Starting phenix.real_space_refine on Wed Aug 7 13:41:36 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v45_42965/08_2024/8v45_42965.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v45_42965/08_2024/8v45_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v45_42965/08_2024/8v45_42965.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v45_42965/08_2024/8v45_42965.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v45_42965/08_2024/8v45_42965.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v45_42965/08_2024/8v45_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 Residue "B TYR 340": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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: 11.40, per 1000 atoms: 0.58 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 - 3.50 Amino acid : False - 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: 7.98 Conformation dependent library (CDL) restraints added in 3.5 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: 2.51 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: 6.59 Time building geometry restraints manager: 8.74 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: 98.39 - 106.67: 448 106.67 - 114.96: 11950 114.96 - 123.24: 13843 123.24 - 131.52: 912 131.52 - 139.80: 35 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: 1.950 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.860 Check model and map are aligned: 0.160 Set scattering table: 0.200 Process input model: 55.650 Find NCS groups from input model: 1.130 Set up NCS constraints: 0.090 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:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 62.950 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 117 poor density : 286 time to evaluate : 2.346 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: 0.3485 time to fit residues: 190.6961 Evaluate side-chains 179 residues out of total 2191 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 144 time to evaluate : 2.278 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7884 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 fitting. rotamer outliers: 62 poor density : 154 time to evaluate : 2.416 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: 0.9588 (mt) cc_final: 0.9251 (pp) REVERT: A 97 TYR cc_start: 0.8452 (p90) cc_final: 0.8131 (p90) REVERT: A 186 GLU cc_start: 0.9151 (tt0) cc_final: 0.8928 (tm-30) REVERT: A 312 GLN cc_start: 0.9145 (tt0) cc_final: 0.8625 (tp-100) REVERT: B 87 PHE cc_start: 0.8500 (OUTLIER) cc_final: 0.8286 (t80) REVERT: B 360 TRP cc_start: 0.8559 (OUTLIER) cc_final: 0.6901 (t60) REVERT: B 376 MET cc_start: 0.9602 (OUTLIER) cc_final: 0.9371 (ttp) REVERT: C 106 MET cc_start: 0.9368 (mtt) cc_final: 0.8835 (tmm) REVERT: C 126 MET cc_start: 0.8599 (mmp) cc_final: 0.8195 (mmp) REVERT: C 372 GLN cc_start: 0.8582 (OUTLIER) cc_final: 0.7064 (mp10) REVERT: C 382 LYS cc_start: 0.9128 (OUTLIER) cc_final: 0.8854 (mptt) REVERT: D 39 LYS cc_start: 0.5579 (OUTLIER) cc_final: 0.2766 (ptpp) REVERT: D 312 GLN cc_start: 0.9547 (tt0) cc_final: 0.9307 (tm-30) REVERT: D 326 MET cc_start: 0.9386 (mmt) cc_final: 0.8782 (mmm) REVERT: D 372 GLN cc_start: 0.8988 (OUTLIER) cc_final: 0.8368 (mm110) REVERT: E 39 LYS cc_start: 0.4952 (OUTLIER) cc_final: 0.2332 (mtmm) REVERT: E 154 MET cc_start: 0.9163 (ptp) cc_final: 0.8832 (ptp) REVERT: E 190 GLN cc_start: 0.9068 (mm-40) cc_final: 0.8330 (tp-100) REVERT: E 201 MET cc_start: 0.8013 (mmm) cc_final: 0.7782 (mmm) REVERT: E 210 GLU cc_start: 0.9138 (mt-10) cc_final: 0.8798 (tt0) REVERT: F 129 MET cc_start: 0.9349 (mtt) cc_final: 0.9063 (mpp) REVERT: F 176 TYR cc_start: 0.5988 (OUTLIER) cc_final: 0.4888 (p90) REVERT: F 202 GLU cc_start: 0.8563 (mt-10) cc_final: 0.8258 (tp30) REVERT: F 309 ARG cc_start: 0.9047 (mtt-85) cc_final: 0.8787 (mtt-85) REVERT: P 5 MET cc_start: 0.7543 (tpp) cc_final: 0.6989 (tmm) REVERT: P 49 TYR cc_start: 0.4963 (OUTLIER) cc_final: 0.4609 (t80) REVERT: P 88 GLN cc_start: 0.8307 (tp40) cc_final: 0.8092 (tp-100) outliers start: 62 outliers final: 31 residues processed: 207 average time/residue: 0.3003 time to fit residues: 97.1575 Evaluate side-chains 169 residues out of total 2191 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 128 time to evaluate : 2.293 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain P residue 49 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 123 optimal weight: 30.0000 chunk 68 optimal weight: 0.8980 chunk 184 optimal weight: 9.9990 chunk 150 optimal weight: 50.0000 chunk 61 optimal weight: 3.9990 chunk 221 optimal weight: 0.9980 chunk 239 optimal weight: 6.9990 chunk 197 optimal weight: 10.0000 chunk 220 optimal weight: 0.9990 chunk 75 optimal weight: 6.9990 chunk 178 optimal weight: 0.