Starting phenix.real_space_refine on Sat Feb 17 02:00:20 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e2l_27842/02_2024/8e2l_27842_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e2l_27842/02_2024/8e2l_27842.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.51 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e2l_27842/02_2024/8e2l_27842.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e2l_27842/02_2024/8e2l_27842.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e2l_27842/02_2024/8e2l_27842_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e2l_27842/02_2024/8e2l_27842_updated.pdb" } resolution = 3.51 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= 0.002 sd= 0.048 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 27 5.49 5 Mg 5 5.21 5 S 54 5.16 5 C 10698 2.51 5 N 3027 2.21 5 O 3281 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 17092 Number of models: 1 Model: "" Number of chains: 12 Chain: "C" Number of atoms: 3122 Number of conformers: 1 Conformer: "" Number of residues, atoms: 461, 3122 Classifications: {'peptide': 461} Incomplete info: {'truncation_to_alanine': 167} Link IDs: {'PTRANS': 20, 'TRANS': 440} Chain breaks: 1 Unresolved chain link angles: 12 Unresolved non-hydrogen bonds: 574 Unresolved non-hydrogen angles: 731 Unresolved non-hydrogen dihedrals: 476 Unresolved non-hydrogen chiralities: 63 Planarities with less than four sites: {'GLN:plan1': 5, 'HIS:plan': 2, 'TYR:plan': 4, 'ASN:plan1': 5, 'TRP:plan': 2, 'ASP:plan': 7, 'PHE:plan': 8, 'GLU:plan': 10, 'ARG:plan': 12} Unresolved non-hydrogen planarities: 260 Chain: "M" Number of atoms: 240 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 240 Classifications: {'DNA': 12} Link IDs: {'rna3p': 11} Chain: "A" Number of atoms: 3114 Number of conformers: 1 Conformer: "" Number of residues, atoms: 460, 3114 Classifications: {'peptide': 460} Incomplete info: {'truncation_to_alanine': 167} Link IDs: {'PTRANS': 20, 'TRANS': 439} Chain breaks: 1 Unresolved chain link angles: 12 Unresolved non-hydrogen bonds: 574 Unresolved non-hydrogen angles: 731 Unresolved non-hydrogen dihedrals: 476 Unresolved non-hydrogen chiralities: 63 Planarities with less than four sites: {'GLN:plan1': 5, 'HIS:plan': 2, 'TYR:plan': 4, 'ASN:plan1': 5, 'TRP:plan': 2, 'ASP:plan': 7, 'PHE:plan': 8, 'GLU:plan': 10, 'ARG:plan': 12} Unresolved non-hydrogen planarities: 260 Chain: "B" Number of atoms: 3122 Number of conformers: 1 Conformer: "" Number of residues, atoms: 461, 3122 Classifications: {'peptide': 461} Incomplete info: {'truncation_to_alanine': 167} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 440} Chain breaks: 1 Unresolved chain link angles: 12 Unresolved non-hydrogen bonds: 574 Unresolved non-hydrogen angles: 731 Unresolved non-hydrogen dihedrals: 476 Unresolved non-hydrogen chiralities: 63 Planarities with less than four sites: {'GLN:plan1': 5, 'HIS:plan': 2, 'TYR:plan': 4, 'ASN:plan1': 5, 'TRP:plan': 2, 'ASP:plan': 7, 'PHE:plan': 8, 'GLU:plan': 10, 'ARG:plan': 12} Unresolved non-hydrogen planarities: 260 Chain: "D" Number of atoms: 3122 Number of conformers: 1 Conformer: "" Number of residues, atoms: 461, 3122 Classifications: {'peptide': 461} Incomplete info: {'truncation_to_alanine': 167} Link IDs: {'PTRANS': 20, 'TRANS': 440} Chain breaks: 1 Unresolved chain link angles: 12 Unresolved non-hydrogen bonds: 574 Unresolved non-hydrogen angles: 731 Unresolved non-hydrogen dihedrals: 476 Unresolved non-hydrogen chiralities: 63 Planarities with less than four sites: {'GLN:plan1': 5, 'HIS:plan': 2, 'TYR:plan': 4, 'ASN:plan1': 5, 'TRP:plan': 2, 'ASP:plan': 7, 'PHE:plan': 8, 'GLU:plan': 10, 'ARG:plan': 12} Unresolved non-hydrogen planarities: 260 Chain: "E" Number of atoms: 2145 Number of conformers: 1 Conformer: "" Number of residues, atoms: 267, 2145 Classifications: {'peptide': 267} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 7, 'TRANS': 259} Chain breaks: 1 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "F" Number of atoms: 2067 Number of conformers: 1 Conformer: "" Number of residues, atoms: 256, 2067 Classifications: {'peptide': 256} Link IDs: {'PTRANS': 7, 'TRANS': 248} Chain breaks: 2 Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 9.21, per 1000 atoms: 0.54 Number of scatterers: 17092 At special positions: 0 Unit cell: (100.58, 167.99, 188.32, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 54 16.00 P 27 15.00 Mg 5 11.99 O 3281 8.00 N 3027 7.00 C 10698 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: 6.77 Conformation dependent library (CDL) restraints added in 3.2 seconds 4680 Ramachandran restraints generated. 2340 Oldfield, 0 Emsley, 2340 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4444 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 92 helices and 18 sheets defined 31.7% alpha, 7.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.43 Creating SS restraints... Processing helix chain 'C' and resid 49 through 51 No H-bonds generated for 'chain 'C' and resid 49 through 51' Processing helix chain 'C' and resid 69 through 72 No H-bonds generated for 'chain 'C' and resid 69 through 72' Processing helix chain 'C' and resid 103 through 105 No H-bonds generated for 'chain 'C' and resid 103 through 105' Processing helix chain 'C' and resid 146 through 153 Processing helix chain 'C' and resid 175 through 179 Processing helix chain 'C' and resid 195 through 204 Processing helix chain 'C' and resid 220 through 225 Processing helix chain 'C' and resid 229 through 234 Processing helix chain 'C' and resid 254 through 262 Processing helix chain 'C' and resid 264 through 267 No H-bonds generated for 'chain 'C' and resid 264 through 267' Processing helix chain 'C' and resid 277 through 279 No H-bonds generated for 'chain 'C' and resid 277 through 279' Processing helix chain 'C' and resid 301 through 313 Processing helix chain 'C' and resid 330 through 340 Processing helix chain 'C' and resid 351 through 357 Processing helix chain 'C' and resid 374 through 388 removed outlier: 3.501A pdb=" N LEU C 378 " --> pdb=" O ILE C 374 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N ASP C 379 " --> pdb=" O LYS C 375 " (cutoff:3.500A) Processing helix chain 'C' and resid 398 through 402 Processing helix chain 'C' and resid 414 through 429 Processing helix chain 'C' and resid 458 through 461 No H-bonds generated for 'chain 'C' and resid 458 through 461' Processing helix chain 'A' and resid 66 through 72 removed outlier: 4.324A pdb=" N LYS A 70 " --> pdb=" O ALA A 67 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N PHE A 72 " --> pdb=" O LEU A 69 " (cutoff:3.500A) Processing helix chain 'A' and resid 103 through 105 No H-bonds generated for 'chain 'A' and resid 103 through 105' Processing helix chain 'A' and resid 146 through 154 Processing helix chain 'A' and resid 175 through 180 Processing helix chain 'A' and resid 195 through 204 removed outlier: 3.778A pdb=" N ARG A 203 " --> pdb=" O LYS A 199 " (cutoff:3.500A) Processing helix chain 'A' and resid 220 through 225 Processing helix chain 'A' and resid 229 through 238 Processing helix chain 'A' and resid 250 through 252 No H-bonds generated for 'chain 'A' and resid 250 through 252' Processing helix chain 'A' and resid 254 through 262 Processing helix chain 'A' and resid 264 through 267 No H-bonds generated for 'chain 'A' and resid 264 through 267' Processing helix chain 'A' and resid 277 through 279 No H-bonds generated for 'chain 'A' and resid 277 through 279' Processing helix