Starting phenix.real_space_refine on Sat Mar 16 20:55:34 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6fo1_4287/03_2024/6fo1_4287_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6fo1_4287/03_2024/6fo1_4287.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.57 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6fo1_4287/03_2024/6fo1_4287.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6fo1_4287/03_2024/6fo1_4287.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6fo1_4287/03_2024/6fo1_4287_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6fo1_4287/03_2024/6fo1_4287_updated.pdb" } resolution = 3.57 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= 0.000 sd= 0.005 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 73 5.16 5 C 9803 2.51 5 N 2729 2.21 5 O 3028 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 276": "NH1" <-> "NH2" Residue "B ARG 357": "NH1" <-> "NH2" Residue "C ARG 117": "NH1" <-> "NH2" Residue "C ARG 333": "NH1" <-> "NH2" Residue "D ARG 400": "NH1" <-> "NH2" Residue "E ARG 273": "NH1" <-> "NH2" Residue "E ARG 353": "NH1" <-> "NH2" Residue "E ARG 400": "NH1" <-> "NH2" Residue "F ARG 124": "NH1" <-> "NH2" Residue "F ARG 253": "NH1" <-> "NH2" Residue "F ARG 400": "NH1" <-> "NH2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 15645 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 2469 Number of conformers: 1 Conformer: "" Number of residues, atoms: 323, 2469 Classifications: {'peptide': 323} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 10, 'TRANS': 312} Chain breaks: 2 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 2389 Number of conformers: 1 Conformer: "" Number of residues, atoms: 313, 2389 Classifications: {'peptide': 313} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 10, 'TRANS': 302} Chain breaks: 2 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "C" Number of atoms: 2416 Number of conformers: 1 Conformer: "" Number of residues, atoms: 319, 2416 Classifications: {'peptide': 319} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 10, 'TRANS': 308} Chain breaks: 2 Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 19 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "D" Number of atoms: 2377 Number of conformers: 1 Conformer: "" Number of residues, atoms: 310, 2377 Classifications: {'peptide': 310} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 9, 'TRANS': 300} Chain breaks: 2 Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 43 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 1, 'ARG:plan': 1, 'ASN:plan1': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 23 Chain: "E" Number of atoms: 2392 Number of conformers: 1 Conformer: "" Number of residues, atoms: 311, 2392 Classifications: {'peptide': 311} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 9, 'TRANS': 301} Chain breaks: 2 Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 14 Chain: "F" Number of atoms: 2400 Number of conformers: 1 Conformer: "" Number of residues, atoms: 311, 2400 Classifications: {'peptide': 311} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 9, 'TRANS': 301} Chain breaks: 2 Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 17 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "G" Number of atoms: 1040 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 1040 Classifications: {'peptide': 125} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 116} Chain: "A" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 8.20, per 1000 atoms: 0.52 Number of scatterers: 15645 At special positions: 0 Unit cell: (129.32, 135.68, 100.7, 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 73 16.00 P 12 15.00 O 3028 8.00 N 2729 7.00 C 9803 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=7, symmetry=0 Number of additional bonds: simple=7, symmetry=0 Coordination: Other bonds: Time building additional restraints: 7.18 Conformation dependent library (CDL) restraints added in 2.8 seconds 3948 Ramachandran restraints generated. 1974 Oldfield, 0 Emsley, 1974 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3748 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 100 helices and 19 sheets defined 51.4% alpha, 10.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.06 Creating SS restraints... Processing helix chain 'A' and resid 15 through 18 Processing helix chain 'A' and resid 43 through 57 Processing helix chain 'A' and resid 76 through 87 removed outlier: 3.504A pdb=" N ALA A 84 " --> pdb=" O ALA A 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 98 through 100 No H-bonds generated for 'chain 'A' and resid 98 through 100' Processing helix chain 'A' and resid 108 through 119 removed outlier: 3.574A pdb=" N ASN A 115 " --> pdb=" O VAL A 111 " (cutoff:3.500A) Processing helix chain 'A' and resid 240 through 246 Processing helix chain 'A' and resid 273 through 289 removed outlier: 3.773A pdb=" N TYR A 286 " --> pdb=" O VAL A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 304 through 306 No H-bonds generated for 'chain 'A' and resid 304 through 306' Processing helix chain 'A' and resid 309 through 319 removed outlier: 3.767A pdb=" N THR A 313 " --> pdb=" O ILE A 309 " (cutoff:3.500A) Processing helix chain 'A' and resid 347 through 349 No H-bonds generated for 'chain 'A' and resid 347 through 349' Processing helix chain 'A' and resid 352 through 357 removed outlier: 5.009A pdb=" N ARG A 357 " --> pdb=" O ASP A 353 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 381 removed outlier: 3.644A pdb=" N ILE A 377 " --> pdb=" O GLN A 373 " (cutoff:3.500A) Processing helix chain 'A' and resid 388 through 400 removed outlier: 3.598A pdb=" N ILE A 397 " --> pdb=" O HIS A 393 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 419 removed outlier: 3.615A pdb=" N GLN A 408 " --> pdb=" O ARG A 404 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N LEU A 410 " --> pdb=" O SER A 406 " (cutoff:3.500A) removed outlier: 4.817A pdb=" N THR A 411 " --> pdb=" O VAL A 407 " (cutoff:3.500A) Proline residue: A 412 - end of helix Processing helix chain 'A' and resid 427 through 436 removed outlier: 3.839A pdb=" N GLU A 435 " --> pdb=" O GLU A 431 " (cutoff:3.500A) Processing helix chain 'A' and resid 440 through 454 removed outlier: 4.434A pdb=" N LYS A 453 " --> pdb=" O ASP A 449 " (cutoff:3.500A) Processing helix chain 'B' and resid 12 through 18 removed outlier: 5.295A pdb=" N SER B 17 " --> pdb=" O GLN B 13 " (cutoff:3.500A) removed outlier: 5.403A pdb=" N HIS B 18 " --> pdb=" O ARG B 14 " (cutoff:3.500A) Processing helix chain 'B' and resid 43 through 57 removed outlier: 3.624A pdb=" N GLU B 54 " --> pdb=" O GLY B 50 " (cutoff:3.500A) Processing helix chain 'B' and resid 76 through 86 Processing helix chain 'B' and resid 98 through 100 No H-bonds generated for 'chain 'B' and resid 98 through 100' Processing helix chain 'B' and resid 108 through 119 Processing helix chain 'B' and resid 242 through 248 removed outlier: 3.896A pdb=" N ASN B 247 " --> pdb=" O LEU B 243 " (cutoff:3.500A) Processing helix chain 'B' and resid 273 through 289 removed outlier: 3.679A pdb=" N GLU B 278 " --> pdb=" O LYS B 274 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ILE B 279 " --> pdb=" O LEU B 275 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ASN B 280 " --> pdb=" O ARG B 276 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N LYS B 281 " --> pdb=" O GLY B 277 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N TYR B 286 " --> pdb=" O VAL B 282 " (cutoff:3.500A) Processing helix chain 'B' and resid 304 through 306 No H-bonds generated for 'chain 'B' and resid 304 through 306' Processing helix chain 'B' and resid 309 through 320 removed outlier: 3.748A pdb=" N THR B 313 " --> pdb=" O ILE B 309 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N GLU B 320 " --> pdb=" O HIS B 316 " (cutoff:3.500A) Processing helix chain 'B' and resid 347 through 349 No H-bonds generated for 'chain 'B' and resid 347 through 349' Processing helix chain 'B' and resid 352 through 355 No H-bonds generated for 'chain 'B' and resid 352 through 355' Processing helix chain 'B' and resid 368 through 382 removed outlier: 3.854A pdb=" N GLN B 373 " --> pdb=" O GLN B 369 " (cutoff:3.500A) Processing helix chain 'B' and resid 388 through 400 removed outlier: 3.710A pdb=" N ASN B 392 " --> pdb=" O GLU B 388 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N GLU B 396 " --> pdb=" O ASN B 392 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 419 removed outlier: 3.893A pdb=" N LEU B 410 " --> pdb=" O SER B 406 " (cutoff:3.500A) removed outlier: 4.842A pdb=" N THR B 411 " --> pdb=" O VAL B 407 " (cutoff:3.500A) Proline residue: B 412 - end of helix Processing helix chain 'B' and resid 427 through 436 removed outlier: 3.855A pdb=" N GLU B 435 " --> pdb=" O GLU B 431 " (cutoff:3.500A) Processing helix chain 'B' and resid 440 through 451 Processing helix chain 'C' and resid 15 through 18 Processing helix chain 'C' and resid 43 through 57 Processing helix chain 'C' and resid 76 through 87 removed outlier: 3.508A pdb=" N