Starting phenix.real_space_refine on Thu Sep 18 21:49:56 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7dmz_30775/09_2025/7dmz_30775.cif Found real_map, /net/cci-nas-00/data/ceres_data/7dmz_30775/09_2025/7dmz_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7dmz_30775/09_2025/7dmz_30775.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7dmz_30775/09_2025/7dmz_30775.map" model { file = "/net/cci-nas-00/data/ceres_data/7dmz_30775/09_2025/7dmz_30775.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7dmz_30775/09_2025/7dmz_30775.cif" } 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-2.0-5805/lib/python3.9/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: 4.65, per 1000 atoms: 0.23 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: 1.54 Conformation dependent library (CDL) restraints added in 1.0 seconds Enol-peptide restraints added in 953.7 nanoseconds 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: 0.72 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: 3.72 Time building geometry restraints manager: 2.13 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: 12412 35.84 - 71.68: 307 71.68 - 107.51: 46 107.51 - 143.35: 6 143.35 - 179.19: 6 Dihedral angle restraints: 12777 sinusoidal: 5376 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 12774 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: 0.170 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: 0.060 Process input model: 19.510 Find NCS groups from input model: 0.810 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: 0.010 Load rotamer database and sin/cos tables:1.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7936 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 : 17.323 179.189 8031 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 aren 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 covalent geometry : bond 0.00858 (20880) covalent geometry : angle 1.01524 (28440) hydrogen bonds : bond 0.17053 ( 921) hydrogen bonds : angle 6.74670 ( 2688) Misc. bond : bond 0.34948 ( 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 : 0.850 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: 0.7268 (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: 0.5927 (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: 0.1629 time to fit residues: 143.7780 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 : 0.575 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.139758 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.123594 restraints weight = 36605.181| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.126552 restraints weight = 21817.029| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.128606 restraints weight = 14622.059| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.130076 restraints weight = 10695.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.131171 restraints weight = 8328.566| |-----------------------------------------------------------------------------| r_work (final): 0.3714 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7796 moved from start: 0.2320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 20883 Z= 0.119 Angle : 0.606 12.518 28440 Z= 0.306 Chirality : 0.044 0.161 3135 Planarity : 0.005 0.063 3681 Dihedral : 11.446 173.424 3339 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 0.18 % Allowed : 3.69 % Favored : 96.12 % 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 aren not related in a simple way. whole: -1.73 (0.15), residues: 2544 helix: -0.25 (0.15), residues: 1122 sheet: -0.29 (0.25), residues: 399 loop : -2.53 (0.16), residues: 1023 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 88 TYR 0.016 0.001 TYR E 36 PHE 0.020 0.001 PHE F 377 TRP 0.015 0.001 TRP D 21 HIS 0.010 0.001 HIS C 309 Details of bonding type rmsd covalent geometry : bond 0.00244 (20880) covalent geometry : angle 0.60608 (28440) hydrogen bonds : bond 0.04316 ( 921) hydrogen bonds : angle 4.73546 ( 2688) Misc. bond : bond 0.00239 ( 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 581 residues out of total 2187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 577 time to evaluate : 0.805 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: symmetry clash REVERT: D 85 GLN cc_start: 0.7902 (mp10) cc_final: 0.5502 (tp-100) REVERT: D 103 TYR cc_start: 0.6696 (t80) cc_final: 0.6444 (t80) REVERT: D 226 ASN cc_start: 0.8267 (m-40) cc_final: 0.7885 (m110) REVERT: D 413 MET cc_start: 0.7585 (ttm) cc_final: 0.7304 (ttm) REVERT: A 128 GLN cc_start: 0.7828 (mm-40) cc_final: 0.7459 (tm-30) REVERT: A 161 TYR cc_start: 0.8531 (m-80) cc_final: 0.8227 (m-80) REVERT: A 413 MET cc_start: 0.7767 (mmm) cc_final: 0.7405 (mmt) REVERT: B 22 GLU cc_start: 0.7973 (tt0) cc_final: 0.7749 (tm-30) REVERT: B 64 ARG cc_start: 0.8724 (mtt90) cc_final: 0.7855 (mtt-85) REVERT: B 90 GLU cc_start: 0.8452 (tp30) cc_final: 0.7904 (tp30) REVERT: B 102 ASN cc_start: 0.8363 (t0) cc_final: 0.8081 (t0) REVERT: B 192 HIS cc_start: 0.7955 (t70) cc_final: 0.7730 (t70) REVERT: B 221 ARG cc_start: 0.7219 (mtt180) cc_final: 0.5590 (ptt180) REVERT: B 256 GLN cc_start: 0.5555 (tm-30) cc_final: 0.5182 (tm-30) REVERT: B 302 MET cc_start: 0.8080 (mmm) cc_final: 0.7709 (tpp) REVERT: B 358 GLN cc_start: 0.9174 (tp40) cc_final: 0.8860 (tp-100) REVERT: B 376 CYS cc_start: 0.8937 (t) cc_final: 0.8534 (p) REVERT: B 377 MET cc_start: 0.7708 (ttp) cc_final: 0.7496 (ttp) REVERT: E 96 GLN cc_start: 0.7624 (mm110) cc_final: 0.7048 (mm-40) REVERT: E 202 TYR cc_start: 0.8838 (m-80) cc_final: 0.8532 (m-80) REVERT: E 320 ARG cc_start: 0.7745 (mtp180) cc_final: 0.7504 (mtm180) REVERT: E 398 MET cc_start: 0.7505 (mtt) cc_final: 0.7235 (mtt) REVERT: C 14 ASN cc_start: 0.8195 (t0) cc_final: 0.7585 (t0) REVERT: C 54 ASN cc_start: 0.8722 (t0) cc_final: 0.8216 (t0) REVERT: C 75 MET cc_start: 0.8118 (mmt) cc_final: 0.7575 (mmt) REVERT: C 103 TRP cc_start: 0.6637 (t60) cc_final: 0.6287 (t60) REVERT: C 113 GLU cc_start: 0.8347 (mt-10) cc_final: 0.8040 (mp0) REVERT: C 278 ARG cc_start: 0.7722 (tpm170) cc_final: 0.7458 (tpm170) REVERT: C 333 LEU cc_start: 0.8544 (tp) cc_final: 0.8224 (tp) REVERT: C 407 TRP cc_start: 0.6728 (m100) cc_final: 0.6176 (m-90) REVERT: C 411 GLU cc_start: 0.6418 (mm-30) cc_final: 0.6044 (tm-30) REVERT: F 37 HIS cc_start: 0.7593 (m-70) cc_final: 0.7242 (m90) REVERT: F 48 ARG cc_start: 0.6568 (mmt180) cc_final: 0.6362 (mmt-90) REVERT: F 61 TYR cc_start: 0.7103 (m-80) cc_final: 0.6845 (m-80) REVERT: F 86 ILE cc_start: 0.8994 (pt) cc_final: 0.8622 (tp) REVERT: F 228 ASN cc_start: 0.9378 (m-40) cc_final: 0.8881 (m-40) REVERT: F 295 MET cc_start: 0.8357 (ttm) cc_final: 0.8132 (ttp) REVERT: F 320 ARG cc_start: 0.7920 (mtp180) cc_final: 0.6782 (mtp-110) REVERT: F 323 MET cc_start: 0.7718 (mtt) cc_final: 0.7321 (mtt) REVERT: F 384 ILE cc_start: 0.7909 (pt) cc_final: 0.7707 (pt) REVERT: F 413 MET cc_start: 0.6841 (mtp) cc_final: 0.6495 (mtm) outliers start: 4 outliers final: 1 residues processed: 579 average time/residue: 0.1552 time to fit residues: 138.1473 Evaluate side-chains 409 residues out of total 2187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 408 time to evaluate : 0.795 ------------------------------------------------------------------------------- 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: 6.9990 chunk 174 optimal weight: 20.0000 chunk 222 optimal weight: 9.9990 chunk 8 optimal weight: 8.9990 chunk 104 optimal weight: 4.9990 chunk 148 optimal weight: 4.9990 chunk 109 optimal weight: 2.9990 chunk 224 optimal weight: 9.9990 chunk 225 optimal weight: 5.9990 chunk 161 optimal weight: 10.0000 chunk 130 optimal weight: 0.6980 overall best weight: 3.