 657 36.00 - 54.00: 117 54.00 - 72.00: 7 72.00 - 90.00: 8 Dihedral angle restraints: 9332 sinusoidal: 3536 harmonic: 5796 Sorted by residual: dihedral pdb=" CA THR F 44 " pdb=" C THR F 44 " pdb=" N GLU F 45 " pdb=" CA GLU F 45 " ideal model delta harmonic sigma weight residual -180.00 -162.09 -17.91 0 5.00e+00 4.00e-02 1.28e+01 dihedral pdb=" CA GLU G 84 " pdb=" C GLU G 84 " pdb=" N ILE G 85 " pdb=" CA ILE G 85 " ideal model delta harmonic sigma weight residual 180.00 162.75 17.25 0 5.00e+00 4.00e-02 1.19e+01 dihedral pdb=" CG ARG D 342 " pdb=" CD ARG D 342 " pdb=" NE ARG D 342 " pdb=" CZ ARG D 342 " ideal model delta sinusoidal sigma weight residual 180.00 135.03 44.97 2 1.50e+01 4.44e-03 1.07e+01 ... (remaining 9329 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 1573 0.030 - 0.060: 721 0.060 - 0.091: 141 0.091 - 0.121: 40 0.121 - 0.151: 5 Chirality restraints: 2480 Sorted by residual: chirality pdb=" CB ILE A 251 " pdb=" CA ILE A 251 " pdb=" CG1 ILE A 251 " pdb=" CG2 ILE A 251 " both_signs ideal model delta sigma weight residual False 2.64 2.80 -0.15 2.00e-01 2.50e+01 5.70e-01 chirality pdb=" CA GLU A 321 " pdb=" N GLU A 321 " pdb=" C GLU A 321 " pdb=" CB GLU A 321 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 5.13e-01 chirality pdb=" CA ASP F 131 " pdb=" N ASP F 131 " pdb=" C ASP F 131 " pdb=" CB ASP F 131 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.69e-01 ... (remaining 2477 not shown) Planarity restraints: 2664 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C HIS D 118 " 0.024 5.00e-02 4.00e+02 3.59e-02 2.06e+00 pdb=" N PRO D 119 " -0.062 5.00e-02 4.00e+02 pdb=" CA PRO D 119 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO D 119 " 0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 318 " -0.006 2.00e-02 2.50e+03 1.29e-02 1.67e+00 pdb=" C VAL A 318 " 0.022 2.00e-02 2.50e+03 pdb=" O VAL A 318 " -0.008 2.00e-02 2.50e+03 pdb=" N LEU A 319 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C HIS A 118 " 0.018 5.00e-02 4.00e+02 2.72e-02 1.19e+00 pdb=" N PRO A 119 " -0.047 5.00e-02 4.00e+02 pdb=" CA PRO A 119 " 0.014 5.00e-02 4.00e+02 pdb=" CD PRO A 119 " 0.015 5.00e-02 4.00e+02 ... (remaining 2661 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.84: 5115 2.84 - 3.42: 15864 3.42 - 3.99: 25212 3.99 - 4.57: 37085 4.57 - 5.14: 53057 Nonbonded interactions: 136333 Sorted by model distance: nonbonded pdb=" OH TYR C 253 " pdb=" OG1 THR D 247 " model vdw 2.271 3.040 nonbonded pdb=" OE2 GLU F 31 " pdb="CA CA F 201 " model vdw 2.272 2.510 nonbonded pdb=" O ARG F 106 " pdb=" OG1 THR F 110 " model vdw 2.279 3.040 nonbonded pdb=" OG1 THR G 44 " pdb=" OE1 GLU G 47 " model vdw 2.291 3.040 nonbonded pdb=" OE2 GLU G 31 " pdb="CA CA G 201 " model vdw 2.292 2.510 ... (remaining 136328 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 9 through 386) selection = (chain 'B' and resid 9 through 386) selection = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } 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 group one per residue 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: 9.660 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.630 Check model and map are aligned: 0.110 Set scattering table: 0.130 Process input model: 34.680 Find NCS groups from input model: 0.720 Set up NCS constraints: 0.080 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: 0.010 Load rotamer database and sin/cos tables:2.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7798 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 15712 Z= 0.096 Angle : 0.489 8.409 21252 Z= 0.277 Chirality : 0.035 0.151 2480 Planarity : 0.003 0.036 2664 Dihedral : 13.057 89.999 5580 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 2.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 0.00 % Allowed : 0.46 % Favored : 99.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -1.17 (0.20), residues: 1996 helix: -0.50 (0.15), residues: 1456 sheet: None (None), residues: 0 loop : -1.14 (0.27), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 242 HIS 0.003 0.000 HIS B 375 PHE 0.013 0.001 PHE H 141 TYR 0.010 0.001 TYR A 179 ARG 0.004 0.000 ARG C 359 Details of bonding type rmsd hydrogen bonds : bond 0.15043 ( 787) hydrogen bonds : angle 4.77613 ( 2346) covalent geometry : bond 0.00182 (15712) covalent geometry : angle 0.48851 (21252) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3992 Ramachandran restraints generated. 1996 Oldfield, 0 Emsley, 1996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3992 Ramachandran restraints generated. 