Starting phenix.real_space_refine on Fri Feb 16 08:36:52 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5wpt_8882/02_2024/5wpt_8882.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5wpt_8882/02_2024/5wpt_8882.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.75 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5wpt_8882/02_2024/5wpt_8882.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5wpt_8882/02_2024/5wpt_8882.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5wpt_8882/02_2024/5wpt_8882.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5wpt_8882/02_2024/5wpt_8882.pdb" } resolution = 3.75 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= 0.010 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 S 96 5.16 5 Na 1 4.78 5 C 9772 2.51 5 N 2444 2.21 5 O 2576 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 146": "NH1" <-> "NH2" Residue "A ARG 168": "NH1" <-> "NH2" Residue "A ARG 172": "NH1" <-> "NH2" Residue "A ARG 322": "NH1" <-> "NH2" Residue "A ARG 336": "NH1" <-> "NH2" Residue "A ARG 337": "NH1" <-> "NH2" Residue "A ARG 340": "NH1" <-> "NH2" Residue "A ARG 347": "NH1" <-> "NH2" Residue "A ARG 455": "NH1" <-> "NH2" Residue "B ARG 146": "NH1" <-> "NH2" Residue "B ARG 168": "NH1" <-> "NH2" Residue "B ARG 172": "NH1" <-> "NH2" Residue "B ARG 322": "NH1" <-> "NH2" Residue "B ARG 336": "NH1" <-> "NH2" Residue "B ARG 337": "NH1" <-> "NH2" Residue "B ARG 340": "NH1" <-> "NH2" Residue "B ARG 347": "NH1" <-> "NH2" Residue "B ARG 455": "NH1" <-> "NH2" Residue "C ARG 146": "NH1" <-> "NH2" Residue "C ARG 168": "NH1" <-> "NH2" Residue "C ARG 172": "NH1" <-> "NH2" Residue "C PHE 235": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 322": "NH1" <-> "NH2" Residue "C ARG 336": "NH1" <-> "NH2" Residue "C ARG 337": "NH1" <-> "NH2" Residue "C ARG 340": "NH1" <-> "NH2" Residue "C ARG 347": "NH1" <-> "NH2" Residue "C ARG 455": "NH1" <-> "NH2" Residue "D ARG 146": "NH1" <-> "NH2" Residue "D ARG 168": "NH1" <-> "NH2" Residue "D ARG 172": "NH1" <-> "NH2" Residue "D PHE 235": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 322": "NH1" <-> "NH2" Residue "D ARG 336": "NH1" <-> "NH2" Residue "D ARG 337": "NH1" <-> "NH2" Residue "D ARG 340": "NH1" <-> "NH2" Residue "D ARG 347": "NH1" <-> "NH2" Residue "D ARG 455": "NH1" <-> "NH2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 14889 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 3694 Number of conformers: 1 Conformer: "" Number of residues, atoms: 454, 3694 Classifications: {'peptide': 454} Link IDs: {'PTRANS': 12, 'TRANS': 441} Chain breaks: 3 Chain: "B" Number of atoms: 3694 Number of conformers: 1 Conformer: "" Number of residues, atoms: 454, 3694 Classifications: {'peptide': 454} Link IDs: {'PTRANS': 12, 'TRANS': 441} Chain breaks: 3 Chain: "C" Number of atoms: 3694 Number of conformers: 1 Conformer: "" Number of residues, atoms: 454, 3694 Classifications: {'peptide': 454} Link IDs: {'PTRANS': 12, 'TRANS': 441} Chain breaks: 3 Chain: "D" Number of atoms: 3694 Number of conformers: 1 Conformer: "" Number of residues, atoms: 454, 3694 Classifications: {'peptide': 454} Link IDs: {'PTRANS': 12, 'TRANS': 441} Chain breaks: 3 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' NA': 1} Classifications: {'undetermined': 1} Time building chain proxies: 7.66, per 1000 atoms: 0.51 Number of scatterers: 14889 At special positions: 0 Unit cell: (110.21, 110.21, 117.7, 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 96 16.00 Na 1 11.00 O 2576 8.00 N 2444 7.00 C 9772 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " NAG-ASN " NAG E 1 " - " ASN A 230 " " NAG F 1 " - " ASN B 230 " " NAG G 1 " - " ASN C 230 " " NAG H 1 " - " ASN D 230 " Time building additional restraints: 5.37 Conformation dependent library (CDL) restraints added in 2.6 seconds 3568 Ramachandran restraints generated. 1784 Oldfield, 0 Emsley, 1784 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3472 Finding SS restraints... Secondary structure from input PDB file: 76 helices and 4 sheets defined 63.1% alpha, 10.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.20 Creating SS restraints... Processing helix chain 'A' and resid 38 through 49 removed outlier: 3.535A pdb=" N ARG A 42 " --> pdb=" O GLU A 38 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N LEU A 45 " --> pdb=" O LEU A 41 " (cutoff:3.500A) Processing helix chain 'A' and resid 51 through 57 removed outlier: 3.612A pdb=" N ARG A 57 " --> pdb=" O CYS A 53 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 106 removed outlier: 3.955A pdb=" N LEU A 68 " --> pdb=" O CYS A 64 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N GLN A 69 " --> pdb=" O LYS A 65 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N SER A 86 " --> pdb=" O LEU A 82 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N PHE A 93 " --> pdb=" O LEU A 89 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ASN A 97 " --> pdb=" O PHE A 93 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ILE A 99 " --> pdb=" O GLU A 95 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LEU A 104 " --> pdb=" O ALA A 100 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 138 removed outlier: 3.645A pdb=" N ALA A 132 " --> pdb=" O ALA A 128 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N TYR A 136 " --> pdb=" O ALA A 132 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ILE A 138 " --> pdb=" O ASP A 134 " (cutoff:3.500A) Processing helix chain 'A' and resid 139 through 142 Processing helix chain 'A' and resid 242 through 246 removed outlier: 3.718A pdb=" N ILE A 246 " --> pdb=" O GLN A 243 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 337 removed outlier: 3.916A pdb=" N VAL A 303 " --> pdb=" O LEU A 299 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ALA A 317 " --> pdb=" O PHE A 313 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N PHE A 330 " --> pdb=" O LEU A 326 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N VAL A 331 " --> pdb=" O GLN A 327 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N PHE A 333 " --> pdb=" O GLU A 329 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ARG A 336 " --> pdb=" O VAL A 332 " (cutoff:3.500A) Processing helix chain 'A' and resid 343 through 348 removed outlier: 3.577A pdb=" N ARG A 347 " --> pdb=" O SER A 343 " (cutoff:3.500A) Processing helix chain 'A' and resid 349 through 351 No H-bonds generated for 'chain 'A' and resid 349 through 351' Processing helix chain 'A' and resid 354 through 376 removed outlier: 3.759A pdb=" N GLU A 376 " --> pdb=" O LYS A 372 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 400 removed outlier: 3.875A pdb=" N THR A 392 " --> pdb=" O ILE A 388 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N LEU A 395 " --> pdb=" O GLY A 391 " (cutoff:3.500A) Processing helix chain 'A' and resid 401 through 407 removed outlier: 3.784A pdb=" N PHE A 407 " --> pdb=" O TYR A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 415 through 419 Processing helix chain 'A' and resid 420 through 447 removed outlier: 4.571A pdb=" N SER A 424 " --> pdb=" O VAL A 420 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N VAL A 425 " --> pdb=" O ALA A 421 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N PHE A 428 " --> pdb=" O SER A 424 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ILE A 435 " --> pdb=" O CYS A 431 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N ILE A 445 " --> pdb=" O PHE A 441 " (cutoff:3.500A) Processing helix chain 'A' and resid 456 through 470 removed outlier: 3.520A pdb=" N VAL A 460 " --> pdb=" O SER A 456 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N ASN A 469 " --> pdb=" O PHE A 465 " (cutoff:3.500A) Processing helix chain 'A' and resid 472 through 483 removed outlier: 3.541A pdb=" N THR A 476 " --> pdb=" O ASP A 472 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N PHE A 477 " --> pdb=" O MET A 473 " (cutoff:3.500A) removed outlier: 4.739A pdb=" N GLN A 483 " --> pdb=" O ALA A 479 " (cutoff:3.500A) Processing helix chain 'A' and resid 484 through 487 removed outlier: 3.589A pdb=" N SER A 487 " --> pdb=" O GLN A 484 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 484 through 487' Processing helix chain 'A' and resid 489 through 507 removed outlier: 3.618A pdb=" N LEU A 496 " --> pdb=" O LEU A 492 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N SER A 500 " --> pdb=" O LEU A 496 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N PHE A 505 " --> pdb=" O PHE A 501 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N TYR A 507 " --> pdb=" O SER A 503 " (cutoff:3.500A) Processing helix chain 'A' and resid 509 through 526 Processing helix chain 'B' and resid 39 through 49 removed outlier: 3.935A pdb=" N LEU B 45 " --> pdb=" O LEU B 41 " (cutoff:3.500A) Processing helix chain 'B' and resid 51 through 57 removed outlier: 3.612A pdb=" N ARG B 57 " --> pdb=" O CYS B 53 " (cutoff:3.500A) Processing helix chain 'B' and resid 63 through 106 removed outlier: 3.954A pdb=" N LEU B 68 " --> pdb=" O CYS B 64 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N GLN B 69 " --> pdb=" O LYS B 65 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N SER B 86 " --> pdb=" O LEU B 82 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N PHE B 93 " --> pdb=" O LEU B 89 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ASN B 97 " --> pdb=" O PHE B 93 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ILE B 99 " --> pdb=" O GLU B 95 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LEU B 104 " --> pdb=" O ALA B 100 " (cutoff:3.500A) Processing helix chain 'B' and resid 122 through 138 removed outlier: 3.645A pdb=" N ALA B 132 " --> pdb=" O ALA B 128 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N TYR B 136 " --> pdb=" O ALA B 132 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ILE B 138 " --> pdb=" O ASP B 134 " (cutoff:3.500A) Processing helix chain 'B' and resid 139 through 142 Processing helix chain 'B' and resid 