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 8 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 192 HIS D 300 ASN D 309 HIS D 358 GLN D 406 HIS ** A 8 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 88 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 192 HIS ** E 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 281 GLN ** E 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 436 GLN ** C 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 294 GLN ** C 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 6 HIS F 8 GLN F 258 ASN ** F 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.132048 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.116342 restraints weight = 37997.290| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.119061 restraints weight = 22881.022| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.120944 restraints weight = 15496.858| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.122221 restraints weight = 11474.791| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.123212 restraints weight = 9139.509| |-----------------------------------------------------------------------------| r_work (final): 0.3605 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7932 moved from start: 0.2736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 20883 Z= 0.189 Angle : 0.661 10.747 28440 Z= 0.337 Chirality : 0.046 0.188 3135 Planarity : 0.005 0.069 3681 Dihedral : 11.221 177.069 3339 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer: Outliers : 0.05 % Allowed : 4.76 % Favored : 95.20 % 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 aren not related in a simple way. whole: -1.04 (0.16), residues: 2544 helix: 0.48 (0.15), residues: 1104 sheet: -0.33 (0.25), residues: 414 loop : -2.18 (0.17), residues: 1026 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 64 TYR 0.018 0.002 TYR A 210 PHE 0.018 0.002 PHE C 319 TRP 0.026 0.002 TRP F 346 HIS 0.006 0.001 HIS E 406 Details of bonding type rmsd covalent geometry : bond 0.00427 (20880) covalent geometry : angle 0.66050 (28440) hydrogen bonds : bond 0.05015 ( 921) hydrogen bonds : angle 4.77585 ( 2688) Misc. bond : bond 0.00351 ( 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 512 residues out of total 2187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 511 time to evaluate : 0.832 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 103 TYR cc_start: 0.6972 (t80) cc_final: 0.6714 (t80) REVERT: D 210 TYR cc_start: 0.8819 (m-10) cc_final: 0.8249 (m-80) REVERT: D 226 ASN cc_start: 0.8876 (m-40) cc_final: 0.8615 (m110) REVERT: D 288 VAL cc_start: 0.8307 (t) cc_final: 0.8099 (p) REVERT: D 300 ASN cc_start: 0.8572 (OUTLIER) cc_final: 0.8203 (t0) REVERT: D 301 GLN cc_start: 0.8145 (mm110) cc_final: 0.7749 (mm110) REVERT: D 386 GLU cc_start: 0.7567 (mm-30) cc_final: 0.7264 (pp20) REVERT: D 413 MET cc_start: 0.7719 (ttm) cc_final: 0.7022 (ttm) REVERT: A 128 GLN cc_start: 0.7977 (mm-40) cc_final: 0.7405 (tm-30) REVERT: A 302 MET cc_start: 0.8727 (mmm) cc_final: 0.7982 (mtt) REVERT: B 51 THR cc_start: 0.9099 (t) cc_final: 0.8836 (t) REVERT: B 64 ARG cc_start: 0.8821 (mtt90) cc_final: 0.8219 (mtt-85) REVERT: B 90 GLU cc_start: 0.8631 (tp30) cc_final: 0.8382 (tp30) REVERT: B 102 ASN cc_start: 0.8613 (t0) cc_final: 0.8242 (t0) REVERT: B 192 HIS cc_start: 0.8044 (t70) cc_final: 0.7812 (t70) REVERT: B 221 ARG cc_start: 0.7150 (mtt90) cc_final: 0.6029 (ptt180) REVERT: B 258 ASN cc_start: 0.9055 (m110) cc_final: 0.8726 (m-40) REVERT: B 302 MET cc_start: 0.8383 (mmm) cc_final: 0.8049 (tpp) REVERT: B 358 GLN cc_start: 0.9158 (tp40) cc_final: 0.8881 (tp-100) REVERT: E 96 GLN cc_start: 0.7571 (mm110) cc_final: 0.7273 (mm-40) REVERT: E 102 ASN cc_start: 0.8836 (m-40) cc_final: 0.8604 (m110) REVERT: E 131 CYS cc_start: 0.6630 (t) cc_final: 0.6337 (t) REVERT: E 132 LEU cc_start: 0.8639 (pp) cc_final: 0.8278 (pp) REVERT: E 259 MET cc_start: 0.8803 (mmm) cc_final: 0.8534 (mmm) REVERT: E 320 ARG cc_start: 0.7822 (mtp180) cc_final: 0.7546 (mtm180) REVERT: E 330 GLU cc_start: 0.8083 (pt0) cc_final: 0.7830 (pt0) REVERT: C 14 ASN cc_start: 0.8328 (t0) cc_final: 0.7766 (t0) REVERT: C 54 ASN cc_start: 0.8940 (t0) cc_final: 0.8381 (t0) REVERT: C 103 TRP cc_start: 0.7085 (t60) cc_final: 0.6666 (t60) REVERT: C 110 GLU cc_start: 0.7724 (mp0) cc_final: 0.7524 (mp0) REVERT: C 113 GLU cc_start: 0.8493 (mt-10) cc_final: 0.8273 (mp0) REVERT: C 166 MET cc_start: 0.9127 (mmt) cc_final: 0.8905 (mmm) REVERT: C 216 THR cc_start: 0.7996 (t) cc_final: 0.7507 (p) REVERT: C 278 ARG cc_start: 0.7870 (tpm170) cc_final: 0.7557 (tpm170) REVERT: C 301 MET cc_start: 0.8974 (mmt) cc_final: 0.8721 (mmt) REVERT: C 333 LEU cc_start: 0.8664 (tp) cc_final: 0.8332 (tp) REVERT: C 372 LYS cc_start: 0.8624 (tppp) cc_final: 0.8382 (tptt) REVERT: C 407 TRP cc_start: 0.6936 (m100) cc_final: 0.6209 (m-90) REVERT: C 411 GLU cc_start: 0.6471 (mm-30) cc_final: 0.6176 (tm-30) REVERT: C 420 GLU cc_start: 0.7816 (mt-10) cc_final: 0.7538 (mp0) REVERT: F 37 HIS cc_start: 0.7783 (m-70) cc_final: 0.7296 (m90) REVERT: F 149 MET cc_start: 0.7789 (mmm) cc_final: 0.7561 (mmp) REVERT: F 154 ILE cc_start: 0.9359 (tt) cc_final: 0.9107 (tt) REVERT: F 228 ASN cc_start: 0.9439 (m-40) cc_final: 0.8909 (m-40) REVERT: F 295 MET cc_start: 0.8530 (ttm) cc_final: 0.8286 (ttp) REVERT: F 320 ARG cc_start: 0.8084 (mtp180) cc_final: 0.7844 (mtp180) REVERT: F 384 ILE cc_start: 0.8153 (pt) cc_final: 0.7832 (pt) REVERT: F 428 LEU cc_start: 0.8870 (tp) cc_final: 0.8657 (tt) outliers start: 1 outliers final: 0 residues processed: 512 average time/residue: 0.1541 time to fit residues: 121.0582 Evaluate side-chains 381 residues out of total 2187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 380 time to evaluate : 0.773 ------------------------------------------------------------------------------- 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: 4.9990 chunk 35 optimal weight: 6.9990 chunk 160 optimal weight: 0.2980 chunk 135 optimal weight: 3.9990 chunk 242 optimal weight: 8.9990 chunk 36 optimal weight: 4.9990 chunk 106 optimal weight: 10.0000 chunk 53 optimal weight: 0.8980 chunk 56 optimal weight: 4.9990 chunk 92 optimal weight: 5.9990 chunk 102 optimal weight: 0.2980 overall best weight: 2.