chain 'A' and resid 301 through 313 Processing helix chain 'A' and resid 328 through 339 Processing helix chain 'A' and resid 349 through 359 removed outlier: 3.826A pdb=" N ASP A 352 " --> pdb=" O GLU A 349 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N PHE A 353 " --> pdb=" O GLN A 350 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N TRP A 354 " --> pdb=" O TYR A 351 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N GLU A 359 " --> pdb=" O ASP A 356 " (cutoff:3.500A) Processing helix chain 'A' and resid 374 through 388 removed outlier: 4.217A pdb=" N ASP A 379 " --> pdb=" O LYS A 375 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N THR A 380 " --> pdb=" O THR A 376 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N MET A 381 " --> pdb=" O VAL A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 398 through 402 Processing helix chain 'A' and resid 414 through 429 Processing helix chain 'A' and resid 457 through 461 Processing helix chain 'B' and resid 66 through 72 removed outlier: 4.324A pdb=" N LYS B 70 " --> pdb=" O ALA B 67 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N PHE B 72 " --> pdb=" O LEU B 69 " (cutoff:3.500A) Processing helix chain 'B' and resid 103 through 105 No H-bonds generated for 'chain 'B' and resid 103 through 105' Processing helix chain 'B' and resid 146 through 154 Processing helix chain 'B' and resid 175 through 180 Processing helix chain 'B' and resid 195 through 204 removed outlier: 3.778A pdb=" N ARG B 203 " --> pdb=" O LYS B 199 " (cutoff:3.500A) Processing helix chain 'B' and resid 220 through 225 Processing helix chain 'B' and resid 229 through 236 Processing helix chain 'B' and resid 250 through 252 No H-bonds generated for 'chain 'B' and resid 250 through 252' Processing helix chain 'B' and resid 254 through 262 Processing helix chain 'B' and resid 264 through 267 No H-bonds generated for 'chain 'B' and resid 264 through 267' Processing helix chain 'B' and resid 277 through 279 No H-bonds generated for 'chain 'B' and resid 277 through 279' Processing helix chain 'B' and resid 301 through 315 removed outlier: 3.501A pdb=" N ILE B 314 " --> pdb=" O LEU B 310 " (cutoff:3.500A) removed outlier: 4.679A pdb=" N GLN B 315 " --> pdb=" O ASP B 311 " (cutoff:3.500A) Processing helix chain 'B' and resid 330 through 340 Processing helix chain 'B' and resid 351 through 359 Processing helix chain 'B' and resid 374 through 388 removed outlier: 3.844A pdb=" N ASP B 379 " --> pdb=" O LYS B 375 " (cutoff:3.500A) Processing helix chain 'B' and resid 398 through 402 Processing helix chain 'B' and resid 414 through 429 Processing helix chain 'B' and resid 458 through 461 No H-bonds generated for 'chain 'B' and resid 458 through 461' Processing helix chain 'D' and resid 67 through 72 removed outlier: 3.836A pdb=" N LYS D 71 " --> pdb=" O ALA D 67 " (cutoff:3.500A) Processing helix chain 'D' and resid 103 through 105 No H-bonds generated for 'chain 'D' and resid 103 through 105' Processing helix chain 'D' and resid 146 through 153 Processing helix chain 'D' and resid 175 through 180 Processing helix chain 'D' and resid 195 through 204 Processing helix chain 'D' and resid 220 through 225 Processing helix chain 'D' and resid 229 through 236 Processing helix chain 'D' and resid 250 through 252 No H-bonds generated for 'chain 'D' and resid 250 through 252' Processing helix chain 'D' and resid 254 through 262 Processing helix chain 'D' and resid 264 through 267 No H-bonds generated for 'chain 'D' and resid 264 through 267' Processing helix chain 'D' and resid 277 through 279 No H-bonds generated for 'chain 'D' and resid 277 through 279' Processing helix chain 'D' and resid 301 through 313 Processing helix chain 'D' and resid 328 through 340 Processing helix chain 'D' and resid 351 through 359 Processing helix chain 'D' and resid 374 through 388 removed outlier: 3.671A pdb=" N ASP D 379 " --> pdb=" O LYS D 375 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N THR D 380 " --> pdb=" O THR D 376 " (cutoff:3.500A) Processing helix chain 'D' and resid 398 through 402 Processing helix chain 'D' and resid 414 through 429 Processing helix chain 'D' and resid 458 through 462 Processing helix chain 'E' and resid 250 through 262 removed outlier: 6.479A pdb=" N GLU E 255 " --> pdb=" O LYS E 251 " (cutoff:3.500A) removed outlier: 5.185A pdb=" N ASP E 256 " --> pdb=" O GLN E 252 " (cutoff:3.500A) Processing helix chain 'E' and resid 264 through 267 No H-bonds generated for 'chain 'E' and resid 264 through 267' Processing helix chain 'E' and resid 301 through 313 Processing helix chain 'E' and resid 328 through 340 Processing helix chain 'E' and resid 351 through 359 Processing helix chain 'E' and resid 374 through 388 removed outlier: 3.576A pdb=" N THR E 380 " --> pdb=" O THR E 376 " (cutoff:3.500A) Processing helix chain 'E' and resid 398 through 402 Processing helix chain 'E' and resid 414 through 429 Processing helix chain 'E' and resid 450 through 452 No H-bonds generated for 'chain 'E' and resid 450 through 452' Processing helix chain 'E' and resid 457 through 461 Processing helix chain 'F' and resid 255 through 258 No H-bonds generated for 'chain 'F' and resid 255 through 258' Processing helix chain 'F' and resid 276 through 280 removed outlier: 4.000A pdb=" N ARG F 280 " --> pdb=" O PRO F 276 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 276 through 280' Processing helix chain 'F' and resid 301 through 313 Processing helix chain 'F' and resid 328 through 340 Processing helix chain 'F' and resid 344 through 346 No H-bonds generated for 'chain 'F' and resid 344 through 346' Processing helix chain 'F' and resid 348 through 359 removed outlier: 4.268A pdb=" N ASP F 352 " --> pdb=" O GLU F 349 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N PHE F 353 " --> pdb=" O GLN F 350 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N TRP F 354 " --> pdb=" O TYR F 351 " (cutoff:3.500A) Processing helix chain 'F' and resid 374 through 388 removed outlier: 3.903A pdb=" N ASP F 379 " --> pdb=" O LYS F 375 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N THR F 380 " --> pdb=" O THR F 376 " (cutoff:3.500A) Processing helix chain 'F' and resid 398 through 402 Processing helix chain 'F' and resid 414 through 429 Processing helix chain 'F' and resid 458 through 462 Processing sheet with id= A, first strand: chain 'C' and resid 140 through 142 No H-bonds generated for sheet with id= A Processing sheet with id= B, first strand: chain 'C' and resid 290 through 293 removed outlier: 6.305A pdb=" N VAL C 433 " --> pdb=" O THR C 291 " (cutoff:3.500A) removed outlier: 7.681A pdb=" N PHE C 293 " --> pdb=" O VAL C 433 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N LEU C 435 " --> pdb=" O PHE C 293 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ILE C 436 " --> pdb=" O ILE C 395 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'C' and resid 467 through 470 removed outlier: 3.691A pdb=" N LEU C 483 " --> pdb=" O PHE C 497 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 183 through 186 Processing sheet with id= E, first strand: chain 'A' and resid 290 through 293 removed outlier: 6.213A pdb=" N VAL A 433 " --> pdb=" O THR A 291 " (cutoff:3.500A) removed outlier: 7.510A pdb=" N PHE A 293 " --> pdb=" O VAL A 433 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N LEU A 435 " --> pdb=" O PHE A 293 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 467 through 470 removed outlier: 3.629A pdb=" N