Starting phenix.real_space_refine on Sat Jul 4 11:32:19 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7dmz_30775/07_2026/7dmz_30775.cif Found real_map, /net/cci-nas-00/data/ceres_data/7dmz_30775/07_2026/7dmz_30775.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7dmz_30775/07_2026/7dmz_30775.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7dmz_30775/07_2026/7dmz_30775.cif" model { file = "/net/cci-nas-00/data/ceres_data/7dmz_30775/07_2026/7dmz_30775.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7dmz_30775/07_2026/7dmz_30775.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7dmz_30775/07_2026/7dmz_30775.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7dmz_30775/07_2026/7dmz_30775.map" } resolution = 4.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.007 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 P 18 5.49 5 Mg 2 5.21 5 S 138 5.16 5 C 12831 2.51 5 N 3462 2.21 5 O 3945 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 50 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 20396 Number of models: 1 Model: "" Number of chains: 12 Chain: "D" Number of atoms: 3346 Number of conformers: 1 Conformer: "" Number of residues, atoms: 428, 3346 Classifications: {'peptide': 428} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 407} Chain breaks: 1 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "A" Number of atoms: 3346 Number of conformers: 1 Conformer: "" Number of residues, atoms: 428, 3346 Classifications: {'peptide': 428} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 407} Chain breaks: 1 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "B" Number of atoms: 3346 Number of conformers: 1 Conformer: "" Number of residues, atoms: 428, 3346 Classifications: {'peptide': 428} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 407} Chain breaks: 1 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "E" Number of atoms: 3340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 426, 3340 Classifications: {'peptide': 426} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 405} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 11 Chain: "C" Number of atoms: 3340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 426, 3340 Classifications: {'peptide': 426} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 405} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 11 Chain: "F" Number of atoms: 3340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 426, 3340 Classifications: {'peptide': 426} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 405} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 11 Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'GTP': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 80 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 80 Unusual residues: {'G2P': 1, 'TAJ': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 80 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 80 Unusual residues: {'G2P': 1, 'TAJ': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 80 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 80 Unusual residues: {'G2P': 1, 'TAJ': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 4.44, per 1000 atoms: 0.22 Number of scatterers: 20396 At special positions: 0 Unit cell: (129.6, 89.1, 167.4, 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) S 138 16.00 P 18 15.00 Mg 2 11.99 O 3945 8.00 N 3462 7.00 C 12831 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=3, symmetry=0 Number of additional bonds: simple=3, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.78 Conformation dependent library (CDL) restraints added in 844.4 milliseconds 5088 Ramachandran restraints generated. 2544 Oldfield, 0 Emsley, 2544 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4746 Finding SS restraints... Secondary structure from input PDB file: 100 helices and 17 sheets defined 49.2% alpha, 12.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.80 Creating SS restraints... Processing helix chain 'D' and resid 10 through 28 Processing helix chain 'D' and resid 71 through 81 removed outlier: 4.481A pdb=" N ILE D 75 " --> pdb=" O GLU D 71 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ASP D 76 " --> pdb=" O PRO D 72 " (cutoff:3.500A) Processing helix chain 'D' and resid 102 through 108 removed outlier: 3.594A pdb=" N TYR D 108 " --> pdb=" O ALA D 104 " (cutoff:3.500A) Processing helix chain 'D' and resid 110 through 113 Processing helix chain 'D' and resid 114 through 127 removed outlier: 3.815A pdb=" N VAL D 118 " --> pdb=" O ILE D 114 " (cutoff:3.500A) Processing helix chain 'D' and resid 144 through 162 removed outlier: 4.532A pdb=" N THR D 150 " --> pdb=" O GLY D 146 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLY D 162 " --> pdb=" O SER D 158 " (cutoff:3.500A) Processing helix chain 'D' and resid 182 through 195 removed outlier: 3.639A pdb=" N ASN D 186 " --> pdb=" O VAL D 182 " (cutoff:3.500A) Processing helix chain 'D' and resid 206 through 216 Processing helix chain 'D' and resid 223 through 244 removed outlier: 3.792A pdb=" N LEU D 227 " --> pdb=" O THR D 223 " (cutoff:3.500A) removed outlier: 4.906A pdb=" N SER D 241 " --> pdb=" O SER D 237 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N LEU D 242 " --> pdb=" O ILE D 238 " (cutoff:3.500A) Processing helix chain 'D' and resid 251 through 260 removed outlier: 4.397A pdb=" N PHE D 255 " --> pdb=" O ASP D 251 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N GLN D 256 " --> pdb=" O LEU D 252 " (cutoff:3.500A) removed outlier: 4.703A pdb=" N THR D 257 " --> pdb=" O THR D 253 " (cutoff:3.500A) Processing helix chain 'D' and resid 287 through 296 removed outlier: 3.849A pdb=" N PHE D 296 " --> pdb=" O THR D 292 " (cutoff:3.500A) Processing helix chain 'D' and resid 297 through 301 removed outlier: 3.536A pdb=" N ASN D 300 " --> pdb=" O GLU D 297 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N GLN D 301 " --> pdb=" O PRO D 298 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 297 through 301' Processing helix chain 'D' and resid 306 through 310 Processing helix chain 'D' and resid 325 through 337 removed outlier: 3.608A pdb=" N THR D 337 " --> pdb=" O ALA D 333 " (cutoff:3.500A) Processing helix chain 'D' and resid 383 through 399 removed outlier: 3.754A pdb=" N ALA D 387 " --> pdb=" O ALA D 383 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LYS D 394 " --> pdb=" O ARG D 390 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU D 397 " --> pdb=" O HIS D 393 " (cutoff:3.500A) Processing helix chain 'D' and resid 405 through 410 Processing helix chain 'D' and resid 415 through 437 removed outlier: 3.800A pdb=" N SER D 419 " --> pdb=" O GLU D 415 " (cutoff:3.500A) Processing helix chain 'A' and resid 10 through 28 removed outlier: 3.635A pdb=" N HIS A 28 " --> pdb=" O TYR A 24 " (cutoff:3.500A) Processing helix chain 'A' and resid 48 through 51 Processing helix chain 'A' and resid 71 through 81 removed outlier: 4.665A pdb=" N ILE A 75 " --> pdb=" O GLU A 71 " (cutoff:3.500A) Processing helix chain 'A' and resid 102 through 108 Processing helix chain 'A' and resid 110 through 113 Processing helix chain 'A' and resid 114 through 126 Processing helix chain 'A' and resid 144 through 161 removed outlier: 4.758A pdb=" N THR A 150 " --> pdb=" O GLY A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 195 Processing helix chain 'A' and resid 206 through 216 Processing helix chain 'A' and resid 223 through 244 removed outlier: 4.071A pdb=" N LEU A 227 " --> pdb=" O THR A 223 " (cutoff:3.500A) removed outlier: 4.941A pdb=" N SER A 241 " --> pdb=" O SER A 237 " (cutoff:3.500A) removed outlier: 5.090A pdb=" N LEU A 242 " --> pdb=" O ILE A 238 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N PHE A 244 " --> pdb=" O ALA A 240 " (cutoff:3.500A) Processing helix chain 'A' and resid 255 through 260 removed outlier: 3.869A pdb=" N VAL A 260 " --> pdb=" O GLN A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 295 removed outlier: 3.798A pdb=" N ILE A 291 " --> pdb=" O SER A 287 " (cutoff:3.500A) Processing helix chain 'A' and resid 296 through 301 removed outlier: 6.198A pdb=" N ALA A 299 " --> pdb=" O PHE A 296 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLN A 301 " --> pdb=" O PRO A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 310 removed outlier: 3.817A pdb=" N GLY A 310 " --> pdb=" O PRO A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 337 removed outlier: 3.946A pdb=" N VAL A 328 " --> pdb=" O VAL A 324 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N THR A 337 " --> pdb=" O ALA A 333 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 401 removed outlier: 3.924A pdb=" N ALA A 387 " --> pdb=" O ALA A 383 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N LYS A 401 " --> pdb=" O LEU A 397 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 Processing helix chain 'A' and resid 415 through 437 removed outlier: 3.944A pdb=" N SER A 419 " --> pdb=" O GLU A 415 " (cutoff:3.500A) Processing helix chain 'B' and resid 10 through 28 removed outlier: 3.517A pdb=" N HIS B 28 " --> pdb=" O TYR B 24 " (cutoff:3.500A) Processing helix chain 'B' and resid 48 through 51 Processing helix chain 'B' and resid 71 through 80 removed outlier: 4.404A pdb=" N ILE B 75 " --> pdb=" O GLU B 71 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ASP B 76 " --> pdb=" O PRO B 72 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N GLU B 77 " --> pdb=" O THR B 73 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N VAL B 78 " --> pdb=" O VAL B 74 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ARG B 79 " --> pdb=" O ILE B 75 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N THR B 80 " --> pdb=" O ASP B 76 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 71 through 80' Processing helix chain 'B' and resid 102 through 108 Processing helix chain 'B' and resid 110 through 113 Processing helix chain 'B' and resid 114 through 127 Processing helix chain 'B' and resid 144 through 161 removed outlier: 4.626A pdb=" N THR B 150 " --> pdb=" O GLY B 146 " (cutoff:3.500A) Processing helix chain 'B' and resid 182 through 194 Processing helix chain 'B' and resid 206 through 216 Processing helix chain 'B' and resid 223 through 244 removed outlier: 3.931A pdb=" N LEU B 227 " --> pdb=" O THR B 223 " (cutoff:3.500A) removed outlier: 4.915A pdb=" N SER B 241 " --> pdb=" O SER B 237 " (cutoff:3.500A) removed outlier: 4.915A pdb=" N LEU B 242 " --> pdb=" O ILE B 238 " (cutoff:3.500A) Processing helix chain 'B' and resid 254 through 259 Processing helix chain 'B' and resid 287 through 295 removed outlier: 3.815A pdb=" N ILE B 291 " --> pdb=" O SER B 287 " (cutoff:3.500A) Processing helix chain 'B' and resid 296 through 301 removed outlier: 6.672A pdb=" N ALA B 299 " --> pdb=" O PHE B 296 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N GLN B 301 " --> pdb=" O PRO B 298 " (cutoff:3.500A) Processing helix chain 'B' and resid 306 through 310 removed outlier: 3.987A pdb=" N GLY B 310 " --> pdb=" O PRO B 307 " (cutoff:3.500A) Processing helix chain 'B' and resid 325 through 337 removed outlier: 3.714A pdb=" N THR B 337 " --> pdb=" O ALA B 333 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 401 removed outlier: 4.217A pdb=" N ALA B 387 " --> pdb=" O ALA B 383 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N LYS B 401 " --> pdb=" O LEU B 397 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 410 Processing helix chain 'B' and resid 415 through 437 removed outlier: 3.960A pdb=" N SER B 419 " --> pdb=" O GLU B 415 " (cutoff:3.500A) Processing helix chain 'E' and resid 11 through 28 Processing helix chain 'E' and resid 48 through 51 removed outlier: 3.517A pdb=" N VAL E 51 " --> pdb=" O ARG E 