ALA C 84 " --> pdb=" O ALA C 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 98 through 100 No H-bonds generated for 'chain 'C' and resid 98 through 100' Processing helix chain 'C' and resid 108 through 119 removed outlier: 3.598A pdb=" N ARG C 117 " --> pdb=" O MET C 113 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ALA C 119 " --> pdb=" O ASN C 115 " (cutoff:3.500A) Processing helix chain 'C' and resid 240 through 245 removed outlier: 3.544A pdb=" N ASP C 244 " --> pdb=" O LEU C 240 " (cutoff:3.500A) Processing helix chain 'C' and resid 273 through 288 removed outlier: 3.597A pdb=" N GLU C 278 " --> pdb=" O LYS C 274 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N TYR C 286 " --> pdb=" O VAL C 282 " (cutoff:3.500A) Processing helix chain 'C' and resid 304 through 306 No H-bonds generated for 'chain 'C' and resid 304 through 306' Processing helix chain 'C' and resid 309 through 320 removed outlier: 3.540A pdb=" N ARG C 317 " --> pdb=" O THR C 313 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N GLU C 320 " --> pdb=" O HIS C 316 " (cutoff:3.500A) Processing helix chain 'C' and resid 347 through 349 No H-bonds generated for 'chain 'C' and resid 347 through 349' Processing helix chain 'C' and resid 352 through 357 removed outlier: 4.547A pdb=" N ARG C 357 " --> pdb=" O ASP C 353 " (cutoff:3.500A) Processing helix chain 'C' and resid 368 through 382 removed outlier: 3.586A pdb=" N ILE C 377 " --> pdb=" O GLN C 373 " (cutoff:3.500A) Processing helix chain 'C' and resid 388 through 400 removed outlier: 3.564A pdb=" N GLU C 396 " --> pdb=" O ASN C 392 " (cutoff:3.500A) Processing helix chain 'C' and resid 403 through 419 removed outlier: 3.934A pdb=" N LEU C 410 " --> pdb=" O SER C 406 " (cutoff:3.500A) removed outlier: 4.872A pdb=" N THR C 411 " --> pdb=" O VAL C 407 " (cutoff:3.500A) Proline residue: C 412 - end of helix Processing helix chain 'C' and resid 427 through 436 Processing helix chain 'C' and resid 440 through 450 removed outlier: 4.196A pdb=" N LYS C 445 " --> pdb=" O LYS C 441 " (cutoff:3.500A) Processing helix chain 'D' and resid 50 through 64 removed outlier: 3.650A pdb=" N ARG D 54 " --> pdb=" O LEU D 50 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLU D 61 " --> pdb=" O GLY D 57 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N MET D 62 " --> pdb=" O VAL D 58 " (cutoff:3.500A) Processing helix chain 'D' and resid 83 through 94 Processing helix chain 'D' and resid 105 through 108 removed outlier: 3.603A pdb=" N ILE D 108 " --> pdb=" O GLY D 105 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 105 through 108' Processing helix chain 'D' and resid 115 through 126 removed outlier: 3.636A pdb=" N ALA D 122 " --> pdb=" O ALA D 118 " (cutoff:3.500A) Processing helix chain 'D' and resid 244 through 252 removed outlier: 4.011A pdb=" N ILE D 250 " --> pdb=" O GLU D 246 " (cutoff:3.500A) Processing helix chain 'D' and resid 270 through 286 removed outlier: 3.845A pdb=" N GLU D 274 " --> pdb=" O SER D 270 " (cutoff:3.500A) Processing helix chain 'D' and resid 301 through 303 No H-bonds generated for 'chain 'D' and resid 301 through 303' Processing helix chain 'D' and resid 306 through 317 removed outlier: 4.261A pdb=" N PHE D 311 " --> pdb=" O GLU D 307 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N GLU D 317 " --> pdb=" O ASN D 313 " (cutoff:3.500A) Processing helix chain 'D' and resid 343 through 345 No H-bonds generated for 'chain 'D' and resid 343 through 345' Processing helix chain 'D' and resid 348 through 351 No H-bonds generated for 'chain 'D' and resid 348 through 351' Processing helix chain 'D' and resid 364 through 377 removed outlier: 3.569A pdb=" N GLU D 376 " --> pdb=" O ARG D 372 " (cutoff:3.500A) Processing helix chain 'D' and resid 384 through 396 Processing helix chain 'D' and resid 399 through 413 removed outlier: 3.780A pdb=" N ILE D 406 " --> pdb=" O ALA D 402 " (cutoff:3.500A) removed outlier: 4.799A pdb=" N THR D 407 " --> pdb=" O ILE D 403 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N ALA D 408 " --> pdb=" O GLN D 404 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N VAL D 412 " --> pdb=" O ALA D 408 " (cutoff:3.500A) Processing helix chain 'D' and resid 423 through 432 Processing helix chain 'D' and resid 436 through 451 removed outlier: 4.110A pdb=" N GLU D 445 " --> pdb=" O GLN D 441 " (cutoff:3.500A) removed outlier: 5.605A pdb=" N TYR D 446 " --> pdb=" O TYR D 442 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N PHE D 450 " --> pdb=" O TYR D 446 " (cutoff:3.500A) Processing helix chain 'E' and resid 50 through 64 removed outlier: 3.576A pdb=" N ARG E 54 " --> pdb=" O LEU E 50 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLU E 61 " --> pdb=" O GLY E 57 " (cutoff:3.500A) Processing helix chain 'E' and resid 83 through 94 Processing helix chain 'E' and resid 115 through 125 Processing helix chain 'E' and resid 244 through 249 removed outlier: 3.524A pdb=" N ASP E 248 " --> pdb=" O LEU E 244 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N VAL E 249 " --> pdb=" O HIS E 245 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 244 through 249' Processing helix chain 'E' and resid 270 through 286 removed outlier: 3.695A pdb=" N GLU E 285 " --> pdb=" O ALA E 281 " (cutoff:3.500A) Processing helix chain 'E' and resid 301 through 303 No H-bonds generated for 'chain 'E' and resid 301 through 303' Processing helix chain 'E' and resid 306 through 313 removed outlier: 3.880A pdb=" N PHE E 311 " --> pdb=" O GLU E 307 " (cutoff:3.500A) Processing helix chain 'E' and resid 343 through 345 No H-bonds generated for 'chain 'E' and resid 343 through 345' Processing helix chain 'E' and resid 348 through 353 removed outlier: 3.637A pdb=" N ASP E 352 " --> pdb=" O ILE E 348 " (cutoff:3.500A) removed outlier: 5.001A pdb=" N ARG E 353 " --> pdb=" O ASP E 349 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 348 through 353' Processing helix chain 'E' and resid 364 through 377 removed outlier: 3.596A pdb=" N GLU E 376 " --> pdb=" O ARG E 372 " (cutoff:3.500A) Processing helix chain 'E' and resid 384 through 396 Processing helix chain 'E' and resid 399 through 416 removed outlier: 3.536A pdb=" N ILE E 403 " --> pdb=" O LEU E 399 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N GLN E 404 " --> pdb=" O ARG E 400 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ILE E 406 " --> pdb=" O ALA E 402 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N THR E 407 " --> pdb=" O ILE E 403 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ALA E 408 " --> pdb=" O GLN E 404 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LEU E 411 " --> pdb=" O THR E 407 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N VAL E 412 " --> pdb=" O ALA E 408 " (cutoff:3.500A) Processing helix chain 'E' and resid 423 through 432 Processing helix chain 'E' and resid 436 through 452 removed outlier: 3.518A pdb=" N ALA E 449 " --> pdb=" O GLU E 445 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N PHE E 450 " --> pdb=" O TYR E 446 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N LEU E 451 " --> pdb=" O GLN E 447 " (cutoff:3.500A) Processing helix chain 'F' and resid 50 through 64 removed outlier: 3.701A pdb=" N GLU F 61 " --> pdb=" O GLY F 57 " (cutoff:3.500A) Processing helix chain 'F' and resid 83 through 94 Processing helix chain 'F' and resid 115 through 125 Processing helix chain 'F' and resid 244 through 252 removed outlier: 3.563A pdb=" N VAL F 249 " --> pdb=" O HIS F 245 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ILE F 250 " --> pdb=" O GLU F 246 " (cutoff:3.500A) Processing helix chain 'F' and resid 270 through 286 removed outlier: 3.518A pdb=" N ALA F 278 " --> pdb=" O GLU F 274 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LYS F 279 " --> pdb=" O GLN F 275 " (cutoff:3.500A) Processing helix chain 'F' and resid 301 through 303 No H-bonds generated for 'chain 'F' and resid 301 through 303' Processing helix chain 'F' and resid 306 through 316 removed outlier: 3.574A pdb=" N PHE F 311 " --> pdb=" O GLU F 307 " (cutoff:3.500A) Processing helix chain 'F' and resid 343 through 345 No H-bonds generated for 'chain 'F' and resid 343 through 345' Processing helix chain 'F' and resid 348 through 353 removed outlier: 3.649A pdb=" N ASP F 352 " --> pdb=" O ILE F 348 " (cutoff:3.500A) removed outlier: 4.847A pdb=" N ARG F 353 " --> pdb=" O ASP F 349 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 348 through 353' Processing helix chain 'F' and resid 364 through 377 removed outlier: 3.664A pdb=" N ILE F 370 " --> pdb=" O ASP F 366 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLU F 376 " --> pdb=" O ARG F 372 " (cutoff:3.500A) Processing helix chain 'F' and resid 384 through 396 Processing helix chain 'F' and resid 399 through 416 removed outlier: 3.509A pdb=" N GLN F 404 " --> pdb=" O ARG F 400 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N THR F 407 " --> pdb=" O ILE F 403 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N ALA F 408 " --> pdb=" O GLN F 404 