242 through 246 removed outlier: 3.717A pdb=" N ILE B 246 " --> pdb=" O GLN B 243 " (cutoff:3.500A) Processing helix chain 'B' and resid 297 through 337 removed outlier: 3.916A pdb=" N VAL B 303 " --> pdb=" O LEU B 299 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ALA B 317 " --> pdb=" O PHE B 313 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N PHE B 330 " --> pdb=" O LEU B 326 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N VAL B 331 " --> pdb=" O GLN B 327 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N PHE B 333 " --> pdb=" O GLU B 329 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ARG B 336 " --> pdb=" O VAL B 332 " (cutoff:3.500A) Processing helix chain 'B' and resid 343 through 348 removed outlier: 3.576A pdb=" N ARG B 347 " --> pdb=" O SER B 343 " (cutoff:3.500A) Processing helix chain 'B' and resid 349 through 351 No H-bonds generated for 'chain 'B' and resid 349 through 351' Processing helix chain 'B' and resid 354 through 376 removed outlier: 3.758A pdb=" N GLU B 376 " --> pdb=" O LYS B 372 " (cutoff:3.500A) Processing helix chain 'B' and resid 384 through 400 removed outlier: 3.876A pdb=" N THR B 392 " --> pdb=" O ILE B 388 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N LEU B 395 " --> pdb=" O GLY B 391 " (cutoff:3.500A) Processing helix chain 'B' and resid 401 through 407 removed outlier: 3.785A pdb=" N PHE B 407 " --> pdb=" O TYR B 404 " (cutoff:3.500A) Processing helix chain 'B' and resid 415 through 419 Processing helix chain 'B' and resid 420 through 447 removed outlier: 4.570A pdb=" N SER B 424 " --> pdb=" O VAL B 420 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N VAL B 425 " --> pdb=" O ALA B 421 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N PHE B 428 " --> pdb=" O SER B 424 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ILE B 435 " --> pdb=" O CYS B 431 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N ILE B 445 " --> pdb=" O PHE B 441 " (cutoff:3.500A) Processing helix chain 'B' and resid 456 through 470 removed outlier: 3.520A pdb=" N VAL B 460 " --> pdb=" O SER B 456 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N ASN B 469 " --> pdb=" O PHE B 465 " (cutoff:3.500A) Processing helix chain 'B' and resid 472 through 483 removed outlier: 3.541A pdb=" N THR B 476 " --> pdb=" O ASP B 472 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N PHE B 477 " --> pdb=" O MET B 473 " (cutoff:3.500A) removed outlier: 4.740A pdb=" N GLN B 483 " --> pdb=" O ALA B 479 " (cutoff:3.500A) Processing helix chain 'B' and resid 484 through 487 removed outlier: 3.588A pdb=" N SER B 487 " --> pdb=" O GLN B 484 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 484 through 487' Processing helix chain 'B' and resid 489 through 507 removed outlier: 3.618A pdb=" N LEU B 496 " --> pdb=" O LEU B 492 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N SER B 500 " --> pdb=" O LEU B 496 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N PHE B 505 " --> pdb=" O PHE B 501 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N TYR B 507 " --> pdb=" O SER B 503 " (cutoff:3.500A) Processing helix chain 'B' and resid 509 through 526 Processing helix chain 'C' and resid 39 through 49 removed outlier: 3.935A pdb=" N LEU C 45 " --> pdb=" O LEU C 41 " (cutoff:3.500A) Processing helix chain 'C' and resid 51 through 57 removed outlier: 3.611A pdb=" N ARG C 57 " --> pdb=" O CYS C 53 " (cutoff:3.500A) Processing helix chain 'C' and resid 63 through 106 removed outlier: 3.955A pdb=" N LEU C 68 " --> pdb=" O CYS C 64 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N GLN C 69 " --> pdb=" O LYS C 65 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N SER C 86 " --> pdb=" O LEU C 82 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N PHE C 93 " --> pdb=" O LEU C 89 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ASN C 97 " --> pdb=" O PHE C 93 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ILE C 99 " --> pdb=" O GLU C 95 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LEU C 104 " --> pdb=" O ALA C 100 " (cutoff:3.500A) Processing helix chain 'C' and resid 122 through 138 removed outlier: 3.646A pdb=" N ALA C 132 " --> pdb=" O ALA C 128 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N TYR C 136 " --> pdb=" O ALA C 132 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ILE C 138 " --> pdb=" O ASP C 134 " (cutoff:3.500A) Processing helix chain 'C' and resid 139 through 142 Processing helix chain 'C' and resid 242 through 246 removed outlier: 3.717A pdb=" N ILE C 246 " --> pdb=" O GLN C 243 " (cutoff:3.500A) Processing helix chain 'C' and resid 297 through 337 removed outlier: 3.915A pdb=" N VAL C 303 " --> pdb=" O LEU C 299 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ALA C 317 " --> pdb=" O PHE C 313 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N PHE C 330 " --> pdb=" O LEU C 326 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N VAL C 331 " --> pdb=" O GLN C 327 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N PHE C 333 " --> pdb=" O GLU C 329 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ARG C 336 " --> pdb=" O VAL C 332 " (cutoff:3.500A) Processing helix chain 'C' and resid 343 through 348 removed outlier: 3.577A pdb=" N ARG C 347 " --> pdb=" O SER C 343 " (cutoff:3.500A) Processing helix chain 'C' and resid 349 through 351 No H-bonds generated for 'chain 'C' and resid 349 through 351' Processing helix chain 'C' and resid 354 through 376 removed outlier: 3.759A pdb=" N GLU C 376 " --> pdb=" O LYS C 372 " (cutoff:3.500A) Processing helix chain 'C' and resid 384 through 400 removed outlier: 3.875A pdb=" N THR C 392 " --> pdb=" O ILE C 388 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N LEU C 395 " --> pdb=" O GLY C 391 " (cutoff:3.500A) Processing helix chain 'C' and resid 401 through 407 removed outlier: 3.785A pdb=" N PHE C 407 " --> pdb=" O TYR C 404 " (cutoff:3.500A) Processing helix chain 'C' and resid 415 through 419 Processing helix chain 'C' and resid 420 through 447 removed outlier: 4.571A pdb=" N SER C 424 " --> pdb=" O VAL C 420 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N VAL C 425 " --> pdb=" O ALA C 421 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N PHE C 428 " --> pdb=" O SER C 424 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ILE C 435 " --> pdb=" O CYS C 431 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N ILE C 445 " --> pdb=" O PHE C 441 " (cutoff:3.500A) Processing helix chain 'C' and resid 456 through 470 removed outlier: 3.519A pdb=" N VAL C 460 " --> pdb=" O SER C 456 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N ASN C 469 " --> pdb=" O PHE C 465 " (cutoff:3.500A) Processing helix chain 'C' and resid 472 through 483 removed outlier: 3.541A pdb=" N THR C 476 " --> pdb=" O ASP C 472 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N PHE C 477 " --> pdb=" O MET C 473 " (cutoff:3.500A) removed outlier: 4.740A pdb=" N GLN C 483 " --> pdb=" O ALA C 479 " (cutoff:3.500A) Processing helix chain 'C' and resid 484 through 487 removed outlier: 3.590A pdb=" N SER C 487 " --> pdb=" O GLN C 484 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 484 through 487' Processing helix chain 'C' and resid 489 through 507 removed outlier: 3.618A pdb=" N LEU C 496 " --> pdb=" O LEU C 492 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N SER C 500 " --> pdb=" O LEU C 496 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N PHE C 505 " --> pdb=" O PHE C 501 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N TYR C 507 " --> pdb=" O SER C 503 " (cutoff:3.500A) Processing helix chain 'C' and resid 509 through 526 Processing helix chain 'D' and resid 39 through 49 removed outlier: 3.935A pdb=" N LEU D 45 " --> pdb=" O LEU D 41 " (cutoff:3.500A) Processing helix chain 'D' and resid 51 through 57 removed outlier: 3.612A pdb=" N ARG D 57 " --> pdb=" O CYS D 53 " (cutoff:3.500A) Processing helix chain 'D' and resid 63 through 106 removed outlier: 3.954A pdb=" N LEU D 68 " --> pdb=" O CYS D 64 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N GLN D 69 " --> pdb=" O LYS D 65 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N SER D 86 " --> pdb=" O LEU D 82 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N PHE D 93 " --> pdb=" O LEU D 89 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ASN D 97 " --> pdb=" O PHE D 93 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ILE D 99 " --> pdb=" O GLU D 95 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LEU D 104 " --> pdb=" O ALA D 100 " (cutoff:3.500A) Processing helix chain 'D' and resid 122 through 138 removed outlier: 3.646A pdb=" N ALA D 132 " --> pdb=" O ALA D 128 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N TYR D 136 " --> pdb=" O ALA D 132 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ILE D 138 " --> pdb=" O ASP D 134 " (cutoff:3.500A) Processing helix chain 'D' and resid 139 through 142 Processing helix chain 'D' and resid 242 through 246 removed outlier: 3.717A pdb=" N ILE D 246 " --> pdb=" O GLN D 243 " (cutoff:3.500A) Processing helix chain 'D' and resid 297 through 337 removed outlier: 3.916A pdb=" N VAL D 303 " --> pdb=" O LEU D 299 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ALA D 317 " --> pdb=" O PHE D 313 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N PHE D 330 " --> pdb=" O LEU D 326 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N VAL D 331 " --> pdb=" O GLN D 327 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N PHE D 333 " --> pdb=" O GLU D 329 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ARG D 336 " --> pdb=" O VAL D 332 " (cutoff:3.500A) Processing helix chain 'D' and resid 343 through 348 removed outlier: 3.576A pdb=" N ARG D 347 " --> pdb=" O SER D 343 " (cutoff:3.500A) Processing helix chain 'D' and resid 349 through 351 No H-bonds generated for 'chain 'D' and resid 349 through 351' Processing helix chain 'D' and resid 354 through 376 