Starting phenix.real_space_refine on Thu Jan 23 09:04:23 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8v45_42965/01_2025/8v45_42965.cif Found real_map, /net/cci-nas-00/data/ceres_data/8v45_42965/01_2025/8v45_42965.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.63 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8v45_42965/01_2025/8v45_42965.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8v45_42965/01_2025/8v45_42965.map" model { file = "/net/cci-nas-00/data/ceres_data/8v45_42965/01_2025/8v45_42965.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8v45_42965/01_2025/8v45_42965.cif" } resolution = 3.63 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.014 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 12 5.49 5 S 82 5.16 5 C 12612 2.51 5 N 3327 2.21 5 O 3780 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 19813 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 2985 Number of conformers: 1 Conformer: "" Number of residues, atoms: 379, 2985 Classifications: {'peptide': 379} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'PTRANS': 10, 'TRANS': 368} Chain breaks: 6 Unresolved non-hydrogen bonds: 85 Unresolved non-hydrogen angles: 107 Unresolved non-hydrogen dihedrals: 66 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 5, 'ARG:plan': 2, 'ASN:plan1': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 44 Chain: "B" Number of atoms: 3050 Number of conformers: 1 Conformer: "" Number of residues, atoms: 383, 3050 Classifications: {'peptide': 383} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 10, 'TRANS': 372} Chain breaks: 7 Unresolved non-hydrogen bonds: 48 Unresolved non-hydrogen angles: 60 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 22 Chain: "C" Number of atoms: 2939 Number of conformers: 1 Conformer: "" Number of residues, atoms: 375, 2939 Classifications: {'peptide': 375} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'PTRANS': 10, 'TRANS': 364} Chain breaks: 7 Unresolved non-hydrogen bonds: 81 Unresolved non-hydrogen angles: 102 Unresolved non-hydrogen dihedrals: 63 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 5, 'ARG:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 40 Chain: "D" Number of atoms: 3042 Number of conformers: 1 Conformer: "" Number of residues, atoms: 382, 3042 Classifications: {'peptide': 382} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 10, 'TRANS': 371} Chain breaks: 7 Unresolved non-hydrogen bonds: 48 Unresolved non-hydrogen angles: 60 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 22 Chain: "E" Number of atoms: 2967 Number of conformers: 1 Conformer: "" Number of residues, atoms: 376, 2967 Classifications: {'peptide': 376} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'PTRANS': 10, 'TRANS': 365} Chain breaks: 6 Unresolved non-hydrogen bonds: 81 Unresolved non-hydrogen angles: 102 Unresolved non-hydrogen dihedrals: 63 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 5, 'ARG:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 40 Chain: "F" Number of atoms: 2962 Number of conformers: 1 Conformer: "" Number of residues, atoms: 378, 2962 Classifications: {'peptide': 378} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'PTRANS': 10, 'TRANS': 367} Chain breaks: 7 Unresolved non-hydrogen bonds: 85 Unresolved non-hydrogen angles: 107 Unresolved non-hydrogen dihedrals: 66 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 5, 'ARG:plan': 2, 'ASN:plan1': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 44 Chain: "O" Number of atoms: 872 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 872 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 2, 'TRANS': 103} Chain: "P" Number of atoms: 872 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 872 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 2, 'TRANS': 103} Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 11.30, per 1000 atoms: 0.57 Number of scatterers: 19813 At special positions: 0 Unit cell: (102.85, 166.43, 168.3, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 82 16.00 P 12 15.00 O 3780 8.00 N 3327 7.00 C 12612 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.48 Conformation dependent library (CDL) restraints added in 2.4 seconds 4778 Ramachandran restraints generated. 2389 Oldfield, 0 Emsley, 2389 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4754 Finding SS restraints... Secondary structure from input PDB file: 95 helices and 18 sheets defined 55.8% alpha, 14.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.32 Creating SS restraints... Processing helix chain 'A' and resid 38 through 50 Processing helix chain 'A' and resid 53 through 60 removed outlier: 3.754A pdb=" N ARG A 56 " --> pdb=" O ASP A 53 " (cutoff:3.500A) Processing helix chain 'A' and resid 102 through 113 removed outlier: 3.772A pdb=" N ILE A 112 " --> pdb=" O THR A 108 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N GLU A 113 " --> pdb=" O VAL A 109 " (cutoff:3.500A) Processing helix chain 'A' and resid 126 through 138 Processing helix chain 'A' and resid 151 through 158 removed outlier: 3.529A pdb=" N LEU A 155 " --> pdb=" O PHE A 151 " (cutoff:3.500A) Processing helix chain 'A' and resid 178 through 189 removed outlier: 4.452A pdb=" N ALA A 182 " --> pdb=" O ARG A 178 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N LEU A 187 " --> pdb=" O PHE A 183 " (cutoff:3.500A) Processing helix chain 'A' and resid 202 through 237 removed outlier: 3.848A pdb=" N SER A 223 " --> pdb=" O ALA A 219 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N VAL A 231 " --> pdb=" O SER A 227 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LEU A 237 " --> pdb=" O VAL A 233 " (cutoff:3.500A) Processing helix chain 'A' and resid 249 through 259 Processing helix chain 'A' and resid 276 through 287 Processing helix chain 'A' and resid 297 through 333 removed outlier: 3.613A pdb=" N LEU A 301 " --> pdb=" O VAL A 297 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N PHE A 319 " --> pdb=" O GLN A 315 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N GLU A 321 " --> pdb=" O LYS A 317 " (cutoff:3.500A) removed outlier: 5.230A pdb=" N ILE A 322 " --> pdb=" O ALA A 318 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N TYR A 325 " --> pdb=" O GLU A 321 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N PHE A 332 " --> pdb=" O SER A 328 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 378 Processing helix chain 'A' and resid 399 through 414 removed outlier: 5.034A pdb=" N LEU A 407 " --> pdb=" O GLN A 403 " (cutoff:3.500A) removed outlier: 4.950A pdb=" N LYS A 408 " --> pdb=" O GLU A 404 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N SER A 412 " --> pdb=" O LYS A 408 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N GLN A 413 " --> pdb=" O ARG A 409 " (cutoff:3.500A) Processing helix chain 'A' and resid 425 through 430 removed outlier: 3.648A pdb=" N THR A 430 " --> pdb=" O SER A 427 " (cutoff:3.500A) Processing helix chain 'A' and resid 432 through 434 No H-bonds generated for 'chain 'A' and resid 432 through 434' Processing helix chain 'B' and resid 38 through 52 Processing helix chain 'B' and resid 53 through 60 removed outlier: 3.565A pdb=" N ARG B 56 " --> pdb=" O ASP B 53 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LEU B 60 " --> pdb=" O PHE B 57 " (cutoff:3.500A) Processing helix chain 'B' and resid 102 through 113 Processing helix chain 'B' and resid 126 through 139 Processing helix chain 'B' and resid 151 through 158 removed outlier: 3.901A pdb=" N LEU B 155 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N GLU B 156 " --> pdb=" O ARG B 152 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ALA B 157 " --> pdb=" O THR B 153 " (cutoff:3.500A) Processing helix chain 'B' and resid 178 through 187 removed outlier: 4.057A pdb=" N ALA B 182 " --> pdb=" O ARG B 178 " (cutoff:3.500A) Processing helix chain 'B' and resid 201 through 233 removed outlier: 4.050A pdb=" N VAL B 231 " --> pdb=" O SER B 227 " (cutoff:3.500A) Processing helix chain 'B' and resid 249 through 261 removed outlier: 4.115A pdb=" N ALA B 261 " --> pdb=" O GLY B 257 " (cutoff:3.500A) Processing helix chain 'B' and resid 271 through 287 removed outlier: 3.682A pdb=" N SER B 275 " --> pdb=" O TYR B 271 " (cutoff:3.500A) Processing helix chain 'B' and resid 297 through 319 removed outlier: 3.706A pdb=" N LEU B 301 " --> pdb=" O VAL B 297 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N VAL B 303 " --> pdb=" O GLY B 299 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N PHE B 319 " --> pdb=" O GLN B 315 " (cutoff:3.500A) Processing helix chain 'B' and resid 319 through 333 removed outlier: 3.987A pdb=" N PHE B 332 " --> pdb=" O SER B 328 " (cutoff:3.500A) Processing helix chain 'B' and resid 362 through 366 removed outlier: 3.700A pdb=" N VAL B 365 " --> pdb=" O PRO B 362 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N LEU B 366 " --> pdb=" O ILE B 363 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 362 through 366' Processing helix chain 'B' and resid 367 through 382 removed outlier: 3.823A pdb=" N ALA B 379 " --> pdb=" O THR B 375 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N SER B 381 " --> pdb=" O LEU B 377 " (cutoff:3.500A) Processing helix chain 'B' and resid 399 through 404 Processing helix chain 'B' and resid 405 through 414 Processing helix chain 'B' and resid 432 through 434 No H-bonds generated for 'chain 'B' and resid 432 through 434' Processing helix chain 'C' and resid 38 through 51 removed outlier: 3.688A pdb=" N VAL C 45 " --> pdb=" O THR C 41 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ASN C 51 " --> pdb=" O ALA C 47 " (cutoff:3.500A) Processing helix chain 'C' and resid 53 through 60 removed outlier: 3.633A pdb=" N ARG C 56 " --> pdb=" O ASP C 53 " (cutoff:3.500A) Processing helix chain 'C' and resid 102 through 113 Processing helix chain 'C' and resid 126 through 138 Processing helix chain 'C' and resid 151 through 158 Processing helix chain 'C' and resid 179 through 189 Processing helix chain 'C' and resid 199 through 237 removed outlier: 3.963A pdb=" N LEU C 237 " --> pdb=" O VAL C 233 " (cutoff:3.500A) Processing helix chain 'C' and resid 249 through 259 Processing helix chain 'C' and resid 276 through 287 Processing helix chain 'C' and resid 297 through 333 removed outlier: 4.874A pdb=" N GLU C 321 " --> pdb=" O LYS C 317 " (cutoff:3.500A) removed outlier: 5.411A pdb=" N ILE C 322 " --> pdb=" O ALA C 318 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N PHE C 332 " --> pdb=" O SER C 328 " (cutoff:3.500A) Processing helix chain 'C' and resid 367 through 382 removed outlier: 3.631A pdb=" N ALA C 379 " --> pdb=" O THR C 375 " (cutoff:3.500A) Processing helix chain 'C' and resid 399 through 414 removed outlier: 4.930A pdb=" N LEU C 407 " --> pdb=" O GLN C 403 " (cutoff:3.500A) removed outlier: 4.973A pdb=" N LYS C 408 " --> pdb=" O GLU C 404 " (cutoff:3.500A) Processing helix chain 'C' and resid 425 through 430 removed outlier: 3.533A pdb=" N ILE C 428 " --> pdb=" O SER C 425 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N THR C 430 " --> pdb=" O SER C 427 " (cutoff:3.500A) Processing helix chain 'C' and resid 432 through 434 No H-bonds generated for 'chain 'C' and resid 432 through 434' Processing helix chain 'D' and resid 38 through 51 removed outlier: 3.748A pdb=" N ASN D 51 " --> pdb=" O ALA D 47 " (cutoff:3.500A) Processing helix chain 'D' and resid 53 through 60 removed outlier: 3.662A pdb=" N ARG D 56 " --> pdb=" O ASP D 53 " (cutoff:3.500A) Processing helix chain 'D' and resid 102 through 113 Processing helix chain 'D' and resid 126 through 138 Processing helix chain 'D' and resid 151 through 158 removed outlier: 3.536A pdb=" N LEU D 155 " --> pdb=" O PHE D 151 " (cutoff:3.500A) Processing helix chain 'D' and resid 178 through 189 removed outlier: 4.195A pdb=" N ALA D 182 " --> pdb=" O ARG D 178 " (cutoff:3.500A) Processing helix chain 'D' and resid 199 through 235 removed outlier: 3.807A pdb=" N GLU D 204 " --> pdb=" O PRO D 200 " (cutoff:3.500A) removed outlier: 4.840A pdb=" N ASP D 205 " --> pdb=" O MET D 201 " (cutoff:3.500A) Processing helix chain 'D' and resid 249 through 261 removed outlier: 4.050A pdb=" N ILE D 260 " --> pdb=" O GLU D 256 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N ALA D 261 " --> pdb=" O GLY D 257 " (cutoff:3.500A) Processing helix chain 'D' and resid 271 through 287 removed outlier: 3.678A pdb=" N SER D 275 " --> pdb=" O TYR D 271 " (cutoff:3.500A) Processing helix chain 'D' and resid 299 through 333 removed outlier: 3.888A pdb=" N PHE D 319 " --> pdb=" O GLN D 315 " (cutoff:3.500A) removed outlier: 4.650A pdb=" N GLU D 321 " --> pdb=" O LYS D 317 " (cutoff:3.500A) removed outlier: 5.383A pdb=" N ILE D 322 " --> pdb=" O ALA D 318 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N PHE D 332 " --> pdb=" O SER D 328 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LEU D 333 " --> pdb=" O VAL D 329 " (cutoff:3.500A) Processing helix chain 'D' and resid 367 through 382 removed outlier: 3.650A pdb=" N ALA D 379 " --> pdb=" O THR D 375 " (cutoff:3.500A) Processing helix chain 'D' and resid 399 through 414 removed outlier: 4.754A pdb=" N LEU D 407 " --> pdb=" O GLN D 403 " (cutoff:3.500A) removed outlier: 4.911A pdb=" N LYS D 408 " --> pdb=" O GLU D 404 " (cutoff:3.500A) Processing helix chain 'D' and resid 425 through 430 removed outlier: 3.772A pdb=" N THR D 430 " --> pdb=" O SER D 427 " (cutoff:3.500A) Processing helix chain 'D' and resid 432 through 434 No H-bonds generated for 'chain 'D' and resid 432 through 434' Processing helix chain 'E' and resid 38 through 50 Processing helix chain 'E' and resid 53 through 60 removed outlier: 3.800A pdb=" N ARG E 56 " --> pdb=" O ASP E 53 " (cutoff:3.500A) Processing helix chain 'E' and resid 102 through 113 removed outlier: 3.769A pdb=" N ILE E 112 " --> pdb=" O THR E 108 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N GLU E 113 " --> pdb=" O VAL E 109 " (cutoff:3.500A) Processing helix chain 'E' and resid 126 through 138 removed outlier: 3.530A pdb=" N ASN E 138 " --> pdb=" O PHE E 134 " (cutoff:3.500A) Processing helix chain 'E' and resid 151 through 158 removed outlier: 3.594A pdb=" N LEU E 155 " --> pdb=" O PHE E 151 " (cutoff:3.500A) Processing helix chain 'E' and resid 178 through 189 removed outlier: 4.199A pdb=" N ALA E 182 " --> pdb=" O ARG E 178 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N LEU E 187 " --> pdb=" O PHE E 183 " (cutoff:3.500A) Processing helix chain 'E' and resid 202 through 236 Processing helix chain 'E' and resid 249 through 259 Processing helix chain 'E' and resid 276 through 287 removed outlier: 3.546A pdb=" N GLU E 280 " --> pdb=" O LYS E 276 " (cutoff:3.500A) Processing helix chain 'E' and resid 297 through 333 removed outlier: 3.826A pdb=" N LEU E 301 " --> pdb=" O VAL E 297 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N GLU E 321 " --> pdb=" O LYS E 317 " (cutoff:3.500A) removed outlier: 5.242A pdb=" N ILE E 322 " --> pdb=" O ALA E 318 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N TYR E 325 " --> pdb=" O GLU E 321 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N PHE E 332 " --> pdb=" O SER E 328 " (cutoff:3.500A) Processing helix chain 'E' and resid 367 through 378 Processing helix chain 'E' and resid 399 through 414 removed outlier: 4.975A pdb=" N LEU E 407 " --> pdb=" O GLN E 403 " (cutoff:3.500A) removed outlier: 4.874A pdb=" N LYS E 408 " --> pdb=" O GLU E 404 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N SER E 412 " --> pdb=" O LYS E 408 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N GLN E 413 " --> pdb=" O ARG E 409 " (cutoff:3.500A) Processing helix chain 'E' and resid 425 through 430 removed outlier: 3.712A pdb=" N THR E 430 " --> pdb=" O SER E 427 " (cutoff:3.500A) Processing helix chain 'E' and resid 432 through 434 No H-bonds generated for 'chain 'E' and resid 432 through 434' Processing helix chain 'F' and resid 38 through 51 removed outlier: 3.815A pdb=" N ASN F 51 " --> pdb=" O ALA F 47 " (cutoff:3.500A) Processing helix chain 'F' and resid 53 through 60 removed outlier: 3.534A pdb=" N ARG F 56 " --> pdb=" O ASP F 53 " (cutoff:3.500A) Processing helix chain 'F' and resid 102 through 113 Processing helix chain 'F' and resid 126 through 138 Processing helix chain 'F' and resid 151 through 158 Processing helix chain 'F' and resid 178 through 189 removed outlier: 4.078A pdb=" N ALA F 182 " --> pdb=" O ARG F 178 " (cutoff:3.500A) Processing helix chain 'F' and resid 199 through 237 removed outlier: 3.749A pdb=" N LEU F 237 " --> pdb=" O VAL F 233 " (cutoff:3.500A) Processing helix chain 'F' and resid 249 through 258 Processing helix chain 'F' and resid 276 through 287 removed outlier: 3.540A pdb=" N GLU F 280 " --> pdb=" O LYS F 276 " (cutoff:3.500A) Processing helix chain 'F' and resid 297 through 333 removed outlier: 4.884A pdb=" N GLU F 321 " --> pdb=" O LYS F 317 " (cutoff:3.500A) removed outlier: 5.304A pdb=" N ILE F 322 " --> pdb=" O ALA F 318 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N PHE F 332 " --> pdb=" O SER F 328 " (cutoff:3.500A) Processing helix chain 'F' and resid 362 through 366 removed outlier: 3.819A pdb=" N LEU F 366 " --> pdb=" O ILE F 363 " (cutoff:3.500A) Processing helix chain 'F' and resid 367 through 382 removed outlier: 3.677A pdb=" N ALA F 379 " --> pdb=" O THR F 375 " (cutoff:3.500A) Processing helix chain 'F' and resid 399 through 414 removed outlier: 4.949A pdb=" N LEU F 407 " --> pdb=" O GLN F 403 " (cutoff:3.500A) removed outlier: 5.033A pdb=" N LYS F 408 " --> pdb=" O GLU F 404 " (cutoff:3.500A) Processing helix chain 'F' and resid 425 through 430 removed outlier: 3.642A pdb=" N THR F 430 " --> pdb=" O SER F 427 " (cutoff:3.500A) Processing helix chain 'F' and resid 432 through 434 No H-bonds generated for 'chain 'F' and resid 432 through 434' Processing helix chain 'O' and resid 6 through 26 removed outlier: 3.538A pdb=" N VAL O 10 " --> pdb=" O THR O 6 " (cutoff:3.500A) Processing helix chain 'O' and resid 29 through 42 removed outlier: 3.524A pdb=" N LEU O 33 " --> pdb=" O ASP O 29 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N ASP O 35 " --> pdb=" O ASP O 31 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N HIS O 38 " --> pdb=" O HIS O 34 " (cutoff:3.500A) Processing helix chain 'O' and resid 49 through 57 removed outlier: 3.598A pdb=" N VAL O 55 " --> pdb=" O ASP O 51 " (cutoff:3.500A) Processing helix chain 'O' and resid 76 through 108 removed outlier: 3.799A pdb=" N GLU O 95 " --> pdb=" O ILE O 91 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ASP O 96 " --> pdb=" O ASP O 92 " (cutoff:3.500A) removed outlier: 4.611A pdb=" N GLU O 98 " --> pdb=" O TRP O 94 " (cutoff:3.500A) removed outlier: 4.865A pdb=" N ASP O 99 " --> pdb=" O GLU O 95 " (cutoff:3.500A) Processing helix chain 'P' and resid 6 through 26 Processing helix chain 'P' and resid 29 through 42 removed outlier: 4.147A pdb=" N ASP P 35 " --> pdb=" O ASP P 31 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N HIS P 38 " --> pdb=" O HIS P 34 " (cutoff:3.500A) Processing helix chain 'P' and resid 49 through 57 Processing helix chain 'P' and resid 76 through 108 removed outlier: 3.623A pdb=" N GLU P 95 " --> pdb=" O ILE P 91 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ASP P 96 " --> pdb=" O ASP P 92 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N GLU P 98 " --> pdb=" O TRP P 94 " (cutoff:3.500A) removed outlier: 4.986A pdb=" N ASP P 99 " --> pdb=" O GLU P 95 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 97 through 101 removed outlier: 5.289A pdb=" N TYR A 18 " --> pdb=" O LYS A 13 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 147 through 148 Processing sheet with id=AA3, first strand: chain 'A' and resid 337 through 342 removed outlier: 3.558A pdb=" N SER A 361 " --> pdb=" O LEU A 353 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 97 through 101 removed outlier: 5.440A pdb=" N TYR B 18 " --> pdb=" O LYS B 13 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 145 through 148 removed outlier: 6.416A pdb=" N VAL B 389 " --> pdb=" O ILE B 420 " (cutoff:3.500A) removed outlier: 7.920A pdb=" N CYS B 422 " --> pdb=" O VAL B 389 " (cutoff:3.500A) removed outlier: 7.140A pdb=" N ILE B 391 " --> pdb=" O CYS B 422 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N ASN B 29 " --> pdb=" O VAL B 421 " (cutoff:3.500A) removed outlier: 7.212A pdb=" N THR B 423 " --> pdb=" O ASN B 29 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N ILE B 31 " --> pdb=" O THR B 423 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N VAL B 30 " --> pdb=" O ILE B 437 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 337 through 339 Processing sheet with id=AA7, first strand: chain 'C' and resid 97 through 101 removed outlier: 5.438A pdb=" N TYR C 18 " --> pdb=" O LYS C 13 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 145 through 148 removed outlier: 6.094A pdb=" N VAL C 30 " --> pdb=" O ILE C 437 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 337 through 339 removed outlier: 3.707A pdb=" N SER C 361 " --> pdb=" O LEU C 353 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 97 through 101 removed outlier: 5.722A pdb=" N TYR D 18 " --> pdb=" O LYS D 13 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 145 through 148 removed outlier: 6.160A pdb=" N SER D 146 " --> pdb=" O LEU D 390 " (cutoff:3.500A) removed outlier: 7.612A pdb=" N ASP D 392 " --> pdb=" O SER D 146 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N PHE D 148 " --> pdb=" O ASP D 392 " (cutoff:3.500A) removed outlier: 5.978A pdb=" N VAL D 389 " --> pdb=" O ILE D 420 " (cutoff:3.500A) removed outlier: 7.650A pdb=" N CYS D 422 " --> pdb=" O VAL D 389 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N ILE D 391 " --> pdb=" O CYS D 422 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N VAL D 30 " --> pdb=" O ILE D 437 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 337 through 339 Processing sheet with id=AB4, first strand: chain 'E' and resid 97 through 101 removed outlier: 3.506A pdb=" N LYS E 8 " --> pdb=" O THR E 68 " (cutoff:3.500A) removed outlier: 5.402A pdb=" N TYR E 18 " --> pdb=" O LYS E 13 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 147 through 148 Processing sheet with id=AB6, first strand: chain 'E' and resid 337 through 341 removed outlier: 3.554A pdb=" N SER E 361 " --> pdb=" O LEU E 353 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 97 through 101 removed outlier: 5.301A pdb=" N TYR F 18 " --> pdb=" O LYS F 13 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 145 through 148 removed outlier: 6.135A pdb=" N VAL F 30 " --> pdb=" O ILE F 437 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 337 through 341 1170 hydrogen bonds defined for protein. 