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LEU F 411 " --> pdb=" O THR F 407 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N VAL F 412 " --> pdb=" O ALA F 408 " (cutoff:3.500A) Processing helix chain 'F' and resid 423 through 432 removed outlier: 3.684A pdb=" N SER F 431 " --> pdb=" O LYS F 427 " (cutoff:3.500A) Processing helix chain 'F' and resid 436 through 450 Processing helix chain 'G' and resid 550 through 560 Processing helix chain 'G' and resid 563 through 565 No H-bonds generated for 'chain 'G' and resid 563 through 565' Processing helix chain 'G' and resid 567 through 572 Processing helix chain 'G' and resid 575 through 582 Proline residue: G 579 - end of helix removed outlier: 4.056A pdb=" N PHE G 582 " --> pdb=" O TYR G 578 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 575 through 582' Processing helix chain 'G' and resid 588 through 602 removed outlier: 3.743A pdb=" N GLN G 593 " --> pdb=" O ASP G 589 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ILE G 594 " --> pdb=" O VAL G 590 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LYS G 596 " --> pdb=" O ASN G 592 " (cutoff:3.500A) Processing helix chain 'G' and resid 608 through 619 removed outlier: 3.609A pdb=" N ARG G 617 " --> pdb=" O GLU G 613 " (cutoff:3.500A) Processing helix chain 'G' and resid 624 through 630 removed outlier: 3.511A pdb=" N VAL G 628 " --> pdb=" O PHE G 624 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N MET G 629 " --> pdb=" O ASP G 625 " (cutoff:3.500A) Processing helix chain 'G' and resid 635 through 649 removed outlier: 3.727A pdb=" N ASP G 647 " --> pdb=" O PHE G 643 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N LYS G 648 " --> pdb=" O ASN G 644 " (cutoff:3.500A) Processing helix chain 'G' and resid 654 through 661 Processing sheet with id= A, first strand: chain 'A' and resid 358 through 363 removed outlier: 6.947A pdb=" N ALA A 65 " --> pdb=" O MET A 359 " (cutoff:3.500A) removed outlier: 8.038A pdb=" N ILE A 361 " --> pdb=" O ALA A 65 " (cutoff:3.500A) removed outlier: 6.096A pdb=" N LEU A 67 " --> pdb=" O ILE A 361 " (cutoff:3.500A) removed outlier: 7.502A pdb=" N THR A 363 " --> pdb=" O LEU A 67 " (cutoff:3.500A) removed outlier: 7.186A pdb=" N ALA A 69 " --> pdb=" O THR A 363 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LEU A 68 " --> pdb=" O PHE A 329 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 293 through 296 Processing sheet with id= C, first strand: chain 'A' and resid 335 through 337 Processing sheet with id= D, first strand: chain 'B' and resid 358 through 363 removed outlier: 6.831A pdb=" N ALA B 65 " --> pdb=" O MET B 359 " (cutoff:3.500A) removed outlier: 8.268A pdb=" N ILE B 361 " --> pdb=" O ALA B 65 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N LEU B 67 " --> pdb=" O ILE B 361 " (cutoff:3.500A) removed outlier: 7.462A pdb=" N THR B 363 " --> pdb=" O LEU B 67 " (cutoff:3.500A) removed outlier: 7.096A pdb=" N ALA B 69 " --> pdb=" O THR B 363 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N SER B 331 " --> pdb=" O LEU B 68 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 120 through 123 Processing sheet with id= F, first strand: chain 'B' and resid 335 through 337 Processing sheet with id= G, first strand: chain 'C' and resid 65 through 70 Processing sheet with id= H, first strand: chain 'C' and resid 93 through 97 removed outlier: 7.169A pdb=" N VAL C 298 " --> pdb=" O CYS C 94 " (cutoff:3.500A) removed outlier: 7.735A pdb=" N MET C 96 " --> pdb=" O VAL C 298 " (cutoff:3.500A) removed outlier: 6.066A pdb=" N PHE C 300 " --> pdb=" O MET C 96 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N ILE C 326 " --> pdb=" O LEU C 299 " (cutoff:3.500A) removed outlier: 7.440A pdb=" N VAL C 301 " --> pdb=" O ILE C 326 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N ILE C 328 " --> pdb=" O VAL C 301 " (cutoff:3.500A) No H-bonds generated for sheet with id= H Processing sheet with id= I, first strand: chain 'C' and resid 294 through 296 removed outlier: 3.507A pdb=" N ILE C 124 " --> pdb=" O GLN C 236 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'C' and resid 335 through 337 Processing sheet with id= K, first strand: chain 'D' and resid 354 through 359 removed outlier: 6.651A pdb=" N ALA D 72 " --> pdb=" O LEU D 355 " (cutoff:3.500A) removed outlier: 7.811A pdb=" N VAL D 357 " --> pdb=" O ALA D 72 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N LEU D 74 " --> pdb=" O VAL D 357 " (cutoff:3.500A) removed outlier: 7.496A pdb=" N THR D 359 " --> pdb=" O LEU D 74 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N ALA D 76 " --> pdb=" O THR D 359 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'D' and resid 127 through 130 Processing sheet with id= M, first strand: chain 'D' and resid 332 through 334 Processing sheet with id= N, first strand: chain 'E' and resid 354 through 359 removed outlier: 6.542A pdb=" N ALA E 72 " --> pdb=" O LEU E 355 " (cutoff:3.500A) removed outlier: 7.778A pdb=" N VAL E 357 " --> pdb=" O ALA E 72 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N LEU E 74 " --> pdb=" O VAL E 357 " (cutoff:3.500A) removed outlier: 7.673A pdb=" N THR E 359 " --> pdb=" O LEU E 74 " (cutoff:3.500A) removed outlier: 7.206A pdb=" N ALA E 76 " --> pdb=" O THR E 359 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'E' and resid 127 through 130 Processing sheet with id= P, first strand: chain 'E' and resid 332 through 334 Processing sheet with id= Q, first strand: chain 'F' and resid 354 through 359 removed outlier: 6.513A pdb=" N ALA F 72 " --> pdb=" O LEU F 355 " (cutoff:3.500A) removed outlier: 7.338A pdb=" N VAL F 357 " --> pdb=" O ALA F 72 " (cutoff:3.500A) removed outlier: 6.076A pdb=" N LEU F 74 " --> pdb=" O VAL F 357 " (cutoff:3.500A) removed outlier: 7.295A pdb=" N THR F 359 " --> pdb=" O LEU F 74 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N ALA F 76 " --> pdb=" O THR F 359 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N THR F 328 " --> pdb=" O ILE F 75 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'F' and resid 127 through 130 Processing sheet with id= S, first strand: chain 'F' and resid 332 through 334 644 hydrogen bonds defined for protein. 1908 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: 4.95 Time building geometry restraints manager: 7.63 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: 5261 1.34 - 1.46: 2682 1.46 - 1.57: 7759 1.57 - 1.69: 18 1.69 - 1.81: 128 Bond restraints: 15848 Sorted by residual: bond pdb=" CA ASP D 352 " pdb=" C ASP D 352 " ideal model delta sigma weight residual 1.524 1.491 0.034 1.66e-02 3.63e+03 4.11e+00 bond pdb=" CA LEU G 559 " pdb=" C LEU G 559 " ideal model delta sigma weight residual 1.523 1.551 -0.028 1.56e-02 4.11e+03 3.15e+00 bond pdb=" C GLU G 574 " pdb=" N PRO G 575 " ideal model delta sigma weight residual 1.333 1.358 -0.025 1.44e-02 4.82e+03 2.95e+00 bond pdb=" C4 ADP A 501 " pdb=" C5 ADP A 501 " ideal model delta sigma weight residual 1.490 1.458 0.032 2.00e-02 2.50e+03 2.63e+00 bond pdb=" CB PHE G 630 " pdb=" CG PHE G 630 " ideal model delta sigma weight residual 1.502 1.468 0.034 2.30e-02 1.89e+03 2.25e+00 ... (remaining 15843 not shown) Histogram of bond angle deviations from ideal: 98.49 - 105.95: 321 105.95 - 113.41: 9404 113.41 - 120.86: 7260 120.86 - 128.32: 4346 128.32 - 135.78: 78 Bond angle restraints: 21409 Sorted by residual: angle pdb=" C THR C 341 " pdb=" N GLU C 342 " pdb=" CA GLU C 342 " ideal model delta sigma weight residual 121.54 129.52 -7.98 1.91e+00 2.74e-01 1.75e+01 angle pdb=" N LEU G 559 " pdb=" CA LEU G 559 " pdb=" C LEU G 559 " ideal model delta sigma weight residual 113.02 117.33 -4.31 1.20e+00 6.94e-01 1.29e+01 angle pdb=" C GLU F 378 " pdb=" N ASP F 379 " pdb=" CA ASP F 379 " ideal model delta sigma weight residual 122.46 127.02 -4.56 1.41e+00 5.03e-01 1.05e+01 angle pdb=" N GLN F 41 " pdb=" CA GLN F 41 " pdb=" CB GLN F 41 " ideal model delta sigma weight residual 114.17 110.54 3.63 1.14e+00 7.69e-01 1.01e+01 angle pdb=" C GLY E 418 " pdb=" N THR E 419 " pdb=" CA THR E 419 " ideal model delta sigma weight residual 121.54 127.30 -5.76 1.91e+00 2.74e-01 9.11e+00 ... (remaining 21404 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.27: 9551 26.27 - 52.53: 164 52.53 - 78.80: 27 78.80 - 105.06: 1 105.06 - 131.33: 6 Dihedral angle restraints: 9749 sinusoidal: 3963 harmonic: 5786 Sorted by residual: dihedral pdb=" O1B ADP E 501 " pdb=" O3A ADP E 501 " pdb=" PB ADP E 501 " pdb=" PA ADP E 501 " ideal model delta sinusoidal sigma weight residual -60.00 71.33 -131.33 1 2.00e+01 2.50e-03 3.98e+01 dihedral pdb=" O1B ADP F 501 " pdb=" O3A ADP F 501 " pdb=" PB ADP F 501 " pdb=" PA ADP F 501 " ideal model delta sinusoidal sigma weight residual -60.00 65.60 -125.60 1 2.00e+01 2.50e-03 3.80e+01 dihedral pdb=" O1B ADP D 501 " pdb=" O3A ADP D 501 " pdb=" PB ADP D 501 " pdb=" PA ADP D 501 " ideal model delta sinusoidal sigma weight residual -60.00 63.10 -123.11 1 2.00e+01 2.50e-03 3.71e+01 ... (remaining 9746 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 1653 0.039 - 