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 8 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 11 GLN D 15 GLN D 88 HIS D 176 GLN D 358 GLN ** A 8 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 18 ASN B 301 GLN ** E 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 167 ASN E 192 HIS E 294 GLN ** C 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 247 GLN ** C 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 385 GLN C 436 GLN F 54 ASN ** F 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 331 GLN ** 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 = 0.3777 r_free = 0.3777 target = 0.135663 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.119838 restraints weight = 37302.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.122724 restraints weight = 22152.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.124685 restraints weight = 14750.074| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.126081 restraints weight = 10789.310| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.127099 restraints weight = 8408.139| |-----------------------------------------------------------------------------| r_work (final): 0.3659 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7870 moved from start: 0.3114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 20883 Z= 0.131 Angle : 0.590 11.779 28440 Z= 0.298 Chirality : 0.044 0.162 3135 Planarity : 0.005 0.067 3681 Dihedral : 10.722 179.675 3339 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 0.14 % Allowed : 2.31 % Favored : 97.55 % 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 aren not related in a simple way. whole: -0.69 (0.16), residues: 2544 helix: 0.83 (0.16), residues: 1107 sheet: -0.15 (0.25), residues: 411 loop : -2.06 (0.18), residues: 1026 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 390 TYR 0.027 0.001 TYR D 432 PHE 0.021 0.001 PHE F 377 TRP 0.024 0.002 TRP B 407 HIS 0.006 0.001 HIS E 192 Details of bonding type rmsd covalent geometry : bond 0.00290 (20880) covalent geometry : angle 0.59012 (28440) hydrogen bonds : bond 0.04141 ( 921) hydrogen bonds : angle 4.46517 ( 2688) Misc. bond : bond 0.00239 ( 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 505 residues out of total 2187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 502 time to evaluate : 0.856 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 88 HIS cc_start: 0.8222 (OUTLIER) cc_final: 0.7248 (t-90) REVERT: D 301 GLN cc_start: 0.7992 (mm110) cc_final: 0.7672 (mm110) REVERT: D 413 MET cc_start: 0.7441 (ttm) cc_final: 0.6750 (ttm) REVERT: D 418 PHE cc_start: 0.7552 (m-80) cc_final: 0.7319 (m-80) REVERT: A 123 ARG cc_start: 0.7920 (mmm-85) cc_final: 0.7537 (mmm-85) REVERT: A 128 GLN cc_start: 0.7916 (mm-40) cc_final: 0.7397 (tm-30) REVERT: A 302 MET cc_start: 0.8662 (mmm) cc_final: 0.8032 (mtt) REVERT: B 22 GLU cc_start: 0.8045 (tt0) cc_final: 0.7685 (tm-30) REVERT: B 64 ARG cc_start: 0.8810 (mtt90) cc_final: 0.8110 (mtt-85) REVERT: B 90 GLU cc_start: 0.8536 (tp30) cc_final: 0.8036 (tp30) REVERT: B 102 ASN cc_start: 0.8594 (t0) cc_final: 0.8288 (t0) REVERT: B 221 ARG cc_start: 0.7113 (mtt90) cc_final: 0.5827 (ptt180) REVERT: B 258 ASN cc_start: 0.9017 (m110) cc_final: 0.8573 (m-40) REVERT: B 301 GLN cc_start: 0.8264 (OUTLIER) cc_final: 0.8018 (mp10) REVERT: B 335 ILE cc_start: 0.9046 (tp) cc_final: 0.8713 (mm) REVERT: B 358 GLN cc_start: 0.9164 (tp40) cc_final: 0.8862 (tp-100) REVERT: B 407 TRP cc_start: 0.7009 (m100) cc_final: 0.6695 (m-10) REVERT: E 69 ASP cc_start: 0.8820 (t0) cc_final: 0.8600 (t0) REVERT: E 96 GLN cc_start: 0.7489 (mm110) cc_final: 0.7077 (mm-40) REVERT: E 132 LEU cc_start: 0.8438 (pp) cc_final: 0.8164 (pp) REVERT: E 299 LYS cc_start: 0.8294 (ptmm) cc_final: 0.8068 (tttm) REVERT: E 320 ARG cc_start: 0.7759 (mtp180) cc_final: 0.7463 (mtm180) REVERT: E 327 GLU cc_start: 0.8088 (mt-10) cc_final: 0.7775 (mt-10) REVERT: C 14 ASN cc_start: 0.8310 (t0) cc_final: 0.7821 (t0) REVERT: C 54 ASN cc_start: 0.8843 (t0) cc_final: 0.8263 (t0) REVERT: C 66 ILE cc_start: 0.9221 (mm) cc_final: 0.8944 (mm) REVERT: C 103 TRP cc_start: 0.7062 (t60) cc_final: 0.6649 (t60) REVERT: C 333 LEU cc_start: 0.8636 (tp) cc_final: 0.8362 (tp) REVERT: C 373 MET cc_start: 0.8122 (ptp) cc_final: 0.7891 (ptm) REVERT: C 407 TRP cc_start: 0.6758 (m100) cc_final: 0.6108 (m-90) REVERT: C 420 GLU cc_start: 0.7821 (mt-10) cc_final: 0.7606 (mp0) REVERT: F 37 HIS cc_start: 0.7579 (m-70) cc_final: 0.7197 (m90) REVERT: F 86 ILE cc_start: 0.9033 (pt) cc_final: 0.8668 (tp) REVERT: F 228 ASN cc_start: 0.9378 (m-40) cc_final: 0.8855 (m-40) REVERT: F 295 MET cc_start: 0.8387 (ttm) cc_final: 0.8017 (ttp) REVERT: F 301 MET cc_start: 0.8836 (mmt) cc_final: 0.8060 (mmm) REVERT: F 413 MET cc_start: 0.6989 (mtp) cc_final: 0.6700 (mtp) outliers start: 3 outliers final: 1 residues processed: 505 average time/residue: 0.1503 time to fit residues: 116.7303 Evaluate side-chains 381 residues out of total 2187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 378 time to evaluate : 0.847 ------------------------------------------------------------------------------- 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: 6.9990 chunk 41 optimal weight: 8.9990 chunk 10 optimal weight: 9.9990 chunk 145 optimal weight: 2.9990 chunk 91 optimal weight: 5.9990 chunk 29 optimal weight: 5.9990 chunk 141 optimal weight: 0.9990 chunk 53 optimal weight: 10.0000 chunk 126 optimal weight: 10.0000 chunk 242 optimal weight: 1.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 8 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 176 GLN D 300 ASN ** A 8 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 31 GLN B 18 ASN E 101 ASN ** E 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 294 GLN ** C 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 102 ASN ** C 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 54 ASN ** F 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.132115 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.116308 restraints weight = 38005.196| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.118981 restraints weight = 23226.