removed outlier: 3.759A pdb=" N GLU D 376 " --> pdb=" O LYS D 372 " (cutoff:3.500A) Processing helix chain 'D' and resid 384 through 400 removed outlier: 3.875A pdb=" N THR D 392 " --> pdb=" O ILE D 388 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N LEU D 395 " --> pdb=" O GLY D 391 " (cutoff:3.500A) Processing helix chain 'D' and resid 401 through 407 removed outlier: 3.785A pdb=" N PHE D 407 " --> pdb=" O TYR D 404 " (cutoff:3.500A) Processing helix chain 'D' and resid 415 through 419 Processing helix chain 'D' and resid 420 through 447 removed outlier: 4.571A pdb=" N SER D 424 " --> pdb=" O VAL D 420 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N VAL D 425 " --> pdb=" O ALA D 421 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N PHE D 428 " --> pdb=" O SER D 424 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ILE D 435 " --> pdb=" O CYS D 431 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N ILE D 445 " --> pdb=" O PHE D 441 " (cutoff:3.500A) Processing helix chain 'D' and resid 456 through 470 removed outlier: 3.520A pdb=" N VAL D 460 " --> pdb=" O SER D 456 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N ASN D 469 " --> pdb=" O PHE D 465 " (cutoff:3.500A) Processing helix chain 'D' and resid 472 through 483 removed outlier: 3.541A pdb=" N THR D 476 " --> pdb=" O ASP D 472 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N PHE D 477 " --> pdb=" O MET D 473 " (cutoff:3.500A) removed outlier: 4.740A pdb=" N GLN D 483 " --> pdb=" O ALA D 479 " (cutoff:3.500A) Processing helix chain 'D' and resid 484 through 487 removed outlier: 3.588A pdb=" N SER D 487 " --> pdb=" O GLN D 484 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 484 through 487' Processing helix chain 'D' and resid 489 through 507 removed outlier: 3.618A pdb=" N LEU D 496 " --> pdb=" O LEU D 492 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N SER D 500 " --> pdb=" O LEU D 496 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N PHE D 505 " --> pdb=" O PHE D 501 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N TYR D 507 " --> pdb=" O SER D 503 " (cutoff:3.500A) Processing helix chain 'D' and resid 509 through 526 Processing sheet with id=AA1, first strand: chain 'A' and resid 118 through 119 removed outlier: 3.600A pdb=" N ILE A 271 " --> pdb=" O ALA A 119 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N GLU A 276 " --> pdb=" O LEU A 259 " (cutoff:3.500A) removed outlier: 7.353A pdb=" N LEU A 228 " --> pdb=" O TYR A 170 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N TYR A 170 " --> pdb=" O LEU A 228 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LEU A 163 " --> pdb=" O VAL A 195 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N TYR A 169 " --> pdb=" O VAL A 189 " (cutoff:3.500A) removed outlier: 7.628A pdb=" N ARG A 187 " --> pdb=" O HIS A 171 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 118 through 119 removed outlier: 3.600A pdb=" N ILE B 271 " --> pdb=" O ALA B 119 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N GLU B 276 " --> pdb=" O LEU B 259 " (cutoff:3.500A) removed outlier: 7.355A pdb=" N LEU B 228 " --> pdb=" O TYR B 170 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N TYR B 170 " --> pdb=" O LEU B 228 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LEU B 163 " --> pdb=" O VAL B 195 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N TYR B 169 " --> pdb=" O VAL B 189 " (cutoff:3.500A) removed outlier: 7.628A pdb=" N ARG B 187 " --> pdb=" O HIS B 171 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 118 through 119 removed outlier: 3.599A pdb=" N ILE C 271 " --> pdb=" O ALA C 119 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N GLU C 276 " --> pdb=" O LEU C 259 " (cutoff:3.500A) removed outlier: 7.354A pdb=" N LEU C 228 " --> pdb=" O TYR C 170 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N TYR C 170 " --> pdb=" O LEU C 228 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LEU C 163 " --> pdb=" O VAL C 195 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N TYR C 169 " --> pdb=" O VAL C 189 " (cutoff:3.500A) removed outlier: 7.628A pdb=" N ARG C 187 " --> pdb=" O HIS C 171 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 118 through 119 removed outlier: 3.599A pdb=" N ILE D 271 " --> pdb=" O ALA D 119 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N GLU D 276 " --> pdb=" O LEU D 259 " (cutoff:3.500A) removed outlier: 7.355A pdb=" N LEU D 228 " --> pdb=" O TYR D 170 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N TYR D 170 " --> pdb=" O LEU D 228 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LEU D 163 " --> pdb=" O VAL D 195 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N TYR D 169 " --> pdb=" O VAL D 189 " (cutoff:3.500A) removed outlier: 7.628A pdb=" N ARG D 187 " --> pdb=" O HIS D 171 " (cutoff:3.500A) 820 hydrogen bonds defined for protein. 2376 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.73 Time building geometry restraints manager: 5.85 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: 4435 1.34 - 1.46: 3038 1.46 - 1.57: 7631 1.57 - 1.69: 0 1.69 - 1.81: 132 Bond restraints: 15236 Sorted by residual: bond pdb=" CB VAL C 434 " pdb=" CG1 VAL C 434 " ideal model delta sigma weight residual 1.521 1.453 0.068 3.30e-02 9.18e+02 4.19e+00 bond pdb=" CB VAL B 434 " pdb=" CG1 VAL B 434 " ideal model delta sigma weight residual 1.521 1.454 0.067 3.30e-02 9.18e+02 4.15e+00 bond pdb=" CB VAL D 434 " pdb=" CG1 VAL D 434 " ideal model delta sigma weight residual 1.521 1.454 0.067 3.30e-02 9.18e+02 4.11e+00 bond pdb=" CB VAL A 434 " pdb=" CG1 VAL A 434 " ideal model delta sigma weight residual 1.521 1.454 0.067 3.30e-02 9.18e+02 4.11e+00 bond pdb=" C GLY A 470 " pdb=" N ASP A 471 " ideal model delta sigma weight residual 1.333 1.296 0.037 1.92e-02 2.71e+03 3.65e+00 ... (remaining 15231 not shown) Histogram of bond angle deviations from ideal: 99.70 - 106.57: 333 106.57 - 113.43: 8476 113.43 - 120.29: 6146 120.29 - 127.15: 5581 127.15 - 134.02: 116 Bond angle restraints: 20652 Sorted by residual: angle pdb=" C ALA D 421 " pdb=" N LEU D 422 " pdb=" CA LEU D 422 " ideal model delta sigma weight residual 120.06 124.44 -4.38 1.19e+00 7.06e-01 1.35e+01 angle pdb=" C ALA B 421 " pdb=" N LEU B 422 " pdb=" CA LEU B 422 " ideal model delta sigma weight residual 120.06 124.42 -4.36 1.19e+00 7.06e-01 1.34e+01 angle pdb=" C ALA A 421 " pdb=" N LEU A 422 " pdb=" CA LEU A 422 " ideal model delta sigma weight residual 120.06 124.39 -4.33 1.19e+00 7.06e-01 1.32e+01 angle pdb=" C ALA C 421 " pdb=" N LEU C 422 " pdb=" CA LEU C 422 " ideal model delta sigma weight residual 120.06 124.39 -4.33 1.19e+00 7.06e-01 1.32e+01 angle pdb=" C ILE A 402 " pdb=" N ARG A 403 " pdb=" CA ARG A 403 " ideal model delta sigma weight residual 120.28 125.09 -4.81 1.44e+00 4.82e-01 1.12e+01 ... (remaining 20647 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.83: 8434 15.83 - 31.66: 485 31.66 - 47.48: 117 47.48 - 63.31: 8 63.31 - 79.14: 12 Dihedral angle restraints: 9056 sinusoidal: 3692 harmonic: 5364 Sorted by residual: dihedral pdb=" CA ASN D 412 " pdb=" C ASN D 412 " pdb=" N ILE D 413 " pdb=" CA ILE D 413 " ideal model delta harmonic sigma weight residual 180.00 125.16 54.84 0 5.00e+00 4.00e-02 1.20e+02 dihedral pdb=" CA ASN C 412 " pdb=" C ASN C 412 " pdb=" N ILE C 413 " pdb=" CA ILE C 413 " ideal model delta harmonic sigma weight residual 180.00 125.16 54.84 0 5.00e+00 4.00e-02 1.20e+02 dihedral pdb=" CA ASN A 412 " pdb=" C ASN A 412 " pdb=" N ILE A 413 " pdb=" CA ILE A 413 " ideal model delta harmonic sigma weight residual 180.00 125.16 54.84 0 5.00e+00 4.00e-02 1.20e+02 ... (remaining 9053 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 1506 0.046 - 0.092: 707 0.092 - 0.139: 155 0.139 - 0.185: 48 0.185 - 0.231: 4 Chirality restraints: 2420 Sorted by residual: chirality pdb=" CB ILE A 193 " pdb=" CA ILE A 193 " pdb=" CG1 ILE A 193 " pdb=" CG2 ILE A 193 " both_signs ideal model delta sigma weight residual False 2.64 2.41 0.23 2.00e-01 2.50e+01 1.33e+00 chirality pdb=" CB ILE B 193 " pdb=" CA ILE B 193 " pdb=" CG1 ILE B 193 " pdb=" CG2 ILE B 193 " both_signs ideal model delta sigma weight residual False 2.64 2.41 0.23 2.00e-01 2.50e+01 1.32e+00 chirality pdb=" CB ILE D 193 " pdb=" CA ILE D 193 " pdb=" CG1 ILE D 193 " pdb=" CG2 ILE D 193 " both_signs ideal model delta sigma weight residual False 2.64 2.42 0.23 2.00e-01 2.50e+01 1.29e+00 ... (remaining 2417 not shown) Planarity restraints: 2520 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C HIS B 526 " -0.048 5.00e-02 4.00e+02 7.31e-02 8.55e+00 pdb=" N PRO B 527 " 0.126 5.00e-02 4.00e+02 pdb=" CA PRO B 527 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO B 527 " -0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS A 526 " -0.048 5.00e-02 4.00e+02 7.30e-02 8.54e+00 pdb=" N PRO A 527 " 0.126 5.00e-02 4.00e+02 pdb=" CA PRO A 527 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO A 527 " -0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS D 526 " -0.048 5.00e-02 4.00e+02 7.30e-02 8.53e+00 pdb=" N PRO D 527 " 0.126 5.00e-02 4.00e+02 pdb=" CA PRO D 527 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO D 527 " -0.043 5.00e-02 4.00e+02 ... (remaining 2517 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 4018 2.80 - 3.33: 13517 3.33 - 3.85: 22826 3.85 - 4.38: 26010 4.38 - 4.90: 44022 Nonbonded interactions: 110393 Sorted by model distance: nonbonded pdb=" O TRP B 335 " pdb=" CG ARG B 338 " model vdw 2.276 3.440 nonbonded pdb=" O TRP A 335 " pdb=" CG ARG A 338 " model vdw 2.277 3.440 nonbonded pdb=" O TRP D 335 " pdb=" CG ARG D 338 " model vdw 2.278 3.440 nonbonded pdb=" O TRP C 335 " pdb=" CG ARG C 338 " model vdw 2.280 3.440 nonbonded pdb=" O PHE D 93 " pdb=" ND2 ASN D 97 " model vdw 2.386 2.520 ... (remaining 110388 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 38 through 527) selection = chain 'B' selection = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.360 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: 2.610 Check model and map are aligned: 0.200 Set scattering table: 0.120 Process input model: 36.940 Find NCS groups from input model: 0.980 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8085 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 : 0.009 0.068 15236 Z= 0.548 Angle : 1.041 10.810 20652 Z= 0.543 Chirality : 0.054 0.231 2420 Planarity : 0.008 0.073 2516 Dihedral : 11.173 79.141 5584 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 2.56 Ramachandran Plot: Outliers : 0.22 % Allowed : 8.07 % Favored : 91.70 % Rotamer: Outliers : 0.24 % Allowed : 3.95 % Favored : 95.