0.077: 659 0.077 - 0.116: 188 0.116 - 0.154: 22 0.154 - 0.193: 6 Chirality restraints: 2528 Sorted by residual: chirality pdb=" CB THR A 402 " pdb=" CA THR A 402 " pdb=" OG1 THR A 402 " pdb=" CG2 THR A 402 " both_signs ideal model delta sigma weight residual False 2.55 2.36 0.19 2.00e-01 2.50e+01 9.32e-01 chirality pdb=" CA PRO G 575 " pdb=" N PRO G 575 " pdb=" C PRO G 575 " pdb=" CB PRO G 575 " both_signs ideal model delta sigma weight residual False 2.72 2.53 0.19 2.00e-01 2.50e+01 8.81e-01 chirality pdb=" CB THR C 402 " pdb=" CA THR C 402 " pdb=" OG1 THR C 402 " pdb=" CG2 THR C 402 " both_signs ideal model delta sigma weight residual False 2.55 2.37 0.18 2.00e-01 2.50e+01 8.51e-01 ... (remaining 2525 not shown) Planarity restraints: 2725 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE E 292 " 0.026 5.00e-02 4.00e+02 3.88e-02 2.41e+00 pdb=" N PRO E 293 " -0.067 5.00e-02 4.00e+02 pdb=" CA PRO E 293 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO E 293 " 0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN D 78 " -0.024 5.00e-02 4.00e+02 3.69e-02 2.18e+00 pdb=" N PRO D 79 " 0.064 5.00e-02 4.00e+02 pdb=" CA PRO D 79 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO D 79 " -0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU G 574 " 0.024 5.00e-02 4.00e+02 3.68e-02 2.16e+00 pdb=" N PRO G 575 " -0.064 5.00e-02 4.00e+02 pdb=" CA PRO G 575 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO G 575 " 0.021 5.00e-02 4.00e+02 ... (remaining 2722 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.61: 225 2.61 - 3.18: 15898 3.18 - 3.76: 22457 3.76 - 4.33: 34415 4.33 - 4.90: 53804 Nonbonded interactions: 126799 Sorted by model distance: nonbonded pdb=" OD1 ASP B 439 " pdb=" OG SER B 442 " model vdw 2.039 2.440 nonbonded pdb=" OD1 ASP C 439 " pdb=" OG SER C 442 " model vdw 2.050 2.440 nonbonded pdb=" O GLU C 396 " pdb=" OG1 THR C 399 " model vdw 2.081 2.440 nonbonded pdb=" OG SER C 17 " pdb=" O3' ADP C 501 " model vdw 2.087 2.440 nonbonded pdb=" OD1 ASP A 439 " pdb=" OG SER A 442 " model vdw 2.089 2.440 ... (remaining 126794 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' and (resid 5 through 123 or resid 238 through 248 or (resid 271 throu \ gh 272 and (name N or name CA or name C or name O or name CB )) or resid 273 or \ (resid 274 through 276 and (name N or name CA or name C or name O or name CB )) \ or resid 277 through 452 or resid 501)) selection = (chain 'B' and (resid 5 through 248 or (resid 271 through 272 and (name N or nam \ e CA or name C or name O or name CB )) or resid 273 or (resid 274 through 276 an \ d (name N or name CA or name C or name O or name CB )) or resid 277 through 452 \ or resid 501)) selection = (chain 'C' and (resid 5 through 123 or resid 238 through 248 or resid 271 throug \ h 452 or resid 501)) } ncs_group { reference = chain 'D' selection = (chain 'E' and (resid 23 through 253 or resid 267 through 269 or (resid 270 and \ (name N or name CA or name C or name O or name CB )) or resid 271 through 451 or \ (resid 452 through 453 and (name N or name CA or name C or name O or name CB )) \ or resid 501)) selection = (chain 'F' and (resid 23 through 252 or (resid 253 through 267 and (name N or na \ me CA or name C or name O or name CB )) or resid 268 through 451 or (resid 452 t \ hrough 453 and (name N or name CA or name C or name O or name CB )) or resid 501 \ )) } 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=0.01 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: 2.000 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: 0.010 Extract box with map and model: 7.450 Check model and map are aligned: 0.240 Set scattering table: 0.150 Process input model: 44.590 Find NCS groups from input model: 1.120 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:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 58.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8357 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 : 0.007 0.049 15848 Z= 0.472 Angle : 0.815 8.461 21409 Z= 0.455 Chirality : 0.044 0.193 2528 Planarity : 0.004 0.039 2725 Dihedral : 10.812 131.330 6001 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 23.07 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.08 % Favored : 93.87 % Rotamer: Outliers : 0.06 % Allowed : 2.88 % Favored : 97.06 % 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: -3.76 (0.16), residues: 1974 helix: -2.86 (0.11), residues: 1067 sheet: -1.50 (0.35), residues: 191 loop : -1.80 (0.23), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP E 283 HIS 0.007 0.002 HIS F 245 PHE 0.025 0.003 PHE G 582 TYR 0.019 0.002 TYR G 569 ARG 0.007 0.001 ARG E 273 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3948 Ramachandran restraints generated. 1974 Oldfield, 0 Emsley, 1974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3948 Ramachandran restraints generated. 1974 Oldfield, 0 Emsley, 1974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 416 residues out of total 1702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 415 time to evaluate : 2.041 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 244 ASP cc_start: 0.7794 (m-30) cc_final: 0.7467 (m-30) REVERT: B 94 CYS cc_start: 0.8568 (t) cc_final: 0.8300 (t) REVERT: B 276 ARG cc_start: 0.7970 (mmt90) cc_final: 0.6980 (ttt180) REVERT: C 343 ASP cc_start: 0.7162 (t70) cc_final: 0.6935 (t70) REVERT: C 438 TYR cc_start: 0.8554 (m-80) cc_final: 0.8338 (m-10) REVERT: D 443 MET cc_start: 0.8106 (ttm) cc_final: 0.7882 (ttm) REVERT: E 126 SER cc_start: 0.9119 (m) cc_final: 0.8642 (t) REVERT: E 279 LYS cc_start: 0.8206 (ttpt) cc_final: 0.7975 (tttp) REVERT: E 411 LEU cc_start: 0.9104 (tp) cc_final: 0.8876 (tp) REVERT: F 78 GLN cc_start: 0.7774 (mm110) cc_final: 0.7354 (mm-40) REVERT: F 126 SER cc_start: 0.9359 (m) cc_final: 0.8827 (t) REVERT: F 314 ARG cc_start: 0.7904 (ttm110) cc_final: 0.7665 (ttm-80) REVERT: F 382 MET cc_start: 0.6922 (ttp) cc_final: 0.6713 (ttt) REVERT: G 622 LYS cc_start: 0.7881 (mttm) cc_final: 0.7676 (ttpp) REVERT: G 626 MET cc_start: 0.8754 (mmp) cc_final: 0.8450 (mmt) outliers start: 1 outliers final: 0 residues processed: 416 average time/residue: 0.3374 time to fit residues: 191.3129 Evaluate side-chains 232 residues out of total 1702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 232 time to evaluate : 1.710 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 168 optimal weight: 9.9990 chunk 150 optimal weight: 0.9990 chunk 83 optimal weight: 0.0870 chunk 51 optimal weight: 0.7980 chunk 101 optimal weight: 0.8980 chunk 80 optimal weight: 0.9990 chunk 155 optimal weight: 4.9990 chunk 60 optimal weight: 3.9990 chunk 94 optimal weight: 0.9980 chunk 116 optimal weight: 0.8980 chunk 180 optimal weight: 0.6980 overall best weight: 0.6758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 18 HIS A 20 HIS A 247 ASN B 18 HIS B 393 HIS B 408 GLN B 450 GLN C 280 ASN C 284 ASN C 316 HIS C 393 HIS D 25 HIS D 404 GLN E 78 GLN E 251 ASN E 277 ASN ** E 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 25 HIS F 277 ASN ** F 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 422 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 moved from start: 0.2788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 15848 Z= 0.217 Angle : 0.677 8.692 21409 Z= 0.331 Chirality : 0.044 0.183 2528 Planarity : 0.004 0.040 2725 Dihedral : 9.238 132.983 2224 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 10.77 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.19 % Favored : 96.76 % Rotamer: Outliers : 1.68 % Allowed : 7.97 % Favored : 90.35 % 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: -1.90 (0.18), residues: 1974 helix: -1.02 (0.15), residues: 1118 sheet: -0.91 (0.35), residues: 199 loop : -1.48 (0.23), residues: 657 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP E 283 HIS 0.006 0.001 HIS B 429 PHE 0.018 0.002 PHE F 450 TYR 0.024 0.002 TYR E 430 ARG 0.008 0.001 ARG F 40 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3948 Ramachandran restraints generated. 1974 Oldfield, 0 Emsley, 1974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3948 Ramachandran restraints generated. 