3318 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: 7.48 Time building geometry restraints manager: 5.19 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6239 1.34 - 1.46: 3281 1.46 - 1.57: 10470 1.57 - 1.69: 16 1.69 - 1.81: 158 Bond restraints: 20164 Sorted by residual: bond pdb=" C HIS B 424 " pdb=" N SER B 425 " ideal model delta sigma weight residual 1.331 1.300 0.031 2.07e-02 2.33e+03 2.31e+00 bond pdb=" O3A ATP F 501 " pdb=" PA ATP F 501 " ideal model delta sigma weight residual 1.592 1.548 0.044 3.00e-02 1.11e+03 2.13e+00 bond pdb=" CB THR A 375 " pdb=" CG2 THR A 375 " ideal model delta sigma weight residual 1.521 1.475 0.046 3.30e-02 9.18e+02 1.91e+00 bond pdb=" CB TRP C 360 " pdb=" CG TRP C 360 " ideal model delta sigma weight residual 1.498 1.456 0.042 3.10e-02 1.04e+03 1.80e+00 bond pdb=" CA GLU C 202 " pdb=" C GLU C 202 " ideal model delta sigma weight residual 1.521 1.503 0.017 1.36e-02 5.41e+03 1.63e+00 ... (remaining 20159 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.02: 26416 2.02 - 4.03: 686 4.03 - 6.05: 73 6.05 - 8.07: 9 8.07 - 10.08: 4 Bond angle restraints: 27188 Sorted by residual: angle pdb=" C HIS D 399 " pdb=" CA HIS D 399 " pdb=" CB HIS D 399 " ideal model delta sigma weight residual 109.68 118.94 -9.26 2.05e+00 2.38e-01 2.04e+01 angle pdb=" C HIS F 399 " pdb=" CA HIS F 399 " pdb=" CB HIS F 399 " ideal model delta sigma weight residual 109.68 118.64 -8.96 2.05e+00 2.38e-01 1.91e+01 angle pdb=" C HIS C 399 " pdb=" CA HIS C 399 " pdb=" CB HIS C 399 " ideal model delta sigma weight residual 109.68 117.92 -8.24 2.05e+00 2.38e-01 1.62e+01 angle pdb=" C SER E 93 " pdb=" N ASN E 94 " pdb=" CA ASN E 94 " ideal model delta sigma weight residual 121.54 128.78 -7.24 1.91e+00 2.74e-01 1.44e+01 angle pdb=" C SER A 93 " pdb=" N ASN A 94 " pdb=" CA ASN A 94 " ideal model delta sigma weight residual 121.54 128.51 -6.97 1.91e+00 2.74e-01 1.33e+01 ... (remaining 27183 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.71: 11343 17.71 - 35.42: 651 35.42 - 53.13: 188 53.13 - 70.84: 47 70.84 - 88.56: 8 Dihedral angle restraints: 12237 sinusoidal: 4941 harmonic: 7296 Sorted by residual: dihedral pdb=" C HIS D 399 " pdb=" N HIS D 399 " pdb=" CA HIS D 399 " pdb=" CB HIS D 399 " ideal model delta harmonic sigma weight residual -122.60 -132.08 9.48 0 2.50e+00 1.60e-01 1.44e+01 dihedral pdb=" C HIS F 399 " pdb=" N HIS F 399 " pdb=" CA HIS F 399 " pdb=" CB HIS F 399 " ideal model delta harmonic sigma weight residual -122.60 -131.58 8.98 0 2.50e+00 1.60e-01 1.29e+01 dihedral pdb=" CA LEU A 377 " pdb=" C LEU A 377 " pdb=" N TYR A 378 " pdb=" CA TYR A 378 " ideal model delta harmonic sigma weight residual 180.00 162.08 17.92 0 5.00e+00 4.00e-02 1.28e+01 ... (remaining 12234 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 2252 0.054 - 0.107: 614 0.107 - 0.161: 139 0.161 - 0.214: 8 0.214 - 0.268: 4 Chirality restraints: 3017 Sorted by residual: chirality pdb=" CB ILE B 98 " pdb=" CA ILE B 98 " pdb=" CG1 ILE B 98 " pdb=" CG2 ILE B 98 " both_signs ideal model delta sigma weight residual False 2.64 2.38 0.27 2.00e-01 2.50e+01 1.79e+00 chirality pdb=" CA HIS D 399 " pdb=" N HIS D 399 " pdb=" C HIS D 399 " pdb=" CB HIS D 399 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.37e+00 chirality pdb=" CB VAL B 233 " pdb=" CA VAL B 233 " pdb=" CG1 VAL B 233 " pdb=" CG2 VAL B 233 " both_signs ideal model delta sigma weight residual False -2.63 -2.40 -0.23 2.00e-01 2.50e+01 1.30e+00 ... (remaining 3014 not shown) Planarity restraints: 3463 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA MET F 201 " -0.033 2.00e-02 2.50e+03 6.57e-02 4.32e+01 pdb=" C MET F 201 " 0.114 2.00e-02 2.50e+03 pdb=" O MET F 201 " -0.043 2.00e-02 2.50e+03 pdb=" N GLU F 202 " -0.038 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET C 201 " 0.029 2.00e-02 2.50e+03 5.88e-02 3.45e+01 pdb=" C MET C 201 " -0.102 2.00e-02 2.50e+03 pdb=" O MET C 201 " 0.038 2.00e-02 2.50e+03 pdb=" N GLU C 202 " 0.034 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS E 317 " -0.017 2.00e-02 2.50e+03 3.53e-02 1.25e+01 pdb=" C LYS E 317 " 0.061 2.00e-02 2.50e+03 pdb=" O LYS E 317 " -0.023 2.00e-02 2.50e+03 pdb=" N ALA E 318 " -0.021 2.00e-02 2.50e+03 ... (remaining 3460 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 4589 2.79 - 3.31: 17495 3.31 - 3.84: 32619 3.84 - 4.37: 36831 4.37 - 4.90: 63354 Nonbonded interactions: 154888 Sorted by model distance: nonbonded pdb=" O SER E 328 " pdb=" OG SER E 331 " model vdw 2.257 3.040 nonbonded pdb=" O TYR C 221 " pdb=" OG1 THR C 225 " model vdw 2.278 3.040 nonbonded pdb=" OG1 THR B 41 " pdb=" O2A ATP B 501 " model vdw 2.295 3.040 nonbonded pdb=" O LEU E 411 " pdb=" OG SER E 415 " model vdw 2.298 3.040 nonbonded pdb=" O TYR B 221 " pdb=" OG1 THR B 225 " model vdw 2.299 3.040 ... (remaining 154883 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 3 through 235 or resid 248 through 260 or resid 275 throug \ h 296 or resid 299 through 342 or resid 349 through 444)) selection = (chain 'B' and (resid 3 through 158 or resid 176 through 260 or (resid 275 throu \ gh 287 and (name N or name CA or name C or name O or name CB )) or resid 296 or \ resid 299 through 342 or resid 349 through 383 or resid 389 through 444)) selection = (chain 'C' and (resid 3 through 235 or resid 248 through 260 or resid 275 throug \ h 296 or resid 299 through 383 or resid 389 through 444)) selection = (chain 'D' and (resid 3 through 158 or resid 176 through 260 or (resid 275 throu \ gh 287 and (name N or name CA or name C or name O or name CB )) or resid 298 thr \ ough 342 or resid 349 through 383 or resid 389 through 444)) selection = (chain 'E' and (resid 3 through 235 or resid 248 through 296 or resid 299 throug \ h 342 or resid 349 through 444)) selection = (chain 'F' and (resid 3 through 158 or resid 176 through 235 or resid 248 throug \ h 260 or resid 275 through 296 or resid 299 through 342 or resid 349 through 383 \ or resid 389 through 444)) } ncs_group { reference = chain 'O' selection = chain 'P' } 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: 10.510 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: 0.000 Extract box with map and model: 3.120 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 41.690 Find NCS groups from input model: 1.120 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 59.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7766 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 20164 Z= 0.297 Angle : 0.752 10.084 27188 Z= 0.436 Chirality : 0.051 0.268 3017 Planarity : 0.006 0.066 3463 Dihedral : 12.903 88.555 7483 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 5.65 % Allowed : 6.71 % Favored : 87.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.11 (0.16), residues: 2389 helix: -0.51 (0.13), residues: 1233 sheet: 0.14 (0.26), residues: 413 loop : -1.37 (0.22), residues: 743 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP D 158 HIS 0.024 0.003 HIS D 399 PHE 0.026 0.002 PHE F 100 TYR 0.018 0.002 TYR B 69 ARG 0.012 0.001 ARG F 185 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4778 Ramachandran restraints generated. 2389 Oldfield, 0 Emsley, 2389 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4778 Ramachandran restraints generated. 2389 Oldfield, 0 Emsley, 2389 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 403 residues out of total 2191 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 286 time to evaluate : 2.527 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: A 11 LEU cc_start: 0.9600 (mt) cc_final: 0.9309 (pp) REVERT: A 97 TYR cc_start: 0.8419 (p90) cc_final: 0.8109 (p90) REVERT: A 186 GLU cc_start: 0.9124 (tt0) cc_final: 0.8824 (tm-30) REVERT: A 203 ILE cc_start: 0.8784 (OUTLIER) cc_final: 0.8497 (mt) REVERT: A 204 GLU cc_start: 0.8046 (tt0) cc_final: 0.7778 (tp30) REVERT: A 312 GLN cc_start: 0.9145 (tt0) cc_final: 0.8585 (tp-100) REVERT: A 351 VAL cc_start: 0.9037 (OUTLIER) cc_final: 0.8271 (p) REVERT: A 376 MET cc_start: 0.8792 (OUTLIER) cc_final: 0.7855 (mmm) REVERT: B 87 PHE cc_start: 0.8562 (OUTLIER) cc_final: 0.8340 (t80) REVERT: B 234 PHE cc_start: 0.7822 (t80) cc_final: 0.7462 (t80) REVERT: B 280 GLU cc_start: 0.8889 (tp30) cc_final: 0.8576 (tp30) REVERT: B 315 GLN cc_start: 0.8485 (tt0) cc_final: 0.8163 (tt0) REVERT: C 106 MET cc_start: 0.9275 (mtt) cc_final: 0.8935 (tmm) REVERT: C 372 GLN cc_start: 0.8308 (OUTLIER) cc_final: 0.7101 (mp10) REVERT: C 382 LYS cc_start: 0.8677 (OUTLIER) cc_final: 0.8322 (mmtm) REVERT: D 39 LYS cc_start: 0.5366 (OUTLIER) cc_final: 0.2513 (ptpp) REVERT: D 154 MET cc_start: 0.8960 (mtt) cc_final: 0.8017 (mtp) REVERT: D 201 MET cc_start: 0.8598 (tpt) cc_final: 0.8313 (mmp) REVERT: D 326 MET cc_start: 0.9329 (mmt) cc_final: 0.8682 (mmm) REVERT: D 372 GLN cc_start: 0.8782 (OUTLIER) cc_final: 0.8229 (mm110) REVERT: D 436 MET cc_start: 0.8183 (mtp) cc_final: 0.7891 (tpp) REVERT: E 39 LYS cc_start: 0.4740 (OUTLIER) cc_final: 0.2111 (mmtp) REVERT: E 153 THR cc_start: 0.8317 (OUTLIER) cc_final: 0.7753 (m) REVERT: E 190 GLN cc_start: 0.9138 (mm-40) cc_final: 0.8351 (tp-100) REVERT: E 326 MET cc_start: 0.9146 (mmt) cc_final: 0.8874 (mmt) REVERT: E 372 GLN cc_start: 0.8991 (mm-40) cc_final: 0.8373 (mm-40) REVERT: E 437 ILE cc_start: 0.8767 (OUTLIER) cc_final: 0.8378 (pt) REVERT: F 176 TYR cc_start: 0.6297 (OUTLIER) cc_final: 0.5766 (p90) REVERT: F 326 MET cc_start: 0.9063 (mmt) cc_final: 0.8732 (mmm) REVERT: F 400 ILE cc_start: 0.9235 (OUTLIER) cc_final: 0.8892 (tp) REVERT: O 48 TYR cc_start: 0.8570 (OUTLIER) cc_final: 0.8255 (m-80) REVERT: P 78 ILE cc_start: 0.4885 (tp) cc_final: 0.3992 (tp) REVERT: P 81 LEU cc_start: 0.8371 (mt) cc_final: 0.7898 (mt) REVERT: P 90 THR cc_start: 0.8615 (p) cc_final: 0.8379 (p) outliers start: 117 outliers final: 21 residues processed: 374 average time/residue: 0.3627 time to fit residues: 199.2579 Evaluate side-chains 179 residues out of total 2191 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 144 time to evaluate : 2.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 ILE Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 351 VAL Chi-restraints excluded: chain A residue 360 TRP Chi-restraints excluded: chain A residue 376 MET Chi-restraints excluded: chain A residue 423 THR Chi-restraints excluded: chain B residue 87 PHE Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 271 TYR Chi-restraints excluded: chain B residue 375 THR Chi-restraints excluded: chain C residue 153 THR Chi-restraints excluded: chain C residue 158 TRP Chi-restraints excluded: chain C residue 176 TYR Chi-restraints excluded: chain C residue 372 GLN Chi-restraints excluded: chain C residue 382 LYS Chi-restraints excluded: chain C residue 383 MET Chi-restraints excluded: chain C residue 423 THR Chi-restraints excluded: chain D residue 39 LYS Chi-restraints excluded: chain D residue 372 GLN Chi-restraints excluded: chain E residue 39 LYS Chi-restraints excluded: chain E residue 82 ILE Chi-restraints excluded: chain E residue 153 THR Chi-restraints excluded: chain E residue 351 VAL Chi-restraints excluded: chain E residue 360 TRP Chi-restraints excluded: chain E residue 437 ILE Chi-restraints excluded: chain F residue 27 ASP Chi-restraints excluded: chain F residue 53 ASP Chi-restraints excluded: chain F residue 176 TYR Chi-restraints excluded: chain F residue 351 VAL Chi-restraints excluded: chain F residue 360 TRP Chi-restraints excluded: chain F residue 400 ILE Chi-restraints excluded: chain O residue 32 ASP Chi-restraints excluded: chain O residue 33 LEU Chi-restraints excluded: chain O residue 48 TYR Chi-restraints excluded: chain O residue 61 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 206 optimal weight: 9.9990 chunk 184 optimal weight: 7.9990 chunk 102 optimal weight: 3.9990 chunk 63 optimal weight: 4.9990 chunk 124 optimal weight: 10.0000 chunk 98 optimal weight: 7.9990 chunk 191 optimal weight: 2.9990 chunk 74 optimal weight: 3.9990 chunk 116 optimal weight: 2.9990 chunk 142 optimal weight: 9.9990 chunk 221 optimal weight: 5.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 15 HIS A 32 HIS A 94 ASN ** A 399 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 403 GLN A 413 GLN B 32 HIS B 85 GLN B 196 ASN B 413 GLN ** C 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 85 GLN C 141 GLN C 215 GLN ** C 399 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 424 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 29 ASN D 32 HIS D 35 ASN D 85 GLN E 32 HIS E 85 GLN E 141 GLN E 399 HIS F 26 ASN F 32 HIS ** F 399 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 438 ASN O 82 GLN P 13 HIS Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.080163 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.052497 restraints weight = 92865.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.054296 restraints weight = 41242.164| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.055539 restraints weight = 26034.871| |-----------------------------------------------------------------------------| r_work (final): 0.3124 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7951 moved from start: 0.2631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 20164 Z= 0.346 Angle : 0.655 11.654 27188 Z= 0.345 Chirality : 0.044 0.164 3017 Planarity : 0.005 0.059 3463 Dihedral : 8.725 77.249 2893 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 2.99 % Allowed : 11.78 % Favored : 85.