LEU A 483 " --> pdb=" O PHE A 497 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N PHE A 497 " --> pdb=" O LEU A 483 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 500 through 502 removed outlier: 4.188A pdb=" N ASP A 500 " --> pdb=" O SER A 509 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 183 through 186 Processing sheet with id= I, first strand: chain 'B' and resid 290 through 293 removed outlier: 6.251A pdb=" N VAL B 433 " --> pdb=" O THR B 291 " (cutoff:3.500A) removed outlier: 7.645A pdb=" N PHE B 293 " --> pdb=" O VAL B 433 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N LEU B 435 " --> pdb=" O PHE B 293 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N VAL B 393 " --> pdb=" O HIS B 432 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'B' and resid 467 through 470 removed outlier: 3.706A pdb=" N LEU B 483 " --> pdb=" O PHE B 497 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N PHE B 497 " --> pdb=" O LEU B 483 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'B' and resid 500 through 502 removed outlier: 4.157A pdb=" N ASP B 500 " --> pdb=" O SER B 509 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N THR B 507 " --> pdb=" O ILE B 502 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'D' and resid 290 through 293 removed outlier: 6.213A pdb=" N VAL D 433 " --> pdb=" O THR D 291 " (cutoff:3.500A) removed outlier: 7.577A pdb=" N PHE D 293 " --> pdb=" O VAL D 433 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N LEU D 435 " --> pdb=" O PHE D 293 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'D' and resid 467 through 470 removed outlier: 3.783A pdb=" N LEU D 483 " --> pdb=" O PHE D 497 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'E' and resid 290 through 293 removed outlier: 6.269A pdb=" N VAL E 433 " --> pdb=" O THR E 291 " (cutoff:3.500A) removed outlier: 7.641A pdb=" N PHE E 293 " --> pdb=" O VAL E 433 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N LEU E 435 " --> pdb=" O PHE E 293 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ILE E 436 " --> pdb=" O ILE E 395 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'E' and resid 467 through 470 removed outlier: 3.678A pdb=" N LEU E 483 " --> pdb=" O PHE E 497 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N PHE E 497 " --> pdb=" O LEU E 483 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'F' and resid 290 through 293 removed outlier: 6.201A pdb=" N VAL F 433 " --> pdb=" O THR F 291 " (cutoff:3.500A) removed outlier: 7.603A pdb=" N PHE F 293 " --> pdb=" O VAL F 433 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N LEU F 435 " --> pdb=" O PHE F 293 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'F' and resid 468 through 470 removed outlier: 3.705A pdb=" N LEU F 483 " --> pdb=" O PHE F 497 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N PHE F 497 " --> pdb=" O LEU F 483 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'F' and resid 500 through 502 removed outlier: 4.300A pdb=" N ASP F 500 " --> pdb=" O SER F 509 " (cutoff:3.500A) 470 hydrogen bonds defined for protein. 1329 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.42 Time building geometry restraints manager: 7.24 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 4895 1.33 - 1.45: 2731 1.45 - 1.57: 9625 1.57 - 1.69: 48 1.69 - 1.81: 90 Bond restraints: 17389 Sorted by residual: bond pdb=" C4 ATP E 601 " pdb=" C5 ATP E 601 " ideal model delta sigma weight residual 1.388 1.469 -0.081 1.00e-02 1.00e+04 6.63e+01 bond pdb=" C4 ATP B 601 " pdb=" C5 ATP B 601 " ideal model delta sigma weight residual 1.388 1.469 -0.081 1.00e-02 1.00e+04 6.61e+01 bond pdb=" C4 ATP F 601 " pdb=" C5 ATP F 601 " ideal model delta sigma weight residual 1.388 1.469 -0.081 1.00e-02 1.00e+04 6.56e+01 bond pdb=" C4 ATP C 601 " pdb=" C5 ATP C 601 " ideal model delta sigma weight residual 1.388 1.468 -0.080 1.00e-02 1.00e+04 6.45e+01 bond pdb=" C4 ATP D 601 " pdb=" C5 ATP D 601 " ideal model delta sigma weight residual 1.388 1.468 -0.080 1.00e-02 1.00e+04 6.41e+01 ... (remaining 17384 not shown) Histogram of bond angle deviations from ideal: 100.23 - 107.43: 565 107.43 - 114.62: 10201 114.62 - 121.82: 8807 121.82 - 129.02: 4048 129.02 - 136.22: 102 Bond angle restraints: 23723 Sorted by residual: angle pdb=" PB ATP F 601 " pdb=" O3B ATP F 601 " pdb=" PG ATP F 601 " ideal model delta sigma weight residual 139.87 119.74 20.13 1.00e+00 1.00e+00 4.05e+02 angle pdb=" PB ATP B 601 " pdb=" O3B ATP B 601 " pdb=" PG ATP B 601 " ideal model delta sigma weight residual 139.87 119.77 20.10 1.00e+00 1.00e+00 4.04e+02 angle pdb=" PB ATP C 601 " pdb=" O3B ATP C 601 " pdb=" PG ATP C 601 " ideal model delta sigma weight residual 139.87 119.95 19.92 1.00e+00 1.00e+00 3.97e+02 angle pdb=" PB ATP E 601 " pdb=" O3B ATP E 601 " pdb=" PG ATP E 601 " ideal model delta sigma weight residual 139.87 119.97 19.90 1.00e+00 1.00e+00 3.96e+02 angle pdb=" PB ATP D 601 " pdb=" O3B ATP D 601 " pdb=" PG ATP D 601 " ideal model delta sigma weight residual 139.87 120.00 19.87 1.00e+00 1.00e+00 3.95e+02 ... (remaining 23718 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.41: 9677 23.41 - 46.81: 536 46.81 - 70.22: 109 70.22 - 93.62: 25 93.62 - 117.03: 1 Dihedral angle restraints: 10348 sinusoidal: 3515 harmonic: 6833 Sorted by residual: dihedral pdb=" CA ILE A 240 " pdb=" C ILE A 240 " pdb=" N PRO A 241 " pdb=" CA PRO A 241 " ideal model delta harmonic sigma weight residual -180.00 -62.97 -117.03 0 5.00e+00 4.00e-02 5.48e+02 dihedral pdb=" CA PHE C 250 " pdb=" C PHE C 250 " pdb=" N LYS C 251 " pdb=" CA LYS C 251 " ideal model delta harmonic sigma weight residual 180.00 157.22 22.78 0 5.00e+00 4.00e-02 2.08e+01 dihedral pdb=" C ASN B 397 " pdb=" N ASN B 397 " pdb=" CA ASN B 397 " pdb=" CB ASN B 397 " ideal model delta harmonic sigma weight residual -122.60 -133.66 11.06 0 2.50e+00 1.60e-01 1.96e+01 ... (remaining 10345 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.077: 2512 0.077 - 0.153: 252 0.153 - 0.230: 6 0.230 - 0.306: 4 0.306 - 0.383: 2 Chirality restraints: 2776 Sorted by residual: chirality pdb=" CA ASN B 397 " pdb=" N ASN B 397 " pdb=" C ASN B 397 " pdb=" CB ASN B 397 " both_signs ideal model delta sigma weight residual False 2.51 2.13 0.38 2.00e-01 2.50e+01 3.67e+00 chirality pdb=" CA ASN E 397 " pdb=" N ASN E 397 " pdb=" C ASN E 397 " pdb=" CB ASN E 397 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.76e+00 chirality pdb=" CA ASN C 397 " pdb=" N ASN C 397 " pdb=" C ASN C 397 " pdb=" CB ASN C 397 " both_signs ideal model delta sigma weight residual False 2.51 2.20 0.31 2.00e-01 2.50e+01 2.34e+00 ... (remaining 2773 not shown) Planarity restraints: 3058 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE B 394 " 0.013 2.00e-02 2.50e+03 2.58e-02 6.64e+00 pdb=" C ILE B 394 " -0.045 2.00e-02 2.50e+03 pdb=" O ILE B 394 " 0.017 2.00e-02 2.50e+03 pdb=" N ILE B 395 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS A 237 " -0.012 2.00e-02 2.50e+03 2.50e-02 6.27e+00 pdb=" C LYS A 237 " 0.043 2.00e-02 2.50e+03 pdb=" O LYS A 237 " -0.016 2.00e-02 2.50e+03 pdb=" N THR A 238 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE A 275 " 0.036 5.00e-02 4.00e+02 5.51e-02 4.86e+00 pdb=" N PRO A 276 " -0.095 5.00e-02 4.00e+02 pdb=" CA PRO A 276 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO A 276 " 0.031 5.00e-02 4.00e+02 ... (remaining 3055 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.60: 129 2.60 - 3.18: 14936 3.18 - 3.75: 25088 3.75 - 4.33: 33116 