1996 Oldfield, 0 Emsley, 1996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 270 time to evaluate : 1.777 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 255 ASP cc_start: 0.6725 (p0) cc_final: 0.6484 (p0) REVERT: B 14 ARG cc_start: 0.7389 (ttt180) cc_final: 0.7146 (ttp80) REVERT: B 46 MET cc_start: 0.7991 (ttm) cc_final: 0.7780 (ttp) REVERT: B 255 ASP cc_start: 0.7051 (p0) cc_final: 0.6577 (p0) REVERT: C 255 ASP cc_start: 0.7029 (p0) cc_final: 0.6607 (p0) REVERT: D 217 LEU cc_start: 0.8716 (tp) cc_final: 0.8503 (tp) REVERT: D 255 ASP cc_start: 0.7090 (p0) cc_final: 0.6598 (p0) REVERT: E 7 GLU cc_start: 0.7023 (tp30) cc_final: 0.6712 (tp30) REVERT: F 24 ASP cc_start: 0.7488 (p0) cc_final: 0.7033 (p0) outliers start: 0 outliers final: 0 residues processed: 270 average time/residue: 0.2889 time to fit residues: 112.3759 Evaluate side-chains 198 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 198 time to evaluate : 1.697 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 168 optimal weight: 0.7980 chunk 151 optimal weight: 0.0010 chunk 84 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 102 optimal weight: 3.9990 chunk 80 optimal weight: 1.9990 chunk 156 optimal weight: 8.9990 chunk 60 optimal weight: 0.7980 chunk 95 optimal weight: 0.6980 chunk 116 optimal weight: 0.0370 chunk 181 optimal weight: 4.9990 overall best weight: 0.4664 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 192 HIS ** E 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 60 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.167558 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.143681 restraints weight = 17329.062| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.142637 restraints weight = 27133.622| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.141307 restraints weight = 29189.056| |-----------------------------------------------------------------------------| r_work (final): 0.3476 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7836 moved from start: 0.0946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 15712 Z= 0.110 Angle : 0.477 7.431 21252 Z= 0.247 Chirality : 0.037 0.145 2480 Planarity : 0.003 0.034 2664 Dihedral : 3.871 18.930 2164 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 1.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 0.72 % Allowed : 6.41 % Favored : 92.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -0.85 (0.20), residues: 1996 helix: -0.35 (0.14), residues: 1480 sheet: None (None), residues: 0 loop : -0.74 (0.28), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 242 HIS 0.003 0.001 HIS A 203 PHE 0.015 0.001 PHE H 141 TYR 0.011 0.001 TYR D 326 ARG 0.005 0.000 ARG D 362 Details of bonding type rmsd hydrogen bonds : bond 0.04215 ( 787) hydrogen bonds : angle 3.74744 ( 2346) covalent geometry : bond 0.00244 (15712) covalent geometry : angle 0.47703 (21252) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3992 Ramachandran restraints generated. 1996 Oldfield, 0 Emsley, 1996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3992 Ramachandran restraints generated. 1996 Oldfield, 0 Emsley, 1996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 217 time to evaluate : 1.760 Fit side-chains revert: symmetry clash REVERT: A 255 ASP cc_start: 0.7042 (p0) cc_final: 0.6757 (p0) REVERT: B 46 MET cc_start: 0.8104 (ttm) cc_final: 0.7881 (ttp) REVERT: B 255 ASP cc_start: 0.7150 (p0) cc_final: 0.6718 (p0) REVERT: C 255 ASP cc_start: 0.7130 (p0) cc_final: 0.6877 (p0) REVERT: C 321 GLU cc_start: 0.8103 (mp0) cc_final: 0.7866 (mp0) REVERT: D 46 MET cc_start: 0.8109 (ttm) cc_final: 0.7883 (ttp) REVERT: D 255 ASP cc_start: 0.7208 (p0) cc_final: 0.6742 (p0) REVERT: E 7 GLU cc_start: 0.7037 (tp30) cc_final: 0.6701 (tp30) outliers start: 11 outliers final: 9 residues processed: 221 average time/residue: 0.2609 time to fit residues: 86.8572 Evaluate side-chains 217 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 208 time to evaluate : 1.744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain C residue 46 MET Chi-restraints excluded: chain C residue 174 LEU Chi-restraints excluded: chain D residue 174 LEU Chi-restraints excluded: chain D residue 329 THR Chi-restraints excluded: chain E residue 145 MET Chi-restraints excluded: chain G residue 17 SER Chi-restraints excluded: chain G residue 78 ASP Chi-restraints excluded: chain H residue 78 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 101 optimal weight: 1.9990 chunk 44 optimal weight: 0.0980 chunk 100 optimal weight: 1.9990 chunk 140 optimal weight: 0.6980 chunk 66 optimal weight: 2.9990 chunk 2 optimal weight: 0.9980 chunk 193 optimal weight: 0.5980 chunk 134 optimal weight: 5.9990 chunk 185 optimal weight: 4.9990 chunk 32 optimal weight: 1.9990 chunk 176 optimal weight: 0.5980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.165274 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.140097 restraints weight = 17459.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 89)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.135282 restraints weight = 28198.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.131300 restraints weight = 27296.719| |-----------------------------------------------------------------------------| r_work (final): 0.3357 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 moved from start: 0.1261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 15712 Z= 0.116 Angle : 0.467 7.072 21252 Z= 0.240 Chirality : 0.037 0.138 2480 Planarity : 0.003 0.032 2664 Dihedral : 3.896 18.109 2164 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 1.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 1.05 % Allowed : 9.49 % Favored : 89.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -0.70 (0.20), residues: 1996 helix: -0.23 (0.15), residues: 1472 sheet: None (None), residues: 0 loop : -0.71 (0.28), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 242 HIS 0.003 0.001 HIS B 299 PHE 0.013 0.001 PHE E 141 TYR 0.010 0.001 TYR D 326 ARG 0.004 0.000 ARG D 362 Details of bonding type rmsd hydrogen bonds : bond 0.03940 ( 787) hydrogen bonds : angle 3.62189 ( 2346) covalent geometry : bond 0.00270 (15712) covalent geometry : angle 0.46660 (21252) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3992 Ramachandran restraints generated. 