Starting phenix.real_space_refine on Fri Feb 16 08:38:09 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5wpq_8881/02_2024/5wpq_8881.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5wpq_8881/02_2024/5wpq_8881.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.64 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5wpq_8881/02_2024/5wpq_8881.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5wpq_8881/02_2024/5wpq_8881.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5wpq_8881/02_2024/5wpq_8881.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5wpq_8881/02_2024/5wpq_8881.pdb" } resolution = 3.64 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= 0.012 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 403": "NH1" <-> "NH2" Residue "A ARG 419": "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 403": "NH1" <-> "NH2" Residue "B ARG 419": "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 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 403": "NH1" <-> "NH2" Residue "C ARG 419": "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 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 403": "NH1" <-> "NH2" Residue "D ARG 419": "NH1" <-> "NH2" Residue "D ARG 455": "NH1" <-> "NH2" Time to flip residues: 0.06s 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: 8.19, per 1000 atoms: 0.55 Number of scatterers: 14889 At special positions: 0 Unit cell: (112.35, 112.35, 116.63, 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: 5.98 Conformation dependent library (CDL) restraints added in 2.8 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: 68 helices and 8 sheets defined 63.4% alpha, 16.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.33 Creating SS restraints... Processing helix chain 'A' and resid 39 through 50 removed outlier: 3.731A pdb=" N ARG A 43 " --> pdb=" O GLU A 39 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N LEU A 45 " --> pdb=" O LEU A 41 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LYS A 46 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N TYR A 47 " --> pdb=" O ARG A 43 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N PHE A 48 " --> pdb=" O ARG A 44 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N MET A 50 " --> pdb=" O LYS A 46 " (cutoff:3.500A) Processing helix chain 'A' and resid 53 through 57 removed outlier: 3.952A pdb=" N PHE A 56 " --> pdb=" O CYS A 53 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ARG A 57 " --> pdb=" O ASP A 54 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 53 through 57' Processing helix chain 'A' and resid 64 through 106 removed outlier: 3.764A pdb=" N SER A 86 " --> pdb=" O LEU A 82 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N PHE A 93 " --> pdb=" O LEU A 89 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ARG A 94 " --> pdb=" O VAL A 90 " (cutoff:3.500A) Processing helix chain 'A' and resid 121 through 138 removed outlier: 3.644A pdb=" N LEU A 125 " --> pdb=" O THR A 121 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ILE A 138 " --> pdb=" O ASP A 134 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 247 removed outlier: 3.845A pdb=" N ILE A 246 " --> pdb=" O LEU A 242 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 327 removed outlier: 3.697A pdb=" N CYS A 309 " --> pdb=" O VAL A 305 " (cutoff:3.500A) Processing helix chain 'A' and resid 327 through 332 removed outlier: 3.627A pdb=" N VAL A 331 " --> pdb=" O GLN A 327 " (cutoff:3.500A) Processing helix chain 'A' and resid 332 through 337 Processing helix chain 'A' and resid 343 through 349 removed outlier: 3.827A pdb=" N ARG A 347 " --> pdb=" O SER A 343 " (cutoff:3.500A) Processing helix chain 'A' and resid 354 through 377 Processing helix chain 'A' and resid 383 through 399 Processing helix chain 'A' and resid 401 through 406 Processing helix chain 'A' and resid 408 through 448 removed outlier: 4.153A pdb=" N LEU A 414 " --> pdb=" O LYS A 410 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N LEU A 418 " --> pdb=" O LEU A 414 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ARG A 419 " --> pdb=" O ILE A 415 " (cutoff:3.500A) Proline residue: A 423 - end of helix removed outlier: 4.106A pdb=" N CYS A 431 " --> pdb=" O ARG A 427 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N ILE A 435 " --> pdb=" O CYS A 431 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ILE A 445 " --> pdb=" O PHE A 441 " (cutoff:3.500A) Processing helix chain 'A' and resid 456 through 470 removed outlier: 4.214A pdb=" N ASN A 469 " --> pdb=" O PHE A 465 " (cutoff:3.500A) Processing helix chain 'A' and resid 472 through 483 removed outlier: 3.555A pdb=" N THR A 476 " --> pdb=" O ASP A 472 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N GLN A 483 " --> pdb=" O ALA A 479 " (cutoff:3.500A) Processing helix chain 'A' and resid 487 through 506 removed outlier: 3.784A pdb=" N TRP A 491 " --> pdb=" O SER A 487 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LEU A 496 " --> pdb=" O LEU A 492 " (cutoff:3.500A) Processing helix chain 'A' and resid 508 through 526 Processing helix chain 'B' and resid 39 through 50 removed outlier: 3.731A pdb=" N ARG B 43 " --> pdb=" O GLU B 39 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N LEU B 45 " --> pdb=" O LEU B 41 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LYS B 46 " --> pdb=" O ARG B 42 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N TYR B 47 " --> pdb=" O ARG B 43 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N PHE B 48 " --> pdb=" O ARG B 44 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N MET B 50 " --> pdb=" O LYS B 46 " (cutoff:3.500A) Processing helix chain 'B' and resid 53 through 57 removed outlier: 3.952A pdb=" N PHE B 56 " --> pdb=" O CYS B 53 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ARG B 57 " --> pdb=" O ASP B 54 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 53 through 57' Processing helix chain 'B' and resid 64 through 106 removed outlier: 3.765A pdb=" N SER B 86 " --> pdb=" O LEU B 82 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N PHE B 93 " --> pdb=" O LEU B 89 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ARG B 94 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing helix chain 'B' and resid 121 through 138 removed outlier: 3.644A pdb=" N LEU B 125 " --> pdb=" O THR B 121 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ILE B 138 " --> pdb=" O ASP B 134 " (cutoff:3.500A) Processing helix chain 'B' and resid 242 through 247 removed outlier: 3.846A pdb=" N ILE B 246 " --> pdb=" O LEU B 242 " (cutoff:3.500A) Processing helix chain 'B' and resid 297 through 327 removed outlier: 3.697A pdb=" N CYS B 309 " --> pdb=" O VAL B 305 " (cutoff:3.500A) Processing helix chain 'B' and resid 327 through 332 removed outlier: 3.628A pdb=" N VAL B 331 " --> pdb=" O GLN B 327 " (cutoff:3.500A) Processing helix chain 'B' and resid 332 through 337 Processing helix chain 'B' and resid 343 through 349 removed outlier: 3.827A pdb=" N ARG B 347 " --> pdb=" O SER B 343 " (cutoff:3.500A) Processing helix chain 'B' and resid 354 through 377 Processing helix chain 'B' and resid 383 through 399 Processing helix chain 'B' and resid 401 through 406 Processing helix chain 'B' and resid 408 through 448 removed outlier: 4.154A pdb=" N LEU B 414 " --> pdb=" O LYS B 410 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N LEU B 418 " --> pdb=" O LEU B 414 