4.33 - 4.90: 54298 Nonbonded interactions: 127567 Sorted by model distance: nonbonded pdb=" O1B ATP D 601 " pdb="MG MG D 602 " model vdw 2.028 2.170 nonbonded pdb=" O3G ATP D 601 " pdb="MG MG D 602 " model vdw 2.030 2.170 nonbonded pdb=" OE1 GLN B 325 " pdb="MG MG B 602 " model vdw 2.038 2.170 nonbonded pdb=" O1B ATP C 601 " pdb="MG MG C 602 " model vdw 2.039 2.170 nonbonded pdb=" O1B ATP E 601 " pdb="MG MG E 602 " model vdw 2.065 2.170 ... (remaining 127562 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and (resid 48 through 404 or resid 410 through 512)) selection = (chain 'C' and (resid 48 through 404 or resid 410 through 512)) selection = (chain 'D' and (resid 48 through 404 or resid 410 through 512)) } ncs_group { reference = (chain 'E' and (resid 244 through 259 or resid 269 through 512 or resid 601 thro \ ugh 602)) selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.210 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 7.860 Check model and map are aligned: 0.240 Set scattering table: 0.140 Process input model: 44.710 Find NCS groups from input model: 1.190 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 59.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7083 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 : 0.004 0.081 17389 Z= 0.231 Angle : 0.729 20.135 23723 Z= 0.559 Chirality : 0.045 0.383 2776 Planarity : 0.003 0.055 3058 Dihedral : 15.288 117.029 5904 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.78 % Favored : 92.09 % Rotamer: Outliers : 0.42 % Allowed : 0.71 % Favored : 98.87 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 1.06 % Cis-general : 0.00 % Twisted Proline : 1.06 % 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: -0.93 (0.18), residues: 2340 helix: 0.79 (0.20), residues: 803 sheet: 0.22 (0.32), residues: 304 loop : -1.88 (0.18), residues: 1233 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP F 272 HIS 0.004 0.001 HIS D 438 PHE 0.023 0.001 PHE B 358 TYR 0.020 0.001 TYR C 386 ARG 0.004 0.000 ARG A 286 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4680 Ramachandran restraints generated. 2340 Oldfield, 0 Emsley, 2340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4680 Ramachandran restraints generated. 2340 Oldfield, 0 Emsley, 2340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 2085 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 145 time to evaluate : 1.838 Fit side-chains REVERT: C 375 LYS cc_start: 0.9049 (mmpt) cc_final: 0.8822 (tppt) REVERT: C 386 TYR cc_start: 0.8901 (m-80) cc_final: 0.8558 (m-80) REVERT: A 386 TYR cc_start: 0.8718 (m-80) cc_final: 0.8242 (m-80) REVERT: A 438 HIS cc_start: 0.5581 (m90) cc_final: 0.4881 (m-70) REVERT: B 491 ASP cc_start: 0.8427 (m-30) cc_final: 0.8127 (m-30) REVERT: E 464 ASP cc_start: 0.8656 (m-30) cc_final: 0.8285 (m-30) REVERT: F 397 ASN cc_start: 0.8324 (m-40) cc_final: 0.8100 (t0) outliers start: 6 outliers final: 1 residues processed: 151 average time/residue: 0.2770 time to fit residues: 64.5453 Evaluate side-chains 109 residues out of total 2085 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 108 time to evaluate : 1.969 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 396 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 199 optimal weight: 0.0470 chunk 178 optimal weight: 0.6980 chunk 99 optimal weight: 40.0000 chunk 61 optimal weight: 10.0000 chunk 120 optimal weight: 4.9990 chunk 95 optimal weight: 50.0000 chunk 184 optimal weight: 3.9990 chunk 71 optimal weight: 9.9990 chunk 112 optimal weight: 4.9990 chunk 137 optimal weight: 5.9990 chunk 214 optimal weight: 5.9990 overall best weight: 2.9484 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 397 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 465 ASN A 392 HIS D 244 HIS D 369 HIS ** D 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 465 ASN E 488 ASN ** F 484 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7186 moved from start: 0.1505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 17389 Z= 0.379 Angle : 0.595 13.353 23723 Z= 0.319 Chirality : 0.045 0.296 2776 Planarity : 0.004 0.088 3058 Dihedral : 11.091 86.903 2750 Min Nonbonded Distance : 1.788 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.23 % Favored : 90.77 % Rotamer: Outliers : 1.34 % Allowed : 9.60 % Favored : 89.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.06 % Cis-general : 0.00 % Twisted Proline : 1.06 % 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: -1.01 (0.18), residues: 2340 helix: 0.85 (0.20), residues: 794 sheet: -0.28 (0.30), residues: 324 loop : -1.89 (0.18), residues: 1222 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP C 195 HIS 0.011 0.002 HIS D 369 PHE 0.031 0.002 PHE F 358 TYR 0.014 0.002 TYR A 388 ARG 0.004 0.001 ARG B 481 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4680 Ramachandran restraints generated. 2340 Oldfield, 0 Emsley, 2340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4680 Ramachandran restraints generated. 2340 Oldfield, 0 Emsley, 2340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 2085 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 116 time to evaluate : 2.152 Fit side-chains revert: symmetry clash REVERT: C 402 MET cc_start: 0.8322 (tmm) cc_final: 0.8044 (tmm) REVERT: A 386 TYR cc_start: 0.8586 (m-80) cc_final: 0.8077 (m-80) REVERT: A 402 MET cc_start: 0.7357 (tmm) cc_final: 0.7156 (tmm) REVERT: B 317 VAL cc_start: 0.8483 (OUTLIER) cc_final: 0.8214 (p) REVERT: D 491 ASP cc_start: 0.8581 (m-30) cc_final: 0.8199 (t0) REVERT: E 402 MET cc_start: 0.8066 (tmm) cc_final: 0.7559 (tmm) REVERT: E 464 ASP cc_start: 0.8773 (m-30) cc_final: 0.8416 (m-30) outliers start: 19 outliers final: 14 residues processed: 125 average time/residue: 0.2670 time to fit residues: 53.7494 Evaluate side-chains 115 residues out of total 2085 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 100 time to evaluate : 2.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 396 ASP Chi-restraints excluded: chain A residue 240 ILE Chi-restraints excluded: chain A residue 353 PHE Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain B residue 431 CYS Chi-restraints excluded: chain D residue 450 THR Chi-restraints excluded: chain E residue 244 HIS Chi-restraints excluded: chain E residue 250 PHE Chi-restraints excluded: chain E residue 257 VAL Chi-restraints excluded: chain E residue 363 LEU Chi-restraints excluded: chain E residue 427 THR Chi-restraints excluded: chain E residue 477 CYS Chi-restraints excluded: chain F residue 250 PHE Chi-restraints excluded: chain F residue 400 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 119 optimal weight: 0.9980 chunk 66 optimal weight: 8.9990 chunk 178 optimal weight: 0.9980 chunk 145 optimal weight: 50.0000 chunk 59 optimal weight: 30.0000 chunk 214 optimal weight: 4.9990 chunk 231 optimal weight: 9.9990 chunk 191 optimal weight: 0.6980 chunk 212 optimal weight: 9.9990 chunk 73 optimal weight: 5.9990 chunk 172 optimal weight: 0.6980 overall best weight: 1.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 488 ASN ** F 484 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7167 moved from start: 0.1695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 17389 Z= 0.220 Angle : 0.477 11.398 23723 Z= 0.260 Chirality : 0.042 0.179 2776 Planarity : 0.003 0.089 3058 Dihedral : 10.926 89.958 2750 Min Nonbonded Distance : 1.855 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.33 % Favored : 91.67 % Rotamer: Outliers : 1.34 % Allowed : 13.70 % Favored : 84.