1996 Oldfield, 0 Emsley, 1996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3992 Ramachandran restraints generated. 1996 Oldfield, 0 Emsley, 1996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 211 time to evaluate : 1.708 Fit side-chains revert: symmetry clash REVERT: E 7 GLU cc_start: 0.7406 (tp30) cc_final: 0.7057 (tp30) REVERT: E 133 ASP cc_start: 0.7181 (p0) cc_final: 0.6959 (p0) REVERT: F 45 GLU cc_start: 0.7166 (tp30) cc_final: 0.6906 (mm-30) REVERT: G 93 ASP cc_start: 0.8527 (t70) cc_final: 0.8248 (t70) REVERT: H 133 ASP cc_start: 0.6912 (p0) cc_final: 0.6685 (p0) outliers start: 16 outliers final: 11 residues processed: 217 average time/residue: 0.2532 time to fit residues: 83.3435 Evaluate side-chains 211 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 200 time to evaluate : 1.703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 291 PHE Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain C residue 46 MET Chi-restraints excluded: chain D residue 174 LEU Chi-restraints excluded: chain D residue 313 GLU Chi-restraints excluded: chain D residue 329 THR Chi-restraints excluded: chain E residue 145 MET Chi-restraints excluded: chain G residue 78 ASP Chi-restraints excluded: chain G residue 81 SER Chi-restraints excluded: chain H residue 17 SER Chi-restraints excluded: chain H residue 78 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 20 optimal weight: 0.0970 chunk 141 optimal weight: 0.7980 chunk 75 optimal weight: 0.5980 chunk 3 optimal weight: 0.8980 chunk 116 optimal weight: 0.6980 chunk 124 optimal weight: 1.9990 chunk 40 optimal weight: 0.7980 chunk 176 optimal weight: 0.9980 chunk 155 optimal weight: 6.9990 chunk 22 optimal weight: 2.9990 chunk 47 optimal weight: 2.9990 overall best weight: 0.5978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 8 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.164779 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.140389 restraints weight = 17334.323| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.138868 restraints weight = 28291.871| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.137772 restraints weight = 32880.015| |-----------------------------------------------------------------------------| r_work (final): 0.3454 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7876 moved from start: 0.1438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 15712 Z= 0.113 Angle : 0.455 6.647 21252 Z= 0.234 Chirality : 0.036 0.135 2480 Planarity : 0.003 0.030 2664 Dihedral : 3.858 17.293 2164 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 1.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 1.57 % Allowed : 10.73 % Favored : 87.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -0.58 (0.20), residues: 1996 helix: -0.12 (0.15), residues: 1468 sheet: None (None), residues: 0 loop : -0.73 (0.28), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 242 HIS 0.003 0.001 HIS B 299 PHE 0.019 0.001 PHE H 141 TYR 0.009 0.001 TYR D 326 ARG 0.004 0.000 ARG A 362 Details of bonding type rmsd hydrogen bonds : bond 0.03748 ( 787) hydrogen bonds : angle 3.55049 ( 2346) covalent geometry : bond 0.00267 (15712) covalent geometry : angle 0.45453 (21252) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3992 Ramachandran restraints generated. 1996 Oldfield, 0 Emsley, 1996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3992 Ramachandran restraints generated. 1996 Oldfield, 0 Emsley, 1996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 199 time to evaluate : 1.705 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 7 GLU cc_start: 0.7057 (tp30) cc_final: 0.6737 (tp30) REVERT: E 133 ASP cc_start: 0.6490 (p0) cc_final: 0.6201 (p0) REVERT: E 145 MET cc_start: 0.6742 (OUTLIER) cc_final: 0.6137 (ttm) REVERT: G 93 ASP cc_start: 0.8510 (t70) cc_final: 0.8219 (t70) REVERT: H 133 ASP cc_start: 0.6210 (p0) cc_final: 0.5953 (p0) outliers start: 24 outliers final: 18 residues processed: 211 average time/residue: 0.2469 time to fit residues: 79.7165 Evaluate side-chains 213 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 194 time to evaluate : 1.674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 291 PHE Chi-restraints excluded: chain B residue 46 MET Chi-restraints excluded: chain B residue 83 GLU Chi-restraints excluded: chain B residue 291 PHE Chi-restraints excluded: chain B residue 321 GLU Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain C residue 46 MET Chi-restraints excluded: chain C residue 291 PHE Chi-restraints excluded: chain D residue 46 MET Chi-restraints excluded: chain D residue 174 LEU Chi-restraints excluded: chain D residue 329 THR Chi-restraints excluded: chain E residue 145 MET Chi-restraints excluded: chain F residue 17 SER Chi-restraints excluded: chain G residue 17 SER Chi-restraints excluded: chain G residue 78 ASP Chi-restraints excluded: chain G residue 81 SER Chi-restraints excluded: chain H residue 17 SER Chi-restraints excluded: chain H residue 78 ASP Chi-restraints excluded: chain H residue 145 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 7 optimal weight: 0.8980 chunk 47 optimal weight: 1.9990 chunk 191 optimal weight: 0.5980 chunk 29 optimal weight: 0.5980 chunk 187 optimal weight: 1.9990 chunk 120 optimal weight: 1.9990 chunk 94 optimal weight: 0.9980 chunk 81 optimal weight: 0.9980 chunk 77 optimal weight: 0.8980 chunk 194 optimal weight: 0.9990 chunk 36 optimal weight: 2.