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** C 312 GLN C 413 GLN ** C 424 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 399 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7846 moved from start: 0.2952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 20164 Z= 0.179 Angle : 0.529 10.340 27188 Z= 0.279 Chirality : 0.042 0.160 3017 Planarity : 0.003 0.039 3463 Dihedral : 7.903 76.622 2864 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 3.04 % Allowed : 11.97 % Favored : 84.98 % 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: 1.24 (0.18), residues: 2389 helix: 1.91 (0.15), residues: 1232 sheet: 0.04 (0.26), residues: 417 loop : -0.51 (0.24), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 158 HIS 0.007 0.001 HIS D 399 PHE 0.022 0.001 PHE F 230 TYR 0.024 0.001 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 218 residues out of total 2191 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 155 time to evaluate : 2.636 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 97 TYR cc_start: 0.8491 (p90) cc_final: 0.8186 (p90) REVERT: A 186 GLU cc_start: 0.9139 (tt0) cc_final: 0.8876 (tm-30) REVERT: A 312 GLN cc_start: 0.9125 (tt0) cc_final: 0.8598 (tp-100) REVERT: A 376 MET cc_start: 0.8749 (OUTLIER) cc_final: 0.8128 (mmm) REVERT: B 204 GLU cc_start: 0.7960 (tp30) cc_final: 0.7710 (tp30) REVERT: B 315 GLN cc_start: 0.8807 (tt0) cc_final: 0.8507 (tt0) REVERT: B 360 TRP cc_start: 0.8334 (OUTLIER) cc_final: 0.6769 (t60) REVERT: C 106 MET cc_start: 0.9358 (mtt) cc_final: 0.8839 (tmm) REVERT: C 372 GLN cc_start: 0.8359 (OUTLIER) cc_final: 0.7245 (mp10) REVERT: C 382 LYS cc_start: 0.9073 (OUTLIER) cc_final: 0.8661 (mmtm) REVERT: C 413 GLN cc_start: 0.8722 (OUTLIER) cc_final: 0.8163 (tm-30) REVERT: D 39 LYS cc_start: 0.5405 (OUTLIER) cc_final: 0.2410 (ptpp) REVERT: D 129 MET cc_start: 0.8942 (mpp) cc_final: 0.8510 (mpp) REVERT: D 338 MET cc_start: 0.8605 (tpt) cc_final: 0.8257 (ttt) REVERT: D 372 GLN cc_start: 0.8851 (OUTLIER) cc_final: 0.8359 (mm110) REVERT: D 436 MET cc_start: 0.8016 (tpp) cc_final: 0.7708 (mmm) REVERT: E 39 LYS cc_start: 0.4808 (OUTLIER) cc_final: 0.2393 (mtmm) REVERT: E 154 MET cc_start: 0.9104 (ptp) cc_final: 0.8678 (ptp) REVERT: E 190 GLN cc_start: 0.9054 (mm-40) cc_final: 0.8368 (tp-100) REVERT: E 201 MET cc_start: 0.7995 (mmm) cc_final: 0.7734 (mmm) REVERT: E 210 GLU cc_start: 0.9143 (mt-10) cc_final: 0.8782 (tt0) REVERT: F 129 MET cc_start: 0.9337 (mtt) cc_final: 0.9077 (mpp) REVERT: F 202 GLU cc_start: 0.8463 (mt-10) cc_final: 0.8154 (tp30) REVERT: F 210 GLU cc_start: 0.9126 (mm-30) cc_final: 0.8811 (tp30) REVERT: F 309 ARG cc_start: 0.9030 (mtt-85) cc_final: 0.8714 (mtt-85) REVERT: F 326 MET cc_start: 0.8996 (mmm) cc_final: 0.8740 (mmm) REVERT: F 392 ASP cc_start: 0.8423 (t0) cc_final: 0.8191 (t0) REVERT: P 82 GLN cc_start: 0.8777 (mt0) cc_final: 0.8455 (mp10) outliers start: 63 outliers final: 32 residues processed: 207 average time/residue: 0.3086 time to fit residues: 100.3404 Evaluate side-chains 166 residues out of total 2191 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 126 time to evaluate : 2.110 ------------------------------------------------------------------------------- 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 376 MET 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 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 176 TYR 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 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 219 optimal weight: 8.9990 chunk 166 optimal weight: 10.0000 chunk 115 optimal weight: 20.0000 chunk 24 optimal weight: 10.0000 chunk 105 optimal weight: 0.7980 chunk 149 optimal weight: 20.0000 chunk 222 optimal weight: 0.7980 chunk 235 optimal weight: 30.0000 chunk 116 optimal weight: 10.0000 chunk 211 optimal weight: 10.0000 chunk 63 optimal weight: 2.9990 overall best weight: 4.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 399 HIS C 32 HIS ** 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 15 HIS D 29 ASN ** D 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 399 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 399 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7932 moved from start: 0.3550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 20164 Z= 0.406 Angle : 0.669 13.001 27188 Z= 0.348 Chirality : 0.045 0.209 3017 Planarity : 0.004 0.042 3463 Dihedral : 8.209 77.794 2859 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 11.