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.46 % 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: -5.18 (0.13), residues: 1784 helix: -3.19 (0.10), residues: 1028 sheet: -2.71 (0.29), residues: 204 loop : -3.76 (0.19), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.003 TRP A 444 HIS 0.011 0.003 HIS D 103 PHE 0.028 0.003 PHE D 407 TYR 0.026 0.004 TYR A 383 ARG 0.009 0.001 ARG D 455 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3568 Ramachandran restraints generated. 1784 Oldfield, 0 Emsley, 1784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3568 Ramachandran restraints generated. 1784 Oldfield, 0 Emsley, 1784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 421 residues out of total 1644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 417 time to evaluate : 1.585 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 LYS cc_start: 0.6011 (mttt) cc_final: 0.5321 (mmtt) REVERT: A 62 LYS cc_start: 0.5648 (mttt) cc_final: 0.5069 (tttt) REVERT: A 63 PRO cc_start: 0.8154 (Cg_endo) cc_final: 0.7729 (Cg_exo) REVERT: A 516 LEU cc_start: 0.9064 (mm) cc_final: 0.8812 (mt) REVERT: B 46 LYS cc_start: 0.5998 (mttt) cc_final: 0.5287 (mmtt) REVERT: B 63 PRO cc_start: 0.8018 (Cg_endo) cc_final: 0.7624 (Cg_exo) REVERT: B 226 HIS cc_start: 0.7376 (m-70) cc_final: 0.7168 (p-80) REVERT: B 322 ARG cc_start: 0.8287 (ttp80) cc_final: 0.7824 (ttt180) REVERT: B 324 PHE cc_start: 0.8548 (t80) cc_final: 0.7658 (m-80) REVERT: B 409 HIS cc_start: 0.7580 (t-90) cc_final: 0.7373 (t-90) REVERT: B 516 LEU cc_start: 0.9093 (mm) cc_final: 0.8866 (mt) REVERT: C 46 LYS cc_start: 0.6058 (mttt) cc_final: 0.5250 (mmtt) REVERT: C 63 PRO cc_start: 0.8071 (Cg_endo) cc_final: 0.7674 (Cg_exo) REVERT: C 226 HIS cc_start: 0.7395 (m-70) cc_final: 0.7189 (p-80) REVERT: C 324 PHE cc_start: 0.8560 (t80) cc_final: 0.7770 (m-80) REVERT: C 516 LEU cc_start: 0.9088 (mm) cc_final: 0.8873 (mt) REVERT: D 46 LYS cc_start: 0.6014 (mttt) cc_final: 0.5224 (mmtt) REVERT: D 63 PRO cc_start: 0.8144 (Cg_endo) cc_final: 0.7758 (Cg_exo) REVERT: D 226 HIS cc_start: 0.7365 (m-70) cc_final: 0.7156 (p-80) REVERT: D 324 PHE cc_start: 0.8596 (t80) cc_final: 0.7776 (m-80) REVERT: D 409 HIS cc_start: 0.7626 (t-90) cc_final: 0.7413 (t-90) REVERT: D 516 LEU cc_start: 0.9068 (mm) cc_final: 0.8847 (mt) outliers start: 4 outliers final: 4 residues processed: 421 average time/residue: 0.3069 time to fit residues: 179.3379 Evaluate side-chains 216 residues out of total 1644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 212 time to evaluate : 1.740 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain D residue 401 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 151 optimal weight: 9.9990 chunk 136 optimal weight: 4.9990 chunk 75 optimal weight: 20.0000 chunk 46 optimal weight: 9.9990 chunk 92 optimal weight: 1.9990 chunk 72 optimal weight: 7.9990 chunk 141 optimal weight: 0.9980 chunk 54 optimal weight: 4.9990 chunk 85 optimal weight: 3.9990 chunk 105 optimal weight: 0.1980 chunk 163 optimal weight: 5.9990 overall best weight: 2.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 328 ASN A 352 ASN ** A 409 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 481 GLN A 526 HIS B 174 HIS B 328 ASN B 352 ASN B 409 HIS B 481 GLN B 526 HIS C 174 HIS C 328 ASN C 352 ASN ** C 409 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 526 HIS D 174 HIS D 328 ASN D 352 ASN D 409 HIS D 526 HIS Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.2785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 15236 Z= 0.241 Angle : 0.704 8.961 20652 Z= 0.367 Chirality : 0.042 0.153 2420 Planarity : 0.005 0.060 2516 Dihedral : 6.498 44.763 2168 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.22 % Allowed : 7.79 % Favored : 91.98 % Rotamer: Outliers : 2.86 % Allowed : 11.74 % Favored : 85.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.46 % 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: -2.45 (0.18), residues: 1784 helix: -0.54 (0.15), residues: 1044 sheet: -2.29 (0.31), residues: 204 loop : -3.40 (0.21), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP C 444 HIS 0.004 0.001 HIS C 526 PHE 0.012 0.002 PHE C 235 TYR 0.015 0.001 TYR A 218 ARG 0.005 0.001 ARG D 427 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3568 Ramachandran restraints generated. 1784 Oldfield, 0 Emsley, 1784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3568 Ramachandran restraints generated. 1784 Oldfield, 0 Emsley, 1784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 329 residues out of total 1644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 282 time to evaluate : 1.685 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 LYS cc_start: 0.5919 (mttt) cc_final: 0.5244 (mptt) REVERT: A 63 PRO cc_start: 0.8211 (Cg_endo) cc_final: 0.7828 (Cg_exo) REVERT: A 324 PHE cc_start: 0.8437 (t80) cc_final: 0.7603 (m-80) REVERT: A 418 LEU cc_start: 0.7177 (pp) cc_final: 0.6953 (tp) REVERT: A 473 MET cc_start: 0.8315 (ttp) cc_final: 0.8036 (ttm) REVERT: A 516 LEU cc_start: 0.8974 (mm) cc_final: 0.8750 (mt) REVERT: B 46 LYS cc_start: 0.5911 (mttt) cc_final: 0.5168 (mptt) REVERT: B 74 LEU cc_start: 0.8670 (tp) cc_final: 0.8156 (mp) REVERT: B 473 MET cc_start: 0.8297 (ttp) cc_final: 0.8034 (ttm) REVERT: C 46 LYS cc_start: 0.5787 (mttt) cc_final: 0.5000 (mptt) REVERT: C 63 PRO cc_start: 0.8198 (Cg_endo) cc_final: 0.7809 (Cg_exo) REVERT: C 74 LEU cc_start: 0.8662 (tp) cc_final: 0.8153 (mp) REVERT: C 473 MET cc_start: 0.8355 (ttp) cc_final: 0.8095 (ttm) REVERT: D 46 LYS cc_start: 0.5788 (mttt) cc_final: 0.5004 (mptt) REVERT: D 63 PRO cc_start: 0.8201 (Cg_endo) cc_final: 0.7818 (Cg_exo) REVERT: D 74 LEU cc_start: 0.8662 (tp) cc_final: 0.8152 (mp) REVERT: D 313 PHE cc_start: 0.8459 (t80) cc_final: 0.8251 (t80) REVERT: D 473 MET cc_start: 0.8258 (ttp) cc_final: 0.7879 (ttm) outliers start: 47 outliers final: 18 residues processed: 324 average time/residue: 0.2510 time to fit residues: 120.8304 Evaluate side-chains 222 residues out of total 1644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 204 time to evaluate : 1.781 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 350 PHE Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 143 SER Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain B residue 350 PHE Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 245 LEU Chi-restraints excluded: chain C residue 350 PHE Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain D residue 71 VAL Chi-restraints excluded: chain D residue 245 LEU Chi-restraints excluded: chain D residue 350 PHE Chi-restraints excluded: chain D residue 401 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 90 optimal weight: 20.0000 chunk 50 optimal weight: 7.9990 chunk 136 optimal weight: 8.9990 chunk 111 optimal weight: 8.9990 chunk 45 optimal weight: 20.0000 chunk 163 optimal weight: 3.9990 chunk 176 optimal weight: 2.9990 chunk 145 optimal weight: 8.9990 chunk 162 optimal weight: 5.9990 chunk 55 optimal weight: 8.9990 chunk 131 optimal weight: 5.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 327 GLN ** B 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 327 GLN ** B 484 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 327 GLN C 481 GLN ** C 484 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 327 GLN ** D 484 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 0.3503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.034 15236 Z= 0.410 Angle : 0.739 8.596 20652 Z= 0.383 Chirality : 0.045 0.138 2420 Planarity : 0.005 0.049 2516 Dihedral : 6.462 48.010 2168 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.14 % Favored : 90.86 % Rotamer: Outliers : 3.71 % Allowed : 12.59 % Favored : 83.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.46 % 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: -1.37 (0.20), residues: 1784 helix: 0.44 (0.17), residues: 1020 sheet: -2.19 (0.33), residues: 204 loop : -2.92 (0.23), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 444 HIS 0.007 0.002 HIS B 409 PHE 0.025 0.002 PHE D 324 TYR 0.024 0.002 TYR A 218 ARG 0.003 0.001 ARG A 455 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3568 Ramachandran restraints generated. 1784 Oldfield, 0 Emsley, 1784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3568 Ramachandran restraints generated. 