1974 Oldfield, 0 Emsley, 1974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 1702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 305 time to evaluate : 2.002 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 294 LEU cc_start: 0.9100 (tp) cc_final: 0.8883 (tp) REVERT: B 276 ARG cc_start: 0.7941 (mmt90) cc_final: 0.6845 (ttt-90) REVERT: C 343 ASP cc_start: 0.6872 (t70) cc_final: 0.6612 (t70) REVERT: C 426 GLU cc_start: 0.8232 (OUTLIER) cc_final: 0.7937 (pt0) REVERT: D 248 ASP cc_start: 0.7417 (m-30) cc_final: 0.7109 (t0) REVERT: D 392 ARG cc_start: 0.8248 (tpt170) cc_final: 0.8026 (tpp80) REVERT: D 427 LYS cc_start: 0.9032 (tttt) cc_final: 0.8732 (ttpp) REVERT: E 46 MET cc_start: 0.8524 (mmm) cc_final: 0.8279 (mmm) REVERT: E 279 LYS cc_start: 0.8059 (ttpt) cc_final: 0.7854 (tttp) REVERT: F 126 SER cc_start: 0.9280 (m) cc_final: 0.8810 (t) REVERT: F 292 ILE cc_start: 0.8775 (OUTLIER) cc_final: 0.8575 (pt) REVERT: G 630 PHE cc_start: 0.7379 (OUTLIER) cc_final: 0.6964 (m-80) outliers start: 28 outliers final: 12 residues processed: 321 average time/residue: 0.2829 time to fit residues: 134.2395 Evaluate side-chains 238 residues out of total 1702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 223 time to evaluate : 1.871 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 THR Chi-restraints excluded: chain A residue 106 ILE Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain C residue 106 ILE Chi-restraints excluded: chain C residue 247 ASN Chi-restraints excluded: chain C residue 426 GLU Chi-restraints excluded: chain D residue 282 GLU Chi-restraints excluded: chain D residue 306 ILE Chi-restraints excluded: chain E residue 306 ILE Chi-restraints excluded: chain E residue 413 CYS Chi-restraints excluded: chain F residue 292 ILE Chi-restraints excluded: chain F residue 413 CYS Chi-restraints excluded: chain G residue 590 VAL Chi-restraints excluded: chain G residue 630 PHE Chi-restraints excluded: chain G residue 636 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 100 optimal weight: 1.9990 chunk 56 optimal weight: 0.9990 chunk 150 optimal weight: 1.9990 chunk 123 optimal weight: 0.5980 chunk 49 optimal weight: 1.9990 chunk 181 optimal weight: 1.9990 chunk 195 optimal weight: 5.9990 chunk 161 optimal weight: 4.9990 chunk 179 optimal weight: 1.9990 chunk 61 optimal weight: 0.8980 chunk 145 optimal weight: 1.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 393 HIS B 408 GLN B 429 HIS B 450 GLN F 25 HIS ** F 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 277 ASN F 341 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8363 moved from start: 0.3191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 15848 Z= 0.289 Angle : 0.644 8.863 21409 Z= 0.311 Chirality : 0.043 0.165 2528 Planarity : 0.003 0.029 2725 Dihedral : 9.082 136.529 2224 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 10.80 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.15 % Favored : 95.80 % Rotamer: Outliers : 3.12 % Allowed : 10.61 % Favored : 86.28 % 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: 1974 helix: -0.39 (0.15), residues: 1133 sheet: -0.35 (0.36), residues: 193 loop : -1.23 (0.23), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP E 283 HIS 0.010 0.001 HIS A 393 PHE 0.016 0.001 PHE D 450 TYR 0.019 0.002 TYR E 430 ARG 0.005 0.001 ARG C 339 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3948 Ramachandran restraints generated. 1974 Oldfield, 0 Emsley, 1974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3948 Ramachandran restraints generated. 1974 Oldfield, 0 Emsley, 1974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 1702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 251 time to evaluate : 1.855 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 276 ARG cc_start: 0.7943 (mmt90) cc_final: 0.6905 (ttt-90) REVERT: B 369 GLN cc_start: 0.8073 (tm-30) cc_final: 0.7681 (tm-30) REVERT: D 427 LYS cc_start: 0.9113 (tttt) cc_final: 0.8764 (ttpp) REVERT: E 46 MET cc_start: 0.8589 (mmm) cc_final: 0.8015 (mmm) REVERT: F 382 MET cc_start: 0.7267 (OUTLIER) cc_final: 0.7053 (mtp) REVERT: G 626 MET cc_start: 0.8809 (mmp) cc_final: 0.8333 (mmm) REVERT: G 630 PHE cc_start: 0.7311 (OUTLIER) cc_final: 0.6983 (m-80) REVERT: G 636 LYS cc_start: 0.8150 (OUTLIER) cc_final: 0.7945 (ptpp) outliers start: 52 outliers final: 26 residues processed: 283 average time/residue: 0.2772 time to fit residues: 115.3592 Evaluate side-chains 253 residues out of total 1702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 224 time to evaluate : 1.879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 THR Chi-restraints excluded: chain A residue 106 ILE Chi-restraints excluded: chain B residue 402 THR Chi-restraints excluded: chain C residue 9 THR Chi-restraints excluded: chain C residue 106 ILE Chi-restraints excluded: chain C residue 247 ASN Chi-restraints excluded: chain C residue 362 ARG Chi-restraints excluded: chain C residue 364 MET Chi-restraints excluded: chain C residue 410 LEU Chi-restraints excluded: chain C residue 428 GLU Chi-restraints excluded: chain C residue 446 ILE Chi-restraints excluded: chain D residue 50 LEU Chi-restraints excluded: chain D residue 90 MET Chi-restraints excluded: chain D residue 280 VAL Chi-restraints excluded: chain D residue 282 GLU Chi-restraints excluded: chain D residue 291 ILE Chi-restraints excluded: chain D residue 301 VAL Chi-restraints excluded: chain D residue 306 ILE Chi-restraints excluded: chain D residue 439 SER Chi-restraints excluded: chain E residue 88 MET Chi-restraints excluded: chain E residue 306 ILE Chi-restraints excluded: chain E residue 413 CYS Chi-restraints excluded: chain F residue 249 VAL Chi-restraints excluded: chain F residue 382 MET Chi-restraints excluded: chain F residue 413 CYS Chi-restraints excluded: chain G residue 590 VAL Chi-restraints excluded: chain G residue 630 PHE Chi-restraints excluded: chain G residue 634 THR Chi-restraints excluded: chain G residue 636 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 178 optimal weight: 0.6980 chunk 136 optimal weight: 5.9990 chunk 93 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 86 optimal weight: 0.9980 chunk 121 optimal weight: 5.9990 chunk 181 optimal weight: 0.6980 chunk 192 optimal weight: 3.9990 chunk 94 optimal weight: 0.6980 chunk 172 optimal weight: 0.7980 chunk 51 optimal weight: 2.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 408 GLN B 450 GLN C 18 HIS ** C 420 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 25 HIS F 25 HIS ** F 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8337 moved from start: 0.3578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 15848 Z= 0.200 Angle : 0.598 9.565 21409 Z= 0.286 Chirality : 0.042 0.184 2528 Planarity : 0.003 0.029 2725 Dihedral : 8.870 143.159 2224 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 9.91 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.95 % Favored : 96.00 % Rotamer: Outliers : 3.00 % Allowed : 11.92 % Favored : 85.08 % 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: -0.48 (0.19), residues: 1974 helix: 0.11 (0.16), residues: 1126 sheet: -0.07 (0.37), residues: 194 loop : -0.94 (0.24), residues: 654 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 283 HIS 0.004 0.001 HIS A 241 PHE 0.019 0.001 PHE F 450 TYR 0.017 0.002 TYR E 430 ARG 0.007 0.000 ARG A 317 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3948 Ramachandran restraints generated. 1974 Oldfield, 0 Emsley, 1974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3948 Ramachandran restraints generated. 1974 Oldfield, 0 Emsley, 1974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 1702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 251 time to evaluate : 1.869 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: B 123 ARG cc_start: 0.4106 (tpm170) cc_final: 0.3836 (tpm170) REVERT: B 276 ARG cc_start: 0.7941 (mmt90) cc_final: 0.6913 (ttt-90) REVERT: B 345 THR cc_start: 0.9145 (m) cc_final: 0.8832 (p) REVERT: E 46 MET cc_start: 0.8517 (mmm) cc_final: 0.7975 (mmm) REVERT: G 557 ARG cc_start: 0.7503 (ttp80) cc_final: 0.7289 (ttp80) outliers start: 50 outliers final: 24 residues processed: 280 average time/residue: 0.2806 time to fit residues: 114.8617 Evaluate side-chains 250 residues out of total 1702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 226 time to evaluate : 1.704 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 THR Chi-restraints excluded: chain A residue 106 ILE Chi-restraints excluded: chain B residue 402 THR Chi-restraints excluded: chain C residue 247 ASN Chi-restraints excluded: chain C residue 362 ARG Chi-restraints excluded: chain C residue 364 MET Chi-restraints excluded: chain C residue 410 LEU Chi-restraints excluded: chain D residue 29 ARG Chi-restraints excluded: chain D residue 90 MET Chi-restraints excluded: chain D residue 280 VAL Chi-restraints excluded: chain D residue 282 GLU Chi-restraints excluded: chain D residue 301 VAL Chi-restraints excluded: chain D residue 306 ILE Chi-restraints excluded: chain D residue 439 SER Chi-restraints excluded: chain E residue 60 LEU Chi-restraints excluded: chain E residue 88 MET Chi-restraints excluded: chain E residue 306 ILE Chi-restraints excluded: chain E residue 413 CYS Chi-restraints excluded: chain F residue 249 VAL Chi-restraints excluded: chain F residue 310 SER Chi-restraints excluded: chain F residue 413 CYS Chi-restraints excluded: chain F residue 436 GLU Chi-restraints excluded: chain G residue 590 VAL Chi-restraints excluded: chain G residue 634 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 160 optimal weight: 3.9990 chunk 109 optimal weight: 1.9990 chunk 2 optimal weight: 0.9980 chunk 143 optimal weight: 2.9990 chunk 79 optimal weight: 3.9990 chunk 164 optimal weight: 0.3980 chunk 132 optimal weight: 2.9990 chunk 0 optimal weight: 8.9990 chunk 98 optimal weight: 0.9990 chunk 172 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 408 GLN C 408 GLN ** C 420 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 251 ASN F 25 HIS ** F 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8369 moved from start: 0.3747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 15848 Z= 0.277 Angle : 0.621 9.909 21409 Z= 0.297 Chirality : 0.043 0.172 2528 Planarity : 0.003 0.028 2725 Dihedral : 8.912 148.154 2224 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 10.68 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.26 % Favored : 95.69 % Rotamer: Outliers : 2.88 % Allowed : 13.48 % Favored : 83.64 % 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: -0.37 (0.19), residues: 1974 helix: 0.20 (0.16), residues: 1133 sheet: -0.02 (0.37), residues: 198 loop : -0.91 (0.24), residues: 643 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP E 283 HIS 0.004 0.001 HIS F 245 PHE 0.013 0.001 PHE G 591 TYR 0.011 0.002 TYR F 430 ARG 0.006 0.000 ARG C 317 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3948 Ramachandran restraints generated. 