48 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 48 through 51' Processing helix chain 'E' and resid 71 through 81 removed outlier: 4.516A pdb=" N MET E 75 " --> pdb=" O GLU E 71 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N GLY E 81 " --> pdb=" O SER E 77 " (cutoff:3.500A) Processing helix chain 'E' and resid 102 through 108 Processing helix chain 'E' and resid 110 through 128 removed outlier: 5.434A pdb=" N ASP E 116 " --> pdb=" O ALA E 112 " (cutoff:3.500A) removed outlier: 5.554A pdb=" N SER E 117 " --> pdb=" O GLU E 113 " (cutoff:3.500A) Processing helix chain 'E' and resid 144 through 161 Processing helix chain 'E' and resid 182 through 198 removed outlier: 3.681A pdb=" N ASN E 186 " --> pdb=" O VAL E 182 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N GLU E 196 " --> pdb=" O HIS E 192 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N THR E 198 " --> pdb=" O LEU E 194 " (cutoff:3.500A) Processing helix chain 'E' and resid 205 through 216 removed outlier: 4.012A pdb=" N LEU E 209 " --> pdb=" O ASP E 205 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N THR E 216 " --> pdb=" O ILE E 212 " (cutoff:3.500A) Processing helix chain 'E' and resid 223 through 239 Processing helix chain 'E' and resid 251 through 260 removed outlier: 4.204A pdb=" N VAL E 260 " --> pdb=" O ALA E 256 " (cutoff:3.500A) Processing helix chain 'E' and resid 287 through 296 removed outlier: 3.535A pdb=" N PHE E 296 " --> pdb=" O THR E 292 " (cutoff:3.500A) Processing helix chain 'E' and resid 324 through 339 removed outlier: 3.530A pdb=" N ASN E 339 " --> pdb=" O VAL E 335 " (cutoff:3.500A) Processing helix chain 'E' and resid 384 through 401 removed outlier: 4.381A pdb=" N GLN E 394 " --> pdb=" O ARG E 390 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ARG E 401 " --> pdb=" O ALA E 397 " (cutoff:3.500A) Processing helix chain 'E' and resid 405 through 410 Processing helix chain 'E' and resid 414 through 435 removed outlier: 4.046A pdb=" N PHE E 418 " --> pdb=" O ASP E 414 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N TYR E 435 " --> pdb=" O GLU E 431 " (cutoff:3.500A) Processing helix chain 'C' and resid 10 through 28 Processing helix chain 'C' and resid 48 through 51 removed outlier: 3.596A pdb=" N VAL C 51 " --> pdb=" O ARG C 48 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 48 through 51' Processing helix chain 'C' and resid 71 through 81 removed outlier: 4.162A pdb=" N MET C 75 " --> pdb=" O GLU C 71 " (cutoff:3.500A) Processing helix chain 'C' and resid 102 through 109 Processing helix chain 'C' and resid 110 through 129 removed outlier: 5.179A pdb=" N ASP C 116 " --> pdb=" O ALA C 112 " (cutoff:3.500A) removed outlier: 4.972A pdb=" N SER C 117 " --> pdb=" O GLU C 113 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N CYS C 129 " --> pdb=" O GLU C 125 " (cutoff:3.500A) Processing helix chain 'C' and resid 144 through 161 removed outlier: 3.540A pdb=" N GLY C 148 " --> pdb=" O GLY C 144 " (cutoff:3.500A) Processing helix chain 'C' and resid 182 through 197 removed outlier: 3.809A pdb=" N ASN C 186 " --> pdb=" O VAL C 182 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N GLU C 196 " --> pdb=" O HIS C 192 " (cutoff:3.500A) Processing helix chain 'C' and resid 205 through 216 removed outlier: 3.635A pdb=" N LEU C 209 " --> pdb=" O ASP C 205 " (cutoff:3.500A) Processing helix chain 'C' and resid 223 through 240 removed outlier: 3.763A pdb=" N LEU C 227 " --> pdb=" O THR C 223 " (cutoff:3.500A) Processing helix chain 'C' and resid 251 through 260 removed outlier: 3.647A pdb=" N VAL C 260 " --> pdb=" O ALA C 256 " (cutoff:3.500A) Processing helix chain 'C' and resid 287 through 296 removed outlier: 3.745A pdb=" N PHE C 296 " --> pdb=" O THR C 292 " (cutoff:3.500A) Processing helix chain 'C' and resid 306 through 310 removed outlier: 3.753A pdb=" N HIS C 309 " --> pdb=" O ASP C 306 " (cutoff:3.500A) Processing helix chain 'C' and resid 324 through 339 removed outlier: 3.534A pdb=" N VAL C 328 " --> pdb=" O SER C 324 " (cutoff:3.500A) Processing helix chain 'C' and resid 384 through 402 removed outlier: 4.397A pdb=" N GLN C 394 " --> pdb=" O ARG C 390 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ARG C 401 " --> pdb=" O ALA C 397 " (cutoff:3.500A) Processing helix chain 'C' and resid 404 through 410 removed outlier: 4.415A pdb=" N TYR C 408 " --> pdb=" O PHE C 404 " (cutoff:3.500A) Processing helix chain 'C' and resid 414 through 435 removed outlier: 4.158A pdb=" N PHE C 418 " --> pdb=" O ASP C 414 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N TYR C 435 " --> pdb=" O GLU C 431 " (cutoff:3.500A) Processing helix chain 'F' and resid 10 through 28 Processing helix chain 'F' and resid 48 through 51 Processing helix chain 'F' and resid 71 through 81 removed outlier: 4.410A pdb=" N MET F 75 " --> pdb=" O GLU F 71 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLY F 81 " --> pdb=" O SER F 77 " (cutoff:3.500A) Processing helix chain 'F' and resid 102 through 109 Processing helix chain 'F' and resid 110 through 128 removed outlier: 4.596A pdb=" N ASP F 116 " --> pdb=" O ALA F 112 " (cutoff:3.500A) removed outlier: 5.591A pdb=" N SER F 117 " --> pdb=" O GLU F 113 " (cutoff:3.500A) Processing helix chain 'F' and resid 144 through 161 Processing helix chain 'F' and resid 182 through 197 removed outlier: 3.532A pdb=" N ASN F 186 " --> pdb=" O VAL F 182 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N GLU F 196 " --> pdb=" O HIS F 192 " (cutoff:3.500A) Processing helix chain 'F' and resid 205 through 216 removed outlier: 3.503A pdb=" N THR F 216 " --> pdb=" O ILE F 212 " (cutoff:3.500A) Processing helix chain 'F' and resid 223 through 240 removed outlier: 3.857A pdb=" N LEU F 227 " --> pdb=" O THR F 223 " (cutoff:3.500A) Processing helix chain 'F' and resid 251 through 260 Processing helix chain 'F' and resid 287 through 296 removed outlier: 3.505A pdb=" N PHE F 296 " --> pdb=" O THR F 292 " (cutoff:3.500A) Processing helix chain 'F' and resid 306 through 310 removed outlier: 3.866A pdb=" N HIS F 309 " --> pdb=" O ASP F 306 " (cutoff:3.500A) Processing helix chain 'F' and resid 324 through 339 removed outlier: 3.566A pdb=" N VAL F 328 " --> pdb=" O SER F 324 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ASN F 339 " --> pdb=" O VAL F 335 " (cutoff:3.500A) Processing helix chain 'F' and resid 384 through 399 removed outlier: 4.464A pdb=" N GLN F 394 " --> pdb=" O ARG F 390 " (cutoff:3.500A) Processing helix chain 'F' and resid 404 through 410 removed outlier: 4.382A pdb=" N TYR F 408 " --> pdb=" O PHE F 404 " (cutoff:3.500A) Processing helix chain 'F' and resid 414 through 435 removed outlier: 3.945A pdb=" N PHE F 418 " --> pdb=" O ASP F 414 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N TYR F 435 " --> pdb=" O GLU F 431 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'D' and resid 65 through 68 removed outlier: 3.573A pdb=" N ILE D 5 " --> pdb=" O GLY D 134 " (cutoff:3.500A) removed outlier: 5.264A pdb=" N SER D 140 " --> pdb=" O VAL D 9 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LEU D 167 " --> pdb=" O PHE D 135 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ILE D 171 " --> pdb=" O HIS D 139 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N PHE D 202 " --> pdb=" O GLU D 168 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 53 through 56 removed outlier: 3.573A pdb=" N LYS D 60 " --> pdb=" O THR D 56 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 269 through 273 removed outlier: 8.588A pdb=" N ASN D 356 " --> pdb=" O LEU D 317 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N TYR D 319 " --> pdb=" O ASN D 356 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 65 through 68 removed outlier: 3.520A pdb=" N PHE A 138 " --> pdb=" O ILE A 7 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N VAL A 9 " --> pdb=" O PHE A 138 " (cutoff:3.500A) removed outlier: 4.973A pdb=" N SER A 140 " --> pdb=" O VAL A 9 " (cutoff:3.500A) removed outlier: 6.096A pdb=" N PHE A 135 " --> pdb=" O LEU A 167 " (cutoff:3.500A) removed outlier: 7.891A pdb=" N PHE A 169 " --> pdb=" O PHE A 135 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N VAL A 137 " --> pdb=" O PHE A 169 " (cutoff:3.500A) removed outlier: 8.524A pdb=" N ILE A 171 " --> pdb=" O VAL A 137 " (cutoff:3.500A) removed outlier: 8.205A pdb=" N HIS A 139 " --> pdb=" O ILE A 171 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N CYS A 200 " --> pdb=" O LYS A 166 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 53 through 55 Processing sheet with id=AA6, first strand: chain 'A' and resid 269 through 273 Processing sheet with id=AA7, first strand: chain 'B' and resid 92 through 94 removed outlier: 8.166A pdb=" N ILE B 93 " --> pdb=" O ALA B 65 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N PHE B 67 " --> pdb=" O ILE B 93 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N ILE B 5 " --> pdb=" O LEU B 136 " (cutoff:3.500A) removed outlier: 7.953A pdb=" N PHE B 138 " --> pdb=" O ILE B 5 " (cutoff:3.500A) removed outlier: 7.104A pdb=" N ILE B 7 " --> pdb=" O PHE B 138 " (cutoff:3.500A) removed outlier: 5.885A pdb=" N PHE B 135 " --> pdb=" O LEU B 167 " (cutoff:3.500A) removed outlier: 7.947A pdb=" N PHE B 169 " --> pdb=" O PHE B 135 " (cutoff:3.500A) removed outlier: 7.088A pdb=" N VAL B 137 " --> pdb=" O PHE B 169 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N LYS B 166 " --> pdb=" O CYS B 200 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 53 through 55 Processing sheet with id=AA9, first strand: chain 'B' and resid 171 through 172 Processing sheet with id=AB1, first strand: chain 'B' and resid 269 through 273 removed outlier: 3.559A pdb=" N ASN B 356 " --> pdb=" O TYR B 319 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 93 through 94 removed outlier: 8.070A pdb=" N VAL E 93 " --> pdb=" O ALA E 65 " (cutoff:3.500A) removed outlier: 5.887A pdb=" N LEU E 67 " --> pdb=" O VAL E 93 " (cutoff:3.500A) removed outlier: 9.020A pdb=" N ILE E 66 " --> pdb=" O ILE E 4 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N HIS E 6 " --> pdb=" O ILE E 66 " (cutoff:3.500A) removed outlier: 7.721A pdb=" N VAL E 68 " --> pdb=" O HIS E 6 " (cutoff:3.500A) removed outlier: 6.084A pdb=" N GLN E 8 " --> pdb=" O VAL E 68 " (cutoff:3.500A) removed outlier: 5.424A pdb=" N GLU E 3 " --> pdb=" O LEU E 132 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N GLY E 134 " --> pdb=" O GLU E 3 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N VAL E 5 " --> pdb=" O GLY E 134 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N GLN E 136 " --> pdb=" O VAL E 5 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N SER E 140 " --> pdb=" O ALA E 9 " (cutoff:3.500A) removed outlier: 7.115A pdb=" N GLN E 133 " --> pdb=" O ILE E 165 " (cutoff:3.500A) removed outlier: 7.987A pdb=" N ASN E 167 " --> pdb=" O GLN E 133 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N PHE E 135 " --> pdb=" O ASN E 167 " (cutoff:3.500A) removed outlier: 8.259A pdb=" N PHE E 169 " --> pdb=" O PHE E 135 " (cutoff:3.500A) removed outlier: 7.024A pdb=" N LEU E 137 " --> pdb=" O PHE E 169 " (cutoff:3.500A) removed outlier: 8.717A pdb=" N VAL E 171 " --> pdb=" O LEU E 137 " (cutoff:3.500A) removed outlier: 7.924A pdb=" N HIS E 139 " --> pdb=" O VAL E 171 " (cutoff:3.500A) removed outlier: 7.806A pdb=" N TYR E 202 " --> pdb=" O MET E 166 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N THR E 168 " --> pdb=" O TYR E 202 " (cutoff:3.500A) removed outlier: 7.853A pdb=" N ILE E 204 " --> pdb=" O THR E 168 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N SER E 170 " --> pdb=" O ILE E 204 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N PHE E 267 " --> pdb=" O SER E 381 " (cutoff:3.500A) removed outlier: 5.007A pdb=" N SER E 381 " --> pdb=" O PHE E 267 " (cutoff:3.500A) removed outlier: 8.221A pdb=" N ALA E 354 " --> pdb=" O VAL E 315 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N ALA E 317 " --> pdb=" O ALA E 354 " (cutoff:3.500A) removed outlier: 7.783A pdb=" N CYS E 356 " --> pdb=" O ALA E 317 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N PHE E 319 " --> pdb=" O CYS E 356 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N VAL E 355 " --> pdb=" O GLN E 247 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 53 through 55 Processing sheet with id=AB4, first strand: chain 'C' and resid 2 through 3 Processing sheet with id=AB5, first strand: chain 'C' and resid 92 through 94 removed outlier: 8.433A pdb=" N VAL C 93 " --> pdb=" O ALA C 65 " (cutoff:3.500A) removed outlier: 5.919A pdb=" N LEU C 67 " --> pdb=" O VAL C 93 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N HIS C 6 " --> pdb=" O ILE C 66 " (cutoff:3.500A) removed outlier: 7.813A pdb=" N VAL C 68 " --> pdb=" O HIS C 6 " (cutoff:3.500A) removed outlier: 5.987A pdb=" N GLN C 8 " --> pdb=" O VAL C 68 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ILE C 7 " --> pdb=" O GLN C 136 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N THR C 138 " --> pdb=" O ILE C 7 " (cutoff:3.500A) removed outlier: 5.184A pdb=" N SER C 140 " --> pdb=" O ALA C 9 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N HIS C 139 " --> pdb=" O PHE C 169 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N VAL C 171 " --> pdb=" O HIS C 139 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N SER C 170 " --> pdb=" O TYR C 202 " (cutoff:3.500A) removed outlier: 7.242A pdb=" N THR C 201 " --> pdb=" O PHE C 268 " (cutoff:3.500A) removed outlier: 7.820A pdb=" N CYS C 203 " --> pdb=" O PRO C 270 " (cutoff:3.500A) removed outlier: 10.362A pdb=" N PHE C 272 " --> pdb=" O CYS C 203 " (cutoff:3.500A) removed outlier: 7.447A pdb=" N PHE C 267 " --> pdb=" O SER C 381 " (cutoff:3.500A) removed outlier: 5.255A pdb=" N SER C 381 " --> pdb=" O PHE C 267 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N SER C 374 " --> pdb=" O PHE C 319 " (cutoff:3.500A) removed outlier: 4.997A pdb=" N PHE C 319 " --> pdb=" O SER C 374 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N THR C 376 " --> pdb=" O ALA C 317 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N ALA C 317 " --> pdb=" O THR C 376 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N ILE C 378 " --> pdb=" O VAL C 315 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N VAL C 315 " --> pdb=" O ILE C 378 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N ASN C 380 " --> pdb=" O LEU C 313 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 53 through 54 Processing sheet with id=AB7, first strand: chain 'F' and resid 93 through 94 removed outlier: 8.018A pdb=" N VAL F 93 " --> pdb=" O ALA F 65 " (cutoff:3.500A) removed outlier: 5.751A pdb=" N LEU F 67 " --> pdb=" O VAL F 93 " (cutoff:3.500A) removed outlier: 9.394A pdb=" N ILE F 66 " --> pdb=" O ILE F 4 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N HIS F 6 " --> pdb=" O ILE F 66 " (cutoff:3.500A) removed outlier: 8.144A pdb=" N VAL F 68 " --> pdb=" O HIS F 6 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N GLN F 8 " --> pdb=" O VAL F 68 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N GLU F 3 " --> pdb=" O GLN F 133 " (cutoff:3.500A) removed outlier: 5.694A pdb=" N PHE F 135 " --> pdb=" O GLU F 3 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N VAL F 5 " --> pdb=" O PHE F 135 " (cutoff:3.500A) removed outlier: 5.805A pdb=" N LEU F 137 " --> pdb=" O VAL F 5 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N ILE F 7 " --> pdb=" O LEU F 137 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N HIS F 139 " --> pdb=" O ILE F 7 " (cutoff:3.500A) removed outlier: 8.059A pdb=" N ALA F 9 " --> pdb=" O HIS F 139 " (cutoff:3.500A) removed outlier: 7.157A pdb=" N GLN F 133 " --> pdb=" O ILE F 165 " (cutoff:3.500A) removed outlier: 8.611A pdb=" N ASN F 167 " --> pdb=" O GLN F 133 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N PHE F 135 " --> pdb=" O ASN F 167 " (cutoff:3.500A) removed outlier: 7.889A pdb=" N PHE F 169 " --> pdb=" O PHE F 135 " (cutoff:3.500A) removed outlier: 7.098A pdb=" N LEU F 137 " --> pdb=" O PHE F 169 " (cutoff:3.500A) removed outlier: 8.846A pdb=" N VAL F 171 " --> pdb=" O LEU F 137 " (cutoff:3.500A) removed outlier: 7.985A pdb=" N HIS F 139 " --> pdb=" O VAL F 171 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N TYR F 202 " --> pdb=" O THR F 168 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ILE F 204 " --> pdb=" O SER F 170 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N THR F 201 " --> pdb=" O PHE F 268 " (cutoff:3.500A) removed outlier: 7.490A pdb=" N CYS F 203 " --> pdb=" O PRO F 270 " (cutoff:3.500A) removed outlier: 10.331A pdb=" N PHE F 272 " --> pdb=" O CYS F 203 " (cutoff:3.500A) removed outlier: 7.134A pdb=" N PHE F 267 " --> pdb=" O SER F 381 " (cutoff:3.500A) removed outlier: 5.114A pdb=" N SER F 381 " --> pdb=" O PHE F 267 " (cutoff:3.500A) removed outlier: 8.326A pdb=" N LYS F 352 " --> pdb=" O LEU F 313 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N VAL F 315 " --> pdb=" O LYS F 352 " (cutoff:3.500A) removed outlier: 8.013A pdb=" N ALA F 354 " --> pdb=" O VAL F 315 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N ALA F 317 " --> pdb=" O ALA F 354 " (cutoff:3.500A) removed outlier: 7.804A pdb=" N CYS F 356 " --> pdb=" O ALA F 317 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N PHE F 319 " --> pdb=" O CYS F 356 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N VAL F 355 " --> pdb=" O LEU F 248 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 53 through 56 921 hydrogen bonds defined for protein. 2688 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: 4.04 Time building geometry restraints manager: 2.44 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 3438 1.31 - 1.44: 5620 1.44 - 1.57: 11573 1.57 - 1.69: 27 1.69 - 1.82: 222 Bond restraints: 20880 Sorted by residual: bond pdb=" C ASP D 98 " pdb=" N ALA D 99 " ideal model delta sigma weight residual 1.334 1.524 -0.190 1.46e-02 4.69e+03 1.69e+02 bond pdb=" C1' GTP A 501 " pdb=" C2' GTP A 501 " ideal model delta sigma weight residual 1.524 1.286 0.238 2.00e-02 2.50e+03 1.41e+02 bond pdb=" C1' GTP B 501 " pdb=" C2' GTP B 501 " ideal model delta sigma weight residual 1.524 1.287 0.237 2.00e-02 2.50e+03 1.41e+02 bond pdb=" C1' GTP D 501 " pdb=" C2' GTP D 501 " ideal model delta sigma weight residual 1.524 1.289 0.235 2.00e-02 2.50e+03 1.38e+02 bond pdb=" C1' GTP B 501 " pdb=" O4' GTP B 501 " ideal model delta sigma weight residual 1.410 1.611 -0.201 2.00e-02 2.50e+03 1.01e+02 ... (remaining 20875 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.17: 28347 5.17 - 10.35: 84 10.35 - 15.52: 7 15.52 - 20.69: 1 20.69 - 25.87: 1 Bond angle restraints: 28440 Sorted by residual: angle pdb=" C PRO E 173 " pdb=" N SER E 174 " pdb=" CA SER E 174 " ideal model delta sigma weight residual 120.68 146.55 -25.87 1.52e+00 4.33e-01 2.90e+02 angle pdb=" C ASP D 98 " pdb=" N ALA D 99 " pdb=" CA ALA D 99 " ideal model delta sigma weight residual 120.68 108.90 11.78 1.70e+00 3.46e-01 4.80e+01 angle pdb=" O ALA D 99 " pdb=" C ALA D 99 " pdb=" N ALA D 100 " ideal model delta sigma weight residual 122.33 130.97 -8.64 1.34e+00 5.57e-01 4.16e+01 angle pdb=" C THR F 287 " pdb=" N VAL F 288 " pdb=" CA VAL F 288 " ideal model delta sigma weight residual 120.24 124.15 -3.91 6.30e-01 2.52e+00 3.85e+01 angle pdb=" CA ALA D 99 " pdb=" C ALA D 99 " pdb=" N ALA D 100 " ideal model delta sigma weight residual 117.82 109.71 8.11 1.42e+00 4.96e-01 3.26e+01 ... (remaining 28435 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.84: 11965 35.84 - 71.68: 278 71.68 - 107.51: 33 107.51 - 143.35: 6 143.35 - 179.19: 6 Dihedral angle restraints: 12288 sinusoidal: 4887 harmonic: 7401 Sorted by residual: dihedral pdb=" C5' GTP B 501 " pdb=" O5' GTP B 501 " pdb=" PA GTP B 501 " pdb=" O3A GTP B 501 " ideal model delta sinusoidal sigma weight residual 69.27 -111.54 -179.19 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" C5' GTP A 501 " pdb=" O5' GTP A 501 " pdb=" PA GTP A 501 " pdb=" O3A GTP A 501 " ideal model delta sinusoidal sigma weight residual 69.27 -96.77 166.04 1 2.00e+01 2.50e-03 4.73e+01 dihedral pdb=" C8 GTP D 501 " pdb=" C1' GTP D 501 " pdb=" N9 GTP D 501 " pdb=" O4' GTP D 501 " ideal model delta sinusoidal sigma weight residual 104.59 -55.07 159.67 1 2.00e+01 2.50e-03 4.65e+01 ... (remaining 12285 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.177: 3107 0.177 - 0.353: 24 0.353 - 0.530: 0 0.530 - 0.706: 3 0.706 - 0.883: 1 Chirality restraints: 3135 Sorted by residual: chirality pdb=" CAZ TAJ E 501 " pdb=" CAV TAJ E 501 " pdb=" CAY TAJ E 501 " pdb=" OAD TAJ E 501 " both_signs ideal model delta sigma weight residual False -2.52 -1.64 -0.88 2.00e-01 2.50e+01 1.95e+01 chirality pdb=" CBB TAJ E 501 " pdb=" CBA TAJ E 501 " pdb=" CBC TAJ E 501 " pdb=" CBD TAJ E 501 " both_signs ideal model delta sigma weight residual False 2.06 2.69 -0.63 2.00e-01 2.50e+01 1.00e+01 chirality pdb=" CBB TAJ F 501 " pdb=" CBA TAJ F 501 " pdb=" CBC TAJ F 501 " pdb=" CBD TAJ F 501 " both_signs ideal model delta sigma weight residual False 2.06 2.61 -0.55 2.00e-01 2.50e+01 7.47e+00 ... (remaining 3132 not shown) Planarity restraints: 3681 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU A 397 " 0.016 2.00e-02 2.50e+03 3.09e-02 9.56e+00 pdb=" C LEU A 397 " -0.053 2.00e-02 2.50e+03 pdb=" O LEU A 397 " 0.020 2.00e-02 2.50e+03 pdb=" N MET A 398 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL A 324 " 0.049 5.00e-02 4.00e+02 7.36e-02 8.66e+00 pdb=" N PRO A 325 " -0.127 5.00e-02 4.00e+02 pdb=" CA PRO A 325 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO A 325 " 0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL C 288 " 0.048 5.00e-02 4.00e+02 7.19e-02 8.28e+00 pdb=" N PRO C 289 " -0.124 5.00e-02 4.00e+02 pdb=" CA PRO C 289 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO C 289 " 0.040 5.00e-02 4.00e+02 ... (remaining 3678 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 280 2.63 - 3.20: 17074 3.20 - 3.77: 31241 3.77 - 4.33: 39846 4.33 - 4.90: 65822 Nonbonded interactions: 154263 Sorted by model distance: nonbonded pdb=" O1B GTP B 501 " pdb="MG MG B 502 " model vdw 2.063 2.170 nonbonded pdb=" O2G GTP B 501 " pdb="MG MG B 502 " model vdw 2.075 2.170 nonbonded pdb=" O ASN C 59 " pdb=" ND2 ASN C 59 " model vdw 2.078 3.120 nonbonded pdb=" O2G GTP A 501 " pdb="MG MG A 502 " model vdw 2.085 2.170 nonbonded pdb=" O3G GTP A 501 " pdb="MG MG A 502 " model vdw 2.125 2.170 ... (remaining 154258 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 1 through 501) selection = (chain 'B' and resid 1 through 501) selection = chain 'D' } ncs_group { reference = chain 'C' selection = chain 'E' selection = chain 'F' } 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: 0.390 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.310 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 20.130 Find NCS groups from input model: 0.510 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7996 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 : 0.010 0.463 20883 Z= 0.598 Angle : 1.015 25.867 28440 Z= 0.576 Chirality : 0.063 0.883 3135 Planarity : 0.008 0.074 3681 Dihedral : 17.089 179.189 7542 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 0.74 % Allowed : 9.46 % Favored : 89.