1784 Oldfield, 0 Emsley, 1784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 1644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 217 time to evaluate : 1.776 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 LYS cc_start: 0.6186 (mttt) cc_final: 0.5575 (mmtt) REVERT: A 469 ASN cc_start: 0.8790 (OUTLIER) cc_final: 0.8502 (m-40) REVERT: A 473 MET cc_start: 0.8497 (ttp) cc_final: 0.8265 (ttm) REVERT: B 46 LYS cc_start: 0.6023 (mttt) cc_final: 0.5168 (mmtt) REVERT: B 74 LEU cc_start: 0.8648 (tp) cc_final: 0.8144 (mp) REVERT: B 324 PHE cc_start: 0.8469 (t80) cc_final: 0.7572 (m-80) REVERT: B 426 MET cc_start: 0.9049 (tpp) cc_final: 0.8141 (mpp) REVERT: B 473 MET cc_start: 0.8531 (ttp) cc_final: 0.8322 (ttm) REVERT: C 46 LYS cc_start: 0.6154 (mttt) cc_final: 0.5585 (mmtt) REVERT: C 324 PHE cc_start: 0.8505 (t80) cc_final: 0.7569 (m-80) REVERT: C 473 MET cc_start: 0.8527 (ttp) cc_final: 0.8297 (ttm) REVERT: C 483 GLN cc_start: 0.6636 (tm-30) cc_final: 0.6423 (tm-30) REVERT: D 46 LYS cc_start: 0.6076 (mttt) cc_final: 0.5521 (mmtt) REVERT: D 324 PHE cc_start: 0.8463 (t80) cc_final: 0.7531 (m-80) REVERT: D 409 HIS cc_start: 0.7583 (t70) cc_final: 0.7382 (t-90) REVERT: D 469 ASN cc_start: 0.8849 (OUTLIER) cc_final: 0.8627 (m-40) REVERT: D 473 MET cc_start: 0.8445 (ttp) cc_final: 0.8070 (ttm) outliers start: 61 outliers final: 49 residues processed: 261 average time/residue: 0.2229 time to fit residues: 90.7977 Evaluate side-chains 255 residues out of total 1644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 204 time to evaluate : 1.711 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 73 ILE Chi-restraints excluded: chain A residue 111 ASP Chi-restraints excluded: chain A residue 143 SER Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 310 SER Chi-restraints excluded: chain A residue 350 PHE Chi-restraints excluded: chain A residue 383 TYR Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 458 SER Chi-restraints excluded: chain A residue 469 ASN Chi-restraints excluded: chain A residue 490 VAL Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 73 ILE Chi-restraints excluded: chain B residue 111 ASP Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain B residue 310 SER Chi-restraints excluded: chain B residue 350 PHE Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 458 SER Chi-restraints excluded: chain B residue 490 VAL Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 73 ILE Chi-restraints excluded: chain C residue 111 ASP Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 245 LEU Chi-restraints excluded: chain C residue 261 THR Chi-restraints excluded: chain C residue 310 SER Chi-restraints excluded: chain C residue 350 PHE Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 458 SER Chi-restraints excluded: chain C residue 490 VAL Chi-restraints excluded: chain D residue 71 VAL Chi-restraints excluded: chain D residue 73 ILE Chi-restraints excluded: chain D residue 111 ASP Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain D residue 245 LEU Chi-restraints excluded: chain D residue 261 THR Chi-restraints excluded: chain D residue 304 VAL Chi-restraints excluded: chain D residue 310 SER Chi-restraints excluded: chain D residue 350 PHE Chi-restraints excluded: chain D residue 401 VAL Chi-restraints excluded: chain D residue 452 VAL Chi-restraints excluded: chain D residue 458 SER Chi-restraints excluded: chain D residue 469 ASN Chi-restraints excluded: chain D residue 490 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 161 optimal weight: 20.0000 chunk 123 optimal weight: 9.9990 chunk 84 optimal weight: 3.9990 chunk 18 optimal weight: 8.9990 chunk 78 optimal weight: 6.9990 chunk 109 optimal weight: 1.9990 chunk 164 optimal weight: 6.9990 chunk 173 optimal weight: 3.9990 chunk 85 optimal weight: 3.9990 chunk 155 optimal weight: 0.6980 chunk 46 optimal weight: 0.6980 overall best weight: 2.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 486 HIS ** B 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 484 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 486 HIS ** C 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 484 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 484 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 486 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 moved from start: 0.3855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 15236 Z= 0.206 Angle : 0.598 8.107 20652 Z= 0.308 Chirality : 0.040 0.140 2420 Planarity : 0.004 0.043 2516 Dihedral : 6.074 44.847 2168 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.51 % Favored : 92.49 % Rotamer: Outliers : 3.04 % Allowed : 14.72 % Favored : 82.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.46 % 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: -0.66 (0.20), residues: 1784 helix: 1.08 (0.17), residues: 1016 sheet: -1.90 (0.33), residues: 204 loop : -2.73 (0.23), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 345 HIS 0.006 0.001 HIS D 409 PHE 0.021 0.002 PHE A 56 TYR 0.027 0.001 TYR A 218 ARG 0.003 0.000 ARG A 419 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3568 Ramachandran restraints generated. 1784 Oldfield, 0 Emsley, 1784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3568 Ramachandran restraints generated. 1784 Oldfield, 0 Emsley, 1784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 1644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 233 time to evaluate : 1.772 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 LYS cc_start: 0.6475 (mttt) cc_final: 0.5764 (mmtt) REVERT: A 61 ARG cc_start: 0.4527 (tpp-160) cc_final: 0.4093 (tpp-160) REVERT: A 62 LYS cc_start: 0.6235 (mttt) cc_final: 0.5669 (tttt) REVERT: A 74 LEU cc_start: 0.8931 (tp) cc_final: 0.8420 (mm) REVERT: A 261 THR cc_start: 0.9437 (m) cc_final: 0.8882 (p) REVERT: A 265 LYS cc_start: 0.8385 (OUTLIER) cc_final: 0.8008 (ttpt) REVERT: A 324 PHE cc_start: 0.8603 (t80) cc_final: 0.8332 (t80) REVERT: B 46 LYS cc_start: 0.6012 (mttt) cc_final: 0.5434 (mptt) REVERT: B 62 LYS cc_start: 0.5925 (mttt) cc_final: 0.5279 (tttt) REVERT: B 74 LEU cc_start: 0.8796 (tp) cc_final: 0.8255 (mp) REVERT: B 261 THR cc_start: 0.9429 (m) cc_final: 0.8873 (p) REVERT: B 324 PHE cc_start: 0.8310 (t80) cc_final: 0.8063 (t80) REVERT: B 473 MET cc_start: 0.8266 (ttp) cc_final: 0.8058 (ttm) REVERT: C 46 LYS cc_start: 0.6090 (mttt) cc_final: 0.5586 (mmtt) REVERT: C 62 LYS cc_start: 0.5949 (mttt) cc_final: 0.5294 (tttt) REVERT: C 74 LEU cc_start: 0.8909 (tp) cc_final: 0.8401 (mm) REVERT: C 324 PHE cc_start: 0.8271 (t80) cc_final: 0.8038 (t80) REVERT: C 483 GLN cc_start: 0.6390 (tm-30) cc_final: 0.5740 (tm-30) REVERT: D 46 LYS cc_start: 0.6013 (mttt) cc_final: 0.5519 (mmtt) REVERT: D 62 LYS cc_start: 0.5923 (mttt) cc_final: 0.5285 (tttt) REVERT: D 74 LEU cc_start: 0.8910 (tp) cc_final: 0.8414 (mm) REVERT: D 324 PHE cc_start: 0.8283 (t80) cc_final: 0.8065 (t80) REVERT: D 409 HIS cc_start: 0.7547 (t70) cc_final: 0.7343 (t-90) outliers start: 50 outliers final: 31 residues processed: 274 average time/residue: 0.2507 time to fit residues: 102.3044 Evaluate side-chains 244 residues out of total 1644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 212 time to evaluate : 1.604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 143 SER Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 265 LYS Chi-restraints excluded: chain A residue 350 PHE Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 458 SER Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 143 SER Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain B residue 350 PHE Chi-restraints excluded: chain B residue 383 TYR Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 490 VAL Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 245 LEU Chi-restraints excluded: chain C residue 350 PHE Chi-restraints excluded: chain C residue 383 TYR Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 458 SER Chi-restraints excluded: chain C residue 490 VAL Chi-restraints excluded: chain D residue 71 VAL Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain D residue 245 LEU Chi-restraints excluded: chain D residue 350 PHE Chi-restraints excluded: chain D residue 383 TYR Chi-restraints excluded: chain D residue 401 VAL Chi-restraints excluded: chain D residue 458 SER Chi-restraints excluded: chain D residue 490 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 144 optimal weight: 8.9990 chunk 98 optimal weight: 1.9990 chunk 2 optimal weight: 5.9990 chunk 129 optimal weight: 2.9990 chunk 71 optimal weight: 5.9990 chunk 148 optimal weight: 0.8980 chunk 120 optimal weight: 7.9990 chunk 0 optimal weight: 20.0000 chunk 88 optimal weight: 5.9990 chunk 156 optimal weight: 6.9990 chunk 43 optimal weight: 0.8980 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 243 GLN ** B 484 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 484 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 481 GLN ** D 484 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8104 moved from start: 0.4134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 15236 Z= 0.221 Angle : 0.600 7.839 20652 Z= 0.304 Chirality : 0.040 0.151 2420 Planarity : 0.004 0.041 2516 Dihedral : 5.896 44.963 2168 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.69 % Favored : 91.31 % Rotamer: Outliers : 4.14 % Allowed : 15.15 % Favored : 80.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.46 % 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: -0.19 (0.21), residues: 1784 helix: 1.46 (0.17), residues: 1012 sheet: -1.65 (0.34), residues: 204 loop : -2.52 (0.24), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 354 HIS 0.006 0.001 HIS D 409 PHE 0.016 0.002 PHE D 324 TYR 0.031 0.001 TYR A 218 ARG 0.004 0.000 ARG A 43 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3568 Ramachandran restraints generated. 1784 Oldfield, 0 Emsley, 1784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3568 Ramachandran restraints generated. 