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.120841 restraints weight = 15937.282| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.122170 restraints weight = 11913.164| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.123142 restraints weight = 9467.226| |-----------------------------------------------------------------------------| r_work (final): 0.3610 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7929 moved from start: 0.3257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 20883 Z= 0.173 Angle : 0.635 12.446 28440 Z= 0.323 Chirality : 0.046 0.185 3135 Planarity : 0.005 0.069 3681 Dihedral : 10.771 179.986 3339 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % Rotamer: Outliers : 0.05 % Allowed : 3.42 % Favored : 96.54 % 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 aren not related in a simple way. whole: -0.64 (0.16), residues: 2544 helix: 0.89 (0.16), residues: 1110 sheet: -0.26 (0.25), residues: 414 loop : -2.00 (0.18), residues: 1020 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 320 TYR 0.017 0.002 TYR D 103 PHE 0.016 0.002 PHE F 377 TRP 0.019 0.002 TRP F 346 HIS 0.005 0.001 HIS E 107 Details of bonding type rmsd covalent geometry : bond 0.00390 (20880) covalent geometry : angle 0.63459 (28440) hydrogen bonds : bond 0.04596 ( 921) hydrogen bonds : angle 4.55273 ( 2688) Misc. bond : bond 0.00330 ( 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 491 residues out of total 2187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 490 time to evaluate : 0.812 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: symmetry clash revert: symmetry clash REVERT: D 210 TYR cc_start: 0.8787 (m-10) cc_final: 0.8223 (m-80) REVERT: D 300 ASN cc_start: 0.8614 (OUTLIER) cc_final: 0.8230 (t0) REVERT: D 413 MET cc_start: 0.7659 (ttm) cc_final: 0.6811 (ttm) REVERT: A 108 TYR cc_start: 0.8441 (m-10) cc_final: 0.8228 (m-10) REVERT: A 123 ARG cc_start: 0.7979 (mmm-85) cc_final: 0.7597 (mmm-85) REVERT: A 128 GLN cc_start: 0.7991 (mm-40) cc_final: 0.7327 (tm-30) REVERT: A 302 MET cc_start: 0.8677 (mmm) cc_final: 0.8113 (mtt) REVERT: B 22 GLU cc_start: 0.8086 (tt0) cc_final: 0.7806 (tm-30) REVERT: B 90 GLU cc_start: 0.8448 (tp30) cc_final: 0.8025 (tp30) REVERT: B 102 ASN cc_start: 0.8690 (t0) cc_final: 0.8367 (t0) REVERT: B 221 ARG cc_start: 0.7237 (mtt90) cc_final: 0.5979 (ptt180) REVERT: B 258 ASN cc_start: 0.9033 (m110) cc_final: 0.8691 (m-40) REVERT: B 302 MET cc_start: 0.8406 (mmm) cc_final: 0.8173 (mtt) REVERT: B 358 GLN cc_start: 0.9148 (tp40) cc_final: 0.8850 (tp-100) REVERT: B 376 CYS cc_start: 0.8461 (t) cc_final: 0.8197 (p) REVERT: E 69 ASP cc_start: 0.8935 (t0) cc_final: 0.8684 (t0) REVERT: E 96 GLN cc_start: 0.7589 (mm110) cc_final: 0.7209 (mm-40) REVERT: E 102 ASN cc_start: 0.8960 (m-40) cc_final: 0.8594 (m110) REVERT: E 299 LYS cc_start: 0.8343 (ptmm) cc_final: 0.8089 (tttm) REVERT: E 320 ARG cc_start: 0.7795 (mtp180) cc_final: 0.7490 (mtm180) REVERT: C 14 ASN cc_start: 0.7993 (t0) cc_final: 0.7542 (t0) REVERT: C 54 ASN cc_start: 0.8805 (t0) cc_final: 0.8277 (t0) REVERT: C 103 TRP cc_start: 0.7153 (t60) cc_final: 0.6737 (t60) REVERT: C 193 GLN cc_start: 0.8243 (mm-40) cc_final: 0.8016 (mm-40) REVERT: C 259 MET cc_start: 0.7710 (tpp) cc_final: 0.7449 (mmm) REVERT: C 269 MET cc_start: 0.8849 (mtp) cc_final: 0.8426 (mtp) REVERT: C 278 ARG cc_start: 0.7877 (tpm170) cc_final: 0.7581 (tpm170) REVERT: C 301 MET cc_start: 0.9107 (mmt) cc_final: 0.8779 (tpp) REVERT: C 314 THR cc_start: 0.7982 (p) cc_final: 0.7498 (p) REVERT: C 333 LEU cc_start: 0.8700 (tp) cc_final: 0.8417 (tp) REVERT: C 373 MET cc_start: 0.8187 (ptp) cc_final: 0.7895 (ptp) REVERT: C 407 TRP cc_start: 0.6723 (m100) cc_final: 0.6056 (m-90) REVERT: C 420 GLU cc_start: 0.7826 (mt-10) cc_final: 0.7555 (mp0) REVERT: F 37 HIS cc_start: 0.7595 (m-70) cc_final: 0.7193 (m90) REVERT: F 86 ILE cc_start: 0.9046 (pt) cc_final: 0.8620 (tp) REVERT: F 228 ASN cc_start: 0.9452 (m-40) cc_final: 0.8929 (m-40) REVERT: F 259 MET cc_start: 0.7706 (mtm) cc_final: 0.7482 (mtm) REVERT: F 295 MET cc_start: 0.8484 (ttm) cc_final: 0.8269 (ttp) REVERT: F 428 LEU cc_start: 0.8675 (tp) cc_final: 0.8470 (tp) outliers start: 1 outliers final: 0 residues processed: 491 average time/residue: 0.1497 time to fit residues: 114.6213 Evaluate side-chains 384 residues out of total 2187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 383 time to evaluate : 0.845 ------------------------------------------------------------------------------- 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: 4.9990 chunk 112 optimal weight: 5.9990 chunk 130 optimal weight: 6.9990 chunk 175 optimal weight: 9.9990 chunk 70 optimal weight: 0.8980 chunk 52 optimal weight: 10.0000 chunk 91 optimal weight: 10.0000 chunk 80 optimal weight: 4.9990 chunk 114 optimal weight: 6.9990 chunk 26 optimal weight: 5.9990 chunk 213 optimal weight: 8.9990 overall best weight: 4.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 8 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 11 GLN D 15 GLN D 35 GLN D 88 HIS D 176 GLN ** A 8 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 167 ASN 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** C 350 ASN ** F 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3709 r_free = 0.3709 target = 0.130041 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.114726 restraints weight = 38094.205| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.117316 restraints weight = 23042.763| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.119129 restraints weight = 15721.758| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.120295 restraints weight = 11685.188| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.121275 restraints weight = 9378.635| |-----------------------------------------------------------------------------| r_work (final): 0.3588 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7962 moved from start: 0.3398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 20883 Z= 0.206 Angle : 0.677 12.847 28440 Z= 0.346 Chirality : 0.048 0.178 3135 Planarity : 0.005 0.069 3681 Dihedral : 10.860 177.721 3339 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 10.