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.58 (0.17), residues: 2389 helix: 1.28 (0.14), residues: 1239 sheet: -0.14 (0.26), residues: 436 loop : -0.72 (0.24), residues: 714 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP D 158 HIS 0.007 0.001 HIS D 399 PHE 0.014 0.002 PHE C 332 TYR 0.019 0.002 TYR P 86 ARG 0.012 0.001 ARG F 110 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4778 Ramachandran restraints generated. 2389 Oldfield, 0 Emsley, 2389 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4778 Ramachandran restraints generated. 2389 Oldfield, 0 Emsley, 2389 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 2191 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 154 time to evaluate : 2.326 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: A 11 LEU cc_start: 0.9597 (mt) cc_final: 0.9254 (pp) REVERT: A 97 TYR cc_start: 0.8545 (p90) cc_final: 0.8209 (p90) REVERT: A 186 GLU cc_start: 0.9160 (tt0) cc_final: 0.8946 (tm-30) REVERT: A 312 GLN cc_start: 0.9163 (tt0) cc_final: 0.8651 (tp-100) REVERT: B 87 PHE cc_start: 0.8914 (OUTLIER) cc_final: 0.8589 (t80) REVERT: B 360 TRP cc_start: 0.8465 (OUTLIER) cc_final: 0.6892 (t60) REVERT: B 376 MET cc_start: 0.9665 (OUTLIER) cc_final: 0.9463 (ttp) REVERT: C 106 MET cc_start: 0.9562 (mtt) cc_final: 0.8944 (tmm) REVERT: C 126 MET cc_start: 0.8895 (mmp) cc_final: 0.8435 (mmp) REVERT: C 372 GLN cc_start: 0.8385 (OUTLIER) cc_final: 0.6986 (mp10) REVERT: C 382 LYS cc_start: 0.9154 (OUTLIER) cc_final: 0.8777 (mptt) REVERT: D 39 LYS cc_start: 0.5168 (OUTLIER) cc_final: 0.2983 (ptpp) REVERT: D 312 GLN cc_start: 0.9812 (tt0) cc_final: 0.9542 (tm-30) REVERT: D 326 MET cc_start: 0.9387 (mmt) cc_final: 0.8855 (mmm) REVERT: D 372 GLN cc_start: 0.8667 (OUTLIER) cc_final: 0.8119 (mm110) REVERT: D 436 MET cc_start: 0.8450 (mtp) cc_final: 0.8114 (tpp) REVERT: E 39 LYS cc_start: 0.4475 (OUTLIER) cc_final: 0.2394 (mtmm) REVERT: E 154 MET cc_start: 0.9275 (ptp) cc_final: 0.8865 (ptp) REVERT: E 190 GLN cc_start: 0.8995 (mm-40) cc_final: 0.8276 (tp-100) REVERT: E 201 MET cc_start: 0.7730 (mmm) cc_final: 0.7521 (mmm) REVERT: E 210 GLU cc_start: 0.9309 (mt-10) cc_final: 0.8958 (tt0) REVERT: F 129 MET cc_start: 0.9341 (mtt) cc_final: 0.9057 (mpp) REVERT: F 176 TYR cc_start: 0.5993 (OUTLIER) cc_final: 0.4904 (p90) REVERT: F 202 GLU cc_start: 0.8571 (mt-10) cc_final: 0.8249 (tp30) REVERT: F 309 ARG cc_start: 0.9060 (mtt-85) cc_final: 0.8819 (mtt-85) REVERT: P 5 MET cc_start: 0.8023 (tpp) cc_final: 0.7514 (tmm) outliers start: 62 outliers final: 31 residues processed: 207 average time/residue: 0.3070 time to fit residues: 99.1679 Evaluate side-chains 168 residues out of total 2191 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 128 time to evaluate : 2.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 ILE Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 218 ILE Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain A residue 375 THR Chi-restraints excluded: chain A residue 376 MET Chi-restraints excluded: chain A residue 423 THR Chi-restraints excluded: chain A residue 437 ILE Chi-restraints excluded: chain B residue 55 ILE Chi-restraints excluded: chain B residue 87 PHE Chi-restraints excluded: chain B residue 88 ILE Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 360 TRP Chi-restraints excluded: chain B residue 376 MET Chi-restraints excluded: chain B residue 419 ILE Chi-restraints excluded: chain B residue 436 MET Chi-restraints excluded: chain C residue 3 ILE Chi-restraints excluded: chain C residue 153 THR Chi-restraints excluded: chain C residue 360 TRP Chi-restraints excluded: chain C residue 372 GLN Chi-restraints excluded: chain C residue 382 LYS Chi-restraints excluded: chain C residue 400 ILE Chi-restraints excluded: chain C residue 407 LEU Chi-restraints excluded: chain D residue 39 LYS Chi-restraints excluded: chain D residue 372 GLN Chi-restraints excluded: chain E residue 39 LYS Chi-restraints excluded: chain E residue 82 ILE Chi-restraints excluded: chain E residue 94 ASN Chi-restraints excluded: chain E residue 351 VAL Chi-restraints excluded: chain E residue 360 TRP Chi-restraints excluded: chain F residue 88 ILE Chi-restraints excluded: chain F residue 153 THR Chi-restraints excluded: chain F residue 176 TYR Chi-restraints excluded: chain F residue 351 VAL Chi-restraints excluded: chain F residue 400 ILE Chi-restraints excluded: chain O residue 32 ASP Chi-restraints excluded: chain O residue 39 MET Chi-restraints excluded: chain O residue 48 TYR Chi-restraints excluded: chain P residue 32 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 19 optimal weight: 3.9990 chunk 10 optimal weight: 9.9990 chunk 55 optimal weight: 0.8980 chunk 121 optimal weight: 30.0000 chunk 235 optimal weight: 40.0000 chunk 195 optimal weight: 10.0000 chunk 73 optimal weight: 1.9990 chunk 227 optimal weight: 0.9980 chunk 123 optimal weight: 6.9990 chunk 137 optimal weight: 8.9990 chunk 149 optimal weight: 9.9990 overall best weight: 2.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 399 HIS C 312 GLN ** C 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 424 HIS D 15 HIS ** F 399 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 88 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.080299 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.053038 restraints weight = 93342.520| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.054862 restraints weight = 44065.212| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 60)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.056116 restraints weight = 28359.202| |-----------------------------------------------------------------------------| r_work (final): 0.3141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8133 moved from start: 0.3106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 20164 Z= 0.275 Angle : 0.577 9.944 27188 Z= 0.304 Chirality : 0.043 0.171 3017 Planarity : 0.004 0.042 3463 Dihedral : 8.112 76.007 2864 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 3.19 % Allowed : 12.41 % Favored : 84.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.13 (0.18), residues: 2389 helix: 1.84 (0.15), residues: 1231 sheet: -0.09 (0.26), residues: 421 loop : -0.51 (0.24), residues: 737 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP D 158 HIS 0.007 0.001 HIS D 399 PHE 0.022 0.001 PHE F 230 TYR 0.020 0.002 TYR P 49 ARG 0.006 0.000 ARG O 23 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4778 Ramachandran restraints generated. 2389 Oldfield, 0 Emsley, 2389 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4778 Ramachandran restraints generated. 2389 Oldfield, 0 Emsley, 2389 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 2191 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 143 time to evaluate : 2.280 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 11 LEU cc_start: 0.9465 (mt) cc_final: 0.9217 (pp) REVERT: A 97 TYR cc_start: 0.8179 (p90) cc_final: 0.7945 (p90) REVERT: A 312 GLN cc_start: 0.8936 (tt0) cc_final: 0.8587 (tp-100) REVERT: B 87 PHE cc_start: 0.8675 (OUTLIER) cc_final: 0.8445 (t80) REVERT: B 315 GLN cc_start: 0.8826 (tt0) cc_final: 0.8559 (tt0) REVERT: B 360 TRP cc_start: 0.8555 (OUTLIER) cc_final: 0.6776 (t60) REVERT: B 376 MET cc_start: 0.9548 (OUTLIER) cc_final: 0.9318 (ttp) REVERT: C 106 MET cc_start: 0.9476 (mtt) cc_final: 0.8891 (tmm) REVERT: C 372 GLN cc_start: 0.8585 (OUTLIER) cc_final: 0.7122 (mp10) REVERT: D 39 LYS cc_start: 0.5136 (OUTLIER) cc_final: 0.2563 (ptpp) REVERT: D 129 MET cc_start: 0.8898 (mpp) cc_final: 0.8498 (mpp) REVERT: D 312 GLN cc_start: 0.9770 (tt0) cc_final: 0.9495 (tm-30) REVERT: D 326 MET cc_start: 0.9420 (mmt) cc_final: 0.8881 (mmp) REVERT: D 338 MET cc_start: 0.9127 (tpt) cc_final: 0.8380 (tpt) REVERT: D 372 GLN cc_start: 0.8715 (OUTLIER) cc_final: 0.8281 (mm110) REVERT: D 436 MET cc_start: 0.8379 (mtp) cc_final: 0.8119 (tpp) REVERT: E 39 LYS cc_start: 0.4681 (OUTLIER) cc_final: 0.2458 (mtmm) REVERT: E 154 MET cc_start: 0.9298 (ptp) cc_final: 0.8869 (ptp) REVERT: E 190 GLN cc_start: 0.8978 (mm-40) cc_final: 0.8265 (tp-100) REVERT: E 201 MET cc_start: 0.7814 (mmm) cc_final: 0.7585 (mmm) REVERT: E 210 GLU cc_start: 0.9264 (mt-10) cc_final: 0.8923 (tt0) REVERT: E 437 ILE cc_start: 0.8642 (OUTLIER) cc_final: 0.8418 (pt) REVERT: F 129 MET cc_start: 0.9207 (mtt) cc_final: 0.8998 (mpp) REVERT: F 210 GLU cc_start: 0.8941 (mm-30) cc_final: 0.8702 (tp30) REVERT: F 309 ARG cc_start: 0.9059 (mtt-85) cc_final: 0.8748 (mtt-85) REVERT: P 82 GLN cc_start: 0.8696 (mt0) cc_final: 0.8473 (mp10) outliers start: 66 outliers final: 39 residues processed: 199 average time/residue: 0.3057 time to fit residues: 96.5960 Evaluate side-chains 166 residues out of total 2191 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 119 time to evaluate : 2.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 ILE Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 218 ILE Chi-restraints excluded: chain A residue 375 THR Chi-restraints excluded: chain A residue 376 MET Chi-restraints excluded: chain A residue 423 THR Chi-restraints excluded: chain A residue 437 ILE Chi-restraints excluded: chain B residue 87 PHE Chi-restraints excluded: chain B residue 88 ILE Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 271 TYR Chi-restraints excluded: chain B residue 360 TRP Chi-restraints excluded: chain B residue 376 MET Chi-restraints excluded: chain B residue 419 ILE Chi-restraints excluded: chain B residue 423 THR Chi-restraints excluded: chain B residue 436 MET Chi-restraints excluded: chain C residue 77 ILE Chi-restraints excluded: chain C residue 153 THR Chi-restraints excluded: chain C residue 223 SER Chi-restraints excluded: chain C residue 360 TRP Chi-restraints excluded: chain C residue 372 GLN Chi-restraints excluded: chain C residue 382 LYS Chi-restraints excluded: chain C residue 400 ILE Chi-restraints excluded: chain C residue 407 LEU Chi-restraints excluded: chain D residue 39 LYS Chi-restraints excluded: chain D residue 97 TYR Chi-restraints excluded: chain D residue 231 VAL Chi-restraints excluded: chain D residue 351 VAL Chi-restraints excluded: chain D residue 372 GLN Chi-restraints excluded: chain E residue 39 LYS Chi-restraints excluded: chain E residue 82 ILE Chi-restraints excluded: chain E residue 94 ASN Chi-restraints excluded: chain E residue 351 VAL Chi-restraints excluded: chain E residue 360 TRP Chi-restraints excluded: chain E residue 437 ILE Chi-restraints excluded: chain F residue 88 ILE Chi-restraints excluded: chain F residue 153 THR Chi-restraints excluded: chain F residue 176 TYR Chi-restraints excluded: chain F residue 351 VAL Chi-restraints excluded: chain O residue 32 ASP Chi-restraints excluded: chain O residue 39 MET Chi-restraints excluded: chain O residue 48 TYR Chi-restraints excluded: chain O residue 61 ILE Chi-restraints excluded: chain P residue 32 ASP Chi-restraints excluded: chain P residue 42 ASP Chi-restraints excluded: chain P residue 61 ILE Chi-restraints excluded: chain P residue 78 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 213 optimal weight: 3.9990 chunk 116 optimal weight: 6.9990 chunk 192 optimal weight: 3.9990 chunk 112 optimal weight: 1.9990 chunk 68 optimal weight: 0.7980 chunk 77 optimal weight: 10.0000 chunk 187 optimal weight: 2.9990 chunk 200 optimal weight: 0.9990 chunk 194 optimal weight: 10.0000 chunk 236 optimal weight: 10.0000 chunk 18 optimal weight: 0.7980 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 399 HIS ** B 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 29 ASN C 32 HIS ** C 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 399 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 13 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.081061 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.054168 restraints weight = 94180.431| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.055988 restraints weight = 43585.745| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.057212 restraints weight = 27768.714| |-----------------------------------------------------------------------------| r_work (final): 0.3175 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 moved from start: 0.3304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 20164 Z= 0.175 Angle : 0.522 8.331 27188 Z= 0.276 Chirality : 0.042 0.198 3017 Planarity : 0.003 0.040 3463 Dihedral : 7.815 76.900 2862 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 2.75 % Allowed : 13.28 % Favored : 83.