1974 Oldfield, 0 Emsley, 1974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3948 Ramachandran restraints generated. 1974 Oldfield, 0 Emsley, 1974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 1702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 236 time to evaluate : 2.005 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 61 MET cc_start: 0.9169 (tpp) cc_final: 0.8770 (mmp) REVERT: A 273 ASP cc_start: 0.7751 (m-30) cc_final: 0.7346 (m-30) REVERT: B 123 ARG cc_start: 0.4348 (tpm170) cc_final: 0.3978 (tpm170) REVERT: B 276 ARG cc_start: 0.7915 (mmt90) cc_final: 0.6943 (ttt-90) REVERT: B 345 THR cc_start: 0.9212 (m) cc_final: 0.8862 (p) REVERT: E 46 MET cc_start: 0.8543 (mmm) cc_final: 0.8022 (mmm) REVERT: G 557 ARG cc_start: 0.7721 (ttp80) cc_final: 0.7511 (ttp80) REVERT: G 586 LEU cc_start: 0.8444 (tm) cc_final: 0.8115 (tp) outliers start: 48 outliers final: 29 residues processed: 267 average time/residue: 0.2755 time to fit residues: 110.2609 Evaluate side-chains 249 residues out of total 1702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 220 time to evaluate : 1.934 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 THR Chi-restraints excluded: chain A residue 106 ILE Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain B residue 402 THR Chi-restraints excluded: chain C residue 9 THR Chi-restraints excluded: chain C residue 106 ILE Chi-restraints excluded: chain C residue 247 ASN Chi-restraints excluded: chain C residue 362 ARG Chi-restraints excluded: chain C residue 410 LEU Chi-restraints excluded: chain C residue 446 ILE Chi-restraints excluded: chain D residue 29 ARG Chi-restraints excluded: chain D residue 50 LEU Chi-restraints excluded: chain D residue 90 MET Chi-restraints excluded: chain D residue 280 VAL Chi-restraints excluded: chain D residue 282 GLU Chi-restraints excluded: chain D residue 291 ILE Chi-restraints excluded: chain D residue 301 VAL Chi-restraints excluded: chain D residue 306 ILE Chi-restraints excluded: chain E residue 88 MET Chi-restraints excluded: chain E residue 129 VAL Chi-restraints excluded: chain E residue 306 ILE Chi-restraints excluded: chain E residue 413 CYS Chi-restraints excluded: chain F residue 60 LEU Chi-restraints excluded: chain F residue 301 VAL Chi-restraints excluded: chain F residue 310 SER Chi-restraints excluded: chain F residue 413 CYS Chi-restraints excluded: chain F residue 436 GLU Chi-restraints excluded: chain G residue 590 VAL Chi-restraints excluded: chain G residue 634 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 64 optimal weight: 5.9990 chunk 173 optimal weight: 0.8980 chunk 38 optimal weight: 2.9990 chunk 112 optimal weight: 1.9990 chunk 47 optimal weight: 6.9990 chunk 192 optimal weight: 1.9990 chunk 159 optimal weight: 2.9990 chunk 89 optimal weight: 0.6980 chunk 16 optimal weight: 0.9980 chunk 63 optimal weight: 5.9990 chunk 101 optimal weight: 2.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 429 HIS ** B 450 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 420 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 78 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8373 moved from start: 0.3851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 15848 Z= 0.283 Angle : 0.625 11.296 21409 Z= 0.299 Chirality : 0.043 0.169 2528 Planarity : 0.003 0.028 2725 Dihedral : 8.911 151.282 2224 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 10.64 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.05 % Favored : 95.90 % Rotamer: Outliers : 2.88 % Allowed : 14.08 % Favored : 83.04 % 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: -0.27 (0.19), residues: 1974 helix: 0.28 (0.16), residues: 1134 sheet: 0.00 (0.37), residues: 199 loop : -0.87 (0.24), residues: 641 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 283 HIS 0.004 0.001 HIS B 429 PHE 0.012 0.001 PHE G 591 TYR 0.013 0.002 TYR G 567 ARG 0.006 0.000 ARG C 317 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3948 Ramachandran restraints generated. 1974 Oldfield, 0 Emsley, 1974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3948 Ramachandran restraints generated. 1974 Oldfield, 0 Emsley, 1974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 1702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 235 time to evaluate : 1.854 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: A 273 ASP cc_start: 0.7660 (m-30) cc_final: 0.7320 (m-30) REVERT: B 42 GLN cc_start: 0.7911 (OUTLIER) cc_final: 0.6217 (mp10) REVERT: B 123 ARG cc_start: 0.4433 (tpm170) cc_final: 0.3961 (tpm170) REVERT: B 276 ARG cc_start: 0.7919 (mmt90) cc_final: 0.6915 (ttt-90) REVERT: B 345 THR cc_start: 0.9234 (m) cc_final: 0.8888 (p) REVERT: E 46 MET cc_start: 0.8531 (mmm) cc_final: 0.8018 (mmm) REVERT: E 273 ARG cc_start: 0.7128 (tpp-160) cc_final: 0.6794 (tpp80) REVERT: G 586 LEU cc_start: 0.8473 (tm) cc_final: 0.8153 (tp) outliers start: 48 outliers final: 36 residues processed: 270 average time/residue: 0.2662 time to fit residues: 107.3272 Evaluate side-chains 259 residues out of total 1702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 222 time to evaluate : 1.878 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 ILE Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain A residue 446 ILE Chi-restraints excluded: chain A residue 447 LEU Chi-restraints excluded: chain B residue 42 GLN Chi-restraints excluded: chain B residue 402 THR Chi-restraints excluded: chain B residue 439 ASP Chi-restraints excluded: chain C residue 106 ILE Chi-restraints excluded: chain C residue 247 ASN Chi-restraints excluded: chain C residue 291 ILE Chi-restraints excluded: chain C residue 362 ARG Chi-restraints excluded: chain C residue 410 LEU Chi-restraints excluded: chain C residue 446 ILE Chi-restraints excluded: chain D residue 29 ARG Chi-restraints excluded: chain D residue 50 LEU Chi-restraints excluded: chain D residue 90 MET Chi-restraints excluded: chain D residue 116 THR Chi-restraints excluded: chain D residue 280 VAL Chi-restraints excluded: chain D residue 282 GLU Chi-restraints excluded: chain D residue 301 VAL Chi-restraints excluded: chain D residue 306 ILE Chi-restraints excluded: chain D residue 319 ASP Chi-restraints excluded: chain D residue 439 SER Chi-restraints excluded: chain E residue 60 LEU Chi-restraints excluded: chain E residue 88 MET Chi-restraints excluded: chain E residue 129 VAL Chi-restraints excluded: chain E residue 280 VAL Chi-restraints excluded: chain E residue 306 ILE Chi-restraints excluded: chain E residue 413 CYS Chi-restraints excluded: chain F residue 60 LEU Chi-restraints excluded: chain F residue 301 VAL Chi-restraints excluded: chain F residue 310 SER Chi-restraints excluded: chain F residue 413 CYS Chi-restraints excluded: chain F residue 436 GLU Chi-restraints excluded: chain G residue 590 VAL Chi-restraints excluded: chain G residue 634 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 185 optimal weight: 0.0970 chunk 21 optimal weight: 1.9990 chunk 109 optimal weight: 0.9990 chunk 140 optimal weight: 6.9990 chunk 108 optimal weight: 0.8980 chunk 162 optimal weight: 1.9990 chunk 107 optimal weight: 0.5980 chunk 191 optimal weight: 5.9990 chunk 120 optimal weight: 0.6980 chunk 116 optimal weight: 0.8980 chunk 88 optimal weight: 0.8980 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 408 GLN ** B 450 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 420 ASN E 25 HIS E 78 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8342 moved from start: 0.4076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 15848 Z= 0.182 Angle : 0.610 13.035 21409 Z= 0.287 Chirality : 0.042 0.172 2528 Planarity : 0.003 0.052 2725 Dihedral : 8.739 154.306 2224 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 9.69 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.70 % Favored : 96.25 % Rotamer: Outliers : 2.70 % Allowed : 14.38 % Favored : 82.92 % 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: -0.03 (0.19), residues: 1974 helix: 0.47 (0.16), residues: 1128 sheet: 0.09 (0.37), residues: 198 loop : -0.75 (0.24), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 283 HIS 0.003 0.001 HIS B 241 PHE 0.011 0.001 PHE G 591 TYR 0.011 0.001 TYR F 430 ARG 0.008 0.000 ARG G 557 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3948 Ramachandran restraints generated. 