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.05 % Favored : 93.95 % Rotamer: Outliers : 0.09 % Allowed : 2.31 % Favored : 97.60 % 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 aren not related in a simple way. whole: -0.71 (0.16), residues: 2544 helix: 0.85 (0.16), residues: 1098 sheet: -0.38 (0.25), residues: 411 loop : -1.97 (0.18), residues: 1035 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 320 TYR 0.017 0.002 TYR D 103 PHE 0.020 0.002 PHE F 404 TRP 0.039 0.002 TRP B 407 HIS 0.006 0.001 HIS E 37 Details of bonding type rmsd covalent geometry : bond 0.00470 (20880) covalent geometry : angle 0.67659 (28440) hydrogen bonds : bond 0.04987 ( 921) hydrogen bonds : angle 4.72377 ( 2688) Misc. bond : bond 0.00316 ( 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 477 residues out of total 2187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 475 time to evaluate : 0.821 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: symmetry clash REVERT: D 85 GLN cc_start: 0.7391 (mp10) cc_final: 0.5589 (tp40) REVERT: D 88 HIS cc_start: 0.8355 (OUTLIER) cc_final: 0.7364 (t-90) REVERT: D 210 TYR cc_start: 0.8879 (m-10) cc_final: 0.8337 (m-80) REVERT: D 413 MET cc_start: 0.7614 (ttm) cc_final: 0.6796 (ttm) REVERT: A 123 ARG cc_start: 0.7788 (mmm-85) cc_final: 0.7477 (mmm-85) REVERT: A 128 GLN cc_start: 0.8025 (mm-40) cc_final: 0.7286 (tm-30) REVERT: A 161 TYR cc_start: 0.8287 (m-80) cc_final: 0.7369 (m-10) REVERT: A 302 MET cc_start: 0.8626 (mmm) cc_final: 0.8178 (mtt) REVERT: B 22 GLU cc_start: 0.8202 (tt0) cc_final: 0.7873 (tm-30) REVERT: B 90 GLU cc_start: 0.8352 (tp30) cc_final: 0.7930 (tp30) REVERT: B 102 ASN cc_start: 0.8840 (t0) cc_final: 0.8473 (t0) REVERT: B 221 ARG cc_start: 0.7292 (mtt90) cc_final: 0.5965 (ptt180) REVERT: B 258 ASN cc_start: 0.8987 (m110) cc_final: 0.8654 (m-40) REVERT: B 301 GLN cc_start: 0.8155 (mm-40) cc_final: 0.7645 (mm-40) REVERT: B 302 MET cc_start: 0.8556 (mmm) cc_final: 0.8012 (mtt) REVERT: B 358 GLN cc_start: 0.9188 (tp40) cc_final: 0.8855 (tp-100) REVERT: B 407 TRP cc_start: 0.6758 (m-10) cc_final: 0.6488 (m-10) REVERT: E 96 GLN cc_start: 0.7585 (mm110) cc_final: 0.7197 (mm-40) REVERT: E 320 ARG cc_start: 0.7829 (mtp180) cc_final: 0.7528 (mtm180) REVERT: E 373 MET cc_start: 0.8100 (mmt) cc_final: 0.7770 (mmm) REVERT: E 374 SER cc_start: 0.9362 (p) cc_final: 0.9120 (p) REVERT: E 413 MET cc_start: 0.8224 (mtp) cc_final: 0.7714 (mtp) REVERT: C 14 ASN cc_start: 0.7941 (t0) cc_final: 0.7552 (t0) REVERT: C 54 ASN cc_start: 0.8926 (t0) cc_final: 0.8368 (t0) REVERT: C 103 TRP cc_start: 0.7038 (t60) cc_final: 0.6583 (t60) REVERT: C 193 GLN cc_start: 0.8388 (mm-40) cc_final: 0.8156 (mm-40) REVERT: C 240 THR cc_start: 0.9261 (t) cc_final: 0.8819 (m) REVERT: C 333 LEU cc_start: 0.8697 (tp) cc_final: 0.8413 (tp) REVERT: C 373 MET cc_start: 0.8131 (ptp) cc_final: 0.7872 (ptt) REVERT: C 407 TRP cc_start: 0.6832 (m100) cc_final: 0.6154 (m-90) REVERT: C 420 GLU cc_start: 0.7837 (mt-10) cc_final: 0.7566 (mp0) REVERT: F 37 HIS cc_start: 0.7638 (m-70) cc_final: 0.7187 (m90) REVERT: F 86 ILE cc_start: 0.9026 (pt) cc_final: 0.8615 (tp) REVERT: F 154 ILE cc_start: 0.9266 (tt) cc_final: 0.8990 (tt) REVERT: F 228 ASN cc_start: 0.9429 (m-40) cc_final: 0.8867 (m-40) REVERT: F 295 MET cc_start: 0.8522 (ttm) cc_final: 0.8303 (ttp) outliers start: 2 outliers final: 1 residues processed: 477 average time/residue: 0.1437 time to fit residues: 106.3083 Evaluate side-chains 370 residues out of total 2187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 368 time to evaluate : 0.802 ------------------------------------------------------------------------------- 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: 0.9980 chunk 250 optimal weight: 0.8980 chunk 84 optimal weight: 10.0000 chunk 46 optimal weight: 4.9990 chunk 195 optimal weight: 8.9990 chunk 66 optimal weight: 0.0770 chunk 200 optimal weight: 2.9990 chunk 61 optimal weight: 6.9990 chunk 56 optimal weight: 5.9990 chunk 36 optimal weight: 0.9990 chunk 185 optimal weight: 0.0670 overall best weight: 0.6078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 8 HIS D 15 GLN D 176 GLN ** A 8 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 197 HIS B 18 ASN ** B 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 101 ASN ** E 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 186 ASN E 192 HIS ** E 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 186 ASN ** C 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 258 ASN F 350 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.138429 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.122476 restraints weight = 36882.851| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.125385 restraints weight = 21974.829| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.127405 restraints weight = 14691.024| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.128694 restraints weight = 10713.710| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.129741 restraints weight = 8490.457| |-----------------------------------------------------------------------------| r_work (final): 0.3701 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7796 moved from start: 0.3773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 20883 Z= 0.108 Angle : 0.575 11.167 28440 Z= 0.290 Chirality : 0.044 0.180 3135 Planarity : 0.005 0.072 3681 Dihedral : 10.134 178.545 3339 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 0.05 % Allowed : 1.34 % Favored : 98.61 % 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 aren not related in a simple way. whole: -0.31 (0.17), residues: 2544 helix: 1.15 (0.16), residues: 1122 sheet: -0.11 (0.25), residues: 414 loop : -1.83 (0.19), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 320 TYR 0.028 0.001 TYR E 36 PHE 0.021 0.001 PHE F 377 TRP 0.018 0.001 TRP F 103 HIS 0.005 0.001 HIS E 6 Details of bonding type rmsd covalent geometry : bond 0.00230 (20880) covalent geometry : angle 0.57487 (28440) hydrogen bonds : bond 0.03625 ( 921) hydrogen bonds : angle 4.24634 ( 2688) Misc. bond : bond 0.00211 ( 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 519 residues out of total 2187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 518 time to evaluate : 0.974 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: symmetry clash revert: symmetry clash REVERT: D 155 GLU cc_start: 0.7921 (tt0) cc_final: 0.7492 (tm-30) REVERT: D 413 MET cc_start: 0.7290 (ttm) cc_final: 0.6616 (ttm) REVERT: A 123 ARG cc_start: 0.7855 (mmm-85) cc_final: 0.7507 (mmm-85) REVERT: A 128 GLN cc_start: 0.7927 (mm-40) cc_final: 0.7280 (tm-30) REVERT: A 161 TYR cc_start: 0.8278 (m-80) cc_final: 0.7351 (m-10) REVERT: A 302 MET cc_start: 0.8496 (mmm) cc_final: 0.8082 (mtt) REVERT: B 22 GLU cc_start: 0.8049 (tt0) cc_final: 0.7658 (tm-30) REVERT: B 51 THR cc_start: 0.9152 (t) cc_final: 0.8789 (t) REVERT: B 64 ARG cc_start: 0.8801 (mtt90) cc_final: 0.7999 (mtt-85) REVERT: B 90 GLU cc_start: 0.8289 (tp30) cc_final: 0.7888 (tp30) REVERT: B 102 ASN cc_start: 0.8563 (t0) cc_final: 0.8257 (t0) REVERT: B 221 ARG cc_start: 0.7167 (mtt90) cc_final: 0.5857 (ptt180) REVERT: B 238 ILE cc_start: 0.8405 (mt) cc_final: 0.8169 (mt) REVERT: B 258 ASN cc_start: 0.8851 (m110) cc_final: 0.8519 (m-40) REVERT: B 301 GLN cc_start: 0.8227 (mm-40) cc_final: 0.7686 (mm-40) REVERT: B 302 MET cc_start: 0.8500 (mmm) cc_final: 