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 3.33 % Allowed : 13.23 % Favored : 83.44 % 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 (0.18), residues: 2389 helix: 1.76 (0.15), residues: 1238 sheet: -0.14 (0.26), residues: 429 loop : -0.38 (0.25), residues: 722 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP D 402 HIS 0.009 0.001 HIS D 399 PHE 0.018 0.002 PHE C 332 TYR 0.021 0.002 TYR P 49 ARG 0.005 0.001 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 195 residues out of total 2191 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 126 time to evaluate : 2.288 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 97 TYR cc_start: 0.8494 (p90) cc_final: 0.8207 (p90) REVERT: A 186 GLU cc_start: 0.9173 (tt0) cc_final: 0.8900 (tm-30) REVERT: A 312 GLN cc_start: 0.9143 (tt0) cc_final: 0.8601 (tp-100) REVERT: B 315 GLN cc_start: 0.8935 (tt0) cc_final: 0.8548 (tt0) REVERT: B 360 TRP cc_start: 0.8682 (OUTLIER) cc_final: 0.6803 (t60) REVERT: C 106 MET cc_start: 0.9353 (mtt) cc_final: 0.8810 (tmm) REVERT: C 372 GLN cc_start: 0.8671 (OUTLIER) cc_final: 0.7112 (mp10) REVERT: D 39 LYS cc_start: 0.5970 (OUTLIER) cc_final: 0.2879 (ptpp) REVERT: D 338 MET cc_start: 0.8686 (tpt) cc_final: 0.8325 (ttt) REVERT: D 372 GLN cc_start: 0.8949 (OUTLIER) cc_final: 0.8406 (mm110) REVERT: D 436 MET cc_start: 0.8136 (tpp) cc_final: 0.7714 (mmm) REVERT: E 39 LYS cc_start: 0.4877 (OUTLIER) cc_final: 0.1922 (mtmm) REVERT: E 154 MET cc_start: 0.9214 (ptp) cc_final: 0.8929 (ptp) REVERT: E 201 MET cc_start: 0.8169 (mmm) cc_final: 0.7789 (mmp) REVERT: F 129 MET cc_start: 0.9332 (mtt) cc_final: 0.9076 (mpp) REVERT: F 202 GLU cc_start: 0.8575 (mt-10) cc_final: 0.8172 (tp30) REVERT: F 309 ARG cc_start: 0.9074 (mtt-85) cc_final: 0.8751 (mtt-85) REVERT: F 326 MET cc_start: 0.8954 (mmm) cc_final: 0.8722 (mmm) REVERT: F 392 ASP cc_start: 0.8623 (t0) cc_final: 0.8393 (t0) REVERT: P 13 HIS cc_start: 0.6395 (t-90) cc_final: 0.6189 (t-170) REVERT: P 82 GLN cc_start: 0.8878 (mt0) cc_final: 0.8508 (mp10) outliers start: 69 outliers final: 42 residues processed: 184 average time/residue: 0.3008 time to fit residues: 88.4174 Evaluate side-chains 164 residues out of total 2191 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 117 time to evaluate : 2.467 ------------------------------------------------------------------------------- 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 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 136 LYS Chi-restraints excluded: chain B residue 203 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 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 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 F residue 88 ILE Chi-restraints excluded: chain F residue 176 TYR Chi-restraints excluded: chain F residue 203 ILE Chi-restraints excluded: chain F residue 351 VAL 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 49 TYR Chi-restraints excluded: chain P residue 61 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 196 optimal weight: 6.9990 chunk 133 optimal weight: 8.9990 chunk 3 optimal weight: 4.9990 chunk 175 optimal weight: 10.0000 chunk 97 optimal weight: 5.9990 chunk 201 optimal weight: 0.9990 chunk 163 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 120 optimal weight: 30.0000 chunk 211 optimal weight: 8.9990 chunk 59 optimal weight: 1.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 399 HIS ** 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 85 GLN ** D 399 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 399 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 413 GLN O 43 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 moved from start: 0.3821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 20164 Z= 0.366 Angle : 0.628 12.055 27188 Z= 0.326 Chirality : 0.044 0.181 3017 Planarity : 0.004 0.044 3463 Dihedral : 8.117 79.031 2856 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 10.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 3.52 % Allowed : 14.20 % Favored : 82.28 % 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 (0.18), residues: 2389 helix: 1.71 (0.15), residues: 1242 sheet: -0.11 (0.26), residues: 430 loop : -0.33 (0.26), residues: 717 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP D 402 HIS 0.007 0.001 HIS A 399 PHE 0.012 0.001 PHE C 332 TYR 0.015 0.002 TYR B 18 ARG 0.004 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 194 residues out of total 2191 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 121 time to evaluate : 2.416 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: A 97 TYR cc_start: 0.8446 (p90) cc_final: 0.8178 (p90) REVERT: A 312 GLN cc_start: 0.9157 (tt0) cc_final: 0.8695 (tp-100) REVERT: B 87 PHE cc_start: 0.8567 (OUTLIER) cc_final: 0.8334 (t80) REVERT: B 315 GLN cc_start: 0.8943 (tt0) cc_final: 0.8624 (tt0) REVERT: B 360 TRP cc_start: 0.8678 (OUTLIER) cc_final: 0.6720 (t60) REVERT: C 106 MET cc_start: 0.9352 (mtt) cc_final: 0.8828 (tmm) REVERT: C 382 LYS cc_start: 0.9263 (OUTLIER) cc_final: 0.8846 (mmtm) REVERT: D 39 LYS cc_start: 0.6015 (OUTLIER) cc_final: 0.1591 (mtmm) REVERT: D 338 MET cc_start: 0.8698 (tpt) cc_final: 0.8337 (ttt) REVERT: D 436 MET cc_start: 0.8142 (tpp) cc_final: 0.7635 (mmm) REVERT: E 39 LYS cc_start: 0.5252 (OUTLIER) cc_final: 0.2417 (ptpp) REVERT: E 201 MET cc_start: 0.8260 (mmm) cc_final: 0.7911 (mmm) REVERT: E 308 LEU cc_start: 0.9029 (OUTLIER) cc_final: 0.8558 (tt) REVERT: F 186 GLU cc_start: 0.8989 (tm-30) cc_final: 0.8696 (tm-30) REVERT: F 202 GLU cc_start: 0.8631 (mt-10) cc_final: 0.8155 (tp30) REVERT: F 309 ARG cc_start: 0.9084 (mtt-85) cc_final: 0.8756 (mtt-85) REVERT: F 326 MET cc_start: 0.8932 (mmm) cc_final: 0.8657 (mmm) REVERT: F 338 MET cc_start: 0.9386 (ttp) cc_final: 0.8788 (ttp) REVERT: F 392 ASP cc_start: 0.8599 (t0) cc_final: 0.8362 (t0) REVERT: F 400 ILE cc_start: 0.9378 (OUTLIER) cc_final: 0.9142 (mp) outliers start: 73 outliers final: 42 residues processed: 186 average time/residue: 0.2957 time to fit residues: 86.9308 Evaluate side-chains 165 residues out of total 2191 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 116 time to evaluate : 2.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 THR 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 407 LEU 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 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 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 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 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 308 LEU 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 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 49 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 79 optimal weight: 0.9990 chunk 212 optimal weight: 7.9990 chunk 46 optimal weight: 4.9990 chunk 138 optimal weight: 5.9990 chunk 58 optimal weight: 9.9990 chunk 236 optimal weight: 10.0000 chunk 195 optimal weight: 0.0040 chunk 109 optimal weight: 8.9990 chunk 19 optimal weight: 3.9990 chunk 78 optimal weight: 0.8980 chunk 123 optimal weight: 8.9990 overall best weight: 2.1798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 399 HIS ** C 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 424 HIS ** D 399 HIS ** 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 P 88 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7894 moved from start: 0.3889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 20164 Z= 0.221 Angle : 0.553 9.498 27188 Z= 0.290 Chirality : 0.043 0.169 3017 Planarity : 0.003 0.041 3463 Dihedral : 7.682 79.202 2850 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 3.24 % Allowed : 14.82 % 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: 1.33 (0.18), residues: 2389 helix: 1.94 (0.15), residues: 1241 sheet: -0.04 (0.26), residues: 423 loop : -0.30 (0.25), residues: 725 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP D 402 HIS 0.005 0.001 HIS A 399 PHE 0.011 0.001 PHE F 188 TYR 0.015 0.001 TYR P 49 ARG 0.009 0.000 ARG B 305 *********************** 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 194 residues out of total 2191 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 127 time to evaluate : 2.538 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 97 TYR cc_start: 0.8462 (p90) cc_final: 0.8225 (p90) REVERT: A 186 GLU cc_start: 0.9165 (tt0) cc_final: 0.8890 (tm-30) REVERT: A 312 GLN cc_start: 0.9126 (tt0) cc_final: 0.8571 (tp-100) REVERT: B 315 GLN cc_start: 0.8916 (tt0) cc_final: 0.8607 (tt0) REVERT: B 360 TRP cc_start: 0.8594 (OUTLIER) cc_final: 0.6727 (t60) REVERT: C 106 MET cc_start: 0.9354 (mtt) cc_final: 0.8883 (tmm) REVERT: C 152 ARG cc_start: 0.8620 (OUTLIER) cc_final: 0.7974 (ptt-90) REVERT: C 382 LYS cc_start: 0.9202 (OUTLIER) cc_final: 0.8798 (mmtm) REVERT: D 39 LYS cc_start: 0.5848 (OUTLIER) cc_final: 0.1279 (mtmm) REVERT: D 201 MET cc_start: 0.8641 (OUTLIER) cc_final: 0.8051 (tpt) REVERT: D 338 MET cc_start: 0.8703 (tpt) cc_final: 0.8379 (ttt) REVERT: D 436 MET cc_start: 0.8195 (tpp) cc_final: 0.7565 (mmm) REVERT: E 39 LYS cc_start: 0.5180 (OUTLIER) cc_final: 0.2408 (ptpp) REVERT: E 152 ARG cc_start: 0.8845 (OUTLIER) cc_final: 0.8486 (ptt-90) REVERT: E 190 GLN cc_start: 0.9039 (mm-40) cc_final: 0.8296 (tp-100) REVERT: E 201 MET cc_start: 0.8214 (mmm) cc_final: 0.7869 (mmm) REVERT: E 383 MET cc_start: 0.8168 (tmm) cc_final: 0.7763 (tmm) REVERT: F 186 GLU cc_start: 0.8977 (tm-30) cc_final: 0.8675 (tm-30) REVERT: F 202 GLU cc_start: 0.8486 (mt-10) cc_final: 0.8127 (tp30) REVERT: F 309 ARG cc_start: 0.9063 (mtt-85) cc_final: 0.8724 (mtt-85) REVERT: F 326 MET cc_start: 0.8953 (mmm) cc_final: 0.8658 (mmm) REVERT: F 338 MET cc_start: 