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.24 (0.14), residues: 2544 helix: -1.96 (0.12), residues: 1083 sheet: -0.93 (0.26), residues: 354 loop : -2.69 (0.15), residues: 1107 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 390 TYR 0.024 0.002 TYR B 224 PHE 0.024 0.003 PHE C 418 TRP 0.017 0.002 TRP F 346 HIS 0.007 0.002 HIS C 406 Details of bonding type rmsd/Z covalent geometry : bond 0.00858 / 0.43 (20880) covalent geometry : angle 1.01524 / 0.58 (28440) hydrogen bonds : bond 0.17053 / 11.96 ( 921) hydrogen bonds : angle 6.74670 / 4.81 ( 2688) Misc. bond : bond 0.34948 / 17.92 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5088 Ramachandran restraints generated. 2544 Oldfield, 0 Emsley, 2544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5088 Ramachandran restraints generated. 2544 Oldfield, 0 Emsley, 2544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 587 residues out of total 2187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 571 time to evaluate : 0.714 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 69 ASP cc_start: 0.8411 (t70) cc_final: 0.7980 (t70) REVERT: D 70 LEU cc_start: 0.8759 (mt) cc_final: 0.8444 (mt) REVERT: D 85 GLN cc_start: 0.7832 (mp10) cc_final: 0.5565 (tp40) REVERT: D 327 ASP cc_start: 0.8754 (OUTLIER) cc_final: 0.8447 (p0) REVERT: D 413 MET cc_start: 0.7682 (ttm) cc_final: 0.7267 (ttm) REVERT: A 128 GLN cc_start: 0.8028 (mm-40) cc_final: 0.7411 (tm-30) REVERT: A 154 MET cc_start: 0.8545 (tpp) cc_final: 0.8265 (tpt) REVERT: A 161 TYR cc_start: 0.8658 (m-80) cc_final: 0.8451 (m-80) REVERT: A 280 LYS cc_start: 0.6198 (mttp) cc_final: 0.5888 (tptt) REVERT: A 284 GLU cc_start: 0.7563 (tp30) cc_final: 0.7108 (pm20) REVERT: A 372 GLN cc_start: 0.8570 (tp40) cc_final: 0.8311 (tp-100) REVERT: A 390 ARG cc_start: 0.8199 (mtt180) cc_final: 0.7882 (mmp80) REVERT: B 35 GLN cc_start: 0.7512 (tt0) cc_final: 0.7300 (tt0) REVERT: B 102 ASN cc_start: 0.8479 (t0) cc_final: 0.8192 (t0) REVERT: B 192 HIS cc_start: 0.7844 (t70) cc_final: 0.7559 (t70) REVERT: B 221 ARG cc_start: 0.7256 (mtt180) cc_final: 0.5732 (ptt180) REVERT: B 290 GLU cc_start: 0.8266 (pt0) cc_final: 0.7931 (pt0) REVERT: B 302 MET cc_start: 0.8202 (mmm) cc_final: 0.7599 (mpp) REVERT: B 358 GLN cc_start: 0.9256 (tp40) cc_final: 0.8872 (tp-100) REVERT: B 398 MET cc_start: 0.7347 (mtt) cc_final: 0.7084 (mtm) REVERT: B 414 GLU cc_start: 0.6176 (mp0) cc_final: 0.5447 (mp0) REVERT: E 71 GLU cc_start: 0.7473 (mp0) cc_final: 0.7000 (pm20) REVERT: E 96 GLN cc_start: 0.7651 (mm110) cc_final: 0.7267 (mm-40) REVERT: E 102 ASN cc_start: 0.9066 (m-40) cc_final: 0.8705 (m110) REVERT: E 282 GLN cc_start: 0.7433 (mt0) cc_final: 0.7117 (pt0) REVERT: E 299 LYS cc_start: 0.8663 (ptmm) cc_final: 0.8264 (tttm) REVERT: E 308 ARG cc_start: 0.7655 (ptt-90) cc_final: 0.6820 (ptt-90) REVERT: E 320 ARG cc_start: 0.7753 (mtp180) cc_final: 0.6363 (mtm110) REVERT: E 325 MET cc_start: 0.8320 (mmm) cc_final: 0.8104 (mmm) REVERT: C 14 ASN cc_start: 0.8448 (t0) cc_final: 0.7843 (t0) REVERT: C 54 ASN cc_start: 0.8676 (t0) cc_final: 0.8375 (t0) REVERT: C 103 TRP cc_start: 0.7213 (t60) cc_final: 0.6495 (t60) REVERT: C 110 GLU cc_start: 0.8360 (mp0) cc_final: 0.8128 (mp0) REVERT: C 113 GLU cc_start: 0.8677 (mt-10) cc_final: 0.8187 (mp0) REVERT: C 259 MET cc_start: 0.8377 (mmm) cc_final: 0.7995 (mmp) REVERT: C 299 LYS cc_start: 0.7722 (tttt) cc_final: 0.7280 (mmmt) REVERT: C 373 MET cc_start: 0.7901 (ptp) cc_final: 0.7572 (ptp) REVERT: C 407 TRP cc_start: 0.6911 (m100) cc_final: 0.6139 (m-90) REVERT: C 411 GLU cc_start: 0.6452 (mm-30) cc_final: 0.5626 (tm-30) REVERT: C 420 GLU cc_start: 0.7893 (mt-10) cc_final: 0.7380 (mt-10) REVERT: F 37 HIS cc_start: 0.8134 (m-70) cc_final: 0.7679 (m90) REVERT: F 61 TYR cc_start: 0.7370 (m-80) cc_final: 0.5926 (m-80) REVERT: F 92 PHE cc_start: 0.8548 (m-80) cc_final: 0.8256 (m-10) REVERT: F 193 GLN cc_start: 0.7887 (mm-40) cc_final: 0.7476 (tp-100) REVERT: F 228 ASN cc_start: 0.9227 (m-40) cc_final: 0.8787 (m-40) REVERT: F 295 MET cc_start: 0.8421 (ttm) cc_final: 0.8198 (ttp) REVERT: F 425 MET cc_start: 0.7014 (tpp) cc_final: 0.6544 (mmm) REVERT: F 428 LEU cc_start: 0.8759 (tp) cc_final: 0.8547 (tp) outliers start: 16 outliers final: 10 residues processed: 583 average time/residue: 0.1532 time to fit residues: 136.0557 Evaluate side-chains 441 residues out of total 2187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 430 time to evaluate : 0.801 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 216 optimal weight: 2.9990 chunk 98 optimal weight: 2.9990 chunk 194 optimal weight: 10.0000 chunk 227 optimal weight: 0.0020 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 0.5980 chunk 66 optimal weight: 2.9990 chunk 247 optimal weight: 5.9990 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 0.6980 chunk 103 optimal weight: 0.9980 overall best weight: 0.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 15 GLN D 88 HIS D 107 HIS ** D 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 258 ASN D 300 ASN D 358 GLN ** A 8 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 88 HIS A 107 HIS A 216 ASN A 226 ASN A 406 HIS B 18 ASN B 107 HIS E 186 ASN ** C 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 59 ASN C 96 GLN C 192 HIS ** C 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 406 HIS F 101 ASN F 192 HIS F 309 HIS F 331 GLN ** F 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.139877 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.123694 restraints weight = 36632.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.126664 restraints weight = 21791.173| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.128756 restraints weight = 14576.202| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.130212 restraints weight = 10605.401| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.131277 restraints weight = 8266.653| |-----------------------------------------------------------------------------| r_work (final): 0.3714 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7835 moved from start: 0.2351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 20883 Z= 0.118 Angle : 0.607 12.530 28440 Z= 0.306 Chirality : 0.044 0.162 3135 Planarity : 0.005 0.064 3681 Dihedral : 10.898 173.628 2850 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 0.18 % Allowed : 3.74 % Favored : 96.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.69 (0.15), residues: 2544 helix: -0.23 (0.15), residues: 1119 sheet: -0.28 (0.25), residues: 399 loop : -2.49 (0.16), residues: 1026 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 401 TYR 0.016 0.001 TYR E 36 PHE 0.021 0.001 PHE F 377 TRP 0.015 0.001 TRP D 21 HIS 0.011 0.001 HIS C 309 Details of bonding type rmsd/Z covalent geometry : bond 0.00244 / 0.12 (20880) covalent geometry : angle 0.60728 / 0.31 (28440) hydrogen bonds : bond 0.04225 / 2.87 ( 921) hydrogen bonds : angle 4.71272 / 3.35 ( 2688) Misc. bond : bond 0.00246 / 0.13 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5088 Ramachandran restraints generated. 2544 Oldfield, 0 Emsley, 2544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5088 Ramachandran restraints generated. 2544 Oldfield, 0 Emsley, 2544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 584 residues out of total 2187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 580 time to evaluate : 0.810 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 85 GLN cc_start: 0.7958 (mp10) cc_final: 0.5467 (tp-100) REVERT: D 103 TYR cc_start: 0.6705 (t80) cc_final: 0.6423 (t80) REVERT: D 226 ASN cc_start: 0.8411 (m-40) cc_final: 0.8027 (m110) REVERT: D 413 MET cc_start: 0.7578 (ttm) cc_final: 0.7245 (ttm) REVERT: A 128 GLN cc_start: 0.7932 (mm-40) cc_final: 0.7503 (tm-30) REVERT: A 161 TYR cc_start: 0.8557 (m-80) cc_final: 0.8228 (m-80) REVERT: A 284 GLU cc_start: 0.7198 (tp30) cc_final: 0.6941 (pm20) REVERT: A 390 ARG cc_start: 0.8044 (mtt180) cc_final: 0.7743 (mmp80) REVERT: A 413 MET cc_start: 0.7831 (mmm) cc_final: 0.7523 (mmt) REVERT: B 22 GLU cc_start: 0.7960 (tt0) cc_final: 0.7684 (tm-30) REVERT: B 64 ARG cc_start: 0.8726 (mtt90) cc_final: 0.7934 (mtt-85) REVERT: B 90 GLU cc_start: 0.8533 (tp30) cc_final: 0.7920 (tp30) REVERT: B 102 ASN cc_start: 0.8367 (t0) cc_final: 0.8072 (t0) REVERT: B 192 HIS cc_start: 0.8000 (t70) cc_final: 0.7731 (t70) REVERT: B 221 ARG cc_start: 0.7140 (mtt180) cc_final: 0.5490 (ptt180) REVERT: B 256 GLN cc_start: 0.5568 (tm-30) cc_final: 0.5168 (tm-30) REVERT: B 302 MET cc_start: 0.8122 (mmm) cc_final: 0.7722 (tpp) REVERT: B 358 GLN cc_start: 0.9181 (tp40) cc_final: 0.8857 (tp-100) REVERT: B 376 CYS cc_start: 0.8927 (t) cc_final: 0.8452 (p) REVERT: E 96 GLN cc_start: 0.7639 (mm110) cc_final: 0.7053 (mm-40) REVERT: E 202 TYR cc_start: 0.8859 (m-80) cc_final: 0.8525 (m-80) REVERT: E 308 ARG cc_start: 0.6835 (ptt-90) cc_final: 0.6595 (ptt-90) REVERT: E 320 ARG cc_start: 0.7749 (mtp180) cc_final: 0.7493 (mtm180) REVERT: E 398 MET cc_start: 0.7428 (mtt) cc_final: 0.7147 (mtt) REVERT: C 14 ASN cc_start: 0.8274 (t0) cc_final: 0.7608 (t0) REVERT: C 54 ASN cc_start: 0.8763 (t0) cc_final: 0.8234 (t0) REVERT: C 75 MET cc_start: 0.8277 (mmt) cc_final: 0.7702 (mmt) REVERT: C 103 TRP cc_start: 0.6637 (t60) cc_final: 0.6281 (t60) REVERT: C 113 GLU cc_start: 0.8431 (mt-10) cc_final: 0.7977 (mp0) REVERT: C 278 ARG cc_start: 0.7721 (tpm170) cc_final: 0.7428 (tpm170) REVERT: C 299 LYS cc_start: 0.7573 (tttt) cc_final: 0.7090 (mmmt) REVERT: C 333 LEU cc_start: 0.8606 (tp) cc_final: 0.8310 (tp) REVERT: C 407 TRP cc_start: 0.6750 (m100) cc_final: 0.6123 (m-90) REVERT: C 411 GLU cc_start: 0.6406 (mm-30) cc_final: 0.6020 (tm-30) REVERT: F 37 HIS cc_start: 0.7702 (m-70) cc_final: 0.7283 (m90) REVERT: F 61 TYR cc_start: 0.7146 (m-80) cc_final: 0.6921 (m-80) REVERT: F 86 ILE cc_start: 0.9049 (pt) cc_final: 0.8642 (tp) REVERT: F 228 ASN cc_start: 0.9342 (m-40) cc_final: 0.8855 (m-40) REVERT: F 295 MET cc_start: 0.8433 (ttm) cc_final: 0.8207 (ttp) REVERT: F 323 MET cc_start: 0.7822 (mtt) cc_final: 0.7402 (mtt) REVERT: F 384 ILE cc_start: 0.7904 (pt) cc_final: 0.7700 (pt) REVERT: F 413 MET cc_start: 0.6791 (mtp) cc_final: 0.6495 (mtm) outliers start: 4 outliers final: 1 residues processed: 582 average time/residue: 0.1410 time to fit residues: 127.1001 Evaluate side-chains 411 residues out of total 2187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 410 time to evaluate : 0.790 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 146 optimal weight: 7.9990 chunk 174 optimal weight: 20.0000 chunk 222 optimal weight: 5.9990 chunk 8 optimal weight: 10.0000 chunk 104 optimal weight: 1.9990 chunk 148 optimal weight: 0.8980 chunk 109 optimal weight: 0.6980 chunk 224 optimal weight: 30.0000 chunk 225 optimal weight: 3.9990 chunk 161 optimal weight: 0.8980 chunk 130 optimal weight: 0.2980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 8 HIS D 176 GLN ** D 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 300 ASN D 309 HIS D 406 HIS ** A 8 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 18 ASN B 28 HIS B 88 HIS B 226 ASN ** B 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 101 ASN ** E 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 186 ASN ** E 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 436 GLN ** C 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 6 HIS F 8 GLN F 247 GLN F 258 ASN F 331 GLN ** F 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.139917 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.123836 restraints weight = 36932.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.126754 restraints weight = 22032.703| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.128772 restraints weight = 14781.813| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.130208 restraints weight = 10828.333| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.131195 restraints weight = 8452.549| |-----------------------------------------------------------------------------| r_work (final): 0.3712 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7833 moved from start: 0.2998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 20883 Z= 0.110 Angle : 0.568 10.982 28440 Z= 0.284 Chirality : 0.044 0.195 3135 Planarity : 0.005 0.066 3681 Dihedral : 10.388 178.184 2850 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 0.05 % Allowed : 3.74 % Favored : 96.