0.8024 (mtt) REVERT: B 358 GLN cc_start: 0.9203 (tp40) cc_final: 0.8877 (tp-100) REVERT: B 407 TRP cc_start: 0.5957 (m100) cc_final: 0.5701 (m-10) REVERT: E 96 GLN cc_start: 0.7453 (mm110) cc_final: 0.7119 (mm-40) REVERT: E 374 SER cc_start: 0.9381 (p) cc_final: 0.9097 (p) REVERT: E 381 SER cc_start: 0.9272 (t) cc_final: 0.9016 (p) REVERT: E 413 MET cc_start: 0.8101 (mtp) cc_final: 0.7639 (mtp) REVERT: C 6 HIS cc_start: 0.8438 (t70) cc_final: 0.7751 (t70) REVERT: C 14 ASN cc_start: 0.7853 (t0) cc_final: 0.7536 (t0) REVERT: C 54 ASN cc_start: 0.8838 (t0) cc_final: 0.8311 (t0) REVERT: C 103 TRP cc_start: 0.6973 (t60) cc_final: 0.6321 (t60) REVERT: C 240 THR cc_start: 0.9016 (t) cc_final: 0.8710 (m) REVERT: C 299 LYS cc_start: 0.8419 (mmtt) cc_final: 0.7354 (mttm) REVERT: C 372 LYS cc_start: 0.8503 (tppp) cc_final: 0.8178 (tptt) REVERT: C 407 TRP cc_start: 0.6728 (m100) cc_final: 0.6034 (m-90) REVERT: C 420 GLU cc_start: 0.7823 (mt-10) cc_final: 0.7604 (mp0) REVERT: F 37 HIS cc_start: 0.7490 (m-70) cc_final: 0.6992 (m90) REVERT: F 86 ILE cc_start: 0.9115 (pt) cc_final: 0.8725 (tp) REVERT: F 202 TYR cc_start: 0.8844 (m-80) cc_final: 0.8135 (m-80) REVERT: F 228 ASN cc_start: 0.9347 (m-40) cc_final: 0.8741 (m-40) REVERT: F 295 MET cc_start: 0.8328 (ttm) cc_final: 0.8034 (ttp) REVERT: F 301 MET cc_start: 0.8846 (mmt) cc_final: 0.7982 (mmm) REVERT: F 372 LYS cc_start: 0.8862 (tppp) cc_final: 0.8330 (tppp) REVERT: F 413 MET cc_start: 0.6614 (mtp) cc_final: 0.6131 (mtp) outliers start: 1 outliers final: 0 residues processed: 519 average time/residue: 0.1513 time to fit residues: 121.8171 Evaluate side-chains 391 residues out of total 2187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 391 time to evaluate : 0.745 ------------------------------------------------------------------------------- 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: 10.0000 chunk 134 optimal weight: 0.4980 chunk 107 optimal weight: 10.0000 chunk 18 optimal weight: 5.9990 chunk 113 optimal weight: 0.9980 chunk 132 optimal weight: 0.3980 chunk 142 optimal weight: 8.9990 chunk 105 optimal weight: 2.9990 chunk 26 optimal weight: 8.9990 overall best weight: 2.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 8 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 88 HIS D 176 GLN ** A 8 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 18 ASN ** 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 167 ASN E 192 HIS ** E 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 258 ASN ** F 406 HIS ** 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 = 0.3787 r_free = 0.3787 target = 0.135705 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.119993 restraints weight = 37587.494| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.122709 restraints weight = 22726.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.124639 restraints weight = 15464.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.125971 restraints weight = 11426.921| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.126966 restraints weight = 9011.369| |-----------------------------------------------------------------------------| r_work (final): 0.3665 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7859 moved from start: 0.3856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 20883 Z= 0.131 Angle : 0.607 12.366 28440 Z= 0.305 Chirality : 0.045 0.287 3135 Planarity : 0.005 0.068 3681 Dihedral : 9.994 177.745 3339 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 0.09 % Allowed : 1.34 % Favored : 98.57 % 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 aren not related in a simple way. whole: -0.24 (0.17), residues: 2544 helix: 1.20 (0.16), residues: 1122 sheet: 0.05 (0.25), residues: 408 loop : -1.85 (0.19), residues: 1014 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG F 320 TYR 0.020 0.001 TYR E 36 PHE 0.023 0.001 PHE F 83 TRP 0.034 0.002 TRP B 407 HIS 0.006 0.001 HIS B 406 Details of bonding type rmsd covalent geometry : bond 0.00295 (20880) covalent geometry : angle 0.60737 (28440) hydrogen bonds : bond 0.04019 ( 921) hydrogen bonds : angle 4.28313 ( 2688) Misc. bond : bond 0.00235 ( 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 490 residues out of total 2187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 488 time to evaluate : 0.833 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: symmetry clash revert: symmetry clash REVERT: D 64 ARG cc_start: 0.8443 (mtt-85) cc_final: 0.8084 (mtt-85) REVERT: D 88 HIS cc_start: 0.8119 (OUTLIER) cc_final: 0.7216 (t-90) REVERT: D 155 GLU cc_start: 0.8121 (tt0) cc_final: 0.7626 (tm-30) REVERT: D 210 TYR cc_start: 0.8850 (m-10) cc_final: 0.8256 (m-80) REVERT: D 220 GLU cc_start: 0.7106 (mm-30) cc_final: 0.6904 (mm-30) REVERT: A 123 ARG cc_start: 0.7970 (mmm-85) cc_final: 0.7629 (mmm-85) REVERT: A 128 GLN cc_start: 0.7965 (mm-40) cc_final: 0.7447 (tm-30) REVERT: A 161 TYR cc_start: 0.8300 (m-80) cc_final: 0.7558 (m-10) REVERT: A 302 MET cc_start: 0.8507 (mmm) cc_final: 0.8152 (mtt) REVERT: B 36 MET cc_start: 0.7336 (ptm) cc_final: 0.7082 (ptm) REVERT: B 90 GLU cc_start: 0.8334 (tp30) cc_final: 0.7862 (tp30) REVERT: B 102 ASN cc_start: 0.8579 (t0) cc_final: 0.8276 (t0) REVERT: B 192 HIS cc_start: 0.7918 (t-90) cc_final: 0.7660 (t-90) REVERT: B 221 ARG cc_start: 0.7200 (mtt90) cc_final: 0.5950 (ptt180) REVERT: B 258 ASN cc_start: 0.8895 (m110) cc_final: 0.8545 (m-40) REVERT: B 301 GLN cc_start: 0.8188 (mm-40) cc_final: 0.7625 (mm-40) REVERT: B 302 MET cc_start: 0.8474 (mmm) cc_final: 0.8162 (mtt) REVERT: B 358 GLN cc_start: 0.9206 (tp40) cc_final: 0.8878 (tp-100) REVERT: B 407 TRP cc_start: 0.6491 (m100) cc_final: 0.6263 (m-10) REVERT: E 96 GLN cc_start: 0.7527 (mm110) cc_final: 0.7163 (mm-40) REVERT: E 320 ARG cc_start: 0.7501 (mtm180) cc_final: 0.6489 (mtm110) REVERT: E 373 MET cc_start: 0.7995 (mmt) cc_final: 0.7658 (mmm) REVERT: E 374 SER cc_start: 0.9227 (p) cc_final: 0.9009 (p) REVERT: E 381 SER cc_start: 0.9287 (t) cc_final: 0.9053 (p) REVERT: E 413 MET cc_start: 0.8196 (mtp) cc_final: 0.7773 (mtp) REVERT: E 416 MET cc_start: 0.8346 (mmm) cc_final: 0.8024 (mmt) REVERT: C 6 HIS cc_start: 0.8421 (t70) cc_final: 0.7596 (t70) REVERT: C 14 ASN cc_start: 0.7859 (t0) cc_final: 0.7552 (t0) REVERT: C 54 ASN cc_start: 0.8871 (t0) cc_final: 0.8328 (t0) REVERT: C 103 TRP cc_start: 0.6857 (t60) cc_final: 0.6337 (t60) REVERT: C 333 LEU cc_start: 0.8724 (tp) cc_final: 0.8471 (tp) REVERT: C 407 TRP cc_start: 0.6850 (m100) cc_final: 0.5974 (m-90) REVERT: C 420 GLU cc_start: 0.7821 (mt-10) cc_final: 0.7619 (mp0) REVERT: F 37 HIS cc_start: 0.7730 (m-70) cc_final: 0.7234 (m90) REVERT: F 69 ASP cc_start: 0.7776 (m-30) cc_final: 0.7569 (m-30) REVERT: F 76 ASP cc_start: 