1974 Oldfield, 0 Emsley, 1974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3948 Ramachandran restraints generated. 1974 Oldfield, 0 Emsley, 1974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 1702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 236 time to evaluate : 1.692 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 MET cc_start: 0.9244 (tpp) cc_final: 0.8739 (mmp) REVERT: A 273 ASP cc_start: 0.7586 (m-30) cc_final: 0.7297 (m-30) REVERT: B 42 GLN cc_start: 0.7803 (OUTLIER) cc_final: 0.6135 (mp10) REVERT: B 123 ARG cc_start: 0.4414 (tpm170) cc_final: 0.4084 (tpm170) REVERT: B 276 ARG cc_start: 0.7890 (mmt90) cc_final: 0.6919 (ttt-90) REVERT: B 345 THR cc_start: 0.9177 (m) cc_final: 0.8853 (p) REVERT: C 317 ARG cc_start: 0.7930 (ttp80) cc_final: 0.7596 (ttp80) REVERT: E 46 MET cc_start: 0.8508 (mmm) cc_final: 0.7996 (mmm) REVERT: G 567 TYR cc_start: 0.7127 (p90) cc_final: 0.6817 (p90) outliers start: 45 outliers final: 34 residues processed: 269 average time/residue: 0.2683 time to fit residues: 106.4562 Evaluate side-chains 254 residues out of total 1702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 219 time to evaluate : 1.798 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 ILE Chi-restraints excluded: chain A residue 294 LEU Chi-restraints excluded: chain A residue 446 ILE Chi-restraints excluded: chain A residue 447 LEU Chi-restraints excluded: chain B residue 42 GLN Chi-restraints excluded: chain B residue 402 THR Chi-restraints excluded: chain B residue 439 ASP Chi-restraints excluded: chain C residue 106 ILE Chi-restraints excluded: chain C residue 247 ASN Chi-restraints excluded: chain C residue 291 ILE Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 362 ARG Chi-restraints excluded: chain C residue 410 LEU Chi-restraints excluded: chain C residue 446 ILE Chi-restraints excluded: chain D residue 29 ARG Chi-restraints excluded: chain D residue 50 LEU Chi-restraints excluded: chain D residue 90 MET Chi-restraints excluded: chain D residue 116 THR Chi-restraints excluded: chain D residue 280 VAL Chi-restraints excluded: chain D residue 282 GLU Chi-restraints excluded: chain D residue 301 VAL Chi-restraints excluded: chain D residue 306 ILE Chi-restraints excluded: chain D residue 319 ASP Chi-restraints excluded: chain D residue 439 SER Chi-restraints excluded: chain E residue 60 LEU Chi-restraints excluded: chain E residue 88 MET Chi-restraints excluded: chain E residue 129 VAL Chi-restraints excluded: chain E residue 280 VAL Chi-restraints excluded: chain E residue 306 ILE Chi-restraints excluded: chain E residue 413 CYS Chi-restraints excluded: chain F residue 301 VAL Chi-restraints excluded: chain F residue 310 SER Chi-restraints excluded: chain F residue 413 CYS Chi-restraints excluded: chain F residue 436 GLU Chi-restraints excluded: chain G residue 631 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 118 optimal weight: 0.9980 chunk 76 optimal weight: 5.9990 chunk 114 optimal weight: 0.1980 chunk 57 optimal weight: 0.8980 chunk 37 optimal weight: 0.9990 chunk 121 optimal weight: 3.9990 chunk 130 optimal weight: 3.9990 chunk 94 optimal weight: 4.9990 chunk 17 optimal weight: 1.9990 chunk 150 optimal weight: 3.9990 chunk 174 optimal weight: 2.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 348 HIS ** B 450 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 408 GLN C 420 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8356 moved from start: 0.4121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 15848 Z= 0.237 Angle : 0.622 9.743 21409 Z= 0.295 Chirality : 0.043 0.175 2528 Planarity : 0.003 0.042 2725 Dihedral : 8.728 153.611 2224 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.00 % Favored : 95.95 % Rotamer: Outliers : 2.28 % Allowed : 15.64 % Favored : 82.09 % 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: -0.01 (0.19), residues: 1974 helix: 0.49 (0.16), residues: 1129 sheet: 0.12 (0.37), residues: 199 loop : -0.76 (0.24), residues: 646 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 283 HIS 0.004 0.001 HIS A 348 PHE 0.011 0.001 PHE G 591 TYR 0.011 0.001 TYR D 446 ARG 0.006 0.000 ARG C 317 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3948 Ramachandran restraints generated. 1974 Oldfield, 0 Emsley, 1974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3948 Ramachandran restraints generated. 1974 Oldfield, 0 Emsley, 1974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 1702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 230 time to evaluate : 1.928 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 MET cc_start: 0.9219 (tpp) cc_final: 0.8742 (mmp) REVERT: A 273 ASP cc_start: 0.7465 (m-30) cc_final: 0.7245 (m-30) REVERT: B 42 GLN cc_start: 0.7901 (OUTLIER) cc_final: 0.6246 (mp10) REVERT: B 123 ARG cc_start: 0.4405 (tpm170) cc_final: 0.3898 (tpm170) REVERT: B 276 ARG cc_start: 0.7860 (mmt90) cc_final: 0.6909 (ttt90) REVERT: B 345 THR cc_start: 0.9251 (m) cc_final: 0.8909 (p) REVERT: C 317 ARG cc_start: 0.7967 (ttp80) cc_final: 0.7616 (ttp80) REVERT: D 444 LYS cc_start: 0.8058 (tttt) cc_final: 0.7649 (tmtt) REVERT: E 46 MET cc_start: 0.8518 (mmm) cc_final: 0.8026 (mmm) REVERT: E 274 GLU cc_start: 0.7929 (tp30) cc_final: 0.7657 (tm-30) REVERT: E 284 ARG cc_start: 0.8245 (ttt-90) cc_final: 0.7830 (ptm-80) outliers start: 38 outliers final: 30 residues processed: 255 average time/residue: 0.2738 time to fit residues: 103.3050 Evaluate side-chains 252 residues out of total 1702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 221 time to evaluate : 1.789 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 ILE Chi-restraints excluded: chain A residue 306 MET Chi-restraints excluded: chain A residue 446 ILE Chi-restraints excluded: chain A residue 447 LEU Chi-restraints excluded: chain B residue 42 GLN Chi-restraints excluded: chain B residue 402 THR Chi-restraints excluded: chain B residue 439 ASP Chi-restraints excluded: chain C residue 247 ASN Chi-restraints excluded: chain C residue 291 ILE Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 362 ARG Chi-restraints excluded: chain C residue 410 LEU Chi-restraints excluded: chain D residue 29 ARG Chi-restraints excluded: chain D residue 50 LEU Chi-restraints excluded: chain D residue 90 MET Chi-restraints excluded: chain D residue 116 THR Chi-restraints excluded: chain D residue 280 VAL Chi-restraints excluded: chain D residue 282 GLU Chi-restraints excluded: chain D residue 301 VAL Chi-restraints excluded: chain D residue 306 ILE Chi-restraints excluded: chain D residue 319 ASP Chi-restraints excluded: chain D residue 450 PHE Chi-restraints excluded: chain E residue 60 LEU Chi-restraints excluded: chain E residue 129 VAL Chi-restraints excluded: chain E residue 280 VAL Chi-restraints excluded: chain E residue 306 ILE Chi-restraints excluded: chain E residue 413 CYS Chi-restraints excluded: chain F residue 301 VAL Chi-restraints excluded: chain F residue 310 SER Chi-restraints excluded: chain F residue 413 CYS Chi-restraints excluded: chain F residue 436 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 183 optimal weight: 0.7980 chunk 167 optimal weight: 3.9990 chunk 178 optimal weight: 0.5980 chunk 107 optimal weight: 6.9990 chunk 77 optimal weight: 5.9990 chunk 140 optimal weight: 0.9980 chunk 54 optimal weight: 1.9990 chunk 161 optimal weight: 0.9980 chunk 169 optimal weight: 4.9990 chunk 117 optimal weight: 0.0670 chunk 189 optimal weight: 3.9990 overall best weight: 0.6918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 450 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 420 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 429 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 302 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8337 moved from start: 0.4282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 15848 Z= 0.188 Angle : 0.609 9.962 21409 Z= 0.288 Chirality : 0.042 0.194 2528 Planarity : 0.003 0.040 2725 Dihedral : 8.623 155.241 2224 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 9.79 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.60 % Favored : 96.35 % Rotamer: Outliers : 1.98 % Allowed : 16.06 % Favored : 81.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.12 (0.19), residues: 1974 helix: 0.59 (0.16), residues: 1120 sheet: 0.14 (0.37), residues: 199 loop : -0.66 (0.24), residues: 655 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.004 TRP E 283 HIS 0.003 0.001 HIS B 241 PHE 0.010 0.001 PHE G 591 TYR 0.012 0.001 TYR G 567 ARG 0.006 0.000 ARG C 317 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3948 Ramachandran restraints generated. 1974 Oldfield, 0 Emsley, 1974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3948 Ramachandran restraints generated. 