1784 Oldfield, 0 Emsley, 1784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 1644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 221 time to evaluate : 1.656 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 LYS cc_start: 0.6430 (mttt) cc_final: 0.5856 (mmtt) REVERT: A 62 LYS cc_start: 0.5986 (mttt) cc_final: 0.5433 (tttt) REVERT: A 265 LYS cc_start: 0.8409 (OUTLIER) cc_final: 0.7998 (ttpt) REVERT: A 324 PHE cc_start: 0.8619 (t80) cc_final: 0.8372 (t80) REVERT: A 483 GLN cc_start: 0.6492 (tm-30) cc_final: 0.6257 (tm-30) REVERT: B 46 LYS cc_start: 0.6366 (mttt) cc_final: 0.5753 (mmtt) REVERT: B 62 LYS cc_start: 0.5952 (mttt) cc_final: 0.5438 (tttt) REVERT: B 74 LEU cc_start: 0.8755 (tp) cc_final: 0.8228 (mp) REVERT: C 46 LYS cc_start: 0.6223 (mttt) cc_final: 0.5719 (mmtt) REVERT: C 62 LYS cc_start: 0.6142 (mttt) cc_final: 0.5522 (tttt) REVERT: C 324 PHE cc_start: 0.8297 (t80) cc_final: 0.8044 (t80) REVERT: C 483 GLN cc_start: 0.6439 (tm-30) cc_final: 0.5739 (tm-30) REVERT: D 46 LYS cc_start: 0.6218 (mttt) cc_final: 0.5758 (mmtt) REVERT: D 62 LYS cc_start: 0.6144 (mttt) cc_final: 0.5493 (tttt) REVERT: D 324 PHE cc_start: 0.8347 (t80) cc_final: 0.8086 (t80) REVERT: D 409 HIS cc_start: 0.7583 (t70) cc_final: 0.7353 (t-90) outliers start: 68 outliers final: 54 residues processed: 261 average time/residue: 0.2257 time to fit residues: 90.2798 Evaluate side-chains 263 residues out of total 1644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 208 time to evaluate : 1.632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 265 LYS Chi-restraints excluded: chain A residue 304 VAL Chi-restraints excluded: chain A residue 310 SER Chi-restraints excluded: chain A residue 350 PHE Chi-restraints excluded: chain A residue 351 VAL Chi-restraints excluded: chain A residue 383 TYR Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 409 HIS Chi-restraints excluded: chain A residue 458 SER Chi-restraints excluded: chain A residue 490 VAL Chi-restraints excluded: chain A residue 513 PHE Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain B residue 306 ILE Chi-restraints excluded: chain B residue 350 PHE Chi-restraints excluded: chain B residue 351 VAL Chi-restraints excluded: chain B residue 383 TYR Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 422 LEU Chi-restraints excluded: chain B residue 458 SER Chi-restraints excluded: chain B residue 490 VAL Chi-restraints excluded: chain B residue 508 MET Chi-restraints excluded: chain B residue 513 PHE Chi-restraints excluded: chain C residue 67 MET Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 245 LEU Chi-restraints excluded: chain C residue 300 LEU Chi-restraints excluded: chain C residue 350 PHE Chi-restraints excluded: chain C residue 351 VAL Chi-restraints excluded: chain C residue 383 TYR Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 409 HIS Chi-restraints excluded: chain C residue 422 LEU Chi-restraints excluded: chain C residue 458 SER Chi-restraints excluded: chain C residue 490 VAL Chi-restraints excluded: chain C residue 508 MET Chi-restraints excluded: chain C residue 513 PHE Chi-restraints excluded: chain D residue 45 LEU Chi-restraints excluded: chain D residue 71 VAL Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain D residue 245 LEU Chi-restraints excluded: chain D residue 350 PHE Chi-restraints excluded: chain D residue 351 VAL Chi-restraints excluded: chain D residue 383 TYR Chi-restraints excluded: chain D residue 401 VAL Chi-restraints excluded: chain D residue 422 LEU Chi-restraints excluded: chain D residue 458 SER Chi-restraints excluded: chain D residue 490 VAL Chi-restraints excluded: chain D residue 508 MET Chi-restraints excluded: chain D residue 513 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 58 optimal weight: 20.0000 chunk 156 optimal weight: 3.9990 chunk 34 optimal weight: 5.9990 chunk 102 optimal weight: 20.0000 chunk 42 optimal weight: 3.9990 chunk 174 optimal weight: 0.6980 chunk 144 optimal weight: 8.9990 chunk 80 optimal weight: 3.9990 chunk 14 optimal weight: 7.9990 chunk 57 optimal weight: 9.9990 chunk 91 optimal weight: 1.9990 overall best weight: 2.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 481 GLN ** B 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 409 HIS ** B 484 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 484 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 484 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8115 moved from start: 0.4305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 15236 Z= 0.241 Angle : 0.605 11.411 20652 Z= 0.309 Chirality : 0.040 0.148 2420 Planarity : 0.004 0.040 2516 Dihedral : 5.848 44.290 2168 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.63 % Favored : 91.37 % Rotamer: Outliers : 4.50 % Allowed : 15.75 % Favored : 79.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.40 % 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: -0.11 (0.21), residues: 1784 helix: 1.50 (0.17), residues: 1020 sheet: -1.57 (0.30), residues: 252 loop : -2.55 (0.26), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 354 HIS 0.005 0.001 HIS D 409 PHE 0.023 0.002 PHE B 56 TYR 0.029 0.001 TYR D 218 ARG 0.003 0.000 ARG A 43 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3568 Ramachandran restraints generated. 1784 Oldfield, 0 Emsley, 1784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3568 Ramachandran restraints generated. 1784 Oldfield, 0 Emsley, 1784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 1644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 215 time to evaluate : 1.681 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 LYS cc_start: 0.6442 (mttt) cc_final: 0.5885 (mmtt) REVERT: A 62 LYS cc_start: 0.6080 (mttt) cc_final: 0.5449 (tttt) REVERT: A 265 LYS cc_start: 0.8362 (OUTLIER) cc_final: 0.7986 (ttpt) REVERT: A 324 PHE cc_start: 0.8255 (t80) cc_final: 0.8027 (t80) REVERT: A 483 GLN cc_start: 0.6555 (tm-30) cc_final: 0.6322 (tm-30) REVERT: A 488 SER cc_start: 0.7695 (t) cc_final: 0.7188 (p) REVERT: B 46 LYS cc_start: 0.6390 (mttt) cc_final: 0.5801 (mmtt) REVERT: B 62 LYS cc_start: 0.5935 (mttt) cc_final: 0.5372 (tttt) REVERT: B 74 LEU cc_start: 0.8741 (tp) cc_final: 0.8218 (mp) REVERT: C 46 LYS cc_start: 0.6457 (mttt) cc_final: 0.5891 (mmtt) REVERT: C 62 LYS cc_start: 0.5957 (mttt) cc_final: 0.5383 (tttt) REVERT: D 46 LYS cc_start: 0.6413 (mttt) cc_final: 0.5873 (mmtt) REVERT: D 62 LYS cc_start: 0.5967 (mttt) cc_final: 0.5426 (tttt) REVERT: D 324 PHE cc_start: 0.8345 (t80) cc_final: 0.8093 (t80) REVERT: D 409 HIS cc_start: 0.7597 (t70) cc_final: 0.7340 (t-90) outliers start: 74 outliers final: 60 residues processed: 255 average time/residue: 0.2751 time to fit residues: 107.4916 Evaluate side-chains 265 residues out of total 1644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 204 time to evaluate : 1.559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 265 LYS Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 350 PHE Chi-restraints excluded: chain A residue 351 VAL Chi-restraints excluded: chain A residue 383 TYR Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 409 HIS Chi-restraints excluded: chain A residue 458 SER Chi-restraints excluded: chain A residue 490 VAL Chi-restraints excluded: chain A residue 513 PHE Chi-restraints excluded: chain B residue 67 MET Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain B residue 304 VAL Chi-restraints excluded: chain B residue 306 ILE Chi-restraints excluded: chain B residue 350 PHE Chi-restraints excluded: chain B residue 351 VAL Chi-restraints excluded: chain B residue 383 TYR Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 422 LEU Chi-restraints excluded: chain B residue 458 SER Chi-restraints excluded: chain B residue 490 VAL Chi-restraints excluded: chain B residue 508 MET Chi-restraints excluded: chain B residue 513 PHE Chi-restraints excluded: chain C residue 67 MET Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain C residue 245 LEU Chi-restraints excluded: chain C residue 300 LEU Chi-restraints excluded: chain C residue 350 PHE Chi-restraints excluded: chain C residue 351 VAL Chi-restraints excluded: chain C residue 383 TYR Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 409 HIS Chi-restraints excluded: chain C residue 422 LEU Chi-restraints excluded: chain C residue 458 SER Chi-restraints excluded: chain C residue 490 VAL Chi-restraints excluded: chain C residue 508 MET Chi-restraints excluded: chain C residue 513 PHE Chi-restraints excluded: chain D residue 67 MET Chi-restraints excluded: chain D residue 71 VAL Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain D residue 245 LEU Chi-restraints excluded: chain D residue 300 LEU Chi-restraints excluded: chain D residue 304 VAL Chi-restraints excluded: chain D residue 321 LEU Chi-restraints excluded: chain D residue 350 PHE Chi-restraints excluded: chain D residue 351 VAL Chi-restraints excluded: chain D residue 383 TYR Chi-restraints excluded: chain D residue 401 VAL Chi-restraints excluded: chain D residue 422 LEU Chi-restraints excluded: chain D residue 458 SER Chi-restraints excluded: chain D residue 490 VAL Chi-restraints excluded: chain D residue 508 MET Chi-restraints excluded: chain D residue 513 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 167 optimal weight: 1.9990 chunk 19 optimal weight: 6.9990 chunk 99 optimal weight: 7.9990 chunk 127 optimal weight: 6.9990 chunk 98 optimal weight: 0.9980 chunk 146 optimal weight: 1.9990 chunk 97 optimal weight: 1.9990 chunk 173 optimal weight: 0.9980 chunk 108 optimal weight: 9.9990 chunk 105 optimal weight: 3.9990 chunk 80 optimal weight: 0.1980 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 469 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8066 moved from start: 0.4571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 15236 Z= 0.157 Angle : 0.566 11.245 20652 Z= 0.287 Chirality : 0.039 0.217 2420 Planarity : 0.003 0.040 2516 Dihedral : 5.596 43.005 2168 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.79 % Favored : 92.21 % Rotamer: Outliers : 3.77 % Allowed : 16.55 % Favored : 79.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.34 % 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: 0.28 (0.21), residues: 1784 helix: 1.75 (0.17), residues: 1020 sheet: -1.10 (0.30), residues: 268 loop : -2.44 (0.27), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 354 HIS 0.008 0.001 HIS B 409 PHE 0.028 0.001 PHE D 56 TYR 0.023 0.001 TYR A 507 ARG 0.004 0.000 ARG A 43 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3568 Ramachandran restraints generated. 1784 Oldfield, 0 Emsley, 1784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3568 Ramachandran restraints generated. 