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ARG B 419 " --> pdb=" O ILE B 415 " (cutoff:3.500A) Proline residue: B 423 - end of helix removed outlier: 4.106A pdb=" N CYS B 431 " --> pdb=" O ARG B 427 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N ILE B 435 " --> pdb=" O CYS B 431 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ILE B 445 " --> pdb=" O PHE B 441 " (cutoff:3.500A) Processing helix chain 'B' and resid 456 through 470 removed outlier: 4.214A pdb=" N ASN B 469 " --> pdb=" O PHE B 465 " (cutoff:3.500A) Processing helix chain 'B' and resid 472 through 483 removed outlier: 3.555A pdb=" N THR B 476 " --> pdb=" O ASP B 472 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N GLN B 483 " --> pdb=" O ALA B 479 " (cutoff:3.500A) Processing helix chain 'B' and resid 487 through 506 removed outlier: 3.785A pdb=" N TRP B 491 " --> pdb=" O SER B 487 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LEU B 496 " --> pdb=" O LEU B 492 " (cutoff:3.500A) Processing helix chain 'B' and resid 508 through 526 Processing helix chain 'C' and resid 39 through 50 removed outlier: 3.731A pdb=" N ARG C 43 " --> pdb=" O GLU C 39 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N LEU C 45 " --> pdb=" O LEU C 41 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LYS C 46 " --> pdb=" O ARG C 42 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N TYR C 47 " --> pdb=" O ARG C 43 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N PHE C 48 " --> pdb=" O ARG C 44 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N MET C 50 " --> pdb=" O LYS C 46 " (cutoff:3.500A) Processing helix chain 'C' and resid 53 through 57 removed outlier: 3.951A pdb=" N PHE C 56 " --> pdb=" O CYS C 53 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ARG C 57 " --> pdb=" O ASP C 54 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 53 through 57' Processing helix chain 'C' and resid 64 through 106 removed outlier: 3.764A pdb=" N SER C 86 " --> pdb=" O LEU C 82 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N PHE C 93 " --> pdb=" O LEU C 89 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ARG C 94 " --> pdb=" O VAL C 90 " (cutoff:3.500A) Processing helix chain 'C' and resid 121 through 138 removed outlier: 3.643A pdb=" N LEU C 125 " --> pdb=" O THR C 121 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ILE C 138 " --> pdb=" O ASP C 134 " (cutoff:3.500A) Processing helix chain 'C' and resid 242 through 247 removed outlier: 3.845A pdb=" N ILE C 246 " --> pdb=" O LEU C 242 " (cutoff:3.500A) Processing helix chain 'C' and resid 297 through 327 removed outlier: 3.697A pdb=" N CYS C 309 " --> pdb=" O VAL C 305 " (cutoff:3.500A) Processing helix chain 'C' and resid 327 through 332 removed outlier: 3.627A pdb=" N VAL C 331 " --> pdb=" O GLN C 327 " (cutoff:3.500A) Processing helix chain 'C' and resid 332 through 337 Processing helix chain 'C' and resid 343 through 349 removed outlier: 3.827A pdb=" N ARG C 347 " --> pdb=" O SER C 343 " (cutoff:3.500A) Processing helix chain 'C' and resid 354 through 377 Processing helix chain 'C' and resid 383 through 399 Processing helix chain 'C' and resid 401 through 406 Processing helix chain 'C' and resid 408 through 448 removed outlier: 4.153A pdb=" N LEU C 414 " --> pdb=" O LYS C 410 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N LEU C 418 " --> pdb=" O LEU C 414 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ARG C 419 " --> pdb=" O ILE C 415 " (cutoff:3.500A) Proline residue: C 423 - end of helix removed outlier: 4.105A pdb=" N CYS C 431 " --> pdb=" O ARG C 427 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N ILE C 435 " --> pdb=" O CYS C 431 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ILE C 445 " --> pdb=" O PHE C 441 " (cutoff:3.500A) Processing helix chain 'C' and resid 456 through 470 removed outlier: 4.214A pdb=" N ASN C 469 " --> pdb=" O PHE C 465 " (cutoff:3.500A) Processing helix chain 'C' and resid 472 through 483 removed outlier: 3.556A pdb=" N THR C 476 " --> pdb=" O ASP C 472 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N GLN C 483 " --> pdb=" O ALA C 479 " (cutoff:3.500A) Processing helix chain 'C' and resid 487 through 506 removed outlier: 3.784A pdb=" N TRP C 491 " --> pdb=" O SER C 487 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LEU C 496 " --> pdb=" O LEU C 492 " (cutoff:3.500A) Processing helix chain 'C' and resid 508 through 526 Processing helix chain 'D' and resid 39 through 50 removed outlier: 3.732A pdb=" N ARG D 43 " --> pdb=" O GLU D 39 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N LEU D 45 " --> pdb=" O LEU D 41 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LYS D 46 " --> pdb=" O ARG D 42 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N TYR D 47 " --> pdb=" O ARG D 43 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N PHE D 48 " --> pdb=" O ARG D 44 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N MET D 50 " --> pdb=" O LYS D 46 " (cutoff:3.500A) Processing helix chain 'D' and resid 53 through 57 removed outlier: 3.952A pdb=" N PHE D 56 " --> pdb=" O CYS D 53 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ARG D 57 " --> pdb=" O ASP D 54 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 53 through 57' Processing helix chain 'D' and resid 64 through 106 removed outlier: 3.764A pdb=" N SER D 86 " --> pdb=" O LEU D 82 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N PHE D 93 " --> pdb=" O LEU D 89 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ARG D 94 " --> pdb=" O VAL D 90 " (cutoff:3.500A) Processing helix chain 'D' and resid 121 through 138 removed outlier: 3.644A pdb=" N LEU D 125 " --> pdb=" O THR D 121 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ILE D 138 " --> pdb=" O ASP D 134 " (cutoff:3.500A) Processing helix chain 'D' and resid 242 through 247 removed outlier: 3.846A pdb=" N ILE D 246 " --> pdb=" O LEU D 242 " (cutoff:3.500A) Processing helix chain 'D' and resid 297 through 327 removed outlier: 3.696A pdb=" N CYS D 309 " --> pdb=" O VAL D 305 " (cutoff:3.500A) Processing helix chain 'D' and resid 327 through 332 removed outlier: 3.627A pdb=" N VAL D 331 " --> pdb=" O GLN D 327 " (cutoff:3.500A) Processing helix chain 'D' and resid 332 through 337 Processing helix chain 'D' and resid 343 through 349 removed outlier: 3.827A pdb=" N ARG D 347 " --> pdb=" O SER D 343 " (cutoff:3.500A) Processing helix chain 'D' and resid 354 through 377 Processing helix chain 'D' and resid 383 through 399 Processing helix chain 'D' and resid 401 through 406 Processing helix chain 'D' and resid 408 through 448 removed outlier: 4.154A pdb=" N LEU D 414 " --> pdb=" O LYS D 410 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N LEU D 418 " --> pdb=" O LEU D 414 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ARG D 419 " --> pdb=" O ILE D 415 " (cutoff:3.500A) Proline residue: D 423 - end of helix removed outlier: 4.106A pdb=" N CYS D 431 " --> pdb=" O ARG D 427 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N ILE D 435 " --> pdb=" O CYS D 431 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ILE D 445 " --> pdb=" O PHE D 441 " (cutoff:3.500A) Processing helix chain 'D' and resid 456 through 470 removed outlier: 4.214A pdb=" N ASN D 469 " --> pdb=" O PHE D 465 " (cutoff:3.500A) Processing helix chain 'D' and resid 472 through 483 removed outlier: 3.556A pdb=" N THR D 476 " --> pdb=" O ASP D 472 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N