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.06 % Cis-general : 0.00 % Twisted Proline : 1.06 % 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: -0.96 (0.18), residues: 2340 helix: 0.97 (0.20), residues: 814 sheet: -0.30 (0.30), residues: 319 loop : -1.95 (0.18), residues: 1207 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 354 HIS 0.005 0.001 HIS A 244 PHE 0.022 0.001 PHE F 358 TYR 0.014 0.001 TYR A 388 ARG 0.002 0.000 ARG F 481 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4680 Ramachandran restraints generated. 2340 Oldfield, 0 Emsley, 2340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4680 Ramachandran restraints generated. 2340 Oldfield, 0 Emsley, 2340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 2085 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 109 time to evaluate : 2.001 Fit side-chains revert: symmetry clash REVERT: C 402 MET cc_start: 0.8158 (tmm) cc_final: 0.7888 (tmm) REVERT: A 431 CYS cc_start: 0.6563 (m) cc_final: 0.6352 (m) REVERT: B 317 VAL cc_start: 0.8514 (OUTLIER) cc_final: 0.8227 (p) REVERT: E 402 MET cc_start: 0.7865 (tmm) cc_final: 0.7346 (tmm) REVERT: E 464 ASP cc_start: 0.8684 (m-30) cc_final: 0.8344 (m-30) outliers start: 19 outliers final: 13 residues processed: 119 average time/residue: 0.2566 time to fit residues: 49.9859 Evaluate side-chains 115 residues out of total 2085 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 101 time to evaluate : 1.971 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 319 THR Chi-restraints excluded: chain C residue 396 ASP Chi-restraints excluded: chain A residue 445 ASP Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 381 MET Chi-restraints excluded: chain B residue 431 CYS Chi-restraints excluded: chain D residue 319 THR Chi-restraints excluded: chain E residue 244 HIS Chi-restraints excluded: chain E residue 248 VAL Chi-restraints excluded: chain E residue 250 PHE Chi-restraints excluded: chain E residue 319 THR Chi-restraints excluded: chain F residue 250 PHE Chi-restraints excluded: chain F residue 335 MET Chi-restraints excluded: chain F residue 400 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 212 optimal weight: 0.0370 chunk 161 optimal weight: 3.9990 chunk 111 optimal weight: 0.0270 chunk 23 optimal weight: 4.9990 chunk 102 optimal weight: 50.0000 chunk 144 optimal weight: 0.3980 chunk 215 optimal weight: 3.9990 chunk 228 optimal weight: 5.9990 chunk 112 optimal weight: 6.9990 chunk 204 optimal weight: 2.9990 chunk 61 optimal weight: 20.0000 overall best weight: 1.4920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 465 ASN ** D 470 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 488 ASN ** F 484 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7171 moved from start: 0.1936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 17389 Z= 0.205 Angle : 0.464 11.163 23723 Z= 0.252 Chirality : 0.041 0.256 2776 Planarity : 0.003 0.082 3058 Dihedral : 10.851 89.019 2750 Min Nonbonded Distance : 1.867 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.19 % Favored : 90.81 % Rotamer: Outliers : 1.55 % Allowed : 15.89 % Favored : 82.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.06 % Cis-general : 0.00 % Twisted Proline : 1.06 % 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: -0.92 (0.18), residues: 2340 helix: 1.05 (0.20), residues: 816 sheet: -0.49 (0.30), residues: 311 loop : -1.90 (0.18), residues: 1213 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 354 HIS 0.006 0.001 HIS B 383 PHE 0.018 0.001 PHE F 358 TYR 0.015 0.001 TYR E 364 ARG 0.003 0.000 ARG E 446 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4680 Ramachandran restraints generated. 2340 Oldfield, 0 Emsley, 2340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4680 Ramachandran restraints generated. 2340 Oldfield, 0 Emsley, 2340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 2085 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 109 time to evaluate : 2.193 Fit side-chains REVERT: C 402 MET cc_start: 0.8181 (tmm) cc_final: 0.7899 (tmm) REVERT: C 443 GLU cc_start: 0.6497 (pp20) cc_final: 0.5978 (pp20) REVERT: A 438 HIS cc_start: 0.6670 (m-70) cc_final: 0.5810 (m-70) REVERT: B 317 VAL cc_start: 0.8419 (OUTLIER) cc_final: 0.8180 (p) REVERT: D 248 VAL cc_start: 0.8821 (t) cc_final: 0.8583 (p) REVERT: E 341 MET cc_start: 0.9115 (tpp) cc_final: 0.8638 (tpp) REVERT: E 464 ASP cc_start: 0.8652 (m-30) cc_final: 0.8325 (m-30) REVERT: F 397 ASN cc_start: 0.7888 (t0) cc_final: 0.7396 (t0) outliers start: 22 outliers final: 16 residues processed: 121 average time/residue: 0.2433 time to fit residues: 48.4681 Evaluate side-chains 119 residues out of total 2085 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 102 time to evaluate : 1.879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 319 THR Chi-restraints excluded: chain C residue 396 ASP Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 318 ASN Chi-restraints excluded: chain B residue 381 MET Chi-restraints excluded: chain D residue 319 THR Chi-restraints excluded: chain E residue 244 HIS Chi-restraints excluded: chain E residue 248 VAL Chi-restraints excluded: chain E residue 250 PHE Chi-restraints excluded: chain E residue 297 THR Chi-restraints excluded: chain E residue 363 LEU Chi-restraints excluded: chain E residue 477 CYS Chi-restraints excluded: chain F residue 250 PHE Chi-restraints excluded: chain F residue 318 ASN Chi-restraints excluded: chain F residue 335 MET Chi-restraints excluded: chain F residue 347 ASN Chi-restraints excluded: chain F residue 400 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 189 optimal weight: 0.0050 chunk 129 optimal weight: 0.9990 chunk 3 optimal weight: 50.0000 chunk 169 optimal weight: 2.9990 chunk 94 optimal weight: 30.0000 chunk 194 optimal weight: 0.9980 chunk 157 optimal weight: 50.0000 chunk 0 optimal weight: 40.0000 chunk 116 optimal weight: 3.9990 chunk 204 optimal weight: 5.9990 chunk 57 optimal weight: 50.0000 overall best weight: 1.8000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 470 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 488 ASN ** F 484 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7186 moved from start: 0.2220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 17389 Z= 0.237 Angle : 0.480 10.406 23723 Z= 0.259 Chirality : 0.042 0.238 2776 Planarity : 0.003 0.090 3058 Dihedral : 10.880 87.393 2750 Min Nonbonded Distance : 1.841 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.27 % Favored : 90.73 % Rotamer: Outliers : 2.40 % Allowed : 16.88 % Favored : 80.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.06 % Cis-general : 0.00 % Twisted Proline : 1.06 % 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: -0.88 (0.18), residues: 2340 helix: 1.22 (0.20), residues: 798 sheet: -0.62 (0.30), residues: 311 loop : -1.88 (0.18), residues: 1231 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 354 HIS 0.006 0.001 HIS B 383 PHE 0.015 0.001 PHE F 250 TYR 0.014 0.001 TYR A 388 ARG 0.003 0.000 ARG C 481 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4680 Ramachandran restraints generated. 2340 Oldfield, 0 Emsley, 2340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4680 Ramachandran restraints generated. 