1784 Oldfield, 0 Emsley, 1784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 1644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 228 time to evaluate : 2.088 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 LYS cc_start: 0.6708 (mttt) cc_final: 0.6013 (mmtt) REVERT: A 62 LYS cc_start: 0.6097 (mttt) cc_final: 0.5436 (tttt) REVERT: A 265 LYS cc_start: 0.8304 (OUTLIER) cc_final: 0.7847 (ttpt) REVERT: A 324 PHE cc_start: 0.8324 (t80) cc_final: 0.8094 (t80) REVERT: A 326 LEU cc_start: 0.8289 (mp) cc_final: 0.8042 (tt) REVERT: A 426 MET cc_start: 0.9151 (tpp) cc_final: 0.8588 (mpp) REVERT: A 483 GLN cc_start: 0.6347 (tm-30) cc_final: 0.6017 (tp40) REVERT: B 46 LYS cc_start: 0.6433 (mttt) cc_final: 0.5886 (mmtt) REVERT: B 62 LYS cc_start: 0.5936 (mttt) cc_final: 0.5358 (tttt) REVERT: B 74 LEU cc_start: 0.8690 (tp) cc_final: 0.8203 (mp) REVERT: B 326 LEU cc_start: 0.8072 (mp) cc_final: 0.7860 (tt) REVERT: C 46 LYS cc_start: 0.6383 (mttt) cc_final: 0.5840 (mmtt) REVERT: C 62 LYS cc_start: 0.6004 (mttt) cc_final: 0.5421 (tttt) REVERT: C 326 LEU cc_start: 0.8050 (mp) cc_final: 0.7829 (tt) REVERT: C 483 GLN cc_start: 0.6461 (tm-30) cc_final: 0.6194 (tp40) REVERT: D 46 LYS cc_start: 0.6379 (mttt) cc_final: 0.5855 (mmtt) REVERT: D 62 LYS cc_start: 0.6021 (mttt) cc_final: 0.5437 (tttt) REVERT: D 409 HIS cc_start: 0.7664 (t70) cc_final: 0.7372 (t-90) outliers start: 62 outliers final: 51 residues processed: 268 average time/residue: 0.2327 time to fit residues: 95.6631 Evaluate side-chains 251 residues out of total 1644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 199 time to evaluate : 1.736 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 265 LYS Chi-restraints excluded: chain A residue 350 PHE Chi-restraints excluded: chain A residue 351 VAL Chi-restraints excluded: chain A residue 383 TYR Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 409 HIS Chi-restraints excluded: chain A residue 458 SER Chi-restraints excluded: chain A residue 490 VAL Chi-restraints excluded: chain A residue 513 PHE Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 67 MET Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain B residue 306 ILE Chi-restraints excluded: chain B residue 350 PHE Chi-restraints excluded: chain B residue 351 VAL Chi-restraints excluded: chain B residue 383 TYR Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 422 LEU Chi-restraints excluded: chain B residue 458 SER Chi-restraints excluded: chain B residue 490 VAL Chi-restraints excluded: chain B residue 508 MET Chi-restraints excluded: chain C residue 67 MET Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain C residue 304 VAL Chi-restraints excluded: chain C residue 350 PHE Chi-restraints excluded: chain C residue 351 VAL Chi-restraints excluded: chain C residue 383 TYR Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 422 LEU Chi-restraints excluded: chain C residue 458 SER Chi-restraints excluded: chain C residue 490 VAL Chi-restraints excluded: chain C residue 508 MET Chi-restraints excluded: chain C residue 513 PHE Chi-restraints excluded: chain D residue 67 MET Chi-restraints excluded: chain D residue 71 VAL Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain D residue 245 LEU Chi-restraints excluded: chain D residue 350 PHE Chi-restraints excluded: chain D residue 351 VAL Chi-restraints excluded: chain D residue 383 TYR Chi-restraints excluded: chain D residue 401 VAL Chi-restraints excluded: chain D residue 422 LEU Chi-restraints excluded: chain D residue 490 VAL Chi-restraints excluded: chain D residue 513 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 107 optimal weight: 9.9990 chunk 69 optimal weight: 4.9990 chunk 103 optimal weight: 0.6980 chunk 52 optimal weight: 9.9990 chunk 34 optimal weight: 4.9990 chunk 33 optimal weight: 5.9990 chunk 110 optimal weight: 0.2980 chunk 118 optimal weight: 0.9990 chunk 85 optimal weight: 4.9990 chunk 16 optimal weight: 0.9980 chunk 136 optimal weight: 10.0000 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 469 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 484 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 486 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 moved from start: 0.4743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 15236 Z= 0.173 Angle : 0.588 11.015 20652 Z= 0.293 Chirality : 0.040 0.192 2420 Planarity : 0.003 0.038 2516 Dihedral : 5.506 42.877 2168 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.07 % Favored : 91.93 % Rotamer: Outliers : 3.16 % Allowed : 18.07 % Favored : 78.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.23 % 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 (0.21), residues: 1784 helix: 1.88 (0.17), residues: 1020 sheet: -0.89 (0.30), residues: 268 loop : -2.37 (0.27), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A 354 HIS 0.005 0.001 HIS B 409 PHE 0.027 0.001 PHE B 56 TYR 0.024 0.001 TYR D 218 ARG 0.003 0.000 ARG A 43 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3568 Ramachandran restraints generated. 1784 Oldfield, 0 Emsley, 1784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3568 Ramachandran restraints generated. 1784 Oldfield, 0 Emsley, 1784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 1644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 211 time to evaluate : 1.696 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 LYS cc_start: 0.6715 (mttt) cc_final: 0.6026 (mmtt) REVERT: A 62 LYS cc_start: 0.6032 (mttt) cc_final: 0.5426 (tttt) REVERT: A 265 LYS cc_start: 0.8331 (OUTLIER) cc_final: 0.7849 (ttpt) REVERT: A 324 PHE cc_start: 0.8320 (t80) cc_final: 0.8070 (t80) REVERT: A 326 LEU cc_start: 0.8295 (mp) cc_final: 0.8045 (tt) REVERT: B 46 LYS cc_start: 0.6706 (mttt) cc_final: 0.6009 (mmtt) REVERT: B 62 LYS cc_start: 0.5873 (mttt) cc_final: 0.5324 (tttt) REVERT: B 74 LEU cc_start: 0.8707 (tp) cc_final: 0.8221 (mp) REVERT: B 313 PHE cc_start: 0.8365 (t80) cc_final: 0.8144 (t80) REVERT: B 340 ARG cc_start: 0.6954 (tpt90) cc_final: 0.6451 (tpt90) REVERT: C 46 LYS cc_start: 0.6391 (mttt) cc_final: 0.5862 (mmtt) REVERT: C 62 LYS cc_start: 0.5868 (mttt) cc_final: 0.5322 (tttt) REVERT: C 326 LEU cc_start: 0.8064 (mp) cc_final: 0.7832 (tt) REVERT: C 340 ARG cc_start: 0.6958 (tpt90) cc_final: 0.6460 (tpt90) REVERT: D 46 LYS cc_start: 0.6392 (mttt) cc_final: 0.5880 (mmtt) REVERT: D 62 LYS cc_start: 0.5924 (mttt) cc_final: 0.5352 (tttt) REVERT: D 340 ARG cc_start: 0.6994 (tpt90) cc_final: 0.6488 (tpt90) REVERT: D 409 HIS cc_start: 0.7674 (t70) cc_final: 0.7372 (t-90) outliers start: 52 outliers final: 45 residues processed: 241 average time/residue: 0.2353 time to fit residues: 86.6108 Evaluate side-chains 244 residues out of total 1644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 198 time to evaluate : 1.831 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 265 LYS Chi-restraints excluded: chain A residue 350 PHE Chi-restraints excluded: chain A residue 351 VAL Chi-restraints excluded: chain A residue 383 TYR Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 409 HIS Chi-restraints excluded: chain A residue 415 ILE Chi-restraints excluded: chain A residue 490 VAL Chi-restraints excluded: chain A residue 513 PHE Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 306 ILE Chi-restraints excluded: chain B residue 350 PHE Chi-restraints excluded: chain B residue 351 VAL Chi-restraints excluded: chain B residue 383 TYR Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 422 LEU Chi-restraints excluded: chain B residue 458 SER Chi-restraints excluded: chain B residue 490 VAL Chi-restraints excluded: chain C residue 67 MET Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain C residue 304 VAL Chi-restraints excluded: chain C residue 350 PHE Chi-restraints excluded: chain C residue 351 VAL Chi-restraints excluded: chain C residue 383 TYR Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 409 HIS Chi-restraints excluded: chain C residue 422 LEU Chi-restraints excluded: chain C residue 458 SER Chi-restraints excluded: chain C residue 490 VAL Chi-restraints excluded: chain C residue 513 PHE Chi-restraints excluded: chain D residue 67 MET Chi-restraints excluded: chain D residue 71 VAL Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain D residue 350 PHE Chi-restraints excluded: chain D residue 351 VAL Chi-restraints excluded: chain D residue 383 TYR Chi-restraints excluded: chain D residue 401 VAL Chi-restraints excluded: chain D residue 422 LEU Chi-restraints excluded: chain D residue 458 SER Chi-restraints excluded: chain D residue 490 VAL Chi-restraints excluded: chain D residue 513 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 157 optimal weight: 1.9990 chunk 166 optimal weight: 0.9980 chunk 151 optimal weight: 6.9990 chunk 161 optimal weight: 3.9990 chunk 97 optimal weight: 9.9990 chunk 70 optimal weight: 10.0000 chunk 126 optimal weight: 0.9980 chunk 49 optimal weight: 7.9990 chunk 146 optimal weight: 4.9990 chunk 152 optimal weight: 0.9990 chunk 106 optimal weight: 1.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 481 GLN ** C 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 481 GLN ** D 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 481 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8060 moved from start: 0.4867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 15236 Z= 0.162 Angle : 0.601 10.714 20652 Z= 0.293 Chirality : 0.039 0.214 2420 Planarity : 0.003 0.037 2516 Dihedral : 5.407 41.866 2168 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.62 % Favored : 92.38 % Rotamer: Outliers : 2.92 % Allowed : 18.80 % Favored : 78.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.23 % 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: 0.62 (0.21), residues: 1784 helix: 1.97 (0.17), residues: 1016 sheet: -0.71 (0.30), residues: 268 loop : -2.30 (0.27), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 354 HIS 0.005 0.001 HIS B 409 PHE 0.031 0.001 PHE A 56 TYR 0.027 0.001 TYR D 218 ARG 0.003 0.000 ARG A 43 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3568 Ramachandran restraints generated. 