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.162939 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.138431 restraints weight = 17673.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 70)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.135855 restraints weight = 30968.818| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 65)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.134326 restraints weight = 37553.425| |-----------------------------------------------------------------------------| r_work (final): 0.3410 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7930 moved from start: 0.1603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 15712 Z= 0.138 Angle : 0.483 6.649 21252 Z= 0.247 Chirality : 0.037 0.134 2480 Planarity : 0.003 0.028 2664 Dihedral : 3.981 17.085 2164 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 1.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 1.83 % Allowed : 11.45 % Favored : 86.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -0.60 (0.20), residues: 1996 helix: -0.15 (0.15), residues: 1472 sheet: None (None), residues: 0 loop : -0.72 (0.28), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 242 HIS 0.004 0.001 HIS B 299 PHE 0.015 0.002 PHE H 141 TYR 0.010 0.001 TYR D 326 ARG 0.003 0.000 ARG A 362 Details of bonding type rmsd hydrogen bonds : bond 0.04090 ( 787) hydrogen bonds : angle 3.60017 ( 2346) covalent geometry : bond 0.00335 (15712) covalent geometry : angle 0.48292 (21252) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3992 Ramachandran restraints generated. 1996 Oldfield, 0 Emsley, 1996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3992 Ramachandran restraints generated. 1996 Oldfield, 0 Emsley, 1996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 201 time to evaluate : 1.572 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 86 ARG cc_start: 0.7898 (ttm-80) cc_final: 0.7633 (ttm-80) REVERT: E 133 ASP cc_start: 0.6635 (p0) cc_final: 0.6282 (p0) REVERT: E 145 MET cc_start: 0.6788 (OUTLIER) cc_final: 0.6375 (ttm) REVERT: G 93 ASP cc_start: 0.8594 (t70) cc_final: 0.8306 (t70) REVERT: H 133 ASP cc_start: 0.6373 (p0) cc_final: 0.6103 (p0) outliers start: 28 outliers final: 20 residues processed: 214 average time/residue: 0.2404 time to fit residues: 78.3876 Evaluate side-chains 218 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 197 time to evaluate : 1.543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 291 PHE Chi-restraints excluded: chain B residue 46 MET Chi-restraints excluded: chain B residue 83 GLU Chi-restraints excluded: chain B residue 291 PHE Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain C residue 46 MET Chi-restraints excluded: chain C residue 291 PHE Chi-restraints excluded: chain C residue 295 GLU Chi-restraints excluded: chain D residue 46 MET Chi-restraints excluded: chain D residue 174 LEU Chi-restraints excluded: chain D residue 313 GLU Chi-restraints excluded: chain D residue 329 THR Chi-restraints excluded: chain E residue 145 MET Chi-restraints excluded: chain F residue 17 SER Chi-restraints excluded: chain G residue 17 SER Chi-restraints excluded: chain G residue 78 ASP Chi-restraints excluded: chain G residue 81 SER Chi-restraints excluded: chain H residue 17 SER Chi-restraints excluded: chain H residue 78 ASP Chi-restraints excluded: chain H residue 91 VAL Chi-restraints excluded: chain H residue 145 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 6 optimal weight: 0.5980 chunk 133 optimal weight: 4.9990 chunk 140 optimal weight: 0.9990 chunk 12 optimal weight: 1.9990 chunk 141 optimal weight: 0.9990 chunk 28 optimal weight: 0.9990 chunk 142 optimal weight: 2.9990 chunk 155 optimal weight: 7.9990 chunk 138 optimal weight: 1.9990 chunk 87 optimal weight: 0.9980 chunk 58 optimal weight: 0.9990 overall best weight: 0.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 340 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.163834 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.136431 restraints weight = 17540.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.136051 restraints weight = 29034.646| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.135759 restraints weight = 29736.184| |-----------------------------------------------------------------------------| r_work (final): 0.3405 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 moved from start: 0.1753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 15712 Z= 0.152 Angle : 0.505 8.451 21252 Z= 0.256 Chirality : 0.038 0.132 2480 Planarity : 0.003 0.027 2664 Dihedral : 4.100 17.153 2164 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 1.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 2.29 % Allowed : 12.04 % Favored : 85.