0.9268 (ttp) cc_final: 0.8664 (ttp) REVERT: F 392 ASP cc_start: 0.8552 (t0) cc_final: 0.8288 (t0) REVERT: F 400 ILE cc_start: 0.9327 (OUTLIER) cc_final: 0.9100 (mp) REVERT: P 82 GLN cc_start: 0.8837 (mt0) cc_final: 0.8486 (mt0) outliers start: 67 outliers final: 44 residues processed: 182 average time/residue: 0.3045 time to fit residues: 87.4689 Evaluate side-chains 170 residues out of total 2191 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 118 time to evaluate : 2.306 ------------------------------------------------------------------------------- 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 234 PHE 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 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 201 MET Chi-restraints excluded: chain D residue 231 VAL Chi-restraints excluded: chain D residue 351 VAL 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 351 VAL 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 195 ILE Chi-restraints excluded: chain F residue 203 ILE 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 39 MET Chi-restraints excluded: chain O residue 48 TYR Chi-restraints excluded: chain O residue 77 VAL Chi-restraints excluded: chain P residue 42 ASP Chi-restraints excluded: chain P residue 49 TYR 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 227 optimal weight: 10.0000 chunk 26 optimal weight: 4.9990 chunk 134 optimal weight: 20.0000 chunk 172 optimal weight: 50.0000 chunk 133 optimal weight: 8.9990 chunk 198 optimal weight: 9.9990 chunk 131 optimal weight: 6.9990 chunk 235 optimal weight: 40.0000 chunk 147 optimal weight: 5.9990 chunk 143 optimal weight: 10.0000 chunk 108 optimal weight: 5.9990 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 286 ASN ** E 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 399 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 424 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 moved from start: 0.4360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.069 20164 Z= 0.558 Angle : 0.769 14.271 27188 Z= 0.397 Chirality : 0.048 0.176 3017 Planarity : 0.004 0.042 3463 Dihedral : 8.203 80.296 2848 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 13.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 3.81 % Allowed : 14.44 % Favored : 81.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.67 (0.18), residues: 2389 helix: 1.34 (0.15), residues: 1253 sheet: -0.19 (0.26), residues: 418 loop : -0.63 (0.25), residues: 718 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 360 HIS 0.016 0.002 HIS A 399 PHE 0.020 0.002 PHE A 435 TYR 0.017 0.002 TYR C 314 ARG 0.009 0.001 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 192 residues out of total 2191 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 113 time to evaluate : 2.335 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 11 LEU cc_start: 0.9592 (OUTLIER) cc_final: 0.9115 (pp) REVERT: A 97 TYR cc_start: 0.8368 (p90) cc_final: 0.8142 (p90) REVERT: A 152 ARG cc_start: 0.8947 (OUTLIER) cc_final: 0.7726 (ptt-90) REVERT: A 312 GLN cc_start: 0.9235 (tt0) cc_final: 0.8696 (tp-100) REVERT: B 315 GLN cc_start: 0.9044 (tt0) cc_final: 0.8685 (tt0) REVERT: B 360 TRP cc_start: 0.8736 (OUTLIER) cc_final: 0.6929 (t60) REVERT: C 106 MET cc_start: 0.9385 (mtt) cc_final: 0.8830 (tmm) REVERT: C 152 ARG cc_start: 0.8620 (OUTLIER) cc_final: 0.7920 (ptt-90) REVERT: C 154 MET cc_start: 0.9362 (mtt) cc_final: 0.9096 (mtt) REVERT: C 326 MET cc_start: 0.8918 (tpp) cc_final: 0.8671 (tpp) REVERT: D 39 LYS cc_start: 0.6147 (OUTLIER) cc_final: 0.2209 (mtmm) REVERT: D 201 MET cc_start: 0.8659 (OUTLIER) cc_final: 0.8112 (tpt) REVERT: D 436 MET cc_start: 0.8300 (tpp) cc_final: 0.7472 (mmt) REVERT: E 39 LYS cc_start: 0.5452 (OUTLIER) cc_final: 0.2482 (mtmm) REVERT: E 201 MET cc_start: 0.8266 (mmm) cc_final: 0.7921 (mmm) REVERT: E 210 GLU cc_start: 0.9328 (mt-10) cc_final: 0.9031 (tt0) REVERT: E 383 MET cc_start: 0.8426 (tmm) cc_final: 0.7945 (tmm) REVERT: F 186 GLU cc_start: 0.9045 (tm-30) cc_final: 0.8750 (tm-30) REVERT: F 202 GLU cc_start: 0.8711 (mt-10) cc_final: 0.8472 (tp30) REVERT: P 27 ILE cc_start: 0.4199 (OUTLIER) cc_final: 0.3987 (tp) REVERT: P 82 GLN cc_start: 0.8922 (mt0) cc_final: 0.8538 (mt0) outliers start: 79 outliers final: 54 residues processed: 178 average time/residue: 0.3052 time to fit residues: 85.0351 Evaluate side-chains 170 residues out of total 2191 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 108 time to evaluate : 2.