2340 Oldfield, 0 Emsley, 2340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 2085 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 105 time to evaluate : 1.914 Fit side-chains REVERT: C 402 MET cc_start: 0.8186 (tmm) cc_final: 0.7915 (tmm) REVERT: C 443 GLU cc_start: 0.6538 (pp20) cc_final: 0.6034 (pp20) REVERT: B 250 PHE cc_start: 0.8248 (OUTLIER) cc_final: 0.8013 (m-80) REVERT: D 248 VAL cc_start: 0.8848 (t) cc_final: 0.8636 (p) REVERT: E 341 MET cc_start: 0.9079 (tpp) cc_final: 0.8525 (tpp) REVERT: E 464 ASP cc_start: 0.8707 (m-30) cc_final: 0.8388 (m-30) outliers start: 34 outliers final: 22 residues processed: 129 average time/residue: 0.2660 time to fit residues: 56.7044 Evaluate side-chains 122 residues out of total 2085 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 99 time to evaluate : 2.124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 319 THR Chi-restraints excluded: chain C residue 396 ASP Chi-restraints excluded: chain C residue 464 ASP Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain B residue 250 PHE Chi-restraints excluded: chain B residue 318 ASN Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain B residue 381 MET Chi-restraints excluded: chain B residue 431 CYS Chi-restraints excluded: chain D residue 319 THR Chi-restraints excluded: chain E residue 244 HIS Chi-restraints excluded: chain E residue 248 VAL Chi-restraints excluded: chain E residue 250 PHE Chi-restraints excluded: chain E residue 297 THR Chi-restraints excluded: chain E residue 319 THR Chi-restraints excluded: chain E residue 363 LEU Chi-restraints excluded: chain E residue 427 THR Chi-restraints excluded: chain E residue 477 CYS Chi-restraints excluded: chain F residue 250 PHE Chi-restraints excluded: chain F residue 318 ASN Chi-restraints excluded: chain F residue 335 MET Chi-restraints excluded: chain F residue 347 ASN Chi-restraints excluded: chain F residue 400 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 76 optimal weight: 20.0000 chunk 205 optimal weight: 0.0770 chunk 45 optimal weight: 5.9990 chunk 133 optimal weight: 0.0980 chunk 56 optimal weight: 50.0000 chunk 228 optimal weight: 6.9990 chunk 189 optimal weight: 0.6980 chunk 105 optimal weight: 40.0000 chunk 18 optimal weight: 50.0000 chunk 75 optimal weight: 7.9990 chunk 119 optimal weight: 3.9990 overall best weight: 2.1742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 470 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 488 ASN ** F 470 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 484 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7201 moved from start: 0.2473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 17389 Z= 0.272 Angle : 0.498 10.491 23723 Z= 0.269 Chirality : 0.042 0.145 2776 Planarity : 0.003 0.077 3058 Dihedral : 10.982 86.416 2750 Min Nonbonded Distance : 1.823 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.04 % Favored : 89.96 % Rotamer: Outliers : 2.97 % Allowed : 18.01 % Favored : 79.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.06 % Cis-general : 0.00 % Twisted Proline : 1.06 % 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: -0.96 (0.18), residues: 2340 helix: 1.17 (0.20), residues: 804 sheet: -0.70 (0.30), residues: 311 loop : -1.96 (0.17), residues: 1225 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 354 HIS 0.013 0.001 HIS B 383 PHE 0.015 0.001 PHE F 250 TYR 0.017 0.001 TYR A 388 ARG 0.003 0.000 ARG C 481 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4680 Ramachandran restraints generated. 2340 Oldfield, 0 Emsley, 2340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4680 Ramachandran restraints generated. 2340 Oldfield, 0 Emsley, 2340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 2085 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 105 time to evaluate : 1.946 Fit side-chains revert: symmetry clash REVERT: C 402 MET cc_start: 0.8204 (tmm) cc_final: 0.7989 (tmm) REVERT: C 443 GLU cc_start: 0.6554 (pp20) cc_final: 0.6180 (pp20) REVERT: B 250 PHE cc_start: 0.8255 (OUTLIER) cc_final: 0.8009 (m-80) REVERT: E 341 MET cc_start: 0.9039 (tpp) cc_final: 0.8545 (tpp) REVERT: E 464 ASP cc_start: 0.8628 (m-30) cc_final: 0.8324 (m-30) outliers start: 42 outliers final: 27 residues processed: 135 average time/residue: 0.2348 time to fit residues: 52.5604 Evaluate side-chains 127 residues out of total 2085 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 99 time to evaluate : 1.899 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 291 THR Chi-restraints excluded: chain C residue 319 THR Chi-restraints excluded: chain C residue 396 ASP Chi-restraints excluded: chain C residue 464 ASP Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain A residue 506 LEU Chi-restraints excluded: chain B residue 250 PHE Chi-restraints excluded: chain B residue 318 ASN Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain B residue 431 CYS Chi-restraints excluded: chain D residue 319 THR Chi-restraints excluded: chain D residue 348 LEU Chi-restraints excluded: chain E residue 244 HIS Chi-restraints excluded: chain E residue 248 VAL Chi-restraints excluded: chain E residue 250 PHE Chi-restraints excluded: chain E residue 297 THR Chi-restraints excluded: chain E residue 318 ASN Chi-restraints excluded: chain E residue 363 LEU Chi-restraints excluded: chain E residue 378 LEU Chi-restraints excluded: chain E residue 414 VAL Chi-restraints excluded: chain E residue 427 THR Chi-restraints excluded: chain E residue 443 GLU Chi-restraints excluded: chain E residue 477 CYS Chi-restraints excluded: chain F residue 250 PHE Chi-restraints excluded: chain F residue 318 ASN Chi-restraints excluded: chain F residue 335 MET Chi-restraints excluded: chain F residue 347 ASN Chi-restraints excluded: chain F residue 400 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 220 optimal weight: 0.0770 chunk 25 optimal weight: 0.8980 chunk 130 optimal weight: 0.9990 chunk 166 optimal weight: 1.9990 chunk 129 optimal weight: 0.7980 chunk 192 optimal weight: 0.8980 chunk 127 optimal weight: 3.9990 chunk 227 optimal weight: 0.9980 chunk 142 optimal weight: 40.0000 chunk 138 optimal weight: 4.9990 chunk 105 optimal weight: 40.0000 overall best weight: 0.7338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 488 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7158 moved from start: 0.2415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 17389 Z= 0.131 Angle : 0.447 12.568 23723 Z= 0.242 Chirality : 0.041 0.221 2776 Planarity : 0.003 0.070 3058 Dihedral : 10.773 88.926 2750 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.76 % Favored : 91.24 % Rotamer: Outliers : 1.62 % Allowed : 19.21 % Favored : 79.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.06 % Cis-general : 0.00 % Twisted Proline : 1.06 % 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: -0.84 (0.18), residues: 2340 helix: 1.27 (0.20), residues: 808 sheet: -0.74 (0.31), residues: 290 loop : -1.85 (0.17), residues: 1242 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 354 HIS 0.008 0.001 HIS B 383 PHE 0.015 0.001 PHE F 250 TYR 0.017 0.001 TYR A 388 ARG 0.003 0.000 ARG C 481 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4680 Ramachandran restraints generated. 2340 Oldfield, 0 Emsley, 2340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4680 Ramachandran restraints generated. 