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -0.70 (0.20), residues: 1996 helix: -0.24 (0.14), residues: 1484 sheet: None (None), residues: 0 loop : -0.69 (0.29), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 242 HIS 0.004 0.001 HIS B 299 PHE 0.015 0.002 PHE H 141 TYR 0.010 0.001 TYR D 326 ARG 0.003 0.000 ARG A 228 Details of bonding type rmsd hydrogen bonds : bond 0.04284 ( 787) hydrogen bonds : angle 3.65094 ( 2346) covalent geometry : bond 0.00374 (15712) covalent geometry : angle 0.50549 (21252) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3992 Ramachandran restraints generated. 1996 Oldfield, 0 Emsley, 1996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3992 Ramachandran restraints generated. 1996 Oldfield, 0 Emsley, 1996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 200 time to evaluate : 1.684 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 321 GLU cc_start: 0.7998 (OUTLIER) cc_final: 0.7664 (mp0) REVERT: B 14 ARG cc_start: 0.7567 (ttt180) cc_final: 0.7342 (ttp80) REVERT: C 321 GLU cc_start: 0.7851 (mp0) cc_final: 0.7276 (mp0) REVERT: E 86 ARG cc_start: 0.7944 (ttm-80) cc_final: 0.7688 (ttm-80) REVERT: E 133 ASP cc_start: 0.6588 (p0) cc_final: 0.6298 (p0) REVERT: E 145 MET cc_start: 0.6803 (OUTLIER) cc_final: 0.6169 (ttm) REVERT: G 93 ASP cc_start: 0.8643 (t70) cc_final: 0.8412 (t70) REVERT: H 133 ASP cc_start: 0.6433 (p0) cc_final: 0.6218 (p0) outliers start: 35 outliers final: 24 residues processed: 220 average time/residue: 0.2426 time to fit residues: 81.4379 Evaluate side-chains 224 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 198 time to evaluate : 1.662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 291 PHE Chi-restraints excluded: chain A residue 321 GLU Chi-restraints excluded: chain B residue 46 MET Chi-restraints excluded: chain B residue 83 GLU Chi-restraints excluded: chain B residue 291 PHE Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain B residue 371 ILE Chi-restraints excluded: chain C residue 19 LEU Chi-restraints excluded: chain C residue 46 MET Chi-restraints excluded: chain C residue 174 LEU Chi-restraints excluded: chain C residue 213 LEU Chi-restraints excluded: chain C residue 291 PHE Chi-restraints excluded: chain C residue 295 GLU Chi-restraints excluded: chain D residue 46 MET Chi-restraints excluded: chain D residue 174 LEU Chi-restraints excluded: chain D residue 329 THR Chi-restraints excluded: chain E residue 91 VAL Chi-restraints excluded: chain E residue 145 MET Chi-restraints excluded: chain G residue 17 SER Chi-restraints excluded: chain G residue 78 ASP Chi-restraints excluded: chain G residue 81 SER Chi-restraints excluded: chain G residue 91 VAL Chi-restraints excluded: chain H residue 17 SER Chi-restraints excluded: chain H residue 78 ASP Chi-restraints excluded: chain H residue 91 VAL Chi-restraints excluded: chain H residue 145 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 69 optimal weight: 0.9990 chunk 157 optimal weight: 2.9990 chunk 9 optimal weight: 0.7980 chunk 97 optimal weight: 0.7980 chunk 75 optimal weight: 0.5980 chunk 87 optimal weight: 0.9990 chunk 160 optimal weight: 3.9990 chunk 10 optimal weight: 0.9980 chunk 181 optimal weight: 0.0980 chunk 127 optimal weight: 0.9990 chunk 42 optimal weight: 0.4980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.163857 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.139236 restraints weight = 17562.327| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.137683 restraints weight = 28500.642| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.136714 restraints weight = 34648.233| |-----------------------------------------------------------------------------| r_work (final): 0.3435 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7892 moved from start: 0.1760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 15712 Z= 0.110 Angle : 0.464 8.680 21252 Z= 0.237 Chirality : 0.036 0.131 2480 Planarity : 0.002 0.027 2664 Dihedral : 3.904 16.049 2164 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 2.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 2.03 % Allowed : 12.83 % Favored : 85.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -0.56 (0.20), residues: 1996 helix: -0.16 (0.15), residues: 1488 sheet: None (None), residues: 0 loop : -0.53 (0.29), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 242 HIS 0.003 0.001 HIS B 203 PHE 0.017 0.001 PHE G 141 TYR 0.009 0.001 TYR D 326 ARG 0.002 0.000 ARG D 362 Details of bonding type rmsd hydrogen bonds : bond 0.03640 ( 787) hydrogen bonds : angle 3.49096 ( 2346) covalent geometry : bond 0.00259 (15712) covalent geometry : angle 0.46447 (21252) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3992 Ramachandran restraints generated. 1996 Oldfield, 0 Emsley, 1996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3992 Ramachandran restraints generated. 