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.39 (0.18), residues: 2389 helix: 2.00 (0.15), residues: 1238 sheet: 0.01 (0.26), residues: 414 loop : -0.32 (0.25), residues: 737 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP D 402 HIS 0.006 0.001 HIS A 399 PHE 0.011 0.001 PHE P 11 TYR 0.016 0.001 TYR P 49 ARG 0.005 0.000 ARG C 110 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4778 Ramachandran restraints generated. 2389 Oldfield, 0 Emsley, 2389 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4778 Ramachandran restraints generated. 2389 Oldfield, 0 Emsley, 2389 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 2191 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 139 time to evaluate : 2.179 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 97 TYR cc_start: 0.8156 (p90) cc_final: 0.7955 (p90) REVERT: A 312 GLN cc_start: 0.8895 (tt0) cc_final: 0.8551 (tp-100) REVERT: A 376 MET cc_start: 0.8620 (OUTLIER) cc_final: 0.8339 (mmm) REVERT: B 204 GLU cc_start: 0.7869 (tp30) cc_final: 0.7605 (tp30) REVERT: B 315 GLN cc_start: 0.8793 (tt0) cc_final: 0.8579 (tt0) REVERT: B 360 TRP cc_start: 0.8383 (OUTLIER) cc_final: 0.6730 (t60) REVERT: C 106 MET cc_start: 0.9426 (mtt) cc_final: 0.8918 (tmm) REVERT: C 129 MET cc_start: 0.9077 (mpp) cc_final: 0.8874 (mpp) REVERT: C 372 GLN cc_start: 0.8472 (OUTLIER) cc_final: 0.7254 (mp10) REVERT: C 382 LYS cc_start: 0.9053 (OUTLIER) cc_final: 0.8620 (mmtm) REVERT: D 39 LYS cc_start: 0.5170 (OUTLIER) cc_final: 0.2834 (ptpp) REVERT: D 312 GLN cc_start: 0.9774 (tt0) cc_final: 0.9493 (tm-30) REVERT: D 338 MET cc_start: 0.9112 (tpt) cc_final: 0.8457 (ttt) REVERT: D 372 GLN cc_start: 0.8677 (OUTLIER) cc_final: 0.8247 (mm110) REVERT: D 436 MET cc_start: 0.8296 (mtp) cc_final: 0.8083 (tpp) REVERT: E 39 LYS cc_start: 0.4531 (OUTLIER) cc_final: 0.2200 (mtmm) REVERT: E 154 MET cc_start: 0.9202 (ptp) cc_final: 0.8763 (ptp) REVERT: E 190 GLN cc_start: 0.9000 (mm-40) cc_final: 0.8267 (tp-100) REVERT: E 201 MET cc_start: 0.8018 (mmm) cc_final: 0.7629 (mmp) REVERT: E 210 GLU cc_start: 0.9278 (mt-10) cc_final: 0.8922 (tt0) REVERT: E 437 ILE cc_start: 0.8493 (OUTLIER) cc_final: 0.8203 (pt) REVERT: F 210 GLU cc_start: 0.8844 (mm-30) cc_final: 0.8610 (tp30) REVERT: F 309 ARG cc_start: 0.9043 (mtt-85) cc_final: 0.8700 (mtt-85) REVERT: F 400 ILE cc_start: 0.9330 (OUTLIER) cc_final: 0.9084 (mp) REVERT: P 82 GLN cc_start: 0.8722 (mt0) cc_final: 0.8473 (mp10) outliers start: 57 outliers final: 35 residues processed: 182 average time/residue: 0.3055 time to fit residues: 88.2452 Evaluate side-chains 166 residues out of total 2191 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 122 time to evaluate : 2.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 ILE Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 218 ILE Chi-restraints excluded: chain A residue 374 LEU Chi-restraints excluded: chain A residue 375 THR Chi-restraints excluded: chain A residue 376 MET Chi-restraints excluded: chain B residue 271 TYR Chi-restraints excluded: chain B residue 360 TRP Chi-restraints excluded: chain B residue 423 THR Chi-restraints excluded: chain B residue 436 MET Chi-restraints excluded: chain C residue 3 ILE Chi-restraints excluded: chain C residue 77 ILE Chi-restraints excluded: chain C residue 153 THR Chi-restraints excluded: chain C residue 223 SER Chi-restraints excluded: chain C residue 360 TRP Chi-restraints excluded: chain C residue 372 GLN Chi-restraints excluded: chain C residue 382 LYS Chi-restraints excluded: chain C residue 400 ILE Chi-restraints excluded: chain C residue 407 LEU Chi-restraints excluded: chain D residue 39 LYS Chi-restraints excluded: chain D residue 97 TYR Chi-restraints excluded: chain D residue 231 VAL Chi-restraints excluded: chain D residue 372 GLN Chi-restraints excluded: chain E residue 39 LYS Chi-restraints excluded: chain E residue 82 ILE Chi-restraints excluded: chain E residue 94 ASN Chi-restraints excluded: chain E residue 351 VAL Chi-restraints excluded: chain E residue 360 TRP Chi-restraints excluded: chain E residue 437 ILE Chi-restraints excluded: chain F residue 88 ILE Chi-restraints excluded: chain F residue 153 THR Chi-restraints excluded: chain F residue 176 TYR Chi-restraints excluded: chain F residue 195 ILE Chi-restraints excluded: chain F residue 351 VAL Chi-restraints excluded: chain F residue 400 ILE Chi-restraints excluded: chain O residue 32 ASP Chi-restraints excluded: chain O residue 39 MET Chi-restraints excluded: chain O residue 48 TYR Chi-restraints excluded: chain O residue 61 ILE Chi-restraints excluded: chain P residue 32 ASP Chi-restraints excluded: chain P residue 42 ASP Chi-restraints excluded: chain P residue 52 ILE Chi-restraints excluded: chain P residue 78 ILE Chi-restraints excluded: chain P residue 99 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 178 optimal weight: 6.9990 chunk 169 optimal weight: 6.9990 chunk 205 optimal weight: 3.9990 chunk 165 optimal weight: 9.9990 chunk 187 optimal weight: 0.9990 chunk 206 optimal weight: 6.9990 chunk 109 optimal weight: 2.9990 chunk 57 optimal weight: 6.9990 chunk 48 optimal weight: 1.9990 chunk 147 optimal weight: 7.9990 chunk 214 optimal weight: 4.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 399 HIS ** C 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 29 ASN D 85 GLN ** D 399 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 399 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.079953 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.052717 restraints weight = 94194.424| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.054502 restraints weight = 44470.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.055644 restraints weight = 28688.067| |-----------------------------------------------------------------------------| r_work (final): 0.3130 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8172 moved from start: 0.3583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 20164 Z= 0.275 Angle : 0.572 10.078 27188 Z= 0.299 Chirality : 0.043 0.163 3017 Planarity : 0.003 0.040 3463 Dihedral : 7.785 77.723 2858 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 3.28 % Allowed : 13.38 % Favored : 83.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.40 (0.18), residues: 2389 helix: 1.98 (0.15), residues: 1236 sheet: 0.00 (0.26), residues: 416 loop : -0.26 (0.25), residues: 737 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.001 TRP D 402 HIS 0.012 0.001 HIS D 399 PHE 0.023 0.001 PHE F 230 TYR 0.013 0.001 TYR P 49 ARG 0.003 0.000 ARG C 56 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4778 Ramachandran restraints generated. 2389 Oldfield, 0 Emsley, 2389 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4778 Ramachandran restraints generated. 2389 Oldfield, 0 Emsley, 2389 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 2191 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 124 time to evaluate : 2.472 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 312 GLN cc_start: 0.8909 (tt0) cc_final: 0.8561 (tp-100) REVERT: B 315 GLN cc_start: 0.8822 (tt0) cc_final: 0.8452 (tt0) REVERT: B 360 TRP cc_start: 0.8596 (OUTLIER) cc_final: 0.6777 (t60) REVERT: B 376 MET cc_start: 0.9485 (OUTLIER) cc_final: 0.9267 (ttp) REVERT: C 106 MET cc_start: 0.9423 (mtt) cc_final: 0.8900 (tmm) REVERT: C 129 MET cc_start: 0.9031 (mpp) cc_final: 0.8755 (mpp) REVERT: C 372 GLN cc_start: 0.8609 (OUTLIER) cc_final: 0.7224 (mp10) REVERT: C 410 MET cc_start: 0.9314 (tpp) cc_final: 0.9009 (mmt) REVERT: C 413 GLN cc_start: 0.8902 (OUTLIER) cc_final: 0.8261 (tm-30) REVERT: D 39 LYS cc_start: 0.5440 (OUTLIER) cc_final: 0.1870 (mtmm) REVERT: D 312 GLN cc_start: 0.9761 (tt0) cc_final: 0.9496 (tm-30) REVERT: D 338 MET cc_start: 0.9150 (tpt) cc_final: 0.8516 (ttt) REVERT: D 372 GLN cc_start: 0.8710 (OUTLIER) cc_final: 0.8290 (mm110) REVERT: D 436 MET cc_start: 0.8326 (mtp) cc_final: 0.8110 (tpp) REVERT: E 39 LYS cc_start: 0.4683 (OUTLIER) cc_final: 0.1909 (mtmm) REVERT: E 154 MET cc_start: 0.9238 (ptp) cc_final: 0.8974 (ptp) REVERT: E 190 GLN cc_start: 0.8962 (mm-40) cc_final: 0.8241 (tp-100) REVERT: E 201 MET cc_start: 0.8103 (mmm) cc_final: 0.7710 (mmp) REVERT: E 437 ILE cc_start: 0.8555 (OUTLIER) cc_final: 0.8313 (pt) REVERT: F 186 GLU cc_start: 0.8672 (tm-30) cc_final: 0.8422 (tm-30) REVERT: F 309 ARG cc_start: 0.9072 (mtt-85) cc_final: 0.8720 (mtt-85) REVERT: F 400 ILE cc_start: 0.9368 (OUTLIER) cc_final: 0.9115 (mp) REVERT: P 82 GLN cc_start: 0.8703 (mt0) cc_final: 0.8456 (mp10) outliers start: 68 outliers final: 42 residues processed: 183 average time/residue: 0.3095 time to fit residues: 90.5970 Evaluate side-chains 167 residues out of total 2191 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 116 time to evaluate : 2.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 218 ILE Chi-restraints excluded: chain A residue 374 LEU Chi-restraints excluded: chain A residue 375 THR Chi-restraints excluded: chain A residue 376 MET Chi-restraints excluded: chain A residue 407 LEU Chi-restraints excluded: chain A residue 437 ILE Chi-restraints excluded: chain B residue 55 ILE Chi-restraints excluded: chain B residue 88 ILE Chi-restraints excluded: chain B residue 271 TYR Chi-restraints excluded: chain B residue 360 TRP Chi-restraints excluded: chain B residue 376 MET Chi-restraints excluded: chain B residue 419 ILE Chi-restraints excluded: chain B residue 423 THR Chi-restraints excluded: chain B residue 436 MET Chi-restraints excluded: chain C residue 3 ILE Chi-restraints excluded: chain C residue 77 ILE Chi-restraints excluded: chain C residue 153 THR Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 223 SER Chi-restraints excluded: chain C residue 360 TRP Chi-restraints excluded: chain C residue 372 GLN Chi-restraints excluded: chain C residue 382 LYS Chi-restraints excluded: chain C residue 400 ILE Chi-restraints excluded: chain C residue 407 LEU Chi-restraints excluded: chain C residue 413 GLN Chi-restraints excluded: chain D residue 39 LYS Chi-restraints excluded: chain D residue 97 TYR Chi-restraints excluded: chain D residue 231 VAL Chi-restraints excluded: chain D residue 351 VAL Chi-restraints excluded: chain D residue 372 GLN Chi-restraints excluded: chain E residue 39 LYS Chi-restraints excluded: chain E residue 82 ILE Chi-restraints excluded: chain E residue 94 ASN Chi-restraints excluded: chain E residue 351 VAL Chi-restraints excluded: chain E residue 360 TRP Chi-restraints excluded: chain E residue 437 ILE Chi-restraints excluded: chain F residue 88 ILE Chi-restraints excluded: chain F residue 155 LEU Chi-restraints excluded: chain F residue 176 TYR Chi-restraints excluded: chain F residue 351 VAL Chi-restraints excluded: chain F residue 400 ILE Chi-restraints excluded: chain O residue 32 ASP Chi-restraints excluded: chain O residue 39 MET Chi-restraints excluded: chain O residue 48 TYR Chi-restraints excluded: chain P residue 32 ASP Chi-restraints excluded: chain P residue 42 ASP Chi-restraints excluded: chain P residue 52 ILE Chi-restraints excluded: chain P residue 53 PHE Chi-restraints excluded: chain P residue 78 ILE Chi-restraints excluded: chain P residue 99 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 1 optimal weight: 1.9990 chunk 11 optimal weight: 0.9990 chunk 232 optimal weight: 5.9990 chunk 139 optimal weight: 9.9990 chunk 225 optimal weight: 9.9990 chunk 149 optimal weight: 6.9990 chunk 70 optimal weight: 0.8980 chunk 213 optimal weight: 5.9990 chunk 164 optimal weight: 10.0000 chunk 113 optimal weight: 0.9990 chunk 40 optimal weight: 5.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 399 HIS ** C 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 399 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 35 ASN ** F 399 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 403 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 43 ASN P 13 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.080383 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.053371 restraints weight = 92810.235| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.055110 restraints weight = 43615.