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 THR Chi-restraints excluded: chain A residue 11 LEU 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 407 LEU 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 88 ILE Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 218 ILE Chi-restraints excluded: chain B residue 234 PHE 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 55 ILE Chi-restraints excluded: chain C residue 77 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 396 ILE Chi-restraints excluded: chain C residue 407 LEU Chi-restraints excluded: chain C residue 423 THR 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 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 351 VAL 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 5 MET 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 61 ILE Chi-restraints excluded: chain O residue 63 LEU Chi-restraints excluded: chain O residue 77 VAL Chi-restraints excluded: chain P residue 27 ILE Chi-restraints excluded: chain P residue 42 ASP 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 145 optimal weight: 9.9990 chunk 93 optimal weight: 0.5980 chunk 140 optimal weight: 20.0000 chunk 70 optimal weight: 0.7980 chunk 46 optimal weight: 2.9990 chunk 45 optimal weight: 5.9990 chunk 149 optimal weight: 4.9990 chunk 160 optimal weight: 30.0000 chunk 116 optimal weight: 9.9990 chunk 21 optimal weight: 5.9990 chunk 184 optimal weight: 0.3980 overall best weight: 1.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 399 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 286 ASN ** 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 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7894 moved from start: 0.4251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 20164 Z= 0.209 Angle : 0.572 10.178 27188 Z= 0.298 Chirality : 0.043 0.218 3017 Planarity : 0.003 0.044 3463 Dihedral : 7.660 80.070 2848 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 2.51 % Allowed : 16.18 % Favored : 81.31 % 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: 1.27 (0.18), residues: 2389 helix: 1.88 (0.15), residues: 1240 sheet: -0.08 (0.26), residues: 421 loop : -0.29 (0.25), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP D 402 HIS 0.010 0.001 HIS A 399 PHE 0.016 0.001 PHE A 435 TYR 0.015 0.001 TYR P 49 ARG 0.008 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 175 residues out of total 2191 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 123 time to evaluate : 2.346 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 97 TYR cc_start: 0.8331 (p90) cc_final: 0.8124 (p90) REVERT: A 186 GLU cc_start: 0.9168 (tt0) cc_final: 0.8883 (tm-30) REVERT: A 312 GLN cc_start: 0.9101 (tt0) cc_final: 0.8637 (tp-100) REVERT: B 315 GLN cc_start: 0.8890 (tt0) cc_final: 0.8599 (tt0) REVERT: B 360 TRP cc_start: 0.8530 (OUTLIER) cc_final: 0.6629 (t60) REVERT: C 106 MET cc_start: 0.9351 (mtt) cc_final: 0.8888 (tmm) REVERT: C 382 LYS cc_start: 0.9228 (OUTLIER) cc_final: 0.8658 (mmtp) REVERT: D 39 LYS cc_start: 0.5959 (OUTLIER) cc_final: 0.1978 (mtmm) REVERT: D 201 MET cc_start: 0.8633 (OUTLIER) cc_final: 0.7989 (tpt) REVERT: D 338 MET cc_start: 0.8518 (tpt) cc_final: 0.8229 (ttt) REVERT: D 436 MET cc_start: 0.8368 (tpp) cc_final: 0.7471 (mmm) REVERT: E 39 LYS cc_start: 0.5323 (OUTLIER) cc_final: 0.2271 (mtmm) REVERT: E 152 ARG cc_start: 0.8822 (OUTLIER) cc_final: 0.8321 (ptt-90) REVERT: E 154 MET cc_start: 0.8957 (ttp) cc_final: 0.8564 (ppp) REVERT: E 201 MET cc_start: 0.8285 (mmm) cc_final: 0.7955 (mmm) REVERT: E 210 GLU cc_start: 0.9256 (mt-10) cc_final: 0.8945 (tt0) REVERT: F 186 GLU cc_start: 0.8995 (tm-30) cc_final: 0.8698 (tm-30) REVERT: F 202 GLU cc_start: 0.8503 (mt-10) cc_final: 0.8056 (tp30) REVERT: F 392 ASP cc_start: 0.8610 (t0) cc_final: 0.8309 (t0) REVERT: P 82 GLN cc_start: 0.8789 (mt0) cc_final: 0.8473 (mt0) outliers start: 52 outliers final: 35 residues processed: 164 average time/residue: 0.2998 time to fit residues: 78.2327 Evaluate side-chains 156 residues out of total 2191 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 115 time to evaluate : 2.307 ------------------------------------------------------------------------------- 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 374 LEU Chi-restraints excluded: chain A residue 376 MET 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 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 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 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 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 351 VAL Chi-restraints excluded: chain F residue 88 ILE Chi-restraints excluded: chain F residue 176 TYR Chi-restraints excluded: chain F residue 203 ILE Chi-restraints excluded: chain F residue 351 VAL Chi-restraints excluded: chain F residue 407 LEU 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 42 ASP 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 213 optimal weight: 4.9990 chunk 225 optimal weight: 9.9990 chunk 205 optimal weight: 5.9990 chunk 219 optimal weight: 2.9990 chunk 131 optimal weight: 3.9990 chunk 95 optimal weight: 8.9990 chunk 172 optimal weight: 20.0000 chunk 67 optimal weight: 0.5980 chunk 198 optimal weight: 10.0000 chunk 207 optimal weight: 9.9990 chunk 218 optimal weight: 0.7980 overall best weight: 2.