2340 Oldfield, 0 Emsley, 2340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 2085 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 114 time to evaluate : 1.948 Fit side-chains revert: symmetry clash REVERT: C 402 MET cc_start: 0.8125 (tmm) cc_final: 0.7849 (tmm) REVERT: C 443 GLU cc_start: 0.6625 (pp20) cc_final: 0.6223 (pp20) REVERT: D 341 MET cc_start: 0.9093 (tpp) cc_final: 0.8806 (tpp) REVERT: E 341 MET cc_start: 0.9087 (tpp) cc_final: 0.8671 (tpp) REVERT: E 364 TYR cc_start: 0.8675 (m-80) cc_final: 0.8446 (m-80) REVERT: E 402 MET cc_start: 0.7892 (tmm) cc_final: 0.7602 (tmm) REVERT: E 464 ASP cc_start: 0.8690 (m-30) cc_final: 0.8388 (m-30) REVERT: F 397 ASN cc_start: 0.7830 (t0) cc_final: 0.7464 (t0) outliers start: 23 outliers final: 17 residues processed: 130 average time/residue: 0.2391 time to fit residues: 51.4649 Evaluate side-chains 123 residues out of total 2085 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 106 time to evaluate : 2.022 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 319 THR Chi-restraints excluded: chain C residue 396 ASP Chi-restraints excluded: chain A residue 347 ASN Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain A residue 506 LEU Chi-restraints excluded: chain B residue 318 ASN Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain B residue 496 ILE Chi-restraints excluded: chain E residue 244 HIS Chi-restraints excluded: chain E residue 248 VAL Chi-restraints excluded: chain E residue 250 PHE Chi-restraints excluded: chain E residue 278 LEU Chi-restraints excluded: chain E residue 297 THR Chi-restraints excluded: chain E residue 318 ASN Chi-restraints excluded: chain F residue 250 PHE Chi-restraints excluded: chain F residue 335 MET Chi-restraints excluded: chain F residue 400 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 140 optimal weight: 50.0000 chunk 90 optimal weight: 8.9990 chunk 135 optimal weight: 0.9980 chunk 68 optimal weight: 6.9990 chunk 44 optimal weight: 6.9990 chunk 144 optimal weight: 50.0000 chunk 154 optimal weight: 20.0000 chunk 112 optimal weight: 5.9990 chunk 21 optimal weight: 5.9990 chunk 178 optimal weight: 3.9990 chunk 206 optimal weight: 4.9990 overall best weight: 4.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 465 ASN ** C 470 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 318 ASN ** D 470 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 488 ASN ** F 470 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 484 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7257 moved from start: 0.3063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.069 17389 Z= 0.529 Angle : 0.680 10.624 23723 Z= 0.362 Chirality : 0.047 0.222 2776 Planarity : 0.004 0.066 3058 Dihedral : 11.441 87.978 2750 Min Nonbonded Distance : 1.740 Molprobity Statistics. All-atom Clashscore : 11.48 Ramachandran Plot: Outliers : 0.04 % Allowed : 11.84 % Favored : 88.12 % Rotamer: Outliers : 2.75 % Allowed : 18.79 % Favored : 78.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.06 % 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: -1.34 (0.18), residues: 2340 helix: 0.72 (0.19), residues: 813 sheet: -1.13 (0.28), residues: 336 loop : -2.04 (0.18), residues: 1191 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 354 HIS 0.009 0.002 HIS B 383 PHE 0.029 0.003 PHE B 293 TYR 0.018 0.002 TYR C 258 ARG 0.004 0.001 ARG E 330 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4680 Ramachandran restraints generated. 2340 Oldfield, 0 Emsley, 2340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4680 Ramachandran restraints generated. 2340 Oldfield, 0 Emsley, 2340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 2085 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 99 time to evaluate : 2.054 Fit side-chains REVERT: C 443 GLU cc_start: 0.6446 (pp20) cc_final: 0.6146 (pp20) REVERT: A 431 CYS cc_start: 0.6489 (m) cc_final: 0.5930 (p) REVERT: B 250 PHE cc_start: 0.8442 (OUTLIER) cc_final: 0.8206 (m-80) REVERT: D 341 MET cc_start: 0.9131 (tpp) cc_final: 0.8895 (tpp) REVERT: E 251 LYS cc_start: 0.8677 (pttp) cc_final: 0.8334 (tppt) REVERT: E 341 MET cc_start: 0.9074 (tpp) cc_final: 0.8558 (tpp) REVERT: E 464 ASP cc_start: 0.8672 (m-30) cc_final: 0.8327 (m-30) outliers start: 39 outliers final: 32 residues processed: 129 average time/residue: 0.2375 time to fit residues: 50.8183 Evaluate side-chains 130 residues out of total 2085 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 97 time to evaluate : 2.046 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 291 THR Chi-restraints excluded: chain C residue 319 THR Chi-restraints excluded: chain C residue 396 ASP Chi-restraints excluded: chain C residue 464 ASP Chi-restraints excluded: chain A residue 318 ASN Chi-restraints excluded: chain A residue 347 ASN Chi-restraints excluded: chain A residue 506 LEU Chi-restraints excluded: chain B residue 250 PHE Chi-restraints excluded: chain B residue 318 ASN Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain B residue 381 MET Chi-restraints excluded: chain B residue 496 ILE Chi-restraints excluded: chain D residue 319 THR Chi-restraints excluded: chain D residue 348 LEU Chi-restraints excluded: chain D residue 378 LEU Chi-restraints excluded: chain D residue 402 MET Chi-restraints excluded: chain E residue 244 HIS Chi-restraints excluded: chain E residue 248 VAL Chi-restraints excluded: chain E residue 250 PHE Chi-restraints excluded: chain E residue 257 VAL Chi-restraints excluded: chain E residue 297 THR Chi-restraints excluded: chain E residue 318 ASN Chi-restraints excluded: chain E residue 378 LEU Chi-restraints excluded: chain E residue 414 VAL Chi-restraints excluded: chain E residue 427 THR Chi-restraints excluded: chain E residue 429 THR Chi-restraints excluded: chain E residue 443 GLU Chi-restraints excluded: chain E residue 466 VAL Chi-restraints excluded: chain F residue 250 PHE Chi-restraints excluded: chain F residue 318 ASN Chi-restraints excluded: chain F residue 335 MET Chi-restraints excluded: chain F residue 347 ASN Chi-restraints excluded: chain F residue 400 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 217 optimal weight: 0.9990 chunk 198 optimal weight: 0.7980 chunk 211 optimal weight: 8.9990 chunk 127 optimal weight: 0.9980 chunk 92 optimal weight: 2.9990 chunk 166 optimal weight: 0.9980 chunk 65 optimal weight: 50.0000 chunk 191 optimal weight: 0.7980 chunk 200 optimal weight: 0.9980 chunk 139 optimal weight: 50.0000 chunk 224 optimal weight: 0.8980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 465 ASN ** D 470 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 470 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7179 moved from start: 0.2861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 17389 Z= 0.150 Angle : 0.475 13.138 23723 Z= 0.257 Chirality : 0.041 0.212 2776 Planarity : 0.003 0.054 3058 Dihedral : 11.068 89.629 2750 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.42 % Favored : 91.58 % Rotamer: Outliers : 1.55 % Allowed : 20.48 % Favored : 77.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.06 % 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: -1.03 (0.18), residues: 2340 helix: 1.05 (0.20), residues: 816 sheet: -0.95 (0.29), residues: 329 loop : -1.92 (0.18), residues: 1195 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 354 HIS 0.009 0.001 HIS B 383 PHE 0.029 0.001 PHE E 358 TYR 0.017 0.001 TYR A 388 ARG 0.003 0.000 ARG C 481 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4680 Ramachandran restraints generated. 2340 Oldfield, 0 Emsley, 2340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4680 Ramachandran restraints generated. 