GLN D 483 " --> pdb=" O ALA D 479 " (cutoff:3.500A) Processing helix chain 'D' and resid 487 through 506 removed outlier: 3.785A pdb=" N TRP D 491 " --> pdb=" O SER D 487 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LEU D 496 " --> pdb=" O LEU D 492 " (cutoff:3.500A) Processing helix chain 'D' and resid 508 through 526 Processing sheet with id=AA1, first strand: chain 'A' and resid 118 through 119 removed outlier: 3.826A pdb=" N ASN A 230 " --> pdb=" O ARG A 168 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N HIS A 234 " --> pdb=" O ALA A 164 " (cutoff:3.500A) removed outlier: 7.634A pdb=" N ARG A 187 " --> pdb=" O HIS A 171 " (cutoff:3.500A) removed outlier: 5.662A pdb=" N GLY A 173 " --> pdb=" O ASP A 185 " (cutoff:3.500A) removed outlier: 7.583A pdb=" N ASP A 185 " --> pdb=" O GLY A 173 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 148 through 149 removed outlier: 3.556A pdb=" N CYS A 253 " --> pdb=" O GLN A 282 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 118 through 119 removed outlier: 3.826A pdb=" N ASN B 230 " --> pdb=" O ARG B 168 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N HIS B 234 " --> pdb=" O ALA B 164 " (cutoff:3.500A) removed outlier: 7.634A pdb=" N ARG B 187 " --> pdb=" O HIS B 171 " (cutoff:3.500A) removed outlier: 5.661A pdb=" N GLY B 173 " --> pdb=" O ASP B 185 " (cutoff:3.500A) removed outlier: 7.583A pdb=" N ASP B 185 " --> pdb=" O GLY B 173 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 148 through 149 removed outlier: 3.556A pdb=" N CYS B 253 " --> pdb=" O GLN B 282 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 118 through 119 removed outlier: 3.827A pdb=" N ASN C 230 " --> pdb=" O ARG C 168 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N HIS C 234 " --> pdb=" O ALA C 164 " (cutoff:3.500A) removed outlier: 7.634A pdb=" N ARG C 187 " --> pdb=" O HIS C 171 " (cutoff:3.500A) removed outlier: 5.662A pdb=" N GLY C 173 " --> pdb=" O ASP C 185 " (cutoff:3.500A) removed outlier: 7.583A pdb=" N ASP C 185 " --> pdb=" O GLY C 173 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 148 through 149 removed outlier: 3.556A pdb=" N CYS C 253 " --> pdb=" O GLN C 282 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 118 through 119 removed outlier: 3.826A pdb=" N ASN D 230 " --> pdb=" O ARG D 168 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N HIS D 234 " --> pdb=" O ALA D 164 " (cutoff:3.500A) removed outlier: 7.633A pdb=" N ARG D 187 " --> pdb=" O HIS D 171 " (cutoff:3.500A) removed outlier: 5.661A pdb=" N GLY D 173 " --> pdb=" O ASP D 185 " (cutoff:3.500A) removed outlier: 7.583A pdb=" N ASP D 185 " --> pdb=" O GLY D 173 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 148 through 149 removed outlier: 3.556A pdb=" N CYS D 253 " --> pdb=" O GLN D 282 " (cutoff:3.500A) 932 hydrogen bonds defined for protein. 2748 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.34 Time building geometry restraints manager: 6.46 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: 4457 1.34 - 1.46: 2844 1.46 - 1.58: 7803 1.58 - 1.69: 0 1.69 - 1.81: 132 Bond restraints: 15236 Sorted by residual: bond pdb=" C1 NAG E 2 " pdb=" O5 NAG E 2 " ideal model delta sigma weight residual 1.406 1.443 -0.037 2.00e-02 2.50e+03 3.50e+00 bond pdb=" C1 NAG F 2 " pdb=" O5 NAG F 2 " ideal model delta sigma weight residual 1.406 1.441 -0.035 2.00e-02 2.50e+03 3.01e+00 bond pdb=" C LEU C 139 " pdb=" N PRO C 140 " ideal model delta sigma weight residual 1.336 1.357 -0.021 1.23e-02 6.61e+03 2.99e+00 bond pdb=" C LEU D 139 " pdb=" N PRO D 140 " ideal model delta sigma weight residual 1.336 1.357 -0.021 1.23e-02 6.61e+03 2.98e+00 bond pdb=" C1 NAG G 2 " pdb=" O5 NAG G 2 " ideal model delta sigma weight residual 1.406 1.441 -0.035 2.00e-02 2.50e+03 2.98e+00 ... (remaining 15231 not shown) Histogram of bond angle deviations from ideal: 100.23 - 107.45: 466 107.45 - 114.66: 8874 114.66 - 121.87: 8524 121.87 - 129.09: 2680 129.09 - 136.30: 108 Bond angle restraints: 20652 Sorted by residual: angle pdb=" CA LEU C 380 " pdb=" CB LEU C 380 " pdb=" CG LEU C 380 " ideal model delta sigma weight residual 116.30 130.41 -14.11 3.50e+00 8.16e-02 1.62e+01 angle pdb=" CA LEU B 380 " pdb=" CB LEU B 380 " pdb=" CG LEU B 380 " ideal model delta sigma weight residual 116.30 130.37 -14.07 3.50e+00 8.16e-02 1.62e+01 angle pdb=" CA LEU A 380 " pdb=" CB LEU A 380 " pdb=" CG LEU A 380 " ideal model delta sigma weight residual 116.30 130.34 -14.04 3.50e+00 8.16e-02 1.61e+01 angle pdb=" CA LEU D 380 " pdb=" CB LEU D 380 " pdb=" CG LEU D 380 " ideal model delta sigma weight residual 116.30 130.33 -14.03 3.50e+00 8.16e-02 1.61e+01 angle pdb=" N HIS D 526 " pdb=" CA HIS D 526 " pdb=" C HIS D 526 " ideal model delta sigma weight residual 109.81 117.27 -7.46 2.21e+00 2.05e-01 1.14e+01 ... (remaining 20647 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.58: 8474 15.58 - 31.15: 410 31.15 - 46.73: 132 46.73 - 62.31: 16 62.31 - 77.89: 24 Dihedral angle restraints: 9056 sinusoidal: 3692 harmonic: 5364 Sorted by residual: dihedral pdb=" CA GLY B 485 " pdb=" C GLY B 485 " pdb=" N HIS B 486 " pdb=" CA HIS B 486 " ideal model delta harmonic sigma weight residual 180.00 148.09 31.91 0 5.00e+00 4.00e-02 4.07e+01 dihedral pdb=" CA GLY D 485 " pdb=" C GLY D 485 " pdb=" N HIS D 486 " pdb=" CA HIS D 486 " ideal model delta harmonic sigma weight residual 180.00 148.10 31.90 0 5.00e+00 4.00e-02 4.07e+01 dihedral pdb=" CA GLY A 485 " pdb=" C GLY A 485 " pdb=" N HIS A 486 " pdb=" CA HIS A 486 " ideal model delta harmonic sigma weight residual 180.00 148.12 31.88 0 5.00e+00 4.00e-02 4.07e+01 ... (remaining 9053 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 1570 0.044 - 0.088: 611 0.088 - 0.132: 184 0.132 - 0.175: 35 0.175 - 0.219: 20 Chirality restraints: 2420 Sorted by residual: chirality pdb=" CG LEU B 389 " pdb=" CB LEU B 389 " pdb=" CD1 LEU B 389 " pdb=" CD2 LEU B 389 " both_signs ideal model delta sigma weight residual False -2.59 -2.37 -0.22 2.00e-01 2.50e+01 1.20e+00 chirality pdb=" CG LEU D 389 " pdb=" CB LEU D 389 " pdb=" CD1 LEU D 389 " pdb=" CD2 LEU D 389 " both_signs ideal model delta sigma weight residual False -2.59 -2.38 -0.21 2.00e-01 2.50e+01 1.14e+00 chirality pdb=" CG LEU C 389 " pdb=" CB LEU C 389 " pdb=" CD1 LEU C 389 " pdb=" CD2 LEU C 389 " both_signs ideal model delta sigma weight residual False -2.59 -2.38 -0.21 2.00e-01 2.50e+01 1.13e+00 ... (remaining 2417 not shown) Planarity restraints: 2520 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY B 448 " 0.038 5.00e-02 4.00e+02 5.68e-02 5.16e+00 pdb=" N PRO B 449 " -0.098 5.00e-02 4.00e+02 pdb=" CA PRO B 449 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO B 449 " 0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY D 448 " -0.037 5.00e-02 4.00e+02 5.65e-02 5.11e+00 pdb=" N PRO D 449 " 0.098 5.00e-02 4.00e+02 pdb=" CA PRO D 449 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO D 449 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY C 448 " -0.037 5.00e-02 4.00e+02 5.65e-02 5.11e+00 pdb=" N PRO C 449 " 0.098 5.00e-02 4.00e+02 pdb=" CA PRO C 449 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO C 449 " -0.031 5.00e-02 4.00e+02 ... (remaining 2517 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.83: 4388 2.83 - 3.35: 13270 3.35 - 3.86: 23074 3.86 - 4.38: 25280 4.38 - 4.90: 44093 Nonbonded interactions: 110105 Sorted by model distance: nonbonded pdb=" O TYR A 439 " pdb=" OH TYR A 497 " model vdw 2.310 2.440 nonbonded pdb=" O TYR D 439 " pdb=" OH TYR D 497 " model vdw 2.310 2.440 nonbonded pdb=" O TYR C 439 " pdb=" OH TYR C 497 " model vdw 2.310 2.440 nonbonded pdb=" O TYR B 439 " pdb=" OH TYR B 497 " model vdw 2.310 2.440 nonbonded pdb=" O LEU B 414 " pdb=" OG1 THR B 417 " model vdw 2.327 2.440 ... (remaining 110100 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: 0.420 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: 2.650 Check model and map are aligned: 0.240 Set scattering table: 0.140 Process input model: 40.480 Find NCS groups from input model: 1.040 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:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7802 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 : 0.006 0.056 15236 Z= 0.355 Angle : 0.970 14.105 20652 Z= 0.499 Chirality : 0.054 0.219 2420 Planarity : 0.007 0.057 2516 Dihedral : 11.534 77.887 5584 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 2.