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7909 moved from start: 0.4329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 20164 Z= 0.259 Angle : 0.604 11.555 27188 Z= 0.310 Chirality : 0.043 0.237 3017 Planarity : 0.003 0.042 3463 Dihedral : 7.599 80.196 2848 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 2.66 % Allowed : 16.08 % Favored : 81.27 % 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: 1.29 (0.18), residues: 2389 helix: 1.91 (0.15), residues: 1240 sheet: -0.09 (0.26), residues: 424 loop : -0.31 (0.25), residues: 725 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 402 HIS 0.010 0.001 HIS A 399 PHE 0.017 0.001 PHE A 435 TYR 0.013 0.001 TYR P 49 ARG 0.009 0.000 ARG F 224 *********************** 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 174 residues out of total 2191 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 119 time to evaluate : 2.396 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 97 TYR cc_start: 0.8348 (p90) cc_final: 0.8147 (p90) REVERT: A 152 ARG cc_start: 0.8861 (OUTLIER) cc_final: 0.7771 (ptt-90) REVERT: A 154 MET cc_start: 0.8959 (mtp) cc_final: 0.8336 (mtp) REVERT: A 186 GLU cc_start: 0.9170 (tt0) cc_final: 0.8873 (tm-30) REVERT: A 312 GLN cc_start: 0.9116 (tt0) cc_final: 0.8696 (tp-100) REVERT: B 315 GLN cc_start: 0.8907 (tt0) cc_final: 0.8600 (tt0) REVERT: B 360 TRP cc_start: 0.8640 (OUTLIER) cc_final: 0.6694 (t60) REVERT: C 382 LYS cc_start: 0.9225 (OUTLIER) cc_final: 0.8676 (mmtp) REVERT: D 39 LYS cc_start: 0.6057 (OUTLIER) cc_final: 0.2131 (mtmm) REVERT: D 201 MET cc_start: 0.8621 (OUTLIER) cc_final: 0.8008 (tpt) REVERT: D 338 MET cc_start: 0.8582 (tpt) cc_final: 0.8245 (ttt) REVERT: D 383 MET cc_start: 0.8589 (tpt) cc_final: 0.8310 (tpt) REVERT: D 436 MET cc_start: 0.8418 (tpp) cc_final: 0.7460 (mmm) REVERT: E 39 LYS cc_start: 0.5387 (OUTLIER) cc_final: 0.2372 (mtmm) REVERT: E 152 ARG cc_start: 0.8823 (OUTLIER) cc_final: 0.8547 (ptt-90) REVERT: E 154 MET cc_start: 0.8969 (ttp) cc_final: 0.8571 (ppp) REVERT: E 201 MET cc_start: 0.8298 (mmm) cc_final: 0.7968 (mmm) REVERT: E 210 GLU cc_start: 0.9280 (mt-10) cc_final: 0.8962 (tt0) REVERT: E 383 MET cc_start: 0.8438 (tmm) cc_final: 0.7907 (tmm) REVERT: F 186 GLU cc_start: 0.9017 (tm-30) cc_final: 0.8723 (tm-30) REVERT: F 202 GLU cc_start: 0.8528 (mt-10) cc_final: 0.8089 (tp30) REVERT: F 392 ASP cc_start: 0.8628 (t0) cc_final: 0.8320 (t0) outliers start: 55 outliers final: 42 residues processed: 165 average time/residue: 0.3111 time to fit residues: 80.5262 Evaluate side-chains 164 residues out of total 2191 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 115 time to evaluate : 2.310 ------------------------------------------------------------------------------- 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 376 MET Chi-restraints excluded: chain A residue 407 LEU Chi-restraints excluded: chain A residue 423 THR 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 423 THR Chi-restraints excluded: chain B residue 436 MET Chi-restraints excluded: chain C residue 77 ILE Chi-restraints excluded: chain C residue 129 MET 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 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 351 VAL 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 195 ILE Chi-restraints excluded: chain F residue 203 ILE Chi-restraints excluded: chain F residue 351 VAL Chi-restraints excluded: chain F residue 407 LEU 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 27 ILE Chi-restraints excluded: chain P residue 42 ASP 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 143 optimal weight: 3.9990 chunk 231 optimal weight: 2.9990 chunk 141 optimal weight: 0.4980 chunk 109 optimal weight: 0.8980 chunk 161 optimal weight: 40.0000 chunk 243 optimal weight: 9.9990 chunk 223 optimal weight: 0.8980 chunk 193 optimal weight: 9.9990 chunk 20 optimal weight: 5.9990 chunk 149 optimal weight: 0.3980 chunk 118 optimal weight: 10.0000 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 413 GLN ** 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 29 ASN ** 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7864 moved from start: 0.4344 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= 0.166 Angle : 0.581 11.347 27188 Z= 0.296 Chirality : 0.042 0.259 3017 Planarity : 0.003 0.041 3463 Dihedral : 7.272 80.077 2847 