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.90 (0.16), residues: 2544 helix: 0.52 (0.15), residues: 1128 sheet: -0.01 (0.25), residues: 411 loop : -2.18 (0.17), residues: 1005 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG F 390 TYR 0.024 0.001 TYR A 210 PHE 0.017 0.001 PHE F 377 TRP 0.017 0.001 TRP D 21 HIS 0.009 0.001 HIS B 28 Details of bonding type rmsd/Z covalent geometry : bond 0.00230 / 0.11 (20880) covalent geometry : angle 0.56806 / 0.28 (28440) hydrogen bonds : bond 0.03893 / 2.62 ( 921) hydrogen bonds : angle 4.40197 / 3.13 ( 2688) Misc. bond : bond 0.00218 / 0.11 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5088 Ramachandran restraints generated. 2544 Oldfield, 0 Emsley, 2544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5088 Ramachandran restraints generated. 2544 Oldfield, 0 Emsley, 2544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 546 residues out of total 2187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 545 time to evaluate : 0.799 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 98 ASP cc_start: 0.7459 (p0) cc_final: 0.7208 (p0) REVERT: D 287 SER cc_start: 0.8724 (p) cc_final: 0.8473 (p) REVERT: D 301 GLN cc_start: 0.7929 (mm110) cc_final: 0.7718 (mm110) REVERT: D 386 GLU cc_start: 0.7487 (mm-30) cc_final: 0.7229 (pp20) REVERT: D 413 MET cc_start: 0.7254 (ttm) cc_final: 0.6662 (ttm) REVERT: A 128 GLN cc_start: 0.7897 (mm-40) cc_final: 0.7453 (tm-30) REVERT: A 390 ARG cc_start: 0.7952 (mtt180) cc_final: 0.7695 (mmp80) REVERT: B 51 THR cc_start: 0.8973 (t) cc_final: 0.8676 (t) REVERT: B 64 ARG cc_start: 0.8705 (mtt90) cc_final: 0.7696 (mtt-85) REVERT: B 90 GLU cc_start: 0.8582 (tp30) cc_final: 0.7855 (tp30) REVERT: B 102 ASN cc_start: 0.8385 (t0) cc_final: 0.8030 (t0) REVERT: B 192 HIS cc_start: 0.7993 (t70) cc_final: 0.7747 (t70) REVERT: B 221 ARG cc_start: 0.6829 (mtt90) cc_final: 0.5850 (ptt180) REVERT: B 224 TYR cc_start: 0.8290 (m-10) cc_final: 0.7911 (m-80) REVERT: B 258 ASN cc_start: 0.9126 (m110) cc_final: 0.8707 (m-40) REVERT: B 358 GLN cc_start: 0.9170 (tp40) cc_final: 0.8915 (tp-100) REVERT: B 414 GLU cc_start: 0.5312 (mp0) cc_final: 0.4907 (pt0) REVERT: E 96 GLN cc_start: 0.7457 (mm110) cc_final: 0.7079 (mm-40) REVERT: E 132 LEU cc_start: 0.8307 (pp) cc_final: 0.7665 (pp) REVERT: E 243 ARG cc_start: 0.8880 (mtm110) cc_final: 0.8614 (ptt90) REVERT: E 308 ARG cc_start: 0.7003 (ptt-90) cc_final: 0.6793 (ptt-90) REVERT: E 320 ARG cc_start: 0.7710 (mtp180) cc_final: 0.6525 (mtm110) REVERT: E 413 MET cc_start: 0.8246 (mtp) cc_final: 0.7700 (mtp) REVERT: E 428 LEU cc_start: 0.8083 (tp) cc_final: 0.7870 (tt) REVERT: C 14 ASN cc_start: 0.8238 (t0) cc_final: 0.7680 (t0) REVERT: C 54 ASN cc_start: 0.8804 (t0) cc_final: 0.8233 (t0) REVERT: C 103 TRP cc_start: 0.7104 (t60) cc_final: 0.6755 (t60) REVERT: C 113 GLU cc_start: 0.8449 (mt-10) cc_final: 0.8183 (mp0) REVERT: C 216 THR cc_start: 0.7828 (t) cc_final: 0.7349 (p) REVERT: C 278 ARG cc_start: 0.7785 (tpm170) cc_final: 0.7460 (tpm170) REVERT: C 333 LEU cc_start: 0.8550 (tp) cc_final: 0.8208 (tp) REVERT: C 356 CYS cc_start: 0.8679 (t) cc_final: 0.7827 (m) REVERT: C 377 PHE cc_start: 0.8727 (t80) cc_final: 0.8174 (t80) REVERT: C 407 TRP cc_start: 0.6764 (m100) cc_final: 0.6227 (m-90) REVERT: C 411 GLU cc_start: 0.6478 (mm-30) cc_final: 0.5979 (tm-30) REVERT: C 420 GLU cc_start: 0.7756 (mt-10) cc_final: 0.7504 (mp0) REVERT: F 6 HIS cc_start: 0.7546 (t70) cc_final: 0.7303 (t-170) REVERT: F 37 HIS cc_start: 0.7698 (m-70) cc_final: 0.7285 (m90) REVERT: F 86 ILE cc_start: 0.9033 (pt) cc_final: 0.8662 (tp) REVERT: F 228 ASN cc_start: 0.9330 (m-40) cc_final: 0.8770 (m-40) REVERT: F 295 MET cc_start: 0.8480 (ttm) cc_final: 0.8265 (ttp) REVERT: F 320 ARG cc_start: 0.7749 (mtp180) cc_final: 0.7419 (mtm110) REVERT: F 323 MET cc_start: 0.7567 (mtt) cc_final: 0.7339 (mtt) REVERT: F 384 ILE cc_start: 0.8118 (pt) cc_final: 0.7900 (pt) REVERT: F 413 MET cc_start: 0.7024 (mtp) cc_final: 0.6807 (mtm) outliers start: 1 outliers final: 0 residues processed: 546 average time/residue: 0.1518 time to fit residues: 127.6660 Evaluate side-chains 404 residues out of total 2187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 404 time to evaluate : 0.800 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 94 optimal weight: 6.9990 chunk 35 optimal weight: 8.9990 chunk 160 optimal weight: 1.9990 chunk 135 optimal weight: 6.9990 chunk 242 optimal weight: 3.9990 chunk 36 optimal weight: 6.9990 chunk 106 optimal weight: 1.9990 chunk 53 optimal weight: 10.0000 chunk 56 optimal weight: 6.9990 chunk 92 optimal weight: 4.9990 chunk 102 optimal weight: 9.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 88 HIS ** D 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 300 ASN D 358 GLN ** A 8 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 88 HIS B 18 ASN ** B 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 101 ASN ** E 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 192 HIS E 281 GLN ** C 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 102 ASN C 294 GLN C 309 HIS ** C 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 350 ASN C 385 GLN C 436 GLN ** F 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.132260 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.116341 restraints weight = 38228.185| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.119043 restraints weight = 23113.136| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.120944 restraints weight = 15743.792| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.122290 restraints weight = 11657.480| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.123250 restraints weight = 9249.337| |-----------------------------------------------------------------------------| r_work (final): 0.3613 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7981 moved from start: 0.3071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 20883 Z= 0.191 Angle : 0.660 10.034 28440 Z= 0.337 Chirality : 0.047 0.152 3135 Planarity : 0.005 0.067 3681 Dihedral : 10.509 179.679 2850 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer: Outliers : 0.09 % Allowed : 4.11 % Favored : 95.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.67 (0.16), residues: 2544 helix: 0.74 (0.16), residues: 1113 sheet: -0.06 (0.25), residues: 414 loop : -1.97 (0.18), residues: 1017 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 121 TYR 0.024 0.002 TYR D 432 PHE 0.020 0.002 PHE C 319 TRP 0.032 0.002 TRP B 407 HIS 0.013 0.002 HIS C 309 Details of bonding type rmsd/Z covalent geometry : bond 0.00432 / 0.19 (20880) covalent geometry : angle 0.66002 / 0.34 (28440) hydrogen bonds : bond 0.04826 / 3.28 ( 921) hydrogen bonds : angle 4.62421 / 3.28 ( 2688) Misc. bond : bond 0.00257 / 0.13 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5088 Ramachandran restraints generated. 2544 Oldfield, 0 Emsley, 2544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5088 Ramachandran restraints generated. 2544 Oldfield, 0 Emsley, 2544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 499 residues out of total 2187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 497 time to evaluate : 0.898 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 49 PHE cc_start: 0.7470 (p90) cc_final: 0.7224 (p90) REVERT: D 88 HIS cc_start: 0.8300 (OUTLIER) cc_final: 0.7187 (t-90) REVERT: D 210 TYR cc_start: 0.8728 (m-10) cc_final: 0.8156 (m-80) REVERT: D 226 ASN cc_start: 0.9126 (m110) cc_final: 0.8751 (m-40) REVERT: D 300 ASN cc_start: 0.8527 (OUTLIER) cc_final: 0.7968 (t0) REVERT: D 367 ASP cc_start: 0.7198 (m-30) cc_final: 0.6755 (m-30) REVERT: D 413 MET cc_start: 0.7493 (ttm) cc_final: 0.6671 (ttm) REVERT: A 123 ARG cc_start: 0.7901 (mmm-85) cc_final: 0.7553 (mmm-85) REVERT: A 128 GLN cc_start: 0.7868 (mm-40) cc_final: 0.7283 (tm-30) REVERT: A 161 TYR cc_start: 0.8419 (m-80) cc_final: 0.7744 (m-80) REVERT: A 186 ASN cc_start: 0.8612 (m-40) cc_final: 0.8405 (m-40) REVERT: A 203 MET cc_start: 0.8266 (mmt) cc_final: 0.7963 (mtm) REVERT: A 390 ARG cc_start: 0.7947 (mtt180) cc_final: 0.7674 (mmp80) REVERT: B 51 THR cc_start: 0.9057 (t) cc_final: 0.8789 (t) REVERT: B 102 ASN cc_start: 0.8661 (t0) cc_final: 0.8370 (t0) REVERT: B 221 ARG cc_start: 0.7228 (mtt90) cc_final: 0.5969 (ptt180) REVERT: B 242 LEU cc_start: 0.9261 (tp) cc_final: 0.9034 (tt) REVERT: B 258 ASN cc_start: 0.9031 (m110) cc_final: 0.8604 (m-40) REVERT: B 302 MET cc_start: 0.8424 (mmm) cc_final: 0.8102 (mtt) REVERT: B 335 ILE cc_start: 0.9107 (tp) cc_final: 0.8798 (mm) REVERT: B 358 GLN cc_start: 0.9111 (tp40) cc_final: 0.8883 (tp-100) REVERT: B 407 TRP cc_start: 0.7543 (m100) cc_final: 0.7076 (m-10) REVERT: E 96 GLN cc_start: 0.7651 (mm110) cc_final: 0.7279 (mm-40) REVERT: E 131 CYS cc_start: 0.7205 (p) cc_final: 0.6712 (m) REVERT: E 215 ARG cc_start: 0.8259 (mmm160) cc_final: 0.8001 (tmm160) REVERT: E 308 ARG cc_start: 0.6760 (ptt-90) cc_final: 0.6492 (ptt-90) REVERT: E 320 ARG cc_start: 0.7811 (mtp180) cc_final: 0.7531 (mtm180) REVERT: C 14 ASN cc_start: 0.8305 (t0) cc_final: 0.7793 (t0) REVERT: C 54 ASN cc_start: 0.8820 (t0) cc_final: 0.8281 (t0) REVERT: C 66 ILE cc_start: 0.9248 (mm) cc_final: 0.8873 (mm) REVERT: C 103 TRP cc_start: 0.7016 (t60) cc_final: 0.6681 (t60) REVERT: C 216 THR cc_start: 0.7752 (t) cc_final: 0.7328 (p) REVERT: C 278 ARG cc_start: 0.7840 (tpm170) cc_final: 0.7554 (tpm170) REVERT: C 301 MET cc_start: 0.9028 (mmp) cc_final: 0.8811 (tpp) REVERT: C 333 LEU cc_start: 0.8642 (tp) cc_final: 0.8355 (tp) REVERT: C 407 TRP cc_start: 0.6906 (m100) cc_final: 0.6208 (m-90) REVERT: C 420 GLU cc_start: 0.7774 (mt-10) cc_final: 0.7558 (mp0) REVERT: F 6 HIS cc_start: 0.7857 (t70) cc_final: 0.7546 (t70) REVERT: F 37 HIS cc_start: 0.7633 (m-70) cc_final: 0.7187 (m90) REVERT: F 228 ASN cc_start: 0.9380 (m-40) cc_final: 0.8973 (m-40) REVERT: F 295 MET cc_start: 0.8478 (ttm) cc_final: 0.8212 (ttp) outliers start: 2 outliers final: 0 residues processed: 499 average time/residue: 0.1523 time to fit residues: 117.2064 Evaluate side-chains 378 residues out of total 2187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 376 time to evaluate : 0.778 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 241 optimal weight: 10.0000 chunk 102 optimal weight: 20.0000 chunk 41 optimal weight: 6.9990 chunk 10 optimal weight: 8.9990 chunk 145 optimal weight: 1.9990 chunk 91 optimal weight: 10.0000 chunk 29 optimal weight: 0.2980 chunk 141 optimal weight: 5.9990 chunk 53 optimal weight: 2.9990 chunk 126 optimal weight: 10.0000 chunk 242 optimal weight: 0.9990 overall best weight: 2.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 176 GLN ** A 8 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 18 ASN B 301 GLN E 101 ASN ** E 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 167 ASN E 192 HIS ** C 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 54 ASN ** F 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.134235 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.118625 restraints weight = 37402.369| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.121361 restraints weight = 22379.434| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.123278 restraints weight = 15077.694| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.124608 restraints weight = 11079.