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.056375 restraints weight = 28231.452| |-----------------------------------------------------------------------------| r_work (final): 0.3148 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 moved from start: 0.3716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 20164 Z= 0.215 Angle : 0.533 10.115 27188 Z= 0.280 Chirality : 0.042 0.168 3017 Planarity : 0.003 0.040 3463 Dihedral : 7.629 78.623 2856 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 3.28 % Allowed : 14.15 % Favored : 82.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.51 (0.18), residues: 2389 helix: 2.10 (0.15), residues: 1237 sheet: 0.02 (0.26), residues: 412 loop : -0.22 (0.25), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP D 402 HIS 0.009 0.001 HIS D 399 PHE 0.012 0.001 PHE F 188 TYR 0.015 0.001 TYR P 49 ARG 0.003 0.000 ARG O 23 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4778 Ramachandran restraints generated. 2389 Oldfield, 0 Emsley, 2389 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4778 Ramachandran restraints generated. 2389 Oldfield, 0 Emsley, 2389 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 2191 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 128 time to evaluate : 2.180 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 312 GLN cc_start: 0.8910 (tt0) cc_final: 0.8546 (tp-100) REVERT: B 87 PHE cc_start: 0.8640 (OUTLIER) cc_final: 0.8374 (t80) REVERT: B 315 GLN cc_start: 0.8837 (tt0) cc_final: 0.8575 (tt0) REVERT: B 360 TRP cc_start: 0.8533 (OUTLIER) cc_final: 0.6744 (t60) REVERT: C 106 MET cc_start: 0.9450 (mtt) cc_final: 0.8938 (tmm) REVERT: C 129 MET cc_start: 0.9024 (mpp) cc_final: 0.8759 (mpp) REVERT: C 152 ARG cc_start: 0.8665 (OUTLIER) cc_final: 0.8139 (ptt-90) REVERT: C 372 GLN cc_start: 0.8476 (OUTLIER) cc_final: 0.7328 (mp10) REVERT: C 410 MET cc_start: 0.9323 (tpp) cc_final: 0.9008 (mmt) REVERT: C 413 GLN cc_start: 0.8869 (OUTLIER) cc_final: 0.8269 (tm-30) REVERT: C 436 MET cc_start: 0.8966 (mmm) cc_final: 0.8714 (mmm) REVERT: D 39 LYS cc_start: 0.5371 (OUTLIER) cc_final: 0.1632 (mtmm) REVERT: D 201 MET cc_start: 0.8710 (OUTLIER) cc_final: 0.8251 (tpt) REVERT: D 312 GLN cc_start: 0.9771 (tt0) cc_final: 0.9450 (tm-30) REVERT: D 372 GLN cc_start: 0.8717 (OUTLIER) cc_final: 0.8247 (mm110) REVERT: D 436 MET cc_start: 0.8382 (mtp) cc_final: 0.8103 (tpp) REVERT: E 39 LYS cc_start: 0.4590 (OUTLIER) cc_final: 0.1661 (mtmm) REVERT: E 154 MET cc_start: 0.9183 (ptp) cc_final: 0.8914 (ptp) REVERT: E 190 GLN cc_start: 0.8978 (mm-40) cc_final: 0.8244 (tp-100) REVERT: E 201 MET cc_start: 0.8115 (mmm) cc_final: 0.7713 (mmp) REVERT: E 437 ILE cc_start: 0.8580 (OUTLIER) cc_final: 0.8333 (pt) REVERT: F 186 GLU cc_start: 0.8697 (tm-30) cc_final: 0.8440 (tm-30) REVERT: F 309 ARG cc_start: 0.9068 (mtt-85) cc_final: 0.8702 (mtt-85) REVERT: F 400 ILE cc_start: 0.9335 (OUTLIER) cc_final: 0.9091 (mp) REVERT: P 82 GLN cc_start: 0.8715 (mt0) cc_final: 0.8450 (mp10) outliers start: 68 outliers final: 40 residues processed: 183 average time/residue: 0.3119 time to fit residues: 89.6630 Evaluate side-chains 169 residues out of total 2191 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 118 time to evaluate : 2.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 THR Chi-restraints excluded: chain A residue 129 MET Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 218 ILE Chi-restraints excluded: chain A residue 374 LEU Chi-restraints excluded: chain A residue 375 THR Chi-restraints excluded: chain A residue 376 MET Chi-restraints excluded: chain B residue 55 ILE Chi-restraints excluded: chain B residue 87 PHE Chi-restraints excluded: chain B residue 88 ILE Chi-restraints excluded: chain B residue 271 TYR Chi-restraints excluded: chain B residue 360 TRP Chi-restraints excluded: chain B residue 419 ILE Chi-restraints excluded: chain B residue 423 THR Chi-restraints excluded: chain B residue 436 MET Chi-restraints excluded: chain C residue 3 ILE Chi-restraints excluded: chain C residue 152 ARG Chi-restraints excluded: chain C residue 153 THR Chi-restraints excluded: chain C residue 223 SER Chi-restraints excluded: chain C residue 360 TRP Chi-restraints excluded: chain C residue 372 GLN Chi-restraints excluded: chain C residue 382 LYS Chi-restraints excluded: chain C residue 400 ILE Chi-restraints excluded: chain C residue 407 LEU Chi-restraints excluded: chain C residue 413 GLN Chi-restraints excluded: chain D residue 39 LYS Chi-restraints excluded: chain D residue 97 TYR Chi-restraints excluded: chain D residue 201 MET Chi-restraints excluded: chain D residue 231 VAL Chi-restraints excluded: chain D residue 351 VAL Chi-restraints excluded: chain D residue 372 GLN Chi-restraints excluded: chain D residue 407 LEU Chi-restraints excluded: chain E residue 39 LYS Chi-restraints excluded: chain E residue 82 ILE Chi-restraints excluded: chain E residue 94 ASN Chi-restraints excluded: chain E residue 351 VAL Chi-restraints excluded: chain E residue 437 ILE Chi-restraints excluded: chain F residue 88 ILE Chi-restraints excluded: chain F residue 176 TYR Chi-restraints excluded: chain F residue 351 VAL Chi-restraints excluded: chain F residue 400 ILE Chi-restraints excluded: chain F residue 407 LEU Chi-restraints excluded: chain O residue 32 ASP Chi-restraints excluded: chain O residue 33 LEU Chi-restraints excluded: chain O residue 39 MET Chi-restraints excluded: chain O residue 48 TYR Chi-restraints excluded: chain P residue 32 ASP Chi-restraints excluded: chain P residue 42 ASP Chi-restraints excluded: chain P residue 52 ILE Chi-restraints excluded: chain P residue 78 ILE Chi-restraints excluded: chain P residue 99 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 222 optimal weight: 3.9990 chunk 236 optimal weight: 1.9990 chunk 226 optimal weight: 3.9990 chunk 100 optimal weight: 5.9990 chunk 44 optimal weight: 5.9990 chunk 102 optimal weight: 4.9990 chunk 93 optimal weight: 3.9990 chunk 213 optimal weight: 4.9990 chunk 231 optimal weight: 5.9990 chunk 136 optimal weight: 20.0000 chunk 178 optimal weight: 30.0000 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 399 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 399 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 403 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 424 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.079432 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.052206 restraints weight = 94775.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 59)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.053984 restraints weight = 45352.863| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 57)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.055209 restraints weight = 29502.550| |-----------------------------------------------------------------------------| r_work (final): 0.3110 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.3947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 20164 Z= 0.334 Angle : 0.605 10.920 27188 Z= 0.315 Chirality : 0.044 0.175 3017 Planarity : 0.003 0.040 3463 Dihedral : 7.731 79.754 2854 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 9.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 3.38 % Allowed : 14.39 % Favored : 82.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.32 (0.18), residues: 2389 helix: 1.91 (0.15), residues: 1245 sheet: -0.05 (0.26), residues: 424 loop : -0.28 (0.25), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP D 402 HIS 0.012 0.001 HIS A 399 PHE 0.016 0.001 PHE D 151 TYR 0.013 0.002 TYR B 18 ARG 0.007 0.000 ARG B 305 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4778 Ramachandran restraints generated. 2389 Oldfield, 0 Emsley, 2389 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4778 Ramachandran restraints generated. 2389 Oldfield, 0 Emsley, 2389 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 2191 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 116 time to evaluate : 2.362 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 312 GLN cc_start: 0.8889 (tt0) cc_final: 0.8553 (tp-100) REVERT: B 87 PHE cc_start: 0.8644 (OUTLIER) cc_final: 0.8378 (t80) REVERT: B 315 GLN cc_start: 0.8849 (tt0) cc_final: 0.8537 (tt0) REVERT: B 360 TRP cc_start: 0.8618 (OUTLIER) cc_final: 0.6702 (t60) REVERT: C 106 MET cc_start: 0.9439 (mtt) cc_final: 0.8922 (tmm) REVERT: C 129 MET cc_start: 0.9041 (mpp) cc_final: 0.8757 (mpp) REVERT: C 152 ARG cc_start: 0.8632 (OUTLIER) cc_final: 0.8190 (ptt-90) REVERT: C 372 GLN cc_start: 0.8594 (OUTLIER) cc_final: 0.7037 (mp10) REVERT: C 413 GLN cc_start: 0.8974 (OUTLIER) cc_final: 0.8314 (tm-30) REVERT: D 39 LYS cc_start: 0.5587 (OUTLIER) cc_final: 0.2024 (mtmm) REVERT: D 201 MET cc_start: 0.8729 (OUTLIER) cc_final: 0.8262 (tpt) REVERT: D 312 GLN cc_start: 0.9768 (tt0) cc_final: 0.9488 (tm-30) REVERT: D 372 GLN cc_start: 0.8744 (OUTLIER) cc_final: 0.8264 (mm110) REVERT: D 436 MET cc_start: 0.8369 (mtp) cc_final: 0.8074 (tpp) REVERT: E 39 LYS cc_start: 0.4607 (OUTLIER) cc_final: 0.1614 (mtmm) REVERT: E 152 ARG cc_start: 0.8984 (OUTLIER) cc_final: 0.8588 (ptt-90) REVERT: E 154 MET cc_start: 0.9269 (ptp) cc_final: 0.9043 (ptp) REVERT: E 190 GLN cc_start: 0.8933 (mm-40) cc_final: 0.8217 (tp-100) REVERT: E 201 MET cc_start: 0.8143 (mmm) cc_final: 0.7798 (mmm) REVERT: E 308 LEU cc_start: 0.8992 (OUTLIER) cc_final: 0.8523 (tt) REVERT: E 383 MET cc_start: 0.8553 (tmm) cc_final: 0.8187 (tmm) REVERT: E 437 ILE cc_start: 0.8567 (OUTLIER) cc_final: 0.8327 (pt) REVERT: F 186 GLU cc_start: 0.8716 (tm-30) cc_final: 0.8478 (tm-30) REVERT: F 309 ARG cc_start: 0.9079 (mtt-85) cc_final: 0.8715 (mtt-85) REVERT: F 400 ILE cc_start: 0.9385 (OUTLIER) cc_final: 0.9142 (mp) REVERT: P 82 GLN cc_start: 0.8791 (mt0) cc_final: 0.8528 (mp10) outliers start: 70 outliers final: 46 residues processed: 176 average time/residue: 0.3143 time to fit residues: 87.4671 Evaluate side-chains 169 residues out of total 2191 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 110 time to evaluate : 2.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 THR Chi-restraints excluded: chain A residue 129 MET Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 218 ILE Chi-restraints excluded: chain A residue 374 LEU Chi-restraints excluded: chain A residue 375 THR Chi-restraints excluded: chain A residue 376 MET Chi-restraints excluded: chain A residue 407 LEU Chi-restraints excluded: chain B residue 55 ILE Chi-restraints excluded: chain B residue 87 PHE Chi-restraints excluded: chain B residue 88 ILE Chi-restraints excluded: chain B residue 106 MET Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 271 TYR Chi-restraints excluded: chain B residue 360 TRP Chi-restraints excluded: chain B residue 419 ILE Chi-restraints excluded: chain B residue 423 THR Chi-restraints excluded: chain B residue 436 MET Chi-restraints excluded: chain C residue 3 ILE Chi-restraints excluded: chain C residue 152 ARG Chi-restraints excluded: chain C residue 153 THR Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 223 SER Chi-restraints excluded: chain C residue 360 TRP Chi-restraints excluded: chain C residue 372 GLN Chi-restraints excluded: chain C residue 382 LYS Chi-restraints excluded: chain C residue 400 ILE Chi-restraints excluded: chain C residue 407 LEU Chi-restraints excluded: chain C residue 413 GLN Chi-restraints excluded: chain D residue 39 LYS Chi-restraints excluded: chain D residue 97 TYR Chi-restraints excluded: chain D residue 201 MET Chi-restraints excluded: chain D residue 231 VAL Chi-restraints excluded: chain D residue 351 VAL Chi-restraints excluded: chain D residue 372 GLN Chi-restraints excluded: chain D residue 391 ILE Chi-restraints excluded: chain D residue 407 LEU Chi-restraints excluded: chain E residue 39 LYS Chi-restraints excluded: chain E residue 82 ILE Chi-restraints excluded: chain E residue 94 ASN Chi-restraints excluded: chain E residue 152 ARG Chi-restraints excluded: chain E residue 308 LEU Chi-restraints excluded: chain E residue 351 VAL Chi-restraints excluded: chain E residue 437 ILE Chi-restraints excluded: chain F residue 88 ILE Chi-restraints excluded: chain F residue 155 LEU Chi-restraints excluded: chain F residue 176 TYR Chi-restraints excluded: chain F residue 351 VAL Chi-restraints excluded: chain F residue 400 ILE Chi-restraints excluded: chain O residue 32 ASP Chi-restraints excluded: chain O residue 33 LEU Chi-restraints excluded: chain O residue 39 MET Chi-restraints excluded: chain O residue 48 TYR Chi-restraints excluded: chain P residue 32 ASP Chi-restraints excluded: chain P residue 42 ASP Chi-restraints excluded: chain P residue 52 ILE Chi-restraints excluded: chain P residue 53 PHE Chi-restraints excluded: chain P residue 78 ILE Chi-restraints excluded: chain P residue 99 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 14 optimal weight: 2.9990 chunk 143 optimal weight: 10.0000 chunk 17 optimal weight: 0.9990 chunk 6 optimal weight: 1.9990 chunk 2 optimal weight: 3.9990 chunk 134 optimal weight: 30.0000 chunk 21 optimal weight: 7.9990 chunk 105 optimal weight: 0.7980 chunk 168 optimal weight: 3.9990 chunk 172 optimal weight: 50.0000 chunk 151 optimal weight: 9.