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 1.98 % Allowed : 16.90 % Favored : 81.12 % 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: 2.13 (0.15), residues: 1232 sheet: 0.03 (0.26), residues: 431 loop : -0.09 (0.26), residues: 726 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 402 HIS 0.008 0.001 HIS A 399 PHE 0.015 0.001 PHE A 435 TYR 0.012 0.001 TYR D 97 ARG 0.008 0.000 ARG F 224 ********************** 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 160 residues out of total 2191 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 119 time to evaluate : 2.354 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 152 ARG cc_start: 0.8764 (OUTLIER) cc_final: 0.7837 (ptt-90) REVERT: A 154 MET cc_start: 0.8761 (mtp) cc_final: 0.8029 (mtp) REVERT: A 186 GLU cc_start: 0.9162 (tt0) cc_final: 0.8869 (tm-30) REVERT: B 315 GLN cc_start: 0.8836 (tt0) cc_final: 0.8623 (tt0) REVERT: B 326 MET cc_start: 0.8773 (mmm) cc_final: 0.8352 (mmm) REVERT: B 360 TRP cc_start: 0.8496 (OUTLIER) cc_final: 0.6660 (t60) REVERT: C 382 LYS cc_start: 0.9142 (OUTLIER) cc_final: 0.8567 (mmtp) REVERT: D 39 LYS cc_start: 0.5885 (OUTLIER) cc_final: 0.1688 (mtmm) REVERT: D 338 MET cc_start: 0.8544 (tpt) cc_final: 0.8263 (ttt) REVERT: E 39 LYS cc_start: 0.5288 (OUTLIER) cc_final: 0.2182 (mtmm) REVERT: E 154 MET cc_start: 0.8937 (ttp) cc_final: 0.8545 (ppp) REVERT: E 190 GLN cc_start: 0.9075 (mm-40) cc_final: 0.8321 (tp-100) REVERT: E 201 MET cc_start: 0.8341 (mmm) cc_final: 0.7988 (mmm) REVERT: E 210 GLU cc_start: 0.9233 (mt-10) cc_final: 0.8933 (tt0) REVERT: E 383 MET cc_start: 0.8298 (tmm) cc_final: 0.7958 (tmm) REVERT: F 186 GLU cc_start: 0.9024 (tm-30) cc_final: 0.8756 (tm-30) REVERT: F 202 GLU cc_start: 0.8418 (mt-10) cc_final: 0.8018 (tp30) REVERT: F 392 ASP cc_start: 0.8527 (t0) cc_final: 0.8246 (t0) REVERT: P 27 ILE cc_start: 0.3832 (OUTLIER) cc_final: 0.3613 (tp) outliers start: 41 outliers final: 32 residues processed: 152 average time/residue: 0.3079 time to fit residues: 74.5038 Evaluate side-chains 155 residues out of total 2191 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 117 time to evaluate : 2.464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 322 ILE Chi-restraints excluded: chain A residue 376 MET Chi-restraints excluded: chain B residue 88 ILE 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 77 ILE Chi-restraints excluded: chain C residue 129 MET 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 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 351 VAL 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 351 VAL Chi-restraints excluded: chain F residue 176 TYR Chi-restraints excluded: chain F residue 187 LEU Chi-restraints excluded: chain F residue 195 ILE Chi-restraints excluded: chain F residue 203 ILE 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 P residue 27 ILE Chi-restraints excluded: chain P residue 42 ASP 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 153 optimal weight: 20.0000 chunk 206 optimal weight: 3.9990 chunk 59 optimal weight: 7.9990 chunk 178 optimal weight: 0.9980 chunk 28 optimal weight: 0.4980 chunk 53 optimal weight: 2.9990 chunk 193 optimal weight: 2.9990 chunk 81 optimal weight: 10.0000 chunk 199 optimal weight: 0.1980 chunk 24 optimal weight: 10.0000 chunk 35 optimal weight: 0.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 403 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.080846 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.054342 restraints weight = 93455.719| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.056160 restraints weight = 43393.736| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 60)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.057466 restraints weight = 27850.113| |-----------------------------------------------------------------------------| r_work (final): 0.3184 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 moved from start: 0.4411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 20164 Z= 0.163 Angle : 0.583 12.994 27188 Z= 0.294 Chirality : 0.043 0.360 3017 Planarity : 0.003 0.039 3463 Dihedral : 7.085 79.725 2847 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 1.98 % Allowed : 17.04 % Favored : 80.98 % 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: 1.73 (0.18), residues: 2389 helix: 2.23 (0.15), residues: 1236 sheet: 0.18 (0.26), residues: 430 loop : -0.06 (0.26), residues: 723 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 402 HIS 0.007 0.001 HIS A 399 PHE 0.013 0.001 PHE A 435 TYR 0.012 0.001 TYR D 97 ARG 0.008 0.000 ARG F 224 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3353.15 seconds wall clock time: 67 minutes 4.92 seconds (4024.92 seconds total)