2340 Oldfield, 0 Emsley, 2340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 2085 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 109 time to evaluate : 1.992 Fit side-chains revert: symmetry clash REVERT: C 443 GLU cc_start: 0.6434 (pp20) cc_final: 0.6073 (pp20) REVERT: D 341 MET cc_start: 0.9152 (tpp) cc_final: 0.8914 (tpp) REVERT: E 341 MET cc_start: 0.9045 (tpp) cc_final: 0.8621 (tpp) REVERT: E 364 TYR cc_start: 0.8683 (m-80) cc_final: 0.8444 (m-80) REVERT: E 464 ASP cc_start: 0.8597 (m-30) cc_final: 0.8281 (m-30) REVERT: E 491 ASP cc_start: 0.8128 (m-30) cc_final: 0.7735 (t0) REVERT: F 397 ASN cc_start: 0.7849 (t0) cc_final: 0.7514 (t0) outliers start: 22 outliers final: 19 residues processed: 126 average time/residue: 0.2371 time to fit residues: 49.8522 Evaluate side-chains 124 residues out of total 2085 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 105 time to evaluate : 1.814 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 291 THR Chi-restraints excluded: chain C residue 318 ASN Chi-restraints excluded: chain C residue 319 THR Chi-restraints excluded: chain C residue 396 ASP Chi-restraints excluded: chain A residue 347 ASN Chi-restraints excluded: chain A residue 506 LEU Chi-restraints excluded: chain B residue 318 ASN Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain D residue 400 PHE Chi-restraints excluded: chain D residue 474 LEU Chi-restraints excluded: chain E residue 244 HIS Chi-restraints excluded: chain E residue 248 VAL Chi-restraints excluded: chain E residue 250 PHE Chi-restraints excluded: chain E residue 297 THR Chi-restraints excluded: chain E residue 318 ASN Chi-restraints excluded: chain E residue 378 LEU Chi-restraints excluded: chain F residue 250 PHE Chi-restraints excluded: chain F residue 335 MET Chi-restraints excluded: chain F residue 400 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 136 optimal weight: 0.5980 chunk 106 optimal weight: 50.0000 chunk 155 optimal weight: 20.0000 chunk 235 optimal weight: 0.7980 chunk 216 optimal weight: 3.9990 chunk 187 optimal weight: 0.0970 chunk 19 optimal weight: 4.9990 chunk 144 optimal weight: 50.0000 chunk 114 optimal weight: 2.9990 chunk 148 optimal weight: 50.0000 chunk 199 optimal weight: 0.5980 overall best weight: 1.0180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 470 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 488 ASN ** F 470 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 484 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7179 moved from start: 0.2856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 17389 Z= 0.161 Angle : 0.467 13.168 23723 Z= 0.251 Chirality : 0.041 0.199 2776 Planarity : 0.003 0.050 3058 Dihedral : 10.878 88.832 2750 Min Nonbonded Distance : 1.870 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.49 % Favored : 90.51 % Rotamer: Outliers : 1.77 % Allowed : 20.27 % Favored : 77.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.06 % 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: -0.88 (0.18), residues: 2340 helix: 1.26 (0.20), residues: 799 sheet: -0.77 (0.30), residues: 312 loop : -1.88 (0.18), residues: 1229 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 354 HIS 0.010 0.001 HIS B 383 PHE 0.028 0.001 PHE E 358 TYR 0.018 0.001 TYR A 388 ARG 0.003 0.000 ARG C 481 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4680 Ramachandran restraints generated. 2340 Oldfield, 0 Emsley, 2340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4680 Ramachandran restraints generated. 2340 Oldfield, 0 Emsley, 2340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 2085 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 109 time to evaluate : 2.166 Fit side-chains revert: symmetry clash REVERT: C 386 TYR cc_start: 0.8892 (m-80) cc_final: 0.8674 (m-80) REVERT: C 443 GLU cc_start: 0.6562 (pp20) cc_final: 0.6162 (pp20) REVERT: A 438 HIS cc_start: 0.6738 (m-70) cc_final: 0.5707 (m-70) REVERT: D 248 VAL cc_start: 0.8797 (t) cc_final: 0.8549 (p) REVERT: D 341 MET cc_start: 0.9127 (tpp) cc_final: 0.8876 (tpp) REVERT: E 341 MET cc_start: 0.9071 (tpp) cc_final: 0.8671 (tpp) REVERT: E 464 ASP cc_start: 0.8654 (m-30) cc_final: 0.8298 (m-30) REVERT: E 491 ASP cc_start: 0.8138 (m-30) cc_final: 0.7732 (t0) REVERT: F 397 ASN cc_start: 0.7864 (t0) cc_final: 0.7504 (t0) outliers start: 25 outliers final: 24 residues processed: 126 average time/residue: 0.2442 time to fit residues: 51.1110 Evaluate side-chains 131 residues out of total 2085 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 107 time to evaluate : 1.868 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 291 THR Chi-restraints excluded: chain C residue 318 ASN Chi-restraints excluded: chain C residue 319 THR Chi-restraints excluded: chain C residue 396 ASP Chi-restraints excluded: chain A residue 347 ASN Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain A residue 506 LEU Chi-restraints excluded: chain B residue 318 ASN Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain B residue 381 MET Chi-restraints excluded: chain B residue 496 ILE Chi-restraints excluded: chain D residue 400 PHE Chi-restraints excluded: chain D residue 474 LEU Chi-restraints excluded: chain E residue 244 HIS Chi-restraints excluded: chain E residue 248 VAL Chi-restraints excluded: chain E residue 250 PHE Chi-restraints excluded: chain E residue 297 THR Chi-restraints excluded: chain E residue 318 ASN Chi-restraints excluded: chain E residue 378 LEU Chi-restraints excluded: chain E residue 443 GLU Chi-restraints excluded: chain E residue 477 CYS Chi-restraints excluded: chain F residue 250 PHE Chi-restraints excluded: chain F residue 335 MET Chi-restraints excluded: chain F residue 400 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 57 optimal weight: 50.0000 chunk 172 optimal weight: 2.9990 chunk 27 optimal weight: 0.7980 chunk 52 optimal weight: 50.0000 chunk 187 optimal weight: 0.0970 chunk 78 optimal weight: 5.9990 chunk 192 optimal weight: 0.8980 chunk 23 optimal weight: 4.9990 chunk 34 optimal weight: 0.9980 chunk 164 optimal weight: 0.6980 chunk 10 optimal weight: 40.0000 overall best weight: 0.6978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 470 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 470 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 = 0.4112 r_free = 0.4112 target = 0.108104 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.073009 restraints weight = 50820.436| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.075615 restraints weight = 22039.990| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.077263 restraints weight = 14033.531| |-----------------------------------------------------------------------------| r_work (final): 0.3497 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7471 moved from start: 0.2834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 17389 Z= 0.127 Angle : 0.451 13.606 23723 Z= 0.242 Chirality : 0.040 0.187 2776 Planarity : 0.003 0.044 3058 Dihedral : 10.673 89.329 2750 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.29 % Favored : 91.71 % Rotamer: Outliers : 1.55 % Allowed : 20.55 % Favored : 77.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.06 % 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: -0.77 (0.18), residues: 2340 helix: 1.40 (0.20), residues: 793 sheet: -0.52 (0.31), residues: 312 loop : -1.88 (0.18), residues: 1235 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 354 HIS 0.009 0.001 HIS B 383 PHE 0.040 0.001 PHE E 358 TYR 0.017 0.001 TYR A 388 ARG 0.003 0.000 ARG C 481 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2792.94 seconds wall clock time: 52 minutes 3.11 seconds (3123.11 seconds total)