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.125493 restraints weight = 8751.756| |-----------------------------------------------------------------------------| r_work (final): 0.3638 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7927 moved from start: 0.3348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 20883 Z= 0.139 Angle : 0.600 10.591 28440 Z= 0.302 Chirality : 0.045 0.246 3135 Planarity : 0.005 0.065 3681 Dihedral : 10.266 178.751 2850 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 0.14 % Allowed : 2.40 % Favored : 97.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.48 (0.16), residues: 2544 helix: 0.94 (0.16), residues: 1113 sheet: 0.02 (0.25), residues: 411 loop : -1.92 (0.18), residues: 1020 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 320 TYR 0.020 0.001 TYR A 210 PHE 0.016 0.001 PHE E 418 TRP 0.017 0.002 TRP B 407 HIS 0.005 0.001 HIS B 192 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.14 (20880) covalent geometry : angle 0.59959 / 0.30 (28440) hydrogen bonds : bond 0.04212 / 2.84 ( 921) hydrogen bonds : angle 4.46697 / 3.17 ( 2688) Misc. bond : bond 0.00399 / 0.20 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5088 Ramachandran restraints generated. 2544 Oldfield, 0 Emsley, 2544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5088 Ramachandran restraints generated. 2544 Oldfield, 0 Emsley, 2544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 494 residues out of total 2187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 491 time to evaluate : 0.771 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 49 PHE cc_start: 0.7546 (p90) cc_final: 0.7256 (p90) REVERT: D 210 TYR cc_start: 0.8785 (m-10) cc_final: 0.8192 (m-80) REVERT: D 413 MET cc_start: 0.7487 (ttm) cc_final: 0.6944 (ttm) REVERT: A 123 ARG cc_start: 0.8009 (mmm-85) cc_final: 0.7634 (mmm-85) REVERT: A 128 GLN cc_start: 0.7938 (mm-40) cc_final: 0.7313 (tm-30) REVERT: A 154 MET cc_start: 0.7948 (tpt) cc_final: 0.7736 (tpt) REVERT: B 22 GLU cc_start: 0.7966 (tt0) cc_final: 0.7594 (tm-30) REVERT: B 64 ARG cc_start: 0.8846 (mtt90) cc_final: 0.8093 (mtt-85) REVERT: B 90 GLU cc_start: 0.8558 (tp30) cc_final: 0.8053 (tp30) REVERT: B 102 ASN cc_start: 0.8671 (t0) cc_final: 0.8318 (t0) REVERT: B 221 ARG cc_start: 0.7193 (mtt90) cc_final: 0.5845 (ptt180) REVERT: B 258 ASN cc_start: 0.9037 (m110) cc_final: 0.8663 (m-40) REVERT: B 301 GLN cc_start: 0.8199 (OUTLIER) cc_final: 0.7998 (mp10) REVERT: B 302 MET cc_start: 0.8531 (mmm) cc_final: 0.8282 (mtp) REVERT: B 358 GLN cc_start: 0.9146 (tp40) cc_final: 0.8855 (tp-100) REVERT: B 407 TRP cc_start: 0.7204 (m100) cc_final: 0.6812 (m-10) REVERT: E 96 GLN cc_start: 0.7476 (mm110) cc_final: 0.7207 (mm-40) REVERT: E 308 ARG cc_start: 0.7051 (ptt-90) cc_final: 0.6840 (ptt-90) REVERT: E 320 ARG cc_start: 0.7852 (mtp180) cc_final: 0.7563 (mtm180) REVERT: E 374 SER cc_start: 0.9310 (p) cc_final: 0.9067 (p) REVERT: C 14 ASN cc_start: 0.8295 (t0) cc_final: 0.7848 (t0) REVERT: C 54 ASN cc_start: 0.8887 (t0) cc_final: 0.8320 (t0) REVERT: C 103 TRP cc_start: 0.7082 (t60) cc_final: 0.6689 (t60) REVERT: C 193 GLN cc_start: 0.8223 (mm-40) cc_final: 0.7980 (mm-40) REVERT: C 216 THR cc_start: 0.7512 (t) cc_final: 0.7106 (p) REVERT: C 269 MET cc_start: 0.9290 (mtp) cc_final: 0.8961 (mtm) REVERT: C 286 LEU cc_start: 0.8038 (mt) cc_final: 0.7428 (pp) REVERT: C 301 MET cc_start: 0.9082 (mmp) cc_final: 0.8818 (tpp) REVERT: C 333 LEU cc_start: 0.8603 (tp) cc_final: 0.8335 (tp) REVERT: C 407 TRP cc_start: 0.6675 (m100) cc_final: 0.6002 (m-90) REVERT: C 420 GLU cc_start: 0.7834 (mt-10) cc_final: 0.7616 (mp0) REVERT: F 37 HIS cc_start: 0.7653 (m-70) cc_final: 0.7202 (m90) REVERT: F 86 ILE cc_start: 0.9052 (pt) cc_final: 0.8654 (tp) REVERT: F 154 ILE cc_start: 0.9325 (tt) cc_final: 0.9102 (tt) REVERT: F 228 ASN cc_start: 0.9266 (m-40) cc_final: 0.8854 (m-40) REVERT: F 295 MET cc_start: 0.8501 (ttm) cc_final: 0.8178 (ttp) REVERT: F 301 MET cc_start: 0.8863 (mmt) cc_final: 0.7995 (mmm) REVERT: F 384 ILE cc_start: 0.8277 (pt) cc_final: 0.7909 (pt) REVERT: F 413 MET cc_start: 0.7099 (mtp) cc_final: 0.6827 (mtm) outliers start: 3 outliers final: 1 residues processed: 493 average time/residue: 0.1448 time to fit residues: 111.9653 Evaluate side-chains 381 residues out of total 2187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 379 time to evaluate : 0.763 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 115 optimal weight: 3.9990 chunk 112 optimal weight: 4.9990 chunk 130 optimal weight: 10.0000 chunk 175 optimal weight: 10.0000 chunk 70 optimal weight: 0.0770 chunk 52 optimal weight: 0.9990 chunk 91 optimal weight: 3.9990 chunk 80 optimal weight: 3.9990 chunk 114 optimal weight: 8.9990 chunk 26 optimal weight: 0.7980 chunk 213 optimal weight: 10.0000 overall best weight: 1.9744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 88 HIS D 176 GLN D 300 ASN D 358 GLN ** A 8 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 197 HIS B 18 ASN B 28 HIS ** B 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 101 ASN ** E 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 192 HIS ** C 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 247 GLN ** C 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 8 GLN F 14 ASN F 54 ASN ** F 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.135432 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.119518 restraints weight = 37437.658| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.122326 restraints weight = 22556.504| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.124272 restraints weight = 15210.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.125648 restraints weight = 11228.525| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.126575 restraints weight = 8846.202| |-----------------------------------------------------------------------------| r_work (final): 0.3658 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7910 moved from start: 0.3588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 20883 Z= 0.123 Angle : 0.578 11.563 28440 Z= 0.290 Chirality : 0.044 0.209 3135 Planarity : 0.005 0.070 3681 Dihedral : 10.032 176.571 2850 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 0.09 % Allowed : 1.89 % Favored : 98.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.29 (0.17), residues: 2544 helix: 1.12 (0.16), residues: 1119 sheet: 0.08 (0.25), residues: 411 loop : -1.84 (0.18), residues: 1014 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 215 TYR 0.023 0.001 TYR E 36 PHE 0.023 0.001 PHE F 377 TRP 0.016 0.001 TRP F 103 HIS 0.004 0.001 HIS B 28 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.12 (20880) covalent geometry : angle 0.57829 / 0.29 (28440) hydrogen bonds : bond 0.03947 / 2.68 ( 921) hydrogen bonds : angle 4.29288 / 3.05 ( 2688) Misc. bond : bond 0.00310 / 0.16 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5088 Ramachandran restraints generated. 2544 Oldfield, 0 Emsley, 2544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5088 Ramachandran restraints generated. 2544 Oldfield, 0 Emsley, 2544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 494 residues out of total 2187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 492 time to evaluate : 0.733 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 88 HIS cc_start: 0.8167 (OUTLIER) cc_final: 0.7149 (t-90) REVERT: D 413 MET cc_start: 0.7356 (ttm) cc_final: 0.6845 (ttm) REVERT: A 123 ARG cc_start: 0.7796 (mmm-85) cc_final: 0.7510 (mmm-85) REVERT: A 128 GLN cc_start: 0.7806 (mm-40) cc_final: 0.7250 (tm-30) REVERT: A 154 MET cc_start: 0.8043 (tpt) cc_final: 0.7821 (tpt) REVERT: A 161 TYR cc_start: 0.8321 (m-80) cc_final: 0.7349 (m-10) REVERT: A 302 MET cc_start: 0.8683 (mmm) cc_final: 0.7814 (mtt) REVERT: B 22 GLU cc_start: 0.7991 (tt0) cc_final: 0.7613 (tm-30) REVERT: B 64 ARG cc_start: 0.8925 (mtt90) cc_final: 0.8103 (mtt-85) REVERT: B 90 GLU cc_start: 0.8275 (tp30) cc_final: 0.7869 (tp30) REVERT: B 102 ASN cc_start: 0.8629 (t0) cc_final: 0.8325 (t0) REVERT: B 221 ARG cc_start: 0.7126 (mtt90) cc_final: 0.5824 (ptt180) REVERT: B 258 ASN cc_start: 0.9032 (m110) cc_final: 0.8644 (m-40) REVERT: B 358 GLN cc_start: 0.9148 (tp40) cc_final: 0.8880 (tp-100) REVERT: B 407 TRP cc_start: 0.7169 (m100) cc_final: 0.6801 (m-10) REVERT: E 96 GLN cc_start: 0.7587 (mm110) cc_final: 0.7283 (mm-40) REVERT: E 131 CYS cc_start: 0.7021 (p) cc_final: 0.6345 (m) REVERT: E 308 ARG cc_start: 0.7026 (ptt-90) cc_final: 0.6594 (ptt-90) REVERT: E 320 ARG cc_start: 0.7803 (mtp180) cc_final: 0.7439 (mtm180) REVERT: E 330 GLU cc_start: 0.8519 (pp20) cc_final: 0.8294 (pt0) REVERT: E 374 SER cc_start: 0.9263 (p) cc_final: 0.9047 (p) REVERT: E 381 SER cc_start: 0.9288 (t) cc_final: 0.8951 (p) REVERT: E 416 MET cc_start: 0.6877 (tpt) cc_final: 0.6417 (mmm) REVERT: C 14 ASN cc_start: 0.7852 (t0) cc_final: 0.7407 (t0) REVERT: C 54 ASN cc_start: 0.8836 (t0) cc_final: 0.8325 (t0) REVERT: C 103 TRP cc_start: 0.7100 (t60) cc_final: 0.6658 (t60) REVERT: C 216 THR cc_start: 0.7807 (t) cc_final: 0.7450 (p) REVERT: C 259 MET cc_start: 0.8367 (mmm) cc_final: 0.8145 (tpp) REVERT: C 269 MET cc_start: 0.9241 (mtp) cc_final: 0.9036 (mtm) REVERT: C 278 ARG cc_start: 0.8015 (tpt170) cc_final: 0.7608 (tpm170) REVERT: C 301 MET cc_start: 0.9079 (mmp) cc_final: 0.8755 (tpp) REVERT: C 333 LEU cc_start: 0.8610 (tp) cc_final: 0.8303 (tp) REVERT: C 373 MET cc_start: 0.8649 (pmm) cc_final: 0.8146 (pmm) REVERT: C 407 TRP cc_start: 0.6647 (m100) cc_final: 0.5972 (m-90) REVERT: F 6 HIS cc_start: 0.7717 (t70) cc_final: 0.7501 (t70) REVERT: F 37 HIS cc_start: 0.7558 (m-70) cc_final: 0.7139 (m90) REVERT: F 86 ILE cc_start: 0.8995 (pt) cc_final: 0.8674 (tp) REVERT: F 228 ASN cc_start: 0.9262 (m-40) cc_final: 0.8796 (m-40) REVERT: F 295 MET cc_start: 0.8384 (ttm) cc_final: 0.7788 (ttp) REVERT: F 301 MET cc_start: 0.8840 (mmt) cc_final: 0.7992 (mmm) REVERT: F 373 MET cc_start: 0.7726 (ptt) cc_final: 0.7513 (ptp) REVERT: F 413 MET cc_start: 0.6894 (mtp) cc_final: 0.6660 (mtm) outliers start: 2 outliers final: 1 residues processed: 494 average time/residue: 0.1374 time to fit residues: 106.6957 Evaluate side-chains 377 residues out of total 2187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 375 time to evaluate : 0.793 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 7 optimal weight: 10.0000 chunk 250 optimal weight: 0.9980 chunk 84 optimal weight: 10.0000 chunk 46 optimal weight: 0.9980 chunk 195 optimal weight: 2.9990 chunk 66 optimal weight: 5.9990 chunk 200 optimal weight: 6.9990 chunk 61 optimal weight: 20.0000 chunk 56 optimal weight: 2.9990 chunk 36 optimal weight: 9.9990 chunk 185 optimal weight: 0.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 8 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 176 GLN D 358 GLN ** A 8 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 31 GLN B 18 ASN ** B 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 28 HIS E 101 ASN ** E 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 192 HIS ** E 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 14 ASN F 54 ASN F 258 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.136069 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.120254 restraints weight = 37375.528| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.123003 restraints weight = 22684.650| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.124911 restraints weight = 15425.030| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.126177 restraints weight = 11439.058| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.127157 restraints weight = 9105.801| |-----------------------------------------------------------------------------| r_work (final): 0.3668 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7897 moved from start: 0.3768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 20883 Z= 0.122 Angle : 0.589 11.286 28440 Z= 0.298 Chirality : 0.044 0.185 3135 Planarity : 0.005 0.066 3681 Dihedral : 9.883 174.365 2850 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 0.09 % Allowed : 1.43 % Favored : 98.