0.8446 (m-30) cc_final: 0.8187 (m-30) REVERT: F 86 ILE cc_start: 0.9083 (pt) cc_final: 0.8665 (tp) REVERT: F 154 ILE cc_start: 0.9259 (tt) cc_final: 0.9057 (tt) REVERT: F 202 TYR cc_start: 0.8854 (m-80) cc_final: 0.8153 (m-80) REVERT: F 228 ASN cc_start: 0.9380 (m-40) cc_final: 0.8804 (m-40) outliers start: 2 outliers final: 1 residues processed: 490 average time/residue: 0.1489 time to fit residues: 114.0135 Evaluate side-chains 374 residues out of total 2187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 372 time to evaluate : 0.773 ------------------------------------------------------------------------------- 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: 5.9990 chunk 40 optimal weight: 10.0000 chunk 175 optimal weight: 7.9990 chunk 33 optimal weight: 9.9990 chunk 247 optimal weight: 9.9990 chunk 55 optimal weight: 6.9990 chunk 190 optimal weight: 5.9990 chunk 46 optimal weight: 1.9990 chunk 99 optimal weight: 7.9990 chunk 236 optimal weight: 5.9990 chunk 68 optimal weight: 0.7980 overall best weight: 4.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 176 GLN D 406 HIS ** A 8 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 18 ASN ** 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 ** E 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 258 ASN ** F 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.131685 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.116035 restraints weight = 38050.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.118650 restraints weight = 23237.049| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.120481 restraints weight = 15938.711| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.121797 restraints weight = 11910.810| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.122753 restraints weight = 9456.642| |-----------------------------------------------------------------------------| r_work (final): 0.3603 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7951 moved from start: 0.3795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 20883 Z= 0.194 Angle : 0.681 11.487 28440 Z= 0.349 Chirality : 0.048 0.362 3135 Planarity : 0.005 0.071 3681 Dihedral : 10.236 179.345 3339 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.97 % Favored : 94.03 % Rotamer: Outliers : 0.00 % Allowed : 0.78 % Favored : 99.22 % 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 aren not related in a simple way. whole: -0.45 (0.17), residues: 2544 helix: 1.01 (0.16), residues: 1125 sheet: -0.30 (0.26), residues: 366 loop : -1.77 (0.18), residues: 1053 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 64 TYR 0.019 0.002 TYR F 432 PHE 0.021 0.002 PHE F 169 TRP 0.040 0.002 TRP B 407 HIS 0.008 0.001 HIS E 192 Details of bonding type rmsd covalent geometry : bond 0.00443 (20880) covalent geometry : angle 0.68148 (28440) hydrogen bonds : bond 0.04743 ( 921) hydrogen bonds : angle 4.64970 ( 2688) Misc. bond : bond 0.00360 ( 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 465 residues out of total 2187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 465 time to evaluate : 0.862 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 155 GLU cc_start: 0.8097 (tt0) cc_final: 0.7638 (tm-30) REVERT: D 210 TYR cc_start: 0.8828 (m-10) cc_final: 0.8263 (m-80) REVERT: D 220 GLU cc_start: 0.7096 (mm-30) cc_final: 0.6868 (mm-30) REVERT: D 413 MET cc_start: 0.7471 (ttm) cc_final: 0.6921 (ttm) REVERT: A 128 GLN cc_start: 0.8010 (mm-40) cc_final: 0.7256 (tm-30) REVERT: A 161 TYR cc_start: 0.8397 (m-80) cc_final: 0.7998 (m-10) REVERT: A 302 MET cc_start: 0.8598 (mmm) cc_final: 0.8130 (mtt) REVERT: B 90 GLU cc_start: 0.8221 (tp30) cc_final: 0.7856 (tp30) REVERT: B 102 ASN cc_start: 0.8680 (t0) cc_final: 0.8369 (t0) REVERT: B 221 ARG cc_start: 0.7326 (mtt90) cc_final: 0.6032 (ptt180) REVERT: B 258 ASN cc_start: 0.8906 (m110) cc_final: 0.8558 (m-40) REVERT: B 301 GLN cc_start: 0.8310 (mm-40) cc_final: 0.7672 (mm-40) REVERT: B 302 MET cc_start: 0.8492 (mmm) cc_final: 0.8164 (mtt) REVERT: B 358 GLN cc_start: 0.9214 (tp40) cc_final: 0.8887 (tp-100) REVERT: B 407 TRP cc_start: 0.7016 (m100) cc_final: 0.6406 (m-10) REVERT: E 96 GLN cc_start: 0.7559 (mm110) cc_final: 0.7178 (mm-40) REVERT: E 320 ARG cc_start: 0.7673 (mtm180) cc_final: 0.6849 (mtm110) REVERT: E 373 MET cc_start: 0.8168 (mmt) cc_final: 0.7790 (mmm) REVERT: E 381 SER cc_start: 0.9281 (t) cc_final: 0.8953 (p) REVERT: E 413 MET cc_start: 0.8124 (mtp) cc_final: 0.7768 (mtp) REVERT: E 416 MET cc_start: 0.8281 (mmm) cc_final: 0.8046 (mmt) REVERT: C 14 ASN cc_start: 0.7856 (t0) cc_final: 0.7549 (t0) REVERT: C 54 ASN cc_start: 0.8732 (t0) cc_final: 0.8212 (t0) REVERT: C 103 TRP cc_start: 0.7048 (t60) cc_final: 0.6740 (t60) REVERT: C 193 GLN cc_start: 0.8292 (mm-40) cc_final: 0.7581 (mm-40) REVERT: C 286 LEU cc_start: 0.8026 (mt) cc_final: 0.7689 (pp) REVERT: C 333 LEU cc_start: 0.8749 (tp) cc_final: 0.8475 (tp) REVERT: C 356 CYS cc_start: 0.8831 (t) cc_final: 0.7767 (m) REVERT: C 407 TRP cc_start: 0.6702 (m100) cc_final: 0.6070 (m-90) REVERT: F 37 HIS cc_start: 0.7632 (m-70) cc_final: 0.7172 (m90) REVERT: F 154 ILE cc_start: 0.9172 (tt) cc_final: 0.8947 (tt) REVERT: F 228 ASN cc_start: 0.9436 (m-40) cc_final: 0.8805 (m-40) REVERT: F 384 ILE cc_start: 0.8369 (pt) cc_final: 0.8071 (pt) outliers start: 0 outliers final: 0 residues processed: 465 average time/residue: 0.1477 time to fit residues: 107.6333 Evaluate side-chains 361 residues out of total 2187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 361 time to evaluate : 0.639 ------------------------------------------------------------------------------- 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: 7.9990 chunk 215 optimal weight: 0.6980 chunk 107 optimal weight: 9.9990 chunk 158 optimal weight: 3.9990 chunk 136 optimal weight: 7.9990 chunk 208 optimal weight: 5.9990 chunk 66 optimal weight: 2.9990 chunk 37 optimal weight: 9.9990 chunk 60 optimal weight: 0.0970 chunk 32 optimal weight: 0.8980 chunk 141 optimal weight: 5.9990 overall best weight: 1.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 11 GLN D 88 HIS D 176 GLN D 406 HIS ** A 8 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 ** E 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 101 ASN ** C 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 258 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.135123 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.119452 restraints weight = 37822.338| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.122180 restraints weight = 22857.648| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.124093 restraints weight = 15506.336| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.125380 restraints weight = 11470.