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.89 % Favored : 94.11 % Rotamer: Outliers : 0.49 % Allowed : 3.89 % Favored : 95.62 % 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: -4.69 (0.14), residues: 1784 helix: -3.01 (0.10), residues: 1040 sheet: -2.15 (0.32), residues: 204 loop : -3.21 (0.21), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.003 TRP B 444 HIS 0.006 0.002 HIS B 451 PHE 0.028 0.003 PHE A 101 TYR 0.022 0.003 TYR B 254 ARG 0.004 0.001 ARG A 102 *********************** 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 557 residues out of total 1644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 549 time to evaluate : 1.586 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 LYS cc_start: 0.8113 (mmpt) cc_final: 0.7437 (ptpt) REVERT: A 225 PHE cc_start: 0.8986 (m-80) cc_final: 0.8494 (m-10) REVERT: A 299 LEU cc_start: 0.8244 (tp) cc_final: 0.8033 (tp) REVERT: A 349 GLU cc_start: 0.7592 (mt-10) cc_final: 0.6677 (mt-10) REVERT: A 426 MET cc_start: 0.8838 (mmt) cc_final: 0.8614 (mmm) REVERT: B 55 LYS cc_start: 0.8042 (mmpt) cc_final: 0.7353 (pttt) REVERT: B 299 LEU cc_start: 0.8231 (tp) cc_final: 0.8018 (tp) REVERT: B 349 GLU cc_start: 0.7609 (mt-10) cc_final: 0.6753 (mt-10) REVERT: B 426 MET cc_start: 0.8845 (mmt) cc_final: 0.8634 (mmm) REVERT: C 55 LYS cc_start: 0.8335 (mmpt) cc_final: 0.7551 (ptpt) REVERT: C 299 LEU cc_start: 0.8244 (tp) cc_final: 0.8042 (tp) REVERT: C 349 GLU cc_start: 0.7475 (mt-10) cc_final: 0.6335 (mt-10) REVERT: C 426 MET cc_start: 0.8797 (mmt) cc_final: 0.8569 (mmm) REVERT: D 55 LYS cc_start: 0.8106 (mmpt) cc_final: 0.7432 (ptpt) REVERT: D 225 PHE cc_start: 0.8950 (m-80) cc_final: 0.8481 (m-10) REVERT: D 299 LEU cc_start: 0.8122 (tp) cc_final: 0.7902 (tp) REVERT: D 349 GLU cc_start: 0.7612 (mt-10) cc_final: 0.6575 (mt-10) REVERT: D 426 MET cc_start: 0.8868 (mmt) cc_final: 0.8649 (mmm) REVERT: D 459 MET cc_start: 0.8075 (mtt) cc_final: 0.7797 (mtt) REVERT: D 473 MET cc_start: 0.8082 (mtt) cc_final: 0.7864 (mtt) outliers start: 8 outliers final: 0 residues processed: 553 average time/residue: 0.2834 time to fit residues: 222.8322 Evaluate side-chains 237 residues out of total 1644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 237 time to evaluate : 1.761 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 151 optimal weight: 5.9990 chunk 136 optimal weight: 7.9990 chunk 75 optimal weight: 5.9990 chunk 46 optimal weight: 10.0000 chunk 92 optimal weight: 20.0000 chunk 72 optimal weight: 6.9990 chunk 141 optimal weight: 4.9990 chunk 54 optimal weight: 3.9990 chunk 85 optimal weight: 3.9990 chunk 105 optimal weight: 0.6980 chunk 163 optimal weight: 0.9990 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 69 GLN A 79 GLN A 234 HIS A 247 ASN A 267 HIS A 328 ASN A 409 HIS A 412 ASN A 481 GLN A 483 GLN B 69 GLN B 79 GLN B 234 HIS B 267 HIS B 328 ASN B 409 HIS B 412 ASN B 481 GLN B 483 GLN C 69 GLN C 234 HIS C 247 ASN C 267 HIS C 328 ASN C 409 HIS C 412 ASN C 481 GLN C 483 GLN D 69 GLN D 234 HIS D 247 ASN D 267 HIS D 328 ASN D 409 HIS D 412 ASN D 481 GLN D 483 GLN Total number of N/Q/H flips: 37 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7906 moved from start: 0.3100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 15236 Z= 0.248 Angle : 0.729 11.446 20652 Z= 0.368 Chirality : 0.044 0.160 2420 Planarity : 0.005 0.042 2516 Dihedral : 6.432 57.638 2164 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.61 % Favored : 94.39 % Rotamer: Outliers : 3.53 % Allowed : 13.26 % Favored : 83.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.02 (0.18), residues: 1784 helix: -0.36 (0.15), residues: 1084 sheet: -1.78 (0.32), residues: 204 loop : -3.17 (0.23), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 444 HIS 0.003 0.001 HIS D 171 PHE 0.016 0.002 PHE C 301 TYR 0.021 0.002 TYR D 218 ARG 0.005 0.000 ARG B 403 *********************** 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: 58 poor density : 271 time to evaluate : 1.769 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 LYS cc_start: 0.8252 (mmpt) cc_final: 0.7428 (ptpt) REVERT: A 67 MET cc_start: 0.7097 (ttp) cc_final: 0.6580 (ttm) REVERT: A 225 PHE cc_start: 0.8950 (m-80) cc_final: 0.8254 (m-10) REVERT: A 349 GLU cc_start: 0.7326 (mt-10) cc_final: 0.6983 (mt-10) REVERT: A 426 MET cc_start: 0.8769 (mmt) cc_final: 0.8542 (mmt) REVERT: B 55 LYS cc_start: 0.8253 (mmpt) cc_final: 0.7424 (ptpt) REVERT: B 349 GLU cc_start: 0.7315 (mt-10) cc_final: 0.6960 (mt-10) REVERT: B 426 MET cc_start: 0.8822 (mmt) cc_final: 0.8556 (mmt) REVERT: C 50 MET cc_start: 0.7496 (tpp) cc_final: 0.7111 (mmm) REVERT: C 55 LYS cc_start: 0.8377 (mmpt) cc_final: 0.7586 (ptpt) REVERT: C 426 MET cc_start: 0.8791 (mmt) cc_final: 0.8576 (mmt) REVERT: D 55 LYS cc_start: 0.8333 (mmpt) cc_final: 0.7558 (ptpt) REVERT: D 67 MET cc_start: 0.7100 (ttp) cc_final: 0.6717 (ttm) REVERT: D 225 PHE cc_start: 0.8937 (m-80) cc_final: 0.8262 (m-10) REVERT: D 349 GLU cc_start: 0.7324 (mt-10) cc_final: 0.6942 (mt-10) REVERT: D 426 MET cc_start: 0.8825 (mmt) cc_final: 0.8591 (mmt) REVERT: D 459 MET cc_start: 0.8146 (mtt) cc_final: 0.7778 (mtt) outliers start: 58 outliers final: 39 residues processed: 312 average time/residue: 0.2470 time to fit residues: 118.8167 Evaluate side-chains 257 residues out of total 1644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 218 time to evaluate : 1.900 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 115 ASP Chi-restraints excluded: chain A residue 222 THR Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 379 ASN Chi-restraints excluded: chain A residue 409 HIS Chi-restraints excluded: chain A residue 415 ILE Chi-restraints excluded: chain A residue 440 CYS Chi-restraints excluded: chain A residue 445 ILE Chi-restraints excluded: chain B residue 68 LEU Chi-restraints excluded: chain B residue 115 ASP Chi-restraints excluded: chain B residue 176 ASP Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain B residue 314 LEU Chi-restraints excluded: chain B residue 379 ASN Chi-restraints excluded: chain B residue 409 HIS Chi-restraints excluded: chain B residue 415 ILE Chi-restraints excluded: chain B residue 440 CYS Chi-restraints excluded: chain B residue 445 ILE Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain C residue 115 ASP Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 222 THR Chi-restraints excluded: chain C residue 314 LEU Chi-restraints excluded: chain C residue 364 LEU Chi-restraints excluded: chain C residue 379 ASN Chi-restraints excluded: chain C residue 409 HIS Chi-restraints excluded: chain C residue 415 ILE Chi-restraints excluded: chain C residue 440 CYS Chi-restraints excluded: chain C residue 445 ILE Chi-restraints excluded: chain D residue 68 LEU Chi-restraints excluded: chain D residue 115 ASP Chi-restraints excluded: chain D residue 222 THR Chi-restraints excluded: chain D residue 314 LEU Chi-restraints excluded: chain D residue 379 ASN Chi-restraints excluded: chain D residue 409 HIS Chi-restraints excluded: chain D residue 415 ILE Chi-restraints excluded: chain D residue 440 CYS Chi-restraints excluded: chain D residue 445 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 90 optimal weight: 30.0000 chunk 50 optimal weight: 7.9990 chunk 136 optimal weight: 0.0170 chunk 111 optimal weight: 0.7980 chunk 45 optimal weight: 40.0000 chunk 163 optimal weight: 1.9990 chunk 176 optimal weight: 3.9990 chunk 145 optimal weight: 0.9980 chunk 162 optimal weight: 9.9990 chunk 55 optimal weight: 0.0980 chunk 131 optimal weight: 0.8980 overall best weight: 0.5618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 247 ASN A 409 HIS A 483 GLN C 247 ASN C 409 HIS C 483 GLN D 247 ASN D 409 HIS D 483 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 moved from start: 0.3539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 15236 Z= 0.154 Angle : 0.618 9.782 20652 Z= 0.311 Chirality : 0.040 0.146 2420 Planarity : 0.004 0.035 2516 Dihedral : 6.032 58.154 2164 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 2.80 % Allowed : 17.46 % Favored : 79.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.94 (0.19), residues: 1784 helix: 0.54 (0.16), residues: 1072 sheet: -1.35 (0.32), residues: 204 loop : -2.79 (0.24), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 345 HIS 0.007 0.001 HIS C 409 PHE 0.014 0.001 PHE C 235 TYR 0.021 0.001 TYR D 218 ARG 0.003 0.000 ARG B 403 *********************** 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 289 residues out of total 1644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 243 time to evaluate : 1.628 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 LYS cc_start: 0.8250 (mmpt) cc_final: 0.7455 (ptpt) REVERT: A 67 MET cc_start: 0.7058 (ttp) cc_final: 0.6667 (ttm) REVERT: A 225 PHE cc_start: 0.8965 (m-80) cc_final: 0.8300 (m-10) REVERT: A 349 GLU cc_start: 0.7291 (mt-10) cc_final: 0.6993 (mt-10) REVERT: A 426 MET cc_start: 0.8652 (mmt) cc_final: 0.8381 (mmt) REVERT: B 55 LYS cc_start: 0.8288 (mmpt) cc_final: 0.7421 (ptpt) REVERT: B 349 GLU cc_start: 0.7287 (mt-10) cc_final: 0.6980 (mt-10) REVERT: B 426 MET cc_start: 0.8699 (mmt) cc_final: 0.8421 (mmt) REVERT: C 50 MET cc_start: 0.7478 (tpp) cc_final: 0.6996 (mmm) REVERT: C 55 LYS cc_start: 0.8371 (mmpt) cc_final: 0.7629 (ptpt) REVERT: C 67 MET cc_start: 0.6721 (ttp) cc_final: 0.6268 (ttm) REVERT: C 114 ASP cc_start: 0.7429 (t0) cc_final: 0.7197 (t0) REVERT: C 426 MET cc_start: 0.8666 (mmt) cc_final: 0.8423 (mmt) REVERT: D 55 LYS cc_start: 0.8260 (mmpt) cc_final: 0.7513 (ptpt) REVERT: D 67 MET cc_start: 0.7078 (ttp) cc_final: 0.6538 (ttm) REVERT: D 225 PHE cc_start: 0.8964 (m-80) cc_final: 0.8291 (m-10) REVERT: D 345 TRP cc_start: 0.6691 (t-100) cc_final: 0.5849 (t-100) REVERT: D 349 GLU cc_start: 0.7351 (mt-10) cc_final: 0.6616 (mt-10) REVERT: D 426 MET cc_start: 0.8690 (mmt) cc_final: 0.8426 (mmt) REVERT: D 459 MET cc_start: 0.8084 (mtt) cc_final: 0.7866 (mtm) outliers start: 46 outliers final: 31 residues processed: 278 average time/residue: 0.2546 time to fit residues: 104.5186 Evaluate side-chains 236 residues out of total 1644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 205 time to evaluate : 1.650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 ASP Chi-restraints excluded: chain A residue 191 ASP Chi-restraints excluded: chain A residue 222 THR Chi-restraints excluded: chain A residue 227 LYS Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain A residue 334 MET Chi-restraints excluded: chain A residue 379 ASN Chi-restraints excluded: chain A residue 415 ILE Chi-restraints excluded: chain B residue 115 ASP Chi-restraints excluded: chain B residue 176 ASP Chi-restraints excluded: chain B residue 191 ASP Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain B residue 227 LYS Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain B residue 334 MET Chi-restraints excluded: chain B residue 379 ASN Chi-restraints excluded: chain C residue 115 ASP Chi-restraints excluded: chain C residue 191 ASP Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 222 THR Chi-restraints excluded: chain C residue 314 LEU Chi-restraints excluded: chain C residue 379 ASN Chi-restraints excluded: chain C residue 409 HIS Chi-restraints excluded: chain C residue 415 ILE Chi-restraints excluded: chain D residue 115 ASP Chi-restraints excluded: chain D residue 191 ASP Chi-restraints excluded: chain D residue 222 THR Chi-restraints excluded: chain D residue 227 LYS Chi-restraints excluded: chain D residue 334 MET Chi-restraints excluded: chain D residue 379 ASN Chi-restraints excluded: chain D residue 415 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 161 optimal weight: 9.9990 chunk 123 optimal weight: 7.9990 chunk 84 optimal weight: 4.9990 chunk 18 optimal weight: 8.9990 chunk 78 optimal weight: 10.0000 chunk 109 optimal weight: 8.9990 chunk 164 optimal weight: 9.9990 chunk 173 optimal weight: 3.9990 chunk 85 optimal weight: 4.9990 chunk 155 optimal weight: 10.0000 chunk 46 optimal weight: 0.0980 overall best weight: 4.4188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 247 ASN ** A 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 327 GLN B 247 ASN ** B 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 327 GLN B 409 HIS C 247 ASN ** C 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 327 GLN D 247 ASN D 327 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 moved from start: 0.3910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 15236 Z= 0.321 Angle : 0.670 8.893 20652 Z= 0.342 Chirality : 0.043 0.171 2420 Planarity : 0.005 0.044 2516 Dihedral : 5.788 51.091 2164 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.50 % Favored : 93.50 % Rotamer: Outliers : 4.32 % Allowed : 16.91 % Favored : 78.