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.21 (0.17), residues: 2544 helix: 1.13 (0.16), residues: 1137 sheet: 0.12 (0.25), residues: 411 loop : -1.80 (0.19), residues: 996 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 320 TYR 0.017 0.001 TYR A 103 PHE 0.018 0.001 PHE F 169 TRP 0.017 0.001 TRP F 103 HIS 0.004 0.001 HIS B 192 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.12 (20880) covalent geometry : angle 0.58939 / 0.30 (28440) hydrogen bonds : bond 0.03923 / 2.63 ( 921) hydrogen bonds : angle 4.30093 / 3.05 ( 2688) Misc. bond : bond 0.00252 / 0.13 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5088 Ramachandran restraints generated. 2544 Oldfield, 0 Emsley, 2544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5088 Ramachandran restraints generated. 2544 Oldfield, 0 Emsley, 2544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 504 residues out of total 2187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 502 time to evaluate : 0.816 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 413 MET cc_start: 0.7583 (ttm) cc_final: 0.6919 (ttm) REVERT: A 123 ARG cc_start: 0.7827 (mmm-85) cc_final: 0.7518 (mmm-85) REVERT: A 128 GLN cc_start: 0.7867 (mm-40) cc_final: 0.7260 (tm-30) REVERT: A 161 TYR cc_start: 0.8340 (m-80) cc_final: 0.7392 (m-10) REVERT: A 203 MET cc_start: 0.8517 (mmp) cc_final: 0.7860 (mmm) REVERT: A 302 MET cc_start: 0.8496 (mmm) cc_final: 0.7981 (mtt) REVERT: B 22 GLU cc_start: 0.7977 (tt0) cc_final: 0.7614 (tm-30) REVERT: B 36 MET cc_start: 0.7408 (ptm) cc_final: 0.7173 (ptm) REVERT: B 64 ARG cc_start: 0.8893 (mtt90) cc_final: 0.8034 (mtt-85) REVERT: B 90 GLU cc_start: 0.8277 (tp30) cc_final: 0.7929 (tp30) REVERT: B 102 ASN cc_start: 0.8603 (t0) cc_final: 0.8286 (t0) REVERT: B 221 ARG cc_start: 0.7122 (mtt90) cc_final: 0.5797 (ptt180) REVERT: B 258 ASN cc_start: 0.8955 (m110) cc_final: 0.8560 (m-40) REVERT: B 302 MET cc_start: 0.8152 (mtp) cc_final: 0.7606 (mtm) REVERT: B 358 GLN cc_start: 0.9158 (tp40) cc_final: 0.8886 (tp-100) REVERT: B 407 TRP cc_start: 0.6979 (m100) cc_final: 0.6635 (m-10) REVERT: E 96 GLN cc_start: 0.7509 (mm110) cc_final: 0.7210 (mm-40) REVERT: E 131 CYS cc_start: 0.7034 (p) cc_final: 0.6465 (m) REVERT: E 308 ARG cc_start: 0.7081 (ptt-90) cc_final: 0.6596 (ptt-90) REVERT: E 320 ARG cc_start: 0.7725 (mtp180) cc_final: 0.6619 (mtm110) REVERT: E 374 SER cc_start: 0.9211 (p) cc_final: 0.8938 (p) REVERT: E 381 SER cc_start: 0.9310 (t) cc_final: 0.8988 (p) REVERT: E 413 MET cc_start: 0.8024 (ttp) cc_final: 0.7508 (ttm) REVERT: E 416 MET cc_start: 0.6994 (tpt) cc_final: 0.6551 (mmm) REVERT: C 6 HIS cc_start: 0.8347 (t70) cc_final: 0.7471 (t70) REVERT: C 14 ASN cc_start: 0.7910 (t0) cc_final: 0.7531 (t0) REVERT: C 54 ASN cc_start: 0.8858 (t0) cc_final: 0.8309 (t0) REVERT: C 103 TRP cc_start: 0.7131 (t60) cc_final: 0.6537 (t60) REVERT: C 216 THR cc_start: 0.7857 (t) cc_final: 0.7502 (p) REVERT: C 301 MET cc_start: 0.9033 (mmp) cc_final: 0.8642 (tpp) REVERT: C 373 MET cc_start: 0.8663 (pmm) cc_final: 0.8119 (pmm) REVERT: C 407 TRP cc_start: 0.6706 (m100) cc_final: 0.6020 (m-90) REVERT: F 6 HIS cc_start: 0.7806 (t70) cc_final: 0.7465 (t70) REVERT: F 37 HIS cc_start: 0.7635 (m-70) cc_final: 0.7188 (m90) REVERT: F 86 ILE cc_start: 0.8987 (pt) cc_final: 0.8666 (tp) REVERT: F 228 ASN cc_start: 0.9243 (m-40) cc_final: 0.8722 (m-40) REVERT: F 291 LEU cc_start: 0.9133 (tt) cc_final: 0.8930 (tt) REVERT: F 295 MET cc_start: 0.8384 (ttm) cc_final: 0.8107 (ttp) REVERT: F 301 MET cc_start: 0.8812 (mmt) cc_final: 0.7983 (mmm) REVERT: F 413 MET cc_start: 0.6857 (mtp) cc_final: 0.6511 (mtm) outliers start: 2 outliers final: 1 residues processed: 503 average time/residue: 0.1356 time to fit residues: 106.5076 Evaluate side-chains 373 residues out of total 2187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 372 time to evaluate : 0.747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 51 optimal weight: 10.0000 chunk 36 optimal weight: 9.9990 chunk 126 optimal weight: 9.9990 chunk 134 optimal weight: 6.9990 chunk 107 optimal weight: 0.9990 chunk 18 optimal weight: 2.9990 chunk 113 optimal weight: 0.6980 chunk 132 optimal weight: 4.9990 chunk 142 optimal weight: 0.9980 chunk 105 optimal weight: 0.0170 chunk 26 optimal weight: 8.9990 overall best weight: 1.1422 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 88 HIS D 176 GLN D 300 ASN ** A 8 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 18 ASN B 139 HIS ** B 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 101 ASN ** E 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 192 HIS ** E 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 258 ASN F 350 ASN F 406 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.138258 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.122279 restraints weight = 37580.809| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.125117 restraints weight = 22622.060| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.127120 restraints weight = 15298.213| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.128526 restraints weight = 11235.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.129432 restraints weight = 8815.202| |-----------------------------------------------------------------------------| r_work (final): 0.3698 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7859 moved from start: 0.3970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 20883 Z= 0.113 Angle : 0.591 10.621 28440 Z= 0.297 Chirality : 0.044 0.294 3135 Planarity : 0.005 0.078 3681 Dihedral : 9.661 169.473 2850 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 0.09 % Allowed : 0.92 % Favored : 98.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.14 (0.17), residues: 2544 helix: 1.25 (0.16), residues: 1140 sheet: 0.09 (0.26), residues: 366 loop : -1.73 (0.18), residues: 1038 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG D 64 TYR 0.026 0.001 TYR E 36 PHE 0.024 0.001 PHE F 377 TRP 0.017 0.001 TRP F 103 HIS 0.004 0.001 HIS E 406 Details of bonding type rmsd/Z covalent geometry : bond 0.00248 / 0.11 (20880) covalent geometry : angle 0.59087 / 0.30 (28440) hydrogen bonds : bond 0.03712 / 2.49 ( 921) hydrogen bonds : angle 4.24654 / 3.02 ( 2688) Misc. bond : bond 0.00222 / 0.11 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5088 Ramachandran restraints generated. 2544 Oldfield, 0 Emsley, 2544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5088 Ramachandran restraints generated. 2544 Oldfield, 0 Emsley, 2544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 498 residues out of total 2187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 496 time to evaluate : 0.690 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 88 HIS cc_start: 0.8037 (OUTLIER) cc_final: 0.7123 (t-90) REVERT: D 155 GLU cc_start: 0.8062 (tt0) cc_final: 0.7570 (tm-30) REVERT: D 358 GLN cc_start: 0.8616 (tp-100) cc_final: 0.8401 (tp-100) REVERT: D 413 MET cc_start: 0.7519 (ttm) cc_final: 0.6769 (ttm) REVERT: A 123 ARG cc_start: 0.7900 (mmm-85) cc_final: 0.7552 (mmm-85) REVERT: A 128 GLN cc_start: 0.7835 (mm-40) cc_final: 0.7440 (tm-30) REVERT: A 161 TYR cc_start: 0.8338 (m-80) cc_final: 0.7357 (m-10) REVERT: A 203 MET cc_start: 0.8546 (mmp) cc_final: 0.7753 (mmm) REVERT: A 302 MET cc_start: 0.8432 (mmm) cc_final: 0.7970 (mtt) REVERT: B 22 GLU cc_start: 0.7974 (tt0) cc_final: 0.7553 (tm-30) REVERT: B 90 GLU cc_start: 0.8210 (tp30) cc_final: 0.7891 (tp30) REVERT: B 102 ASN cc_start: 0.8562 (t0) cc_final: 0.8222 (t0) REVERT: B 221 ARG cc_start: 0.7131 (mtt90) cc_final: 0.5907 (ptt180) REVERT: B 302 MET cc_start: 0.8001 (mtp) cc_final: 0.7424 (mtm) REVERT: B 358 GLN cc_start: 0.9167 (tp40) cc_final: 0.8913 (tp-100) REVERT: B 407 TRP cc_start: 0.6911 (m100) cc_final: 0.6560 (m-10) REVERT: E 23 VAL cc_start: 0.8979 (t) cc_final: 0.8766 (t) REVERT: E 96 GLN cc_start: 0.7511 (mm110) cc_final: 0.7115 (mm-40) REVERT: E 238 VAL cc_start: 0.7961 (t) cc_final: 0.7744 (t) REVERT: E 308 ARG cc_start: 0.7232 (ptt-90) cc_final: 0.6716 (ptt-90) REVERT: E 320 ARG cc_start: 0.7743 (mtp180) cc_final: 0.6717 (mtm110) REVERT: E 373 MET cc_start: 0.7806 (mmt) cc_final: 0.7605 (mmp) REVERT: E 374 SER cc_start: 0.9170 (p) cc_final: 0.8902 (p) REVERT: E 381 SER cc_start: 0.9316 (t) cc_final: 0.9019 (p) REVERT: E 416 MET cc_start: 0.6865 (tpt) cc_final: 0.6484 (mmm) REVERT: C 6 HIS cc_start: 0.8288 (t70) cc_final: 0.7432 (t70) REVERT: C 14 ASN cc_start: 0.7856 (t0) cc_final: 0.7488 (t0) REVERT: C 54 ASN cc_start: 0.8811 (t0) cc_final: 0.8305 (t0) REVERT: C 103 TRP cc_start: 0.6956 (t60) cc_final: 0.6288 (t60) REVERT: C 216 THR cc_start: 0.7849 (t) cc_final: 0.7467 (p) REVERT: C 278 ARG cc_start: 0.7883 (tpt170) cc_final: 0.7619 (tpm170) REVERT: C 373 MET cc_start: 0.8507 (pmm) cc_final: 0.8075 (pmm) REVERT: C 407 TRP cc_start: 0.6691 (m100) cc_final: 0.5972 (m-90) REVERT: F 37 HIS cc_start: 0.7568 (m-70) cc_final: 0.7141 (m90) REVERT: F 154 ILE cc_start: 0.9285 (tt) cc_final: 0.9030 (tt) REVERT: F 228 ASN cc_start: 0.9178 (m-40) cc_final: 0.8655 (m-40) REVERT: F 295 MET cc_start: 0.8275 (ttm) cc_final: 0.7993 (ttp) REVERT: F 301 MET cc_start: 0.8782 (mmt) cc_final: 0.7905 (mmm) REVERT: F 372 LYS cc_start: 0.8792 (tppp) cc_final: 0.8305 (tppp) REVERT: F 413 MET cc_start: 0.6756 (mtp) cc_final: 0.6487 (mtm) outliers start: 2 outliers final: 1 residues processed: 498 average time/residue: 0.1355 time to fit residues: 104.6574 Evaluate side-chains 384 residues out of total 2187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 382 time to evaluate : 0.717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 125 optimal weight: 10.0000 chunk 40 optimal weight: 5.9990 chunk 175 optimal weight: 30.0000 chunk 33 optimal weight: 5.9990 chunk 247 optimal weight: 0.8980 chunk 55 optimal weight: 10.0000 chunk 190 optimal weight: 9.9990 chunk 46 optimal weight: 9.9990 chunk 99 optimal weight: 8.9990 chunk 236 optimal weight: 9.9990 chunk 68 optimal weight: 0.3980 overall best weight: 4.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 15 GLN D 35 GLN D 176 GLN D 372 GLN ** A 8 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 31 GLN B 139 HIS E 101 ASN ** E 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 192 HIS ** E 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 193 GLN C 197 ASN ** C 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.130824 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.115389 restraints weight = 38150.087| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.118001 restraints weight = 23206.386| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.119814 restraints weight = 15871.133| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.121125 restraints weight = 11813.726| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.122051 restraints weight = 9346.631| |-----------------------------------------------------------------------------| r_work (final): 0.3598 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7999 moved from start: 0.3824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 20883 Z= 0.205 Angle : 0.708 10.846 28440 Z= 0.361 Chirality : 0.048 0.330 3135 Planarity : 0.005 0.079 3681 Dihedral : 10.097 174.962 2850 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 10.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.01 % Favored : 93.99 % Rotamer: Outliers : 0.05 % Allowed : 0.97 % Favored : 98.