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 413 GLN ** D 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 399 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 399 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 403 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 13 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.080102 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.053079 restraints weight = 93902.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.054836 restraints weight = 44231.948| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.056062 restraints weight = 28694.338| |-----------------------------------------------------------------------------| r_work (final): 0.3145 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 moved from start: 0.3987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 20164 Z= 0.218 Angle : 0.562 9.858 27188 Z= 0.292 Chirality : 0.042 0.168 3017 Planarity : 0.003 0.042 3463 Dihedral : 7.560 80.197 2854 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 3.24 % Allowed : 14.53 % Favored : 82.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.56 (0.18), residues: 2389 helix: 2.10 (0.15), residues: 1236 sheet: 0.04 (0.26), residues: 434 loop : -0.12 (0.26), residues: 719 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP D 402 HIS 0.010 0.001 HIS A 399 PHE 0.020 0.001 PHE D 151 TYR 0.013 0.001 TYR B 18 ARG 0.006 0.000 ARG B 305 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4778 Ramachandran restraints generated. 2389 Oldfield, 0 Emsley, 2389 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4778 Ramachandran restraints generated. 2389 Oldfield, 0 Emsley, 2389 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 2191 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 120 time to evaluate : 2.243 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 312 GLN cc_start: 0.8891 (tt0) cc_final: 0.8530 (tp-100) REVERT: B 87 PHE cc_start: 0.8662 (OUTLIER) cc_final: 0.8387 (t80) REVERT: B 315 GLN cc_start: 0.8842 (tt0) cc_final: 0.8588 (tt0) REVERT: B 360 TRP cc_start: 0.8551 (OUTLIER) cc_final: 0.6746 (t60) REVERT: C 106 MET cc_start: 0.9441 (mtt) cc_final: 0.8955 (tmm) REVERT: C 129 MET cc_start: 0.9083 (mpp) cc_final: 0.8778 (mpp) REVERT: C 152 ARG cc_start: 0.8550 (OUTLIER) cc_final: 0.7951 (ptt-90) REVERT: C 372 GLN cc_start: 0.8469 (OUTLIER) cc_final: 0.7172 (mp10) REVERT: C 382 LYS cc_start: 0.9158 (OUTLIER) cc_final: 0.8627 (mmtp) REVERT: C 413 GLN cc_start: 0.8798 (OUTLIER) cc_final: 0.8219 (tm-30) REVERT: C 436 MET cc_start: 0.8985 (mmm) cc_final: 0.8772 (mmm) REVERT: D 39 LYS cc_start: 0.5489 (OUTLIER) cc_final: 0.1916 (mtmm) REVERT: D 312 GLN cc_start: 0.9780 (tt0) cc_final: 0.9490 (tm-30) REVERT: D 338 MET cc_start: 0.9207 (tpt) cc_final: 0.8514 (ttt) REVERT: D 372 GLN cc_start: 0.8641 (OUTLIER) cc_final: 0.8193 (mm110) REVERT: D 436 MET cc_start: 0.8383 (mtp) cc_final: 0.8072 (tpp) REVERT: E 39 LYS cc_start: 0.4542 (OUTLIER) cc_final: 0.1639 (mtmm) REVERT: E 152 ARG cc_start: 0.8957 (OUTLIER) cc_final: 0.8579 (ptt-90) REVERT: E 154 MET cc_start: 0.9231 (ptp) cc_final: 0.8996 (ptp) REVERT: E 190 GLN cc_start: 0.8992 (mm-40) cc_final: 0.8254 (tp-100) REVERT: E 201 MET cc_start: 0.8069 (mmm) cc_final: 0.7734 (mmm) REVERT: E 308 LEU cc_start: 0.9010 (OUTLIER) cc_final: 0.8551 (tt) REVERT: E 383 MET cc_start: 0.8583 (tmm) cc_final: 0.8237 (tmm) REVERT: E 437 ILE cc_start: 0.8587 (OUTLIER) cc_final: 0.8337 (pt) REVERT: F 186 GLU cc_start: 0.8741 (tm-30) cc_final: 0.8497 (tm-30) REVERT: F 309 ARG cc_start: 0.9070 (mtt-85) cc_final: 0.8698 (mtt-85) REVERT: F 400 ILE cc_start: 0.9337 (OUTLIER) cc_final: 0.9106 (mp) REVERT: P 82 GLN cc_start: 0.8801 (mt0) cc_final: 0.8538 (mp10) outliers start: 67 outliers final: 47 residues processed: 178 average time/residue: 0.3306 time to fit residues: 94.1095 Evaluate side-chains 174 residues out of total 2191 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 114 time to evaluate : 2.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 THR Chi-restraints excluded: chain A residue 129 MET Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 218 ILE Chi-restraints excluded: chain A residue 374 LEU Chi-restraints excluded: chain A residue 375 THR Chi-restraints excluded: chain A residue 376 MET Chi-restraints excluded: chain A residue 407 LEU Chi-restraints excluded: chain A residue 437 ILE Chi-restraints excluded: chain B residue 55 ILE Chi-restraints excluded: chain B residue 87 PHE Chi-restraints excluded: chain B residue 88 ILE Chi-restraints excluded: chain B residue 271 TYR Chi-restraints excluded: chain B residue 360 TRP Chi-restraints excluded: chain B residue 376 MET Chi-restraints excluded: chain B residue 419 ILE Chi-restraints excluded: chain B residue 423 THR Chi-restraints excluded: chain B residue 436 MET Chi-restraints excluded: chain C residue 3 ILE Chi-restraints excluded: chain C residue 152 ARG Chi-restraints excluded: chain C residue 153 THR Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 223 SER Chi-restraints excluded: chain C residue 360 TRP Chi-restraints excluded: chain C residue 372 GLN Chi-restraints excluded: chain C residue 382 LYS Chi-restraints excluded: chain C residue 400 ILE Chi-restraints excluded: chain C residue 407 LEU Chi-restraints excluded: chain C residue 413 GLN Chi-restraints excluded: chain D residue 39 LYS Chi-restraints excluded: chain D residue 97 TYR Chi-restraints excluded: chain D residue 231 VAL Chi-restraints excluded: chain D residue 351 VAL Chi-restraints excluded: chain D residue 372 GLN Chi-restraints excluded: chain D residue 391 ILE Chi-restraints excluded: chain D residue 407 LEU Chi-restraints excluded: chain E residue 35 ASN Chi-restraints excluded: chain E residue 39 LYS Chi-restraints excluded: chain E residue 82 ILE Chi-restraints excluded: chain E residue 94 ASN Chi-restraints excluded: chain E residue 152 ARG Chi-restraints excluded: chain E residue 308 LEU Chi-restraints excluded: chain E residue 351 VAL Chi-restraints excluded: chain E residue 437 ILE Chi-restraints excluded: chain F residue 88 ILE Chi-restraints excluded: chain F residue 176 TYR Chi-restraints excluded: chain F residue 351 VAL Chi-restraints excluded: chain F residue 400 ILE Chi-restraints excluded: chain F residue 407 LEU Chi-restraints excluded: chain O residue 32 ASP Chi-restraints excluded: chain O residue 33 LEU Chi-restraints excluded: chain O residue 39 MET Chi-restraints excluded: chain O residue 48 TYR Chi-restraints excluded: chain O residue 77 VAL Chi-restraints excluded: chain P residue 32 ASP Chi-restraints excluded: chain P residue 42 ASP Chi-restraints excluded: chain P residue 52 ILE Chi-restraints excluded: chain P residue 53 PHE Chi-restraints excluded: chain P residue 78 ILE Chi-restraints excluded: chain P residue 99 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 114 optimal weight: 9.9990 chunk 84 optimal weight: 8.9990 chunk 107 optimal weight: 1.9990 chunk 139 optimal weight: 9.9990 chunk 38 optimal weight: 1.9990 chunk 170 optimal weight: 20.0000 chunk 237 optimal weight: 30.0000 chunk 143 optimal weight: 9.9990 chunk 122 optimal weight: 50.0000 chunk 183 optimal weight: 3.9990 chunk 222 optimal weight: 3.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 399 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 438 ASN D 32 HIS ** D 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 399 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 399 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 403 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.078825 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.051427 restraints weight = 93035.010| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.053076 restraints weight = 45479.427| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.054136 restraints weight = 29946.055| |-----------------------------------------------------------------------------| r_work (final): 0.3098 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8222 moved from start: 0.4184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 20164 Z= 0.373 Angle : 0.661 11.059 27188 Z= 0.338 Chirality : 0.045 0.159 3017 Planarity : 0.004 0.041 3463 Dihedral : 7.810 81.014 2854 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 10.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 3.43 % Allowed : 14.39 % Favored : 82.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.26 (0.18), residues: 2389 helix: 1.83 (0.15), residues: 1247 sheet: -0.04 (0.26), residues: 429 loop : -0.27 (0.26), residues: 713 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP D 402 HIS 0.010 0.001 HIS A 399 PHE 0.027 0.001 PHE A 435 TYR 0.014 0.002 TYR B 18 ARG 0.007 0.000 ARG C 152 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4778 Ramachandran restraints generated. 2389 Oldfield, 0 Emsley, 2389 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4778 Ramachandran restraints generated. 2389 Oldfield, 0 Emsley, 2389 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 2191 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 115 time to evaluate : 2.266 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 312 GLN cc_start: 0.8892 (tt0) cc_final: 0.8657 (tp-100) REVERT: B 87 PHE cc_start: 0.8636 (OUTLIER) cc_final: 0.8372 (t80) REVERT: B 315 GLN cc_start: 0.8823 (tt0) cc_final: 0.8526 (tt0) REVERT: B 360 TRP cc_start: 0.8656 (OUTLIER) cc_final: 0.6702 (t60) REVERT: C 106 MET cc_start: 0.9413 (mtt) cc_final: 0.8917 (tmm) REVERT: C 129 MET cc_start: 0.9039 (mpp) cc_final: 0.8723 (mpp) REVERT: C 372 GLN cc_start: 0.8597 (OUTLIER) cc_final: 0.7138 (mp10) REVERT: D 39 LYS cc_start: 0.5683 (OUTLIER) cc_final: 0.2072 (mtmm) REVERT: D 154 MET cc_start: 0.9279 (mtm) cc_final: 0.8587 (mpp) REVERT: D 312 GLN cc_start: 0.9766 (tt0) cc_final: 0.9509 (tm-30) REVERT: D 372 GLN cc_start: 0.8702 (OUTLIER) cc_final: 0.8210 (mm110) REVERT: D 436 MET cc_start: 0.8338 (mtp) cc_final: 0.8053 (tpp) REVERT: E 39 LYS cc_start: 0.4785 (OUTLIER) cc_final: 0.1809 (mtmm) REVERT: E 152 ARG cc_start: 0.8958 (OUTLIER) cc_final: 0.8672 (ptt-90) REVERT: E 154 MET cc_start: 0.9268 (ptp) cc_final: 0.8986 (ptp) REVERT: E 201 MET cc_start: 0.8116 (mmm) cc_final: 0.7767 (mmm) REVERT: E 308 LEU cc_start: 0.9001 (OUTLIER) cc_final: 0.8534 (tt) REVERT: E 383 MET cc_start: 0.8733 (tmm) cc_final: 0.8403 (tmm) REVERT: E 437 ILE cc_start: 0.8586 (OUTLIER) cc_final: 0.8352 (pt) REVERT: F 186 GLU cc_start: 0.8716 (tm-30) cc_final: 0.8483 (tm-30) REVERT: F 309 ARG cc_start: 0.9078 (mtt-85) cc_final: 0.8710 (mtt-85) REVERT: F 400 ILE cc_start: 0.9395 (OUTLIER) cc_final: 0.9155 (mp) REVERT: P 82 GLN cc_start: 0.8698 (mt0) cc_final: 0.8484 (mt0) outliers start: 71 outliers final: 51 residues processed: 176 average time/residue: 0.3134 time to fit residues: 87.0453 Evaluate side-chains 173 residues out of total 2191 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 112 time to evaluate : 2.