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.126363 restraints weight = 9094.768| |-----------------------------------------------------------------------------| r_work (final): 0.3652 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7864 moved from start: 0.4039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 20883 Z= 0.127 Angle : 0.629 10.698 28440 Z= 0.317 Chirality : 0.046 0.356 3135 Planarity : 0.005 0.065 3681 Dihedral : 9.842 179.545 3339 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 0.09 % Allowed : 0.28 % Favored : 99.63 % 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 aren not related in a simple way. whole: -0.22 (0.17), residues: 2544 helix: 1.19 (0.16), residues: 1122 sheet: -0.04 (0.25), residues: 408 loop : -1.75 (0.19), residues: 1014 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 84 TYR 0.027 0.001 TYR E 36 PHE 0.022 0.001 PHE D 138 TRP 0.026 0.002 TRP B 407 HIS 0.005 0.001 HIS E 37 Details of bonding type rmsd covalent geometry : bond 0.00281 (20880) covalent geometry : angle 0.62868 (28440) hydrogen bonds : bond 0.04054 ( 921) hydrogen bonds : angle 4.41834 ( 2688) Misc. bond : bond 0.00265 ( 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 478 residues out of total 2187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 476 time to evaluate : 0.670 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 64 ARG cc_start: 0.8384 (mpt-90) cc_final: 0.8025 (mpt-90) REVERT: D 88 HIS cc_start: 0.8170 (OUTLIER) cc_final: 0.7287 (t-90) REVERT: D 155 GLU cc_start: 0.8134 (tt0) cc_final: 0.7562 (tm-30) REVERT: D 210 TYR cc_start: 0.8853 (m-10) cc_final: 0.8243 (m-80) REVERT: D 287 SER cc_start: 0.8693 (t) cc_final: 0.8444 (p) REVERT: D 413 MET cc_start: 0.7487 (ttm) cc_final: 0.7093 (ttm) REVERT: A 128 GLN cc_start: 0.8029 (mm-40) cc_final: 0.7429 (tm-30) REVERT: A 161 TYR cc_start: 0.8567 (m-80) cc_final: 0.7064 (m-10) REVERT: A 203 MET cc_start: 0.7170 (mtp) cc_final: 0.6910 (mtp) REVERT: A 302 MET cc_start: 0.8559 (mmm) cc_final: 0.8039 (mtt) REVERT: B 22 GLU cc_start: 0.8107 (tt0) cc_final: 0.7714 (tm-30) REVERT: B 90 GLU cc_start: 0.8263 (tp30) cc_final: 0.7884 (tp30) REVERT: B 102 ASN cc_start: 0.8659 (t0) cc_final: 0.8275 (t0) REVERT: B 192 HIS cc_start: 0.7682 (t-90) cc_final: 0.7472 (t70) REVERT: B 221 ARG cc_start: 0.7158 (mtt90) cc_final: 0.5947 (ptt180) REVERT: B 301 GLN cc_start: 0.8241 (mm-40) cc_final: 0.7695 (mm-40) REVERT: B 302 MET cc_start: 0.8495 (mmm) cc_final: 0.8128 (mtt) REVERT: B 358 GLN cc_start: 0.9198 (tp40) cc_final: 0.8866 (tp-100) REVERT: B 407 TRP cc_start: 0.6790 (m100) cc_final: 0.6237 (m-10) REVERT: E 74 THR cc_start: 0.8526 (p) cc_final: 0.8251 (p) REVERT: E 96 GLN cc_start: 0.7609 (mm110) cc_final: 0.7200 (mm-40) REVERT: E 320 ARG cc_start: 0.7403 (mtm180) cc_final: 0.6396 (mtm110) REVERT: E 374 SER cc_start: 0.9298 (p) cc_final: 0.9023 (p) REVERT: E 381 SER cc_start: 0.9333 (t) cc_final: 0.9090 (p) REVERT: E 413 MET cc_start: 0.8129 (mtp) cc_final: 0.7708 (mtp) REVERT: C 6 HIS cc_start: 0.8286 (t70) cc_final: 0.7263 (t70) REVERT: C 14 ASN cc_start: 0.7704 (t0) cc_final: 0.7388 (t0) REVERT: C 54 ASN cc_start: 0.8726 (t0) cc_final: 0.8219 (t0) REVERT: C 75 MET cc_start: 0.8204 (mmt) cc_final: 0.7926 (mmm) REVERT: C 103 TRP cc_start: 0.6969 (t60) cc_final: 0.6496 (t60) REVERT: C 278 ARG cc_start: 0.8051 (tpt170) cc_final: 0.7471 (tpm170) REVERT: C 282 GLN cc_start: 0.7457 (mp10) cc_final: 0.7166 (mp10) REVERT: C 286 LEU cc_start: 0.7995 (mt) cc_final: 0.7457 (pp) REVERT: C 333 LEU cc_start: 0.8704 (tp) cc_final: 0.8435 (tp) REVERT: C 407 TRP cc_start: 0.6677 (m100) cc_final: 0.6002 (m-90) REVERT: F 37 HIS cc_start: 0.7623 (m-70) cc_final: 0.7044 (m90) REVERT: F 76 ASP cc_start: 0.8452 (m-30) cc_final: 0.8146 (m-30) REVERT: F 154 ILE cc_start: 0.9206 (tt) cc_final: 0.8959 (tt) REVERT: F 202 TYR cc_start: 0.8788 (m-80) cc_final: 0.8056 (m-80) REVERT: F 228 ASN cc_start: 0.9370 (m-40) cc_final: 0.8748 (m-40) REVERT: F 259 MET cc_start: 0.7387 (mtm) cc_final: 0.7166 (mtm) outliers start: 2 outliers final: 1 residues processed: 478 average time/residue: 0.1425 time to fit residues: 107.2925 Evaluate side-chains 376 residues out of total 2187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 374 time to evaluate : 0.710 ------------------------------------------------------------------------------- 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: 6.9990 chunk 10 optimal weight: 0.0870 chunk 175 optimal weight: 7.9990 chunk 122 optimal weight: 5.9990 chunk 33 optimal weight: 7.9990 chunk 128 optimal weight: 3.9990 chunk 70 optimal weight: 2.9990 chunk 230 optimal weight: 0.6980 chunk 180 optimal weight: 3.9990 chunk 96 optimal weight: 8.9990 chunk 154 optimal weight: 0.8980 overall best weight: 1.7362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 176 GLN ** A 8 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 258 ASN ** 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 28 HIS F 258 ASN F 406 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.136188 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.120460 restraints weight = 37651.893| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.123155 restraints weight = 22671.305| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.125014 restraints weight = 15437.661| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.126375 restraints weight = 11487.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.127353 restraints weight = 9069.064| |-----------------------------------------------------------------------------| r_work (final): 0.3663 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7853 moved from start: 0.4118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 20883 Z= 0.125 Angle : 0.617 10.898 28440 Z= 0.312 Chirality : 0.046 0.350 3135 Planarity : 0.005 0.063 3681 Dihedral : 9.685 179.941 3339 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 0.00 % Allowed : 0.32 % 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 aren not related in a simple way. whole: -0.13 (0.17), residues: 2544 helix: 1.27 (0.16), residues: 1122 sheet: 0.03 (0.25), residues: 411 loop : -1.73 (0.19), residues: 1011 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG F 320 TYR 0.021 0.001 TYR F 432 PHE 0.022 0.001 PHE D 138 TRP 0.028 0.002 TRP B 407 HIS 0.005 0.001 HIS E 6 Details of bonding type rmsd covalent geometry : bond 0.00279 (20880) covalent geometry : angle 0.61712 (28440) hydrogen bonds : bond 0.03998 ( 921) hydrogen bonds : angle 4.35442 ( 2688) Misc. bond : bond 0.00258 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3220.36 seconds wall clock time: 56 minutes 43.29 seconds (3403.29 seconds total)