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.35 (0.17), residues: 2544 helix: 1.04 (0.16), residues: 1122 sheet: -0.06 (0.25), residues: 408 loop : -1.78 (0.19), residues: 1014 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 284 TYR 0.025 0.002 TYR E 161 PHE 0.026 0.002 PHE F 169 TRP 0.028 0.002 TRP F 346 HIS 0.007 0.002 HIS E 37 Details of bonding type rmsd/Z covalent geometry : bond 0.00466 / 0.21 (20880) covalent geometry : angle 0.70773 / 0.36 (28440) hydrogen bonds : bond 0.05008 / 3.37 ( 921) hydrogen bonds : angle 4.75214 / 3.37 ( 2688) Misc. bond : bond 0.00473 / 0.24 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5088 Ramachandran restraints generated. 2544 Oldfield, 0 Emsley, 2544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5088 Ramachandran restraints generated. 2544 Oldfield, 0 Emsley, 2544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 472 residues out of total 2187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 471 time to evaluate : 0.714 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 155 GLU cc_start: 0.8204 (tt0) cc_final: 0.7653 (tm-30) REVERT: D 210 TYR cc_start: 0.8811 (m-10) cc_final: 0.8273 (m-80) REVERT: D 220 GLU cc_start: 0.7610 (tp30) cc_final: 0.6686 (mm-30) REVERT: D 413 MET cc_start: 0.7648 (ttm) cc_final: 0.6918 (ttm) REVERT: A 123 ARG cc_start: 0.7936 (mmm-85) cc_final: 0.7638 (mmm-85) REVERT: A 128 GLN cc_start: 0.7883 (mm-40) cc_final: 0.7397 (tm-30) REVERT: A 161 TYR cc_start: 0.8298 (m-80) cc_final: 0.7683 (m-10) REVERT: A 203 MET cc_start: 0.8712 (mmp) cc_final: 0.7748 (mmm) REVERT: A 211 ASP cc_start: 0.7605 (t0) cc_final: 0.7160 (t0) REVERT: A 302 MET cc_start: 0.8490 (mmm) cc_final: 0.7942 (mtt) REVERT: B 22 GLU cc_start: 0.8020 (tt0) cc_final: 0.7642 (tm-30) REVERT: B 90 GLU cc_start: 0.8278 (tp30) cc_final: 0.7915 (tp30) REVERT: B 102 ASN cc_start: 0.8742 (t0) cc_final: 0.8366 (t0) REVERT: B 221 ARG cc_start: 0.7278 (mtt90) cc_final: 0.6063 (ptt180) REVERT: B 302 MET cc_start: 0.8104 (mtp) cc_final: 0.7618 (mtm) REVERT: B 358 GLN cc_start: 0.9157 (tp40) cc_final: 0.8871 (tp-100) REVERT: B 407 TRP cc_start: 0.7309 (m100) cc_final: 0.6923 (m-10) REVERT: B 414 GLU cc_start: 0.5899 (mt-10) cc_final: 0.5552 (mt-10) REVERT: E 75 MET cc_start: 0.9001 (mmm) cc_final: 0.8664 (mmt) REVERT: E 96 GLN cc_start: 0.7639 (mm110) cc_final: 0.7250 (mm-40) REVERT: E 308 ARG cc_start: 0.7220 (ptt-90) cc_final: 0.6456 (ptt-90) REVERT: E 374 SER cc_start: 0.9197 (p) cc_final: 0.8996 (p) REVERT: E 381 SER cc_start: 0.9347 (t) cc_final: 0.8924 (p) REVERT: C 14 ASN cc_start: 0.7827 (t0) cc_final: 0.7439 (t0) REVERT: C 54 ASN cc_start: 0.8847 (t0) cc_final: 0.8301 (t0) REVERT: C 75 MET cc_start: 0.8212 (mmt) cc_final: 0.7989 (mmm) REVERT: C 103 TRP cc_start: 0.6960 (t60) cc_final: 0.6374 (t60) REVERT: C 216 THR cc_start: 0.7953 (t) cc_final: 0.7556 (p) REVERT: C 278 ARG cc_start: 0.8109 (tpt170) cc_final: 0.7571 (tpm170) REVERT: C 372 LYS cc_start: 0.8305 (tppp) cc_final: 0.8037 (tptt) REVERT: C 373 MET cc_start: 0.8586 (pmm) cc_final: 0.8225 (pmm) REVERT: C 407 TRP cc_start: 0.6745 (m100) cc_final: 0.6051 (m-90) REVERT: F 37 HIS cc_start: 0.7712 (m-70) cc_final: 0.7225 (m90) REVERT: F 76 ASP cc_start: 0.8445 (m-30) cc_final: 0.8208 (m-30) REVERT: F 154 ILE cc_start: 0.9308 (tt) cc_final: 0.9018 (tt) REVERT: F 228 ASN cc_start: 0.9302 (m-40) cc_final: 0.8930 (m-40) REVERT: F 295 MET cc_start: 0.8445 (ttm) cc_final: 0.8241 (ttp) REVERT: F 299 LYS cc_start: 0.9084 (pptt) cc_final: 0.8701 (pttm) REVERT: F 372 LYS cc_start: 0.8835 (tppp) cc_final: 0.8322 (tppp) REVERT: F 384 ILE cc_start: 0.8358 (pt) cc_final: 0.8028 (pt) REVERT: F 413 MET cc_start: 0.7011 (mtp) cc_final: 0.6572 (mtm) outliers start: 1 outliers final: 1 residues processed: 472 average time/residue: 0.1288 time to fit residues: 95.1112 Evaluate side-chains 376 residues out of total 2187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 375 time to evaluate : 0.755 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 29 optimal weight: 4.9990 chunk 215 optimal weight: 0.9980 chunk 107 optimal weight: 8.9990 chunk 158 optimal weight: 0.5980 chunk 136 optimal weight: 6.9990 chunk 208 optimal weight: 0.8980 chunk 66 optimal weight: 8.9990 chunk 37 optimal weight: 9.9990 chunk 60 optimal weight: 0.7980 chunk 32 optimal weight: 5.9990 chunk 141 optimal weight: 1.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 88 HIS D 176 GLN D 358 GLN ** A 8 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 139 HIS ** B 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 101 ASN ** E 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 192 HIS ** E 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 14 ASN F 54 ASN F 258 ASN ** F 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.137035 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.121387 restraints weight = 37571.942| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.124181 restraints weight = 22437.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.126125 restraints weight = 15064.479| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.127408 restraints weight = 11048.418| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.128458 restraints weight = 8725.888| |-----------------------------------------------------------------------------| r_work (final): 0.3687 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7878 moved from start: 0.4128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 20883 Z= 0.120 Angle : 0.629 9.683 28440 Z= 0.315 Chirality : 0.046 0.337 3135 Planarity : 0.005 0.066 3681 Dihedral : 9.754 175.692 2850 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 0.05 % Allowed : 0.28 % Favored : 99.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.14 (0.17), residues: 2544 helix: 1.21 (0.16), residues: 1137 sheet: 0.05 (0.25), residues: 408 loop : -1.71 (0.19), residues: 999 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG C 284 TYR 0.024 0.001 TYR E 36 PHE 0.023 0.001 PHE F 377 TRP 0.018 0.001 TRP F 103 HIS 0.007 0.001 HIS B 192 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.12 (20880) covalent geometry : angle 0.62889 / 0.31 (28440) hydrogen bonds : bond 0.03888 / 2.61 ( 921) hydrogen bonds : angle 4.38828 / 3.10 ( 2688) Misc. bond : bond 0.00305 / 0.15 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5088 Ramachandran restraints generated. 2544 Oldfield, 0 Emsley, 2544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5088 Ramachandran restraints generated. 2544 Oldfield, 0 Emsley, 2544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 477 residues out of total 2187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 476 time to evaluate : 0.804 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 3 GLU cc_start: 0.7740 (tt0) cc_final: 0.7231 (tt0) REVERT: D 88 HIS cc_start: 0.8102 (OUTLIER) cc_final: 0.7130 (t-90) REVERT: D 155 GLU cc_start: 0.7946 (tt0) cc_final: 0.7516 (tm-30) REVERT: D 413 MET cc_start: 0.7515 (ttm) cc_final: 0.6811 (ttm) REVERT: A 128 GLN cc_start: 0.7902 (mm-40) cc_final: 0.7408 (tm-30) REVERT: A 161 TYR cc_start: 0.8283 (m-80) cc_final: 0.7653 (m-10) REVERT: A 211 ASP cc_start: 0.7415 (t0) cc_final: 0.6904 (t0) REVERT: A 302 MET cc_start: 0.8391 (mmm) cc_final: 0.7869 (mtt) REVERT: B 22 GLU cc_start: 0.8032 (tt0) cc_final: 0.7589 (tm-30) REVERT: B 60 LYS cc_start: 0.6749 (mmpt) cc_final: 0.6425 (mmtt) REVERT: B 90 GLU cc_start: 0.8197 (tp30) cc_final: 0.7823 (tp30) REVERT: B 102 ASN cc_start: 0.8600 (t0) cc_final: 0.8269 (t0) REVERT: B 221 ARG cc_start: 0.7020 (mtt90) cc_final: 0.5792 (ptt180) REVERT: B 302 MET cc_start: 0.8120 (mtp) cc_final: 0.7598 (mtm) REVERT: B 358 GLN cc_start: 0.9192 (tp40) cc_final: 0.8895 (tp-100) REVERT: B 407 TRP cc_start: 0.6892 (m100) cc_final: 0.6540 (m-10) REVERT: E 96 GLN cc_start: 0.7602 (mm110) cc_final: 0.7144 (mm-40) REVERT: E 131 CYS cc_start: 0.6412 (p) cc_final: 0.6141 (m) REVERT: E 308 ARG cc_start: 0.7270 (ptt-90) cc_final: 0.6439 (ptt-90) REVERT: E 320 ARG cc_start: 0.7603 (mtm180) cc_final: 0.6820 (mtm110) REVERT: E 373 MET cc_start: 0.7863 (mmp) cc_final: 0.6649 (mtm) REVERT: E 381 SER cc_start: 0.9323 (t) cc_final: 0.8979 (p) REVERT: C 14 ASN cc_start: 0.7751 (t0) cc_final: 0.7406 (t0) REVERT: C 54 ASN cc_start: 0.8638 (t0) cc_final: 0.8179 (t0) REVERT: C 75 MET cc_start: 0.8075 (mmt) cc_final: 0.7803 (mmm) REVERT: C 103 TRP cc_start: 0.6822 (t60) cc_final: 0.6145 (t60) REVERT: C 216 THR cc_start: 0.7848 (t) cc_final: 0.7486 (p) REVERT: C 373 MET cc_start: 0.8994 (pmm) cc_final: 0.8480 (pmm) REVERT: C 407 TRP cc_start: 0.6669 (m100) cc_final: 0.5996 (m-90) REVERT: F 37 HIS cc_start: 0.7540 (m-70) cc_final: 0.7064 (m90) REVERT: F 76 ASP cc_start: 0.8397 (m-30) cc_final: 0.8158 (m-30) REVERT: F 154 ILE cc_start: 0.9264 (tt) cc_final: 0.8998 (tt) REVERT: F 228 ASN cc_start: 0.9078 (m-40) cc_final: 0.8609 (m-40) REVERT: F 259 MET cc_start: 0.7567 (mtm) cc_final: 0.7303 (mtm) REVERT: F 372 LYS cc_start: 0.8736 (tppp) cc_final: 0.8231 (tppp) REVERT: F 413 MET cc_start: 0.6662 (mtp) cc_final: 0.6204 (mtm) outliers start: 1 outliers final: 0 residues processed: 477 average time/residue: 0.1424 time to fit residues: 105.3645 Evaluate side-chains 373 residues out of total 2187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 372 time to evaluate : 0.763 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 18 optimal weight: 5.9990 chunk 10 optimal weight: 10.0000 chunk 175 optimal weight: 9.9990 chunk 122 optimal weight: 3.9990 chunk 33 optimal weight: 0.8980 chunk 128 optimal weight: 6.9990 chunk 70 optimal weight: 0.0970 chunk 230 optimal weight: 3.9990 chunk 180 optimal weight: 0.0070 chunk 96 optimal weight: 9.9990 chunk 154 optimal weight: 0.9990 overall best weight: 1.2000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 176 GLN D 358 GLN ** A 8 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 28 HIS E 101 ASN ** E 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 192 HIS ** E 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 37 HIS F 258 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.138409 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.122675 restraints weight = 37455.550| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.125469 restraints weight = 22500.253| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.127403 restraints weight = 15181.912| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.128768 restraints weight = 11201.800| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.129765 restraints weight = 8824.113| |-----------------------------------------------------------------------------| r_work (final): 0.3703 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7859 moved from start: 0.4273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 20883 Z= 0.116 Angle : 0.617 10.686 28440 Z= 0.307 Chirality : 0.045 0.333 3135 Planarity : 0.005 0.064 3681 Dihedral : 9.573 174.861 2850 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 0.05 % Allowed : 0.28 % Favored : 99.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.11 (0.17), residues: 2544 helix: 1.16 (0.16), residues: 1155 sheet: 0.26 (0.25), residues: 393 loop : -1.72 (0.19), residues: 996 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A 121 TYR 0.023 0.001 TYR E 161 PHE 0.029 0.001 PHE D 138 TRP 0.019 0.001 TRP F 103 HIS 0.004 0.001 HIS E 406 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.12 (20880) covalent geometry : angle 0.61670 / 0.31 (28440) hydrogen bonds : bond 0.03781 / 2.52 ( 921) hydrogen bonds : angle 4.27592 / 3.04 ( 2688) Misc. bond : bond 0.00278 / 0.14 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3220.62 seconds wall clock time: 56 minutes 40.20 seconds (3400.20 seconds total)