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.61 (0.20), residues: 1784 helix: 0.88 (0.16), residues: 1080 sheet: -1.34 (0.32), residues: 204 loop : -2.85 (0.23), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 444 HIS 0.018 0.002 HIS C 409 PHE 0.015 0.002 PHE D 235 TYR 0.031 0.002 TYR D 218 ARG 0.004 0.001 ARG A 403 *********************** 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: 71 poor density : 212 time to evaluate : 1.799 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 LYS cc_start: 0.8246 (mmpt) cc_final: 0.7370 (ptpt) REVERT: A 225 PHE cc_start: 0.9030 (m-80) cc_final: 0.8388 (m-10) REVERT: A 349 GLU cc_start: 0.7436 (mt-10) cc_final: 0.7086 (mt-10) REVERT: A 426 MET cc_start: 0.8737 (mmt) cc_final: 0.8520 (mmt) REVERT: A 480 MET cc_start: 0.8476 (mmm) cc_final: 0.8149 (mpp) REVERT: B 55 LYS cc_start: 0.8269 (mmpt) cc_final: 0.7324 (ptpt) REVERT: B 349 GLU cc_start: 0.7437 (mt-10) cc_final: 0.7098 (mt-10) REVERT: B 480 MET cc_start: 0.8505 (mmm) cc_final: 0.8208 (mpp) REVERT: C 55 LYS cc_start: 0.8347 (mmpt) cc_final: 0.7447 (ptpt) REVERT: C 88 GLN cc_start: 0.7942 (tp40) cc_final: 0.7439 (tp40) REVERT: C 330 PHE cc_start: 0.7944 (OUTLIER) cc_final: 0.7349 (t80) REVERT: C 345 TRP cc_start: 0.6998 (t-100) cc_final: 0.6316 (t-100) REVERT: C 480 MET cc_start: 0.8485 (mmm) cc_final: 0.8140 (mpp) REVERT: D 55 LYS cc_start: 0.8260 (mmpt) cc_final: 0.7384 (ptpt) REVERT: D 225 PHE cc_start: 0.8986 (m-80) cc_final: 0.8383 (m-10) REVERT: D 349 GLU cc_start: 0.7363 (mt-10) cc_final: 0.7062 (mt-10) REVERT: D 459 MET cc_start: 0.8143 (mtt) cc_final: 0.7779 (mtt) REVERT: D 480 MET cc_start: 0.8480 (mmm) cc_final: 0.8209 (mpp) outliers start: 71 outliers final: 39 residues processed: 270 average time/residue: 0.2544 time to fit residues: 106.6080 Evaluate side-chains 230 residues out of total 1644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 190 time to evaluate : 1.925 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 ASP Chi-restraints excluded: chain A residue 191 ASP Chi-restraints excluded: chain A residue 222 THR Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain A residue 379 ASN Chi-restraints excluded: chain A residue 415 ILE Chi-restraints excluded: chain A residue 445 ILE Chi-restraints excluded: chain A residue 510 LEU Chi-restraints excluded: chain B residue 115 ASP Chi-restraints excluded: chain B residue 176 ASP Chi-restraints excluded: chain B residue 191 ASP Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain B residue 314 LEU Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain B residue 334 MET Chi-restraints excluded: chain B residue 379 ASN Chi-restraints excluded: chain B residue 445 ILE Chi-restraints excluded: chain C residue 115 ASP Chi-restraints excluded: chain C residue 191 ASP Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 222 THR Chi-restraints excluded: chain C residue 314 LEU Chi-restraints excluded: chain C residue 330 PHE Chi-restraints excluded: chain C residue 364 LEU Chi-restraints excluded: chain C residue 379 ASN Chi-restraints excluded: chain C residue 415 ILE Chi-restraints excluded: chain C residue 445 ILE Chi-restraints excluded: chain C residue 510 LEU Chi-restraints excluded: chain D residue 115 ASP Chi-restraints excluded: chain D residue 191 ASP Chi-restraints excluded: chain D residue 222 THR Chi-restraints excluded: chain D residue 279 THR Chi-restraints excluded: chain D residue 307 LEU Chi-restraints excluded: chain D residue 314 LEU Chi-restraints excluded: chain D residue 364 LEU Chi-restraints excluded: chain D residue 379 ASN Chi-restraints excluded: chain D residue 415 ILE Chi-restraints excluded: chain D residue 445 ILE Chi-restraints excluded: chain D residue 510 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 144 optimal weight: 2.9990 chunk 98 optimal weight: 5.9990 chunk 2 optimal weight: 0.0070 chunk 129 optimal weight: 3.9990 chunk 71 optimal weight: 8.9990 chunk 148 optimal weight: 7.9990 chunk 120 optimal weight: 8.9990 chunk 0 optimal weight: 30.0000 chunk 88 optimal weight: 4.9990 chunk 156 optimal weight: 1.9990 chunk 43 optimal weight: 0.9990 overall best weight: 2.0006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 247 ASN A 267 HIS B 247 ASN B 267 HIS C 267 HIS D 247 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7912 moved from start: 0.4198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 15236 Z= 0.183 Angle : 0.587 8.984 20652 Z= 0.297 Chirality : 0.040 0.138 2420 Planarity : 0.003 0.035 2516 Dihedral : 5.692 55.019 2164 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 4.01 % Allowed : 17.15 % Favored : 78.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (0.20), residues: 1784 helix: 1.19 (0.16), residues: 1112 sheet: -1.03 (0.33), residues: 204 loop : -2.79 (0.24), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 345 HIS 0.005 0.001 HIS B 234 PHE 0.014 0.001 PHE B 235 TYR 0.027 0.002 TYR D 218 ARG 0.003 0.000 ARG D 403 *********************** 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 287 residues out of total 1644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 221 time to evaluate : 2.122 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 LYS cc_start: 0.8227 (mmpt) cc_final: 0.7278 (ptpt) REVERT: A 225 PHE cc_start: 0.9015 (m-80) cc_final: 0.8441 (m-10) REVERT: A 330 PHE cc_start: 0.7889 (OUTLIER) cc_final: 0.7550 (t80) REVERT: A 349 GLU cc_start: 0.7423 (mt-10) cc_final: 0.7038 (mt-10) REVERT: A 426 MET cc_start: 0.8600 (mmt) cc_final: 0.8386 (mmt) REVERT: A 480 MET cc_start: 0.8485 (mmm) cc_final: 0.8138 (mpp) REVERT: B 55 LYS cc_start: 0.8267 (mmpt) cc_final: 0.7199 (mtmt) REVERT: B 313 PHE cc_start: 0.7951 (t80) cc_final: 0.7691 (t80) REVERT: B 330 PHE cc_start: 0.7876 (OUTLIER) cc_final: 0.7508 (t80) REVERT: B 349 GLU cc_start: 0.7420 (mt-10) cc_final: 0.7055 (mt-10) REVERT: B 480 MET cc_start: 0.8466 (mmm) cc_final: 0.8124 (mpp) REVERT: C 50 MET cc_start: 0.7511 (tpp) cc_final: 0.7005 (mmm) REVERT: C 55 LYS cc_start: 0.8244 (mmpt) cc_final: 0.7410 (ptpt) REVERT: C 88 GLN cc_start: 0.7754 (tp40) cc_final: 0.7442 (tp40) REVERT: C 330 PHE cc_start: 0.7903 (OUTLIER) cc_final: 0.7418 (t80) REVERT: C 345 TRP cc_start: 0.7241 (t-100) cc_final: 0.6605 (t-100) REVERT: C 480 MET cc_start: 0.8474 (mmm) cc_final: 0.8158 (mpp) REVERT: D 55 LYS cc_start: 0.8255 (mmpt) cc_final: 0.7311 (ptpt) REVERT: D 225 PHE cc_start: 0.9008 (m-80) cc_final: 0.8410 (m-10) REVERT: D 330 PHE cc_start: 0.7882 (OUTLIER) cc_final: 0.7527 (t80) REVERT: D 349 GLU cc_start: 0.7465 (mt-10) cc_final: 0.7056 (mt-10) REVERT: D 459 MET cc_start: 0.8098 (mtt) cc_final: 0.7733 (mtt) REVERT: D 480 MET cc_start: 0.8452 (mmm) cc_final: 0.8148 (mpp) outliers start: 66 outliers final: 37 residues processed: 268 average time/residue: 0.2977 time to fit residues: 119.8329 Evaluate side-chains 232 residues out of total 1644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 191 time to evaluate : 1.839 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 ASP Chi-restraints excluded: chain A residue 191 ASP Chi-restraints excluded: chain A residue 222 THR Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 330 PHE Chi-restraints excluded: chain A residue 334 MET Chi-restraints excluded: chain A residue 379 ASN Chi-restraints excluded: chain A residue 445 ILE Chi-restraints excluded: chain A residue 489 LEU Chi-restraints excluded: chain A residue 510 LEU Chi-restraints excluded: chain B residue 115 ASP Chi-restraints excluded: chain B residue 176 ASP Chi-restraints excluded: chain B residue 191 ASP Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain B residue 314 LEU Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain B residue 330 PHE Chi-restraints excluded: chain B residue 334 MET Chi-restraints excluded: chain B residue 379 ASN Chi-restraints excluded: chain B residue 445 ILE Chi-restraints excluded: chain C residue 115 ASP Chi-restraints excluded: chain C residue 191 ASP Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 222 THR Chi-restraints excluded: chain C residue 314 LEU Chi-restraints excluded: chain C residue 330 PHE Chi-restraints excluded: chain C residue 334 MET Chi-restraints excluded: chain C residue 379 ASN Chi-restraints excluded: chain C residue 415 ILE Chi-restraints excluded: chain C residue 445 ILE Chi-restraints excluded: chain C residue 489 LEU Chi-restraints excluded: chain D residue 115 ASP Chi-restraints excluded: chain D residue 191 ASP Chi-restraints excluded: chain D residue 222 THR Chi-restraints excluded: chain D residue 314 LEU Chi-restraints excluded: chain D residue 330 PHE Chi-restraints excluded: chain D residue 334 MET Chi-restraints excluded: chain D residue 379 ASN Chi-restraints excluded: chain D residue 445 ILE Chi-restraints excluded: chain D residue 489 LEU Chi-restraints excluded: chain D residue 510 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 58 optimal weight: 8.9990 chunk 156 optimal weight: 5.9990 chunk 34 optimal weight: 2.9990 chunk 102 optimal weight: 9.9990 chunk 42 optimal weight: 0.9980 chunk 174 optimal weight: 4.9990 chunk 144 optimal weight: 2.9990 chunk 80 optimal weight: 0.9990 chunk 14 optimal weight: 20.0000 chunk 57 optimal weight: 9.9990 chunk 91 optimal weight: 9.