1996 Oldfield, 0 Emsley, 1996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 199 time to evaluate : 1.549 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 321 GLU cc_start: 0.7923 (OUTLIER) cc_final: 0.7668 (mp0) REVERT: B 14 ARG cc_start: 0.7475 (ttt180) cc_final: 0.7250 (ttp80) REVERT: E 86 ARG cc_start: 0.7916 (ttm-80) cc_final: 0.7660 (ttm-80) REVERT: E 133 ASP cc_start: 0.6482 (p0) cc_final: 0.6192 (p0) REVERT: E 145 MET cc_start: 0.6683 (OUTLIER) cc_final: 0.6011 (ttm) REVERT: H 133 ASP cc_start: 0.6328 (p0) cc_final: 0.6118 (p0) outliers start: 31 outliers final: 26 residues processed: 217 average time/residue: 0.2455 time to fit residues: 80.7217 Evaluate side-chains 226 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 198 time to evaluate : 1.524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 291 PHE Chi-restraints excluded: chain A residue 321 GLU Chi-restraints excluded: chain B residue 19 LEU Chi-restraints excluded: chain B residue 83 GLU Chi-restraints excluded: chain B residue 179 TYR Chi-restraints excluded: chain B residue 291 PHE Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain B residue 371 ILE Chi-restraints excluded: chain C residue 19 LEU Chi-restraints excluded: chain C residue 46 MET Chi-restraints excluded: chain C residue 179 TYR Chi-restraints excluded: chain C residue 291 PHE Chi-restraints excluded: chain C residue 295 GLU Chi-restraints excluded: chain D residue 19 LEU Chi-restraints excluded: chain D residue 46 MET Chi-restraints excluded: chain D residue 174 LEU Chi-restraints excluded: chain D residue 313 GLU Chi-restraints excluded: chain D residue 329 THR Chi-restraints excluded: chain E residue 76 MET Chi-restraints excluded: chain E residue 91 VAL Chi-restraints excluded: chain E residue 145 MET Chi-restraints excluded: chain F residue 17 SER Chi-restraints excluded: chain G residue 17 SER Chi-restraints excluded: chain G residue 81 SER Chi-restraints excluded: chain G residue 91 VAL Chi-restraints excluded: chain G residue 145 MET Chi-restraints excluded: chain H residue 17 SER Chi-restraints excluded: chain H residue 145 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 67 optimal weight: 1.9990 chunk 185 optimal weight: 5.9990 chunk 162 optimal weight: 3.9990 chunk 85 optimal weight: 0.3980 chunk 40 optimal weight: 0.0670 chunk 112 optimal weight: 0.9980 chunk 89 optimal weight: 0.9990 chunk 117 optimal weight: 0.8980 chunk 174 optimal weight: 0.1980 chunk 28 optimal weight: 0.8980 chunk 49 optimal weight: 0.3980 overall best weight: 0.3918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.165479 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.140975 restraints weight = 17401.036| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 88)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.136871 restraints weight = 29090.206| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.134908 restraints weight = 33162.936| |-----------------------------------------------------------------------------| r_work (final): 0.3409 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7911 moved from start: 0.1809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 15712 Z= 0.093 Angle : 0.454 10.630 21252 Z= 0.229 Chirality : 0.035 0.131 2480 Planarity : 0.002 0.027 2664 Dihedral : 3.715 15.140 2164 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 1.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 2.23 % Allowed : 12.70 % Favored : 85.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -0.40 (0.20), residues: 1996 helix: -0.03 (0.15), residues: 1492 sheet: None (None), residues: 0 loop : -0.55 (0.29), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 242 HIS 0.003 0.001 HIS B 203 PHE 0.015 0.001 PHE G 141 TYR 0.008 0.001 TYR D 326 ARG 0.002 0.000 ARG A 362 Details of bonding type rmsd hydrogen bonds : bond 0.03208 ( 787) hydrogen bonds : angle 3.34869 ( 2346) covalent geometry : bond 0.00211 (15712) covalent geometry : angle 0.45394 (21252) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3992 Ramachandran restraints generated. 1996 Oldfield, 0 Emsley, 1996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3992 Ramachandran restraints generated. 1996 Oldfield, 0 Emsley, 1996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 199 time to evaluate : 1.798 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 321 GLU cc_start: 0.7908 (OUTLIER) cc_final: 0.7591 (mp0) REVERT: E 86 ARG cc_start: 0.7924 (ttm-80) cc_final: 0.7659 (ttm-80) REVERT: E 133 ASP cc_start: 0.6887 (p0) cc_final: 0.6610 (p0) REVERT: H 133 ASP cc_start: 0.6663 (p0) cc_final: 0.6432 (p0) outliers start: 34 outliers final: 27 residues processed: 219 average time/residue: 0.2509 time to fit residues: 83.3825 Evaluate side-chains 222 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 194 time to evaluate : 1.677 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 291 PHE Chi-restraints excluded: chain A residue 321 GLU Chi-restraints excluded: chain B residue 19 LEU Chi-restraints excluded: chain B residue 46 MET Chi-restraints excluded: chain B residue 83 GLU Chi-restraints excluded: chain B residue 179 TYR Chi-restraints excluded: chain B residue 291 PHE Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain B residue 371 ILE Chi-restraints excluded: chain C residue 19 LEU Chi-restraints excluded: chain C residue 46 MET Chi-restraints excluded: chain C residue 174 LEU Chi-restraints excluded: chain C residue 179 TYR Chi-restraints excluded: chain C residue 291 PHE Chi-restraints excluded: chain C residue 295 GLU Chi-restraints excluded: chain D residue 46 MET Chi-restraints excluded: chain D residue 83 GLU Chi-restraints excluded: chain D residue 174 LEU Chi-restraints excluded: chain D residue 179 TYR Chi-restraints excluded: chain D residue 313 GLU Chi-restraints excluded: chain D residue 329 THR Chi-restraints excluded: chain E residue 76 MET Chi-restraints excluded: chain E residue 91 VAL Chi-restraints excluded: chain F residue 17 SER Chi-restraints excluded: chain G residue 17 SER Chi-restraints excluded: chain G residue 81 SER Chi-restraints excluded: chain H residue 17 SER Chi-restraints excluded: chain H residue 145 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 130 optimal weight: 0.6980 chunk 77 optimal weight: 0.9990 chunk 131 optimal weight: 0.0770 chunk 20 optimal weight: 2.9990 chunk 44 optimal weight: 0.8980 chunk 191 optimal weight: 3.9990 chunk 112 optimal weight: 0.9990 chunk 166 optimal weight: 1.9990 chunk 61 optimal weight: 4.9990 chunk 7 optimal weight: 0.5980 chunk 51 optimal weight: 1.9990 overall best weight: 0.6540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 340 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.163784 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.139491 restraints weight = 17456.917| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 61)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.137097 restraints weight = 29220.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.136208 restraints weight = 34775.087| |-----------------------------------------------------------------------------| r_work (final): 0.3431 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7900 moved from start: 0.1878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 15712 Z= 0.121 Angle : 0.490 11.779 21252 Z= 0.244 Chirality : 0.037 0.129 2480 Planarity : 0.003 0.027 2664 Dihedral : 3.819 15.464 2164 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 2.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 2.29 % Allowed : 13.02 % Favored : 84.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -0.45 (0.20), residues: 1996 helix: -0.06 (0.15), residues: 1492 sheet: None (None), residues: 0 loop : -0.57 (0.29), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 242 HIS 0.003 0.001 HIS B 203 PHE 0.014 0.001 PHE H 141 TYR 0.017 0.001 TYR C 326 ARG 0.002 0.000 ARG D 362 Details of bonding type rmsd hydrogen bonds : bond 0.03669 ( 787) hydrogen bonds : angle 3.41708 ( 2346) covalent geometry : bond 0.00293 (15712) covalent geometry : angle 0.48994 (21252) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3992 Ramachandran restraints generated. 1996 Oldfield, 0 Emsley, 1996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3992 Ramachandran restraints generated. 1996 Oldfield, 0 Emsley, 1996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 195 time to evaluate : 1.531 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 321 GLU cc_start: 0.7927 (OUTLIER) cc_final: 0.7638 (mp0) REVERT: B 14 ARG cc_start: 0.7493 (ttt180) cc_final: 0.7241 (ttp80) REVERT: E 86 ARG cc_start: 0.7932 (ttm-80) cc_final: 0.7661 (ttm-80) REVERT: E 133 ASP cc_start: 0.6567 (p0) cc_final: 0.6296 (p0) REVERT: H 133 ASP cc_start: 0.6296 (p0) cc_final: 0.6076 (p0) outliers start: 35 outliers final: 32 residues processed: 216 average time/residue: 0.2477 time to fit residues: 81.0894 Evaluate side-chains 222 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 189 time to evaluate : 1.759 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain A residue 291 PHE Chi-restraints excluded: chain A residue 321 GLU Chi-restraints excluded: chain B residue 19 LEU Chi-restraints excluded: chain B residue 46 MET Chi-restraints excluded: chain B residue 83 GLU Chi-restraints excluded: chain B residue 291 PHE Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain B residue 371 ILE Chi-restraints excluded: chain C residue 19 LEU Chi-restraints excluded: chain C residue 46 MET Chi-restraints excluded: chain C residue 174 LEU Chi-restraints excluded: chain C residue 179 TYR Chi-restraints excluded: chain C residue 213 LEU Chi-restraints excluded: chain C residue 291 PHE Chi-restraints excluded: chain C residue 295 GLU Chi-restraints excluded: chain D residue 46 MET Chi-restraints excluded: chain D residue 83 GLU Chi-restraints excluded: chain D residue 174 LEU Chi-restraints excluded: chain D residue 179 TYR Chi-restraints excluded: chain D residue 313 GLU Chi-restraints excluded: chain D residue 329 THR Chi-restraints excluded: chain E residue 76 MET Chi-restraints excluded: chain E residue 91 VAL Chi-restraints excluded: chain F residue 17 SER Chi-restraints excluded: chain G residue 17 SER Chi-restraints excluded: chain G residue 78 ASP Chi-restraints excluded: chain G residue 81 SER Chi-restraints excluded: chain G residue 91 VAL Chi-restraints excluded: chain H residue 17 SER Chi-restraints excluded: chain H residue 78 ASP Chi-restraints excluded: chain H residue 91 VAL Chi-restraints excluded: chain H residue 145 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 60 optimal weight: 0.9980 chunk 61 optimal weight: 1.9990 chunk 22 optimal weight: 3.9990 chunk 149 optimal weight: 0.8980 chunk 189 optimal weight: 1.9990 chunk 43 optimal weight: 0.6980 chunk 37 optimal weight: 0.4980 chunk 157 optimal weight: 5.9990 chunk 23 optimal weight: 0.6980 chunk 110 optimal weight: 0.5980 chunk 47 optimal weight: 0.6980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.163208 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.138565 restraints weight = 17516.307| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.136892 restraints weight = 28850.471| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.135984 restraints weight = 34087.060| |-----------------------------------------------------------------------------| r_work (final): 0.3438 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7893 moved from start: 0.1911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 15712 Z= 0.118 Angle : 0.488 12.736 21252 Z= 0.243 Chirality : 0.036 0.128 2480 Planarity : 0.003 0.026 2664 Dihedral : 3.807 15.374 2164 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 2.