1784 Oldfield, 0 Emsley, 1784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3568 Ramachandran restraints generated. 1784 Oldfield, 0 Emsley, 1784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 1644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 216 time to evaluate : 1.747 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 LYS cc_start: 0.6760 (mttt) cc_final: 0.6156 (mmtt) REVERT: A 62 LYS cc_start: 0.6123 (mttt) cc_final: 0.5517 (tttt) REVERT: A 265 LYS cc_start: 0.8318 (OUTLIER) cc_final: 0.7831 (ttpt) REVERT: A 313 PHE cc_start: 0.8332 (t80) cc_final: 0.8128 (t80) REVERT: A 326 LEU cc_start: 0.8190 (mp) cc_final: 0.7967 (tt) REVERT: B 46 LYS cc_start: 0.6716 (mttt) cc_final: 0.6015 (mmtt) REVERT: B 62 LYS cc_start: 0.6075 (mttt) cc_final: 0.5520 (tttt) REVERT: B 74 LEU cc_start: 0.8700 (tp) cc_final: 0.8223 (mp) REVERT: B 340 ARG cc_start: 0.6736 (tpt90) cc_final: 0.6247 (tpt90) REVERT: C 46 LYS cc_start: 0.6700 (mttt) cc_final: 0.6040 (mmtt) REVERT: C 62 LYS cc_start: 0.6099 (mttt) cc_final: 0.5545 (tttt) REVERT: C 340 ARG cc_start: 0.6749 (tpt90) cc_final: 0.6264 (tpt90) REVERT: D 46 LYS cc_start: 0.6751 (mttt) cc_final: 0.6097 (mmtt) REVERT: D 62 LYS cc_start: 0.6111 (mttt) cc_final: 0.5524 (tttt) REVERT: D 340 ARG cc_start: 0.6782 (tpt90) cc_final: 0.6304 (tpt90) REVERT: D 341 GLU cc_start: 0.5815 (tt0) cc_final: 0.5521 (tt0) REVERT: D 409 HIS cc_start: 0.7509 (t70) cc_final: 0.7207 (t70) REVERT: D 473 MET cc_start: 0.7904 (ttp) cc_final: 0.7677 (ttp) outliers start: 48 outliers final: 42 residues processed: 248 average time/residue: 0.2368 time to fit residues: 89.9340 Evaluate side-chains 234 residues out of total 1644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 191 time to evaluate : 1.683 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 265 LYS Chi-restraints excluded: chain A residue 304 VAL Chi-restraints excluded: chain A residue 350 PHE Chi-restraints excluded: chain A residue 351 VAL Chi-restraints excluded: chain A residue 383 TYR Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 409 HIS Chi-restraints excluded: chain A residue 490 VAL Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 310 SER Chi-restraints excluded: chain B residue 350 PHE Chi-restraints excluded: chain B residue 351 VAL Chi-restraints excluded: chain B residue 383 TYR Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 422 LEU Chi-restraints excluded: chain B residue 458 SER Chi-restraints excluded: chain B residue 490 VAL Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain C residue 350 PHE Chi-restraints excluded: chain C residue 351 VAL Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 409 HIS Chi-restraints excluded: chain C residue 422 LEU Chi-restraints excluded: chain C residue 490 VAL Chi-restraints excluded: chain C residue 513 PHE Chi-restraints excluded: chain D residue 45 LEU Chi-restraints excluded: chain D residue 71 VAL Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain D residue 350 PHE Chi-restraints excluded: chain D residue 351 VAL Chi-restraints excluded: chain D residue 383 TYR Chi-restraints excluded: chain D residue 401 VAL Chi-restraints excluded: chain D residue 422 LEU Chi-restraints excluded: chain D residue 458 SER Chi-restraints excluded: chain D residue 490 VAL Chi-restraints excluded: chain D residue 513 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 170 optimal weight: 7.9990 chunk 104 optimal weight: 8.9990 chunk 81 optimal weight: 3.9990 chunk 118 optimal weight: 3.9990 chunk 179 optimal weight: 5.9990 chunk 165 optimal weight: 0.0370 chunk 142 optimal weight: 6.9990 chunk 14 optimal weight: 8.9990 chunk 110 optimal weight: 6.9990 chunk 87 optimal weight: 0.9980 chunk 113 optimal weight: 9.9990 overall best weight: 3.0064 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 484 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 486 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8109 moved from start: 0.4872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 15236 Z= 0.246 Angle : 0.642 10.388 20652 Z= 0.319 Chirality : 0.041 0.226 2420 Planarity : 0.004 0.037 2516 Dihedral : 5.513 41.671 2168 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.80 % Favored : 91.20 % Rotamer: Outliers : 2.80 % Allowed : 19.10 % Favored : 78.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.23 % 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: 0.55 (0.21), residues: 1784 helix: 1.91 (0.17), residues: 1016 sheet: -0.81 (0.30), residues: 268 loop : -2.30 (0.27), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 354 HIS 0.005 0.001 HIS D 409 PHE 0.028 0.002 PHE D 56 TYR 0.033 0.002 TYR C 218 ARG 0.002 0.000 ARG A 43 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3568 Ramachandran restraints generated. 1784 Oldfield, 0 Emsley, 1784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3568 Ramachandran restraints generated. 1784 Oldfield, 0 Emsley, 1784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 196 time to evaluate : 1.614 Fit side-chains REVERT: A 46 LYS cc_start: 0.6836 (mttt) cc_final: 0.6227 (mmtt) REVERT: A 62 LYS cc_start: 0.6204 (mttt) cc_final: 0.5572 (tttt) REVERT: A 265 LYS cc_start: 0.8375 (OUTLIER) cc_final: 0.7900 (ttpt) REVERT: A 326 LEU cc_start: 0.8169 (mp) cc_final: 0.7913 (tt) REVERT: B 46 LYS cc_start: 0.6772 (mttt) cc_final: 0.6076 (mmtt) REVERT: B 62 LYS cc_start: 0.6204 (mttt) cc_final: 0.5619 (tttt) REVERT: B 74 LEU cc_start: 0.8691 (tp) cc_final: 0.8229 (mp) REVERT: B 313 PHE cc_start: 0.8429 (t80) cc_final: 0.8209 (t80) REVERT: B 340 ARG cc_start: 0.6812 (tpt90) cc_final: 0.6326 (tpt90) REVERT: B 483 GLN cc_start: 0.6132 (tp40) cc_final: 0.5728 (tp40) REVERT: C 46 LYS cc_start: 0.6795 (mttt) cc_final: 0.6135 (mmtt) REVERT: C 62 LYS cc_start: 0.6199 (mttt) cc_final: 0.5576 (tttt) REVERT: C 313 PHE cc_start: 0.8475 (t80) cc_final: 0.8261 (t80) REVERT: C 340 ARG cc_start: 0.6765 (tpt90) cc_final: 0.6276 (tpt90) REVERT: C 483 GLN cc_start: 0.6349 (tm-30) cc_final: 0.6019 (tp40) REVERT: D 46 LYS cc_start: 0.6815 (mttt) cc_final: 0.6160 (mmtt) REVERT: D 62 LYS cc_start: 0.6214 (mttt) cc_final: 0.5600 (tttt) REVERT: D 409 HIS cc_start: 0.7588 (t70) cc_final: 0.7291 (t70) REVERT: D 462 GLU cc_start: 0.7621 (mt-10) cc_final: 0.7323 (mt-10) REVERT: D 473 MET cc_start: 0.8017 (ttp) cc_final: 0.7585 (ttm) outliers start: 46 outliers final: 42 residues processed: 226 average time/residue: 0.2467 time to fit residues: 84.3694 Evaluate side-chains 229 residues out of total 1644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 186 time to evaluate : 1.765 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 265 LYS Chi-restraints excluded: chain A residue 304 VAL Chi-restraints excluded: chain A residue 350 PHE Chi-restraints excluded: chain A residue 351 VAL Chi-restraints excluded: chain A residue 383 TYR Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 409 HIS Chi-restraints excluded: chain A residue 490 VAL Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 350 PHE Chi-restraints excluded: chain B residue 351 VAL Chi-restraints excluded: chain B residue 383 TYR Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 422 LEU Chi-restraints excluded: chain B residue 458 SER Chi-restraints excluded: chain B residue 490 VAL Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain C residue 304 VAL Chi-restraints excluded: chain C residue 350 PHE Chi-restraints excluded: chain C residue 351 VAL Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 409 HIS Chi-restraints excluded: chain C residue 422 LEU Chi-restraints excluded: chain C residue 490 VAL Chi-restraints excluded: chain C residue 513 PHE Chi-restraints excluded: chain D residue 45 LEU Chi-restraints excluded: chain D residue 71 VAL Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain D residue 350 PHE Chi-restraints excluded: chain D residue 351 VAL Chi-restraints excluded: chain D residue 383 TYR Chi-restraints excluded: chain D residue 401 VAL Chi-restraints excluded: chain D residue 422 LEU Chi-restraints excluded: chain D residue 458 SER Chi-restraints excluded: chain D residue 490 VAL Chi-restraints excluded: chain D residue 513 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 152 optimal weight: 2.9990 chunk 43 optimal weight: 0.8980 chunk 131 optimal weight: 0.3980 chunk 21 optimal weight: 9.9990 chunk 39 optimal weight: 2.9990 chunk 143 optimal weight: 5.9990 chunk 59 optimal weight: 10.0000 chunk 146 optimal weight: 9.9990 chunk 18 optimal weight: 9.9990 chunk 26 optimal weight: 6.9990 chunk 125 optimal weight: 0.9990 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 483 GLN ** B 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.129441 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.102664 restraints weight = 28493.527| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.105161 restraints weight = 17114.050| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.106763 restraints weight = 12643.642| |-----------------------------------------------------------------------------| r_work (final): 0.3295 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.4983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 15236 Z= 0.178 Angle : 0.625 10.696 20652 Z= 0.307 Chirality : 0.040 0.200 2420 Planarity : 0.003 0.037 2516 Dihedral : 5.461 40.420 2168 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.85 % Favored : 92.15 % Rotamer: Outliers : 2.68 % Allowed : 19.95 % Favored : 77.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.23 % 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: 0.63 (0.21), residues: 1784 helix: 1.94 (0.17), residues: 1016 sheet: -0.68 (0.30), residues: 268 loop : -2.23 (0.27), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP A 354 HIS 0.005 0.001 HIS D 409 PHE 0.032 0.001 PHE D 56 TYR 0.031 0.001 TYR B 218 ARG 0.003 0.000 ARG A 43 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2680.35 seconds wall clock time: 50 minutes 6.53 seconds (3006.53 seconds total)