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 247 ASN B 247 ASN D 247 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 moved from start: 0.4409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 15236 Z= 0.215 Angle : 0.600 10.132 20652 Z= 0.301 Chirality : 0.041 0.132 2420 Planarity : 0.004 0.034 2516 Dihedral : 5.377 49.154 2164 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.77 % Favored : 94.23 % Rotamer: Outliers : 4.44 % Allowed : 17.03 % Favored : 78.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.11 (0.20), residues: 1784 helix: 1.37 (0.16), residues: 1112 sheet: -0.78 (0.34), residues: 200 loop : -2.75 (0.24), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 345 HIS 0.005 0.001 HIS C 234 PHE 0.024 0.001 PHE D 428 TYR 0.030 0.002 TYR D 218 ARG 0.002 0.000 ARG A 44 *********************** 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 285 residues out of total 1644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 212 time to evaluate : 1.814 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 LYS cc_start: 0.8321 (mmpt) cc_final: 0.7267 (ptpt) REVERT: A 225 PHE cc_start: 0.9035 (m-80) cc_final: 0.8438 (m-10) REVERT: A 313 PHE cc_start: 0.7868 (t80) cc_final: 0.7559 (t80) REVERT: A 330 PHE cc_start: 0.8000 (OUTLIER) cc_final: 0.7697 (t80) REVERT: A 349 GLU cc_start: 0.7413 (mt-10) cc_final: 0.7152 (mt-10) REVERT: A 426 MET cc_start: 0.8642 (mmt) cc_final: 0.8350 (mmm) REVERT: A 480 MET cc_start: 0.8432 (mmm) cc_final: 0.8155 (mpp) REVERT: B 55 LYS cc_start: 0.8274 (mmpt) cc_final: 0.7144 (mtmt) REVERT: B 313 PHE cc_start: 0.7966 (t80) cc_final: 0.7714 (t80) REVERT: B 330 PHE cc_start: 0.7999 (OUTLIER) cc_final: 0.7651 (t80) REVERT: B 349 GLU cc_start: 0.7418 (mt-10) cc_final: 0.7179 (mt-10) REVERT: B 480 MET cc_start: 0.8482 (mmm) cc_final: 0.8211 (mpp) REVERT: C 50 MET cc_start: 0.7467 (tpp) cc_final: 0.6934 (mmm) REVERT: C 55 LYS cc_start: 0.8269 (mmpt) cc_final: 0.7394 (ptpt) REVERT: C 88 GLN cc_start: 0.7761 (tp40) cc_final: 0.7500 (tp40) REVERT: C 330 PHE cc_start: 0.7994 (OUTLIER) cc_final: 0.7539 (t80) REVERT: C 345 TRP cc_start: 0.7344 (t-100) cc_final: 0.6847 (t-100) REVERT: C 480 MET cc_start: 0.8417 (mmm) cc_final: 0.8154 (mpp) REVERT: D 55 LYS cc_start: 0.8347 (mmpt) cc_final: 0.7281 (ptpt) REVERT: D 225 PHE cc_start: 0.9021 (m-80) cc_final: 0.8400 (m-10) REVERT: D 330 PHE cc_start: 0.8005 (OUTLIER) cc_final: 0.7695 (t80) REVERT: D 349 GLU cc_start: 0.7454 (mt-10) cc_final: 0.7188 (mt-10) REVERT: D 459 MET cc_start: 0.8105 (mtt) cc_final: 0.7724 (mtt) REVERT: D 480 MET cc_start: 0.8493 (mmm) cc_final: 0.8229 (mpp) outliers start: 73 outliers final: 41 residues processed: 267 average time/residue: 0.2680 time to fit residues: 109.9586 Evaluate side-chains 233 residues out of total 1644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 188 time to evaluate : 1.997 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 ASP Chi-restraints excluded: chain A residue 191 ASP Chi-restraints excluded: chain A residue 222 THR Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 330 PHE Chi-restraints excluded: chain A residue 334 MET Chi-restraints excluded: chain A residue 379 ASN Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 445 ILE Chi-restraints excluded: chain A residue 489 LEU Chi-restraints excluded: chain A residue 510 LEU Chi-restraints excluded: chain B residue 115 ASP Chi-restraints excluded: chain B residue 191 ASP Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain B residue 314 LEU Chi-restraints excluded: chain B residue 324 PHE Chi-restraints excluded: chain B residue 330 PHE Chi-restraints excluded: chain B residue 334 MET Chi-restraints excluded: chain B residue 379 ASN Chi-restraints excluded: chain B residue 380 LEU Chi-restraints excluded: chain B residue 445 ILE Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain C residue 115 ASP Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 314 LEU Chi-restraints excluded: chain C residue 324 PHE Chi-restraints excluded: chain C residue 330 PHE Chi-restraints excluded: chain C residue 334 MET Chi-restraints excluded: chain C residue 379 ASN Chi-restraints excluded: chain C residue 380 LEU Chi-restraints excluded: chain C residue 445 ILE Chi-restraints excluded: chain C residue 489 LEU Chi-restraints excluded: chain C residue 510 LEU Chi-restraints excluded: chain D residue 91 VAL Chi-restraints excluded: chain D residue 115 ASP Chi-restraints excluded: chain D residue 191 ASP Chi-restraints excluded: chain D residue 222 THR Chi-restraints excluded: chain D residue 314 LEU Chi-restraints excluded: chain D residue 330 PHE Chi-restraints excluded: chain D residue 334 MET Chi-restraints excluded: chain D residue 364 LEU Chi-restraints excluded: chain D residue 379 ASN Chi-restraints excluded: chain D residue 380 LEU Chi-restraints excluded: chain D residue 445 ILE Chi-restraints excluded: chain D residue 510 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 167 optimal weight: 7.9990 chunk 19 optimal weight: 9.9990 chunk 99 optimal weight: 2.9990 chunk 127 optimal weight: 3.9990 chunk 98 optimal weight: 5.9990 chunk 146 optimal weight: 10.0000 chunk 97 optimal weight: 0.8980 chunk 173 optimal weight: 0.7980 chunk 108 optimal weight: 6.9990 chunk 105 optimal weight: 5.9990 chunk 80 optimal weight: 0.8980 overall best weight: 1.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 247 ASN B 171 HIS B 247 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7914 moved from start: 0.4654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 15236 Z= 0.176 Angle : 0.586 11.018 20652 Z= 0.291 Chirality : 0.040 0.135 2420 Planarity : 0.003 0.034 2516 Dihedral : 5.053 39.987 2164 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 3.77 % Allowed : 18.25 % Favored : 77.