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 2.36 % Allowed : 12.89 % Favored : 84.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -0.41 (0.20), residues: 1996 helix: -0.06 (0.15), residues: 1488 sheet: None (None), residues: 0 loop : -0.49 (0.29), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 242 HIS 0.004 0.001 HIS B 328 PHE 0.015 0.001 PHE G 141 TYR 0.015 0.001 TYR C 326 ARG 0.002 0.000 ARG D 362 Details of bonding type rmsd hydrogen bonds : bond 0.03656 ( 787) hydrogen bonds : angle 3.41353 ( 2346) covalent geometry : bond 0.00284 (15712) covalent geometry : angle 0.48752 (21252) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3992 Ramachandran restraints generated. 1996 Oldfield, 0 Emsley, 1996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3992 Ramachandran restraints generated. 1996 Oldfield, 0 Emsley, 1996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 189 time to evaluate : 1.782 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 14 ARG cc_start: 0.7516 (ttt180) cc_final: 0.7237 (ttp80) REVERT: E 86 ARG cc_start: 0.7931 (ttm-80) cc_final: 0.7656 (ttm-80) REVERT: E 133 ASP cc_start: 0.6486 (p0) cc_final: 0.6223 (p0) REVERT: H 133 ASP cc_start: 0.6333 (p0) cc_final: 0.6105 (p0) outliers start: 36 outliers final: 33 residues processed: 213 average time/residue: 0.2474 time to fit residues: 80.5382 Evaluate side-chains 222 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 189 time to evaluate : 1.629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain A residue 291 PHE Chi-restraints excluded: chain B residue 19 LEU Chi-restraints excluded: chain B residue 46 MET Chi-restraints excluded: chain B residue 83 GLU Chi-restraints excluded: chain B residue 291 PHE Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain B residue 371 ILE Chi-restraints excluded: chain C residue 19 LEU Chi-restraints excluded: chain C residue 46 MET Chi-restraints excluded: chain C residue 174 LEU Chi-restraints excluded: chain C residue 179 TYR Chi-restraints excluded: chain C residue 213 LEU Chi-restraints excluded: chain C residue 291 PHE Chi-restraints excluded: chain C residue 295 GLU Chi-restraints excluded: chain D residue 19 LEU Chi-restraints excluded: chain D residue 46 MET Chi-restraints excluded: chain D residue 83 GLU Chi-restraints excluded: chain D residue 174 LEU Chi-restraints excluded: chain D residue 179 TYR Chi-restraints excluded: chain D residue 313 GLU Chi-restraints excluded: chain D residue 329 THR Chi-restraints excluded: chain E residue 76 MET Chi-restraints excluded: chain E residue 91 VAL Chi-restraints excluded: chain F residue 17 SER Chi-restraints excluded: chain G residue 17 SER Chi-restraints excluded: chain G residue 81 SER Chi-restraints excluded: chain G residue 91 VAL Chi-restraints excluded: chain G residue 95 ASP Chi-restraints excluded: chain H residue 17 SER Chi-restraints excluded: chain H residue 78 ASP Chi-restraints excluded: chain H residue 91 VAL Chi-restraints excluded: chain H residue 145 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 101 optimal weight: 0.9980 chunk 132 optimal weight: 0.8980 chunk 167 optimal weight: 5.9990 chunk 90 optimal weight: 6.9990 chunk 81 optimal weight: 1.9990 chunk 170 optimal weight: 3.9990 chunk 107 optimal weight: 5.9990 chunk 5 optimal weight: 1.9990 chunk 173 optimal weight: 0.8980 chunk 51 optimal weight: 0.1980 chunk 43 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.162597 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.137955 restraints weight = 17407.411| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.136836 restraints weight = 28546.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.135558 restraints weight = 32307.350| |-----------------------------------------------------------------------------| r_work (final): 0.3432 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7902 moved from start: 0.1949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 15712 Z= 0.130 Angle : 0.503 12.621 21252 Z= 0.250 Chirality : 0.037 0.128 2480 Planarity : 0.003 0.027 2664 Dihedral : 3.869 15.580 2164 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 2.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 2.36 % Allowed : 13.42 % Favored : 84.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -0.36 (0.20), residues: 1996 helix: 0.01 (0.15), residues: 1464 sheet: None (None), residues: 0 loop : -0.55 (0.28), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 242 HIS 0.003 0.001 HIS B 328 PHE 0.016 0.001 PHE G 141 TYR 0.015 0.001 TYR C 326 ARG 0.002 0.000 ARG D 362 Details of bonding type rmsd hydrogen bonds : bond 0.03845 ( 787) hydrogen bonds : angle 3.45357 ( 2346) covalent geometry : bond 0.00317 (15712) covalent geometry : angle 0.50266 (21252) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4631.88 seconds wall clock time: 82 minutes 15.37 seconds (4935.37 seconds total)