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 THR Chi-restraints excluded: chain A residue 129 MET Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 218 ILE Chi-restraints excluded: chain A residue 374 LEU Chi-restraints excluded: chain A residue 375 THR Chi-restraints excluded: chain A residue 376 MET Chi-restraints excluded: chain A residue 407 LEU Chi-restraints excluded: chain A residue 437 ILE Chi-restraints excluded: chain B residue 55 ILE Chi-restraints excluded: chain B residue 87 PHE Chi-restraints excluded: chain B residue 88 ILE Chi-restraints excluded: chain B residue 106 MET Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 271 TYR Chi-restraints excluded: chain B residue 360 TRP Chi-restraints excluded: chain B residue 419 ILE Chi-restraints excluded: chain B residue 423 THR Chi-restraints excluded: chain B residue 436 MET Chi-restraints excluded: chain C residue 152 ARG Chi-restraints excluded: chain C residue 153 THR Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 223 SER Chi-restraints excluded: chain C residue 360 TRP Chi-restraints excluded: chain C residue 372 GLN Chi-restraints excluded: chain C residue 382 LYS Chi-restraints excluded: chain C residue 400 ILE Chi-restraints excluded: chain C residue 407 LEU Chi-restraints excluded: chain D residue 39 LYS Chi-restraints excluded: chain D residue 97 TYR Chi-restraints excluded: chain D residue 231 VAL Chi-restraints excluded: chain D residue 351 VAL Chi-restraints excluded: chain D residue 372 GLN Chi-restraints excluded: chain D residue 391 ILE Chi-restraints excluded: chain D residue 407 LEU Chi-restraints excluded: chain E residue 14 ILE Chi-restraints excluded: chain E residue 35 ASN Chi-restraints excluded: chain E residue 39 LYS Chi-restraints excluded: chain E residue 82 ILE Chi-restraints excluded: chain E residue 94 ASN Chi-restraints excluded: chain E residue 152 ARG Chi-restraints excluded: chain E residue 308 LEU Chi-restraints excluded: chain E residue 351 VAL Chi-restraints excluded: chain E residue 437 ILE Chi-restraints excluded: chain F residue 88 ILE Chi-restraints excluded: chain F residue 176 TYR Chi-restraints excluded: chain F residue 187 LEU Chi-restraints excluded: chain F residue 338 MET Chi-restraints excluded: chain F residue 351 VAL Chi-restraints excluded: chain F residue 400 ILE Chi-restraints excluded: chain O residue 32 ASP Chi-restraints excluded: chain O residue 33 LEU Chi-restraints excluded: chain O residue 39 MET Chi-restraints excluded: chain O residue 48 TYR Chi-restraints excluded: chain O residue 77 VAL Chi-restraints excluded: chain P residue 32 ASP Chi-restraints excluded: chain P residue 42 ASP Chi-restraints excluded: chain P residue 52 ILE Chi-restraints excluded: chain P residue 53 PHE Chi-restraints excluded: chain P residue 78 ILE Chi-restraints excluded: chain P residue 99 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 238 optimal weight: 8.9990 chunk 186 optimal weight: 10.0000 chunk 10 optimal weight: 10.0000 chunk 58 optimal weight: 10.0000 chunk 176 optimal weight: 9.9990 chunk 126 optimal weight: 6.9990 chunk 231 optimal weight: 0.7980 chunk 102 optimal weight: 0.9990 chunk 242 optimal weight: 20.0000 chunk 138 optimal weight: 2.9990 chunk 48 optimal weight: 6.9990 overall best weight: 3.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 399 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 399 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 399 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 403 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 13 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.079122 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.052160 restraints weight = 94560.888| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.053814 restraints weight = 46564.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.054998 restraints weight = 30932.437| |-----------------------------------------------------------------------------| r_work (final): 0.3108 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 moved from start: 0.4272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 20164 Z= 0.335 Angle : 0.648 11.200 27188 Z= 0.333 Chirality : 0.044 0.244 3017 Planarity : 0.003 0.041 3463 Dihedral : 7.811 81.131 2854 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 10.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 3.19 % Allowed : 14.92 % Favored : 81.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.22 (0.18), residues: 2389 helix: 1.77 (0.15), residues: 1250 sheet: -0.02 (0.26), residues: 431 loop : -0.27 (0.26), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP D 402 HIS 0.008 0.001 HIS D 399 PHE 0.021 0.001 PHE A 435 TYR 0.015 0.002 TYR B 18 ARG 0.006 0.000 ARG C 152 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4778 Ramachandran restraints generated. 2389 Oldfield, 0 Emsley, 2389 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4778 Ramachandran restraints generated. 2389 Oldfield, 0 Emsley, 2389 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 2191 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 117 time to evaluate : 2.279 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 152 ARG cc_start: 0.8986 (OUTLIER) cc_final: 0.7877 (ptt-90) REVERT: A 154 MET cc_start: 0.8806 (mtp) cc_final: 0.8326 (mtp) REVERT: A 312 GLN cc_start: 0.8940 (tt0) cc_final: 0.8581 (tp-100) REVERT: B 87 PHE cc_start: 0.8684 (OUTLIER) cc_final: 0.8410 (t80) REVERT: B 315 GLN cc_start: 0.8889 (tt0) cc_final: 0.8604 (tt0) REVERT: B 360 TRP cc_start: 0.8660 (OUTLIER) cc_final: 0.6743 (t60) REVERT: C 106 MET cc_start: 0.9465 (mtt) cc_final: 0.8959 (tmm) REVERT: C 129 MET cc_start: 0.9076 (mpp) cc_final: 0.8755 (mpp) REVERT: D 39 LYS cc_start: 0.5703 (OUTLIER) cc_final: 0.2152 (mtmm) REVERT: D 154 MET cc_start: 0.9270 (mtm) cc_final: 0.8567 (mpp) REVERT: D 201 MET cc_start: 0.8732 (OUTLIER) cc_final: 0.8237 (tpt) REVERT: D 312 GLN cc_start: 0.9770 (tt0) cc_final: 0.9520 (tm-30) REVERT: D 338 MET cc_start: 0.9125 (tpt) cc_final: 0.8434 (ttt) REVERT: D 372 GLN cc_start: 0.8660 (OUTLIER) cc_final: 0.8158 (mm110) REVERT: D 436 MET cc_start: 0.8415 (mtp) cc_final: 0.8099 (tpp) REVERT: E 39 LYS cc_start: 0.4749 (OUTLIER) cc_final: 0.1857 (mtmm) REVERT: E 152 ARG cc_start: 0.8978 (OUTLIER) cc_final: 0.8564 (ptt-90) REVERT: E 154 MET cc_start: 0.9257 (ptp) cc_final: 0.8988 (ptp) REVERT: E 201 MET cc_start: 0.8177 (mmm) cc_final: 0.7850 (mmm) REVERT: E 308 LEU cc_start: 0.9017 (OUTLIER) cc_final: 0.8551 (tt) REVERT: E 437 ILE cc_start: 0.8552 (OUTLIER) cc_final: 0.8307 (pt) REVERT: F 186 GLU cc_start: 0.8741 (tm-30) cc_final: 0.8503 (tm-30) REVERT: F 309 ARG cc_start: 0.9071 (mtt-85) cc_final: 0.8708 (mtt-85) REVERT: F 400 ILE cc_start: 0.9378 (OUTLIER) cc_final: 0.9166 (mp) outliers start: 66 outliers final: 52 residues processed: 175 average time/residue: 0.3219 time to fit residues: 87.7605 Evaluate side-chains 175 residues out of total 2191 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 112 time to evaluate : 2.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 THR Chi-restraints excluded: chain A residue 129 MET Chi-restraints excluded: chain A residue 152 ARG Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 218 ILE Chi-restraints excluded: chain A residue 374 LEU Chi-restraints excluded: chain A residue 375 THR Chi-restraints excluded: chain A residue 376 MET Chi-restraints excluded: chain A residue 407 LEU Chi-restraints excluded: chain A residue 437 ILE Chi-restraints excluded: chain B residue 55 ILE Chi-restraints excluded: chain B residue 87 PHE Chi-restraints excluded: chain B residue 88 ILE Chi-restraints excluded: chain B residue 106 MET Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 271 TYR Chi-restraints excluded: chain B residue 360 TRP Chi-restraints excluded: chain B residue 419 ILE Chi-restraints excluded: chain B residue 423 THR Chi-restraints excluded: chain B residue 436 MET Chi-restraints excluded: chain C residue 153 THR Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 223 SER Chi-restraints excluded: chain C residue 360 TRP Chi-restraints excluded: chain C residue 372 GLN Chi-restraints excluded: chain C residue 382 LYS Chi-restraints excluded: chain C residue 400 ILE Chi-restraints excluded: chain C residue 407 LEU Chi-restraints excluded: chain D residue 25 PHE Chi-restraints excluded: chain D residue 39 LYS Chi-restraints excluded: chain D residue 97 TYR Chi-restraints excluded: chain D residue 201 MET Chi-restraints excluded: chain D residue 231 VAL Chi-restraints excluded: chain D residue 351 VAL Chi-restraints excluded: chain D residue 372 GLN Chi-restraints excluded: chain D residue 391 ILE Chi-restraints excluded: chain D residue 407 LEU Chi-restraints excluded: chain E residue 14 ILE Chi-restraints excluded: chain E residue 39 LYS Chi-restraints excluded: chain E residue 82 ILE Chi-restraints excluded: chain E residue 94 ASN Chi-restraints excluded: chain E residue 152 ARG Chi-restraints excluded: chain E residue 308 LEU Chi-restraints excluded: chain E residue 351 VAL Chi-restraints excluded: chain E residue 437 ILE Chi-restraints excluded: chain F residue 88 ILE Chi-restraints excluded: chain F residue 155 LEU Chi-restraints excluded: chain F residue 176 TYR Chi-restraints excluded: chain F residue 187 LEU Chi-restraints excluded: chain F residue 351 VAL Chi-restraints excluded: chain F residue 400 ILE Chi-restraints excluded: chain O residue 32 ASP Chi-restraints excluded: chain O residue 33 LEU Chi-restraints excluded: chain O residue 39 MET Chi-restraints excluded: chain O residue 48 TYR Chi-restraints excluded: chain O residue 77 VAL Chi-restraints excluded: chain P residue 32 ASP Chi-restraints excluded: chain P residue 42 ASP Chi-restraints excluded: chain P residue 52 ILE Chi-restraints excluded: chain P residue 53 PHE Chi-restraints excluded: chain P residue 78 ILE Chi-restraints excluded: chain P residue 99 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 31 optimal weight: 0.7980 chunk 205 optimal weight: 5.9990 chunk 40 optimal weight: 9.9990 chunk 72 optimal weight: 1.9990 chunk 159 optimal weight: 7.9990 chunk 73 optimal weight: 2.9990 chunk 60 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 240 optimal weight: 40.0000 chunk 120 optimal weight: 5.9990 chunk 74 optimal weight: 0.9980 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 413 GLN ** D 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 399 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 403 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 82 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.080355 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.053557 restraints weight = 93579.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.055335 restraints weight = 43807.997| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 58)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.056587 restraints weight = 28243.824| |-----------------------------------------------------------------------------| r_work (final): 0.3160 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8137 moved from start: 0.4262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 20164 Z= 0.185 Angle : 0.595 13.684 27188 Z= 0.302 Chirality : 0.043 0.249 3017 Planarity : 0.003 0.041 3463 Dihedral : 7.523 81.264 2854 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 2.70 % Allowed : 15.35 % Favored : 81.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.59 (0.18), residues: 2389 helix: 2.09 (0.15), residues: 1240 sheet: 0.09 (0.26), residues: 434 loop : -0.08 (0.26), residues: 715 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP D 402 HIS 0.008 0.001 HIS D 399 PHE 0.021 0.001 PHE D 151 TYR 0.014 0.001 TYR B 18 ARG 0.005 0.000 ARG B 305 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6459.67 seconds wall clock time: 117 minutes 34.83 seconds (7054.83 seconds total)