1974 Oldfield, 0 Emsley, 1974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 1702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 235 time to evaluate : 1.956 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: A 61 MET cc_start: 0.9180 (tpp) cc_final: 0.8737 (mmp) REVERT: A 273 ASP cc_start: 0.7399 (m-30) cc_final: 0.7187 (m-30) REVERT: B 42 GLN cc_start: 0.7802 (OUTLIER) cc_final: 0.6163 (mp10) REVERT: B 123 ARG cc_start: 0.4275 (tpm170) cc_final: 0.3859 (tpm170) REVERT: B 276 ARG cc_start: 0.7837 (mmt90) cc_final: 0.6896 (ttt90) REVERT: B 345 THR cc_start: 0.9227 (m) cc_final: 0.8888 (p) REVERT: C 317 ARG cc_start: 0.7907 (ttp80) cc_final: 0.7533 (ttp80) REVERT: E 46 MET cc_start: 0.8500 (mmm) cc_final: 0.8002 (mmm) REVERT: E 274 GLU cc_start: 0.7961 (tp30) cc_final: 0.7666 (tm-30) REVERT: E 283 TRP cc_start: 0.7754 (m-90) cc_final: 0.7514 (m-90) REVERT: G 586 LEU cc_start: 0.8357 (tm) cc_final: 0.8078 (tp) outliers start: 33 outliers final: 29 residues processed: 258 average time/residue: 0.2783 time to fit residues: 106.5405 Evaluate side-chains 252 residues out of total 1702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 222 time to evaluate : 1.580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 ILE Chi-restraints excluded: chain A residue 306 MET Chi-restraints excluded: chain A residue 439 ASP Chi-restraints excluded: chain A residue 446 ILE Chi-restraints excluded: chain A residue 447 LEU Chi-restraints excluded: chain B residue 42 GLN Chi-restraints excluded: chain B residue 402 THR Chi-restraints excluded: chain B residue 439 ASP Chi-restraints excluded: chain C residue 106 ILE Chi-restraints excluded: chain C residue 247 ASN Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 362 ARG Chi-restraints excluded: chain C residue 410 LEU Chi-restraints excluded: chain D residue 29 ARG Chi-restraints excluded: chain D residue 50 LEU Chi-restraints excluded: chain D residue 90 MET Chi-restraints excluded: chain D residue 116 THR Chi-restraints excluded: chain D residue 280 VAL Chi-restraints excluded: chain D residue 282 GLU Chi-restraints excluded: chain D residue 301 VAL Chi-restraints excluded: chain D residue 306 ILE Chi-restraints excluded: chain D residue 319 ASP Chi-restraints excluded: chain D residue 450 PHE Chi-restraints excluded: chain E residue 60 LEU Chi-restraints excluded: chain E residue 129 VAL Chi-restraints excluded: chain E residue 306 ILE Chi-restraints excluded: chain E residue 413 CYS Chi-restraints excluded: chain F residue 301 VAL Chi-restraints excluded: chain F residue 413 CYS Chi-restraints excluded: chain F residue 436 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 115 optimal weight: 1.9990 chunk 89 optimal weight: 0.8980 chunk 131 optimal weight: 1.9990 chunk 198 optimal weight: 10.0000 chunk 182 optimal weight: 0.7980 chunk 157 optimal weight: 2.9990 chunk 16 optimal weight: 0.3980 chunk 121 optimal weight: 0.8980 chunk 96 optimal weight: 0.0570 chunk 125 optimal weight: 3.9990 chunk 168 optimal weight: 2.9990 overall best weight: 0.6098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 316 HIS ** B 450 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 408 GLN C 420 ASN C 429 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8331 moved from start: 0.4372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 15848 Z= 0.181 Angle : 0.615 10.768 21409 Z= 0.291 Chirality : 0.042 0.192 2528 Planarity : 0.003 0.053 2725 Dihedral : 8.584 155.182 2224 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 9.98 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.80 % Favored : 96.15 % Rotamer: Outliers : 2.10 % Allowed : 16.36 % Favored : 81.55 % 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: 0.18 (0.19), residues: 1974 helix: 0.63 (0.16), residues: 1119 sheet: 0.06 (0.37), residues: 203 loop : -0.56 (0.24), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.003 TRP E 283 HIS 0.004 0.001 HIS B 316 PHE 0.010 0.001 PHE G 591 TYR 0.011 0.001 TYR G 567 ARG 0.006 0.000 ARG G 557 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3948 Ramachandran restraints generated. 1974 Oldfield, 0 Emsley, 1974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3948 Ramachandran restraints generated. 1974 Oldfield, 0 Emsley, 1974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 1702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 230 time to evaluate : 1.940 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 61 MET cc_start: 0.9183 (tpp) cc_final: 0.8738 (mmp) REVERT: B 42 GLN cc_start: 0.7779 (OUTLIER) cc_final: 0.6152 (mp10) REVERT: B 123 ARG cc_start: 0.4411 (tpm170) cc_final: 0.3935 (tpm170) REVERT: B 276 ARG cc_start: 0.7811 (mmt90) cc_final: 0.6899 (ttt90) REVERT: B 345 THR cc_start: 0.9220 (m) cc_final: 0.8880 (p) REVERT: C 317 ARG cc_start: 0.7846 (ttp80) cc_final: 0.7519 (ttp80) REVERT: D 443 MET cc_start: 0.7807 (ptm) cc_final: 0.7536 (ptm) REVERT: D 444 LYS cc_start: 0.8177 (tttt) cc_final: 0.7888 (tmtt) REVERT: E 46 MET cc_start: 0.8504 (mmm) cc_final: 0.8010 (mmm) REVERT: E 274 GLU cc_start: 0.7875 (tp30) cc_final: 0.7632 (tm-30) REVERT: E 283 TRP cc_start: 0.7839 (m-90) cc_final: 0.7378 (m-90) REVERT: G 586 LEU cc_start: 0.8344 (tm) cc_final: 0.8113 (tp) outliers start: 35 outliers final: 29 residues processed: 254 average time/residue: 0.2744 time to fit residues: 103.1831 Evaluate side-chains 257 residues out of total 1702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 227 time to evaluate : 1.740 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 ILE Chi-restraints excluded: chain A residue 306 MET Chi-restraints excluded: chain A residue 439 ASP Chi-restraints excluded: chain A residue 447 LEU Chi-restraints excluded: chain B residue 42 GLN Chi-restraints excluded: chain B residue 402 THR Chi-restraints excluded: chain B residue 439 ASP Chi-restraints excluded: chain C residue 106 ILE Chi-restraints excluded: chain C residue 247 ASN Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 362 ARG Chi-restraints excluded: chain C residue 364 MET Chi-restraints excluded: chain C residue 385 ASN Chi-restraints excluded: chain D residue 29 ARG Chi-restraints excluded: chain D residue 50 LEU Chi-restraints excluded: chain D residue 90 MET Chi-restraints excluded: chain D residue 116 THR Chi-restraints excluded: chain D residue 280 VAL Chi-restraints excluded: chain D residue 282 GLU Chi-restraints excluded: chain D residue 301 VAL Chi-restraints excluded: chain D residue 306 ILE Chi-restraints excluded: chain D residue 319 ASP Chi-restraints excluded: chain E residue 60 LEU Chi-restraints excluded: chain E residue 129 VAL Chi-restraints excluded: chain E residue 280 VAL Chi-restraints excluded: chain E residue 306 ILE Chi-restraints excluded: chain E residue 413 CYS Chi-restraints excluded: chain F residue 301 VAL Chi-restraints excluded: chain F residue 413 CYS Chi-restraints excluded: chain F residue 436 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 48 optimal weight: 2.9990 chunk 145 optimal weight: 0.7980 chunk 23 optimal weight: 0.5980 chunk 43 optimal weight: 0.9990 chunk 158 optimal weight: 3.9990 chunk 66 optimal weight: 1.9990 chunk 162 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 138 optimal weight: 0.8980 chunk 9 optimal weight: 0.2980 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 429 HIS ** B 450 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 85 GLN ** C 429 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 25 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.105608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.083692 restraints weight = 33381.660| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.086402 restraints weight = 18223.327| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.088151 restraints weight = 12389.573| |-----------------------------------------------------------------------------| r_work (final): 0.3152 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3152 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3152 r_free = 0.3152 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3151 r_free = 0.3151 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3151 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 moved from start: 0.4426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 15848 Z= 0.193 Angle : 0.620 11.139 21409 Z= 0.293 Chirality : 0.042 0.176 2528 Planarity : 0.003 0.053 2725 Dihedral : 8.562 154.985 2224 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.80 % Favored : 96.15 % Rotamer: Outliers : 1.68 % Allowed : 16.90 % Favored : 81.43 % 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: 0.24 (0.19), residues: 1974 helix: 0.65 (0.16), residues: 1115 sheet: 0.16 (0.37), residues: 200 loop : -0.51 (0.24), residues: 659 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.003 TRP E 283 HIS 0.003 0.001 HIS B 241 PHE 0.009 0.001 PHE G 591 TYR 0.015 0.001 TYR E 401 ARG 0.010 0.000 ARG F 414 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3215.66 seconds wall clock time: 58 minutes 49.85 seconds (3529.85 seconds total)