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.28 (0.20), residues: 1784 helix: 1.47 (0.16), residues: 1108 sheet: -0.62 (0.34), residues: 200 loop : -2.59 (0.25), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 345 HIS 0.004 0.001 HIS C 234 PHE 0.015 0.001 PHE D 428 TYR 0.026 0.002 TYR D 218 ARG 0.002 0.000 ARG B 403 *********************** 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 262 residues out of total 1644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 200 time to evaluate : 1.811 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 LYS cc_start: 0.8291 (mmpt) cc_final: 0.7238 (ptpt) REVERT: A 225 PHE cc_start: 0.9016 (m-80) cc_final: 0.8454 (m-10) REVERT: A 330 PHE cc_start: 0.8045 (OUTLIER) cc_final: 0.7789 (t80) REVERT: A 349 GLU cc_start: 0.7421 (mt-10) cc_final: 0.7166 (mt-10) REVERT: A 426 MET cc_start: 0.8586 (mmt) cc_final: 0.8307 (mmm) REVERT: B 55 LYS cc_start: 0.8254 (mmpt) cc_final: 0.7269 (ptpt) REVERT: B 330 PHE cc_start: 0.8054 (OUTLIER) cc_final: 0.7807 (t80) REVERT: B 349 GLU cc_start: 0.7442 (mt-10) cc_final: 0.7209 (mt-10) REVERT: C 50 MET cc_start: 0.7511 (tpp) cc_final: 0.6991 (mmm) REVERT: C 55 LYS cc_start: 0.8264 (mmpt) cc_final: 0.7396 (ptpt) REVERT: C 330 PHE cc_start: 0.8086 (OUTLIER) cc_final: 0.7738 (t80) REVERT: C 345 TRP cc_start: 0.7354 (t-100) cc_final: 0.6938 (t-100) REVERT: D 55 LYS cc_start: 0.8316 (mmpt) cc_final: 0.7244 (ptpt) REVERT: D 191 ASP cc_start: 0.7483 (OUTLIER) cc_final: 0.7267 (m-30) REVERT: D 225 PHE cc_start: 0.9012 (m-80) cc_final: 0.8424 (m-10) REVERT: D 330 PHE cc_start: 0.8023 (OUTLIER) cc_final: 0.7800 (t80) REVERT: D 345 TRP cc_start: 0.6670 (t-100) cc_final: 0.5965 (t-100) REVERT: D 349 GLU cc_start: 0.7479 (mt-10) cc_final: 0.6815 (mt-10) REVERT: D 459 MET cc_start: 0.8102 (mtt) cc_final: 0.7828 (mtt) outliers start: 62 outliers final: 43 residues processed: 243 average time/residue: 0.2390 time to fit residues: 89.0747 Evaluate side-chains 234 residues out of total 1644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 186 time to evaluate : 1.890 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 115 ASP Chi-restraints excluded: chain A residue 191 ASP Chi-restraints excluded: chain A residue 222 THR Chi-restraints excluded: chain A residue 227 LYS Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 330 PHE Chi-restraints excluded: chain A residue 334 MET Chi-restraints excluded: chain A residue 379 ASN Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 445 ILE Chi-restraints excluded: chain A residue 510 LEU Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 115 ASP Chi-restraints excluded: chain B residue 191 ASP Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain B residue 314 LEU Chi-restraints excluded: chain B residue 324 PHE Chi-restraints excluded: chain B residue 330 PHE Chi-restraints excluded: chain B residue 334 MET Chi-restraints excluded: chain B residue 379 ASN Chi-restraints excluded: chain B residue 380 LEU Chi-restraints excluded: chain B residue 445 ILE Chi-restraints excluded: chain B residue 489 LEU Chi-restraints excluded: chain C residue 115 ASP Chi-restraints excluded: chain C residue 191 ASP Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 314 LEU Chi-restraints excluded: chain C residue 324 PHE Chi-restraints excluded: chain C residue 330 PHE Chi-restraints excluded: chain C residue 334 MET Chi-restraints excluded: chain C residue 379 ASN Chi-restraints excluded: chain C residue 380 LEU Chi-restraints excluded: chain C residue 445 ILE Chi-restraints excluded: chain C residue 489 LEU Chi-restraints excluded: chain D residue 91 VAL Chi-restraints excluded: chain D residue 115 ASP Chi-restraints excluded: chain D residue 191 ASP Chi-restraints excluded: chain D residue 222 THR Chi-restraints excluded: chain D residue 314 LEU Chi-restraints excluded: chain D residue 324 PHE Chi-restraints excluded: chain D residue 330 PHE Chi-restraints excluded: chain D residue 334 MET Chi-restraints excluded: chain D residue 379 ASN Chi-restraints excluded: chain D residue 380 LEU Chi-restraints excluded: chain D residue 445 ILE Chi-restraints excluded: chain D residue 489 LEU Chi-restraints excluded: chain D residue 510 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 107 optimal weight: 7.9990 chunk 69 optimal weight: 3.9990 chunk 103 optimal weight: 4.9990 chunk 52 optimal weight: 5.9990 chunk 34 optimal weight: 6.9990 chunk 33 optimal weight: 4.9990 chunk 110 optimal weight: 6.9990 chunk 118 optimal weight: 2.9990 chunk 85 optimal weight: 5.9990 chunk 16 optimal weight: 3.9990 chunk 136 optimal weight: 9.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 247 ASN ** B 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7976 moved from start: 0.4722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 15236 Z= 0.304 Angle : 0.655 8.932 20652 Z= 0.326 Chirality : 0.043 0.156 2420 Planarity : 0.004 0.039 2516 Dihedral : 5.148 33.463 2164 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.11 % Favored : 93.89 % Rotamer: Outliers : 3.89 % Allowed : 18.49 % Favored : 77.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.10 (0.20), residues: 1784 helix: 1.41 (0.16), residues: 1104 sheet: -0.97 (0.34), residues: 204 loop : -2.72 (0.24), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 444 HIS 0.008 0.002 HIS C 234 PHE 0.014 0.002 PHE B 235 TYR 0.037 0.002 TYR D 218 ARG 0.002 0.000 ARG A 403 *********************** 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 251 residues out of total 1644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 187 time to evaluate : 1.889 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 LYS cc_start: 0.8298 (mmpt) cc_final: 0.7229 (ptpt) REVERT: A 225 PHE cc_start: 0.9046 (m-80) cc_final: 0.8463 (m-10) REVERT: A 330 PHE cc_start: 0.8160 (OUTLIER) cc_final: 0.7903 (t80) REVERT: A 349 GLU cc_start: 0.7408 (mt-10) cc_final: 0.7143 (mt-10) REVERT: B 49 PHE cc_start: 0.7532 (OUTLIER) cc_final: 0.6975 (t80) REVERT: B 55 LYS cc_start: 0.8323 (mmpt) cc_final: 0.7258 (ptpt) REVERT: B 330 PHE cc_start: 0.8048 (OUTLIER) cc_final: 0.7830 (t80) REVERT: B 349 GLU cc_start: 0.7430 (mt-10) cc_final: 0.7155 (mt-10) REVERT: C 50 MET cc_start: 0.7452 (tpp) cc_final: 0.6949 (mmm) REVERT: C 55 LYS cc_start: 0.8315 (mmpt) cc_final: 0.7386 (ptpt) REVERT: C 330 PHE cc_start: 0.8104 (OUTLIER) cc_final: 0.7777 (t80) REVERT: C 345 TRP cc_start: 0.7167 (t-100) cc_final: 0.6513 (t-100) REVERT: D 55 LYS cc_start: 0.8317 (mmpt) cc_final: 0.7222 (ptpt) REVERT: D 67 MET cc_start: 0.6559 (ttp) cc_final: 0.6106 (ttm) REVERT: D 225 PHE cc_start: 0.9050 (m-80) cc_final: 0.8499 (m-10) REVERT: D 330 PHE cc_start: 0.8154 (OUTLIER) cc_final: 0.7908 (t80) REVERT: D 349 GLU cc_start: 0.7463 (mt-10) cc_final: 0.7175 (mt-10) outliers start: 64 outliers final: 47 residues processed: 235 average time/residue: 0.2336 time to fit residues: 84.8917 Evaluate side-chains 225 residues out of total 1644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 173 time to evaluate : 1.935 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 115 ASP Chi-restraints excluded: chain A residue 191 ASP Chi-restraints excluded: chain A residue 222 THR Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 330 PHE Chi-restraints excluded: chain A residue 334 MET Chi-restraints excluded: chain A residue 379 ASN Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 445 ILE Chi-restraints excluded: chain A residue 510 LEU Chi-restraints excluded: chain B residue 49 PHE Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 115 ASP Chi-restraints excluded: chain B residue 191 ASP Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain B residue 314 LEU Chi-restraints excluded: chain B residue 324 PHE Chi-restraints excluded: chain B residue 330 PHE Chi-restraints excluded: chain B residue 334 MET Chi-restraints excluded: chain B residue 364 LEU Chi-restraints excluded: chain B residue 379 ASN Chi-restraints excluded: chain B residue 380 LEU Chi-restraints excluded: chain B residue 445 ILE Chi-restraints excluded: chain B residue 489 LEU Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain C residue 115 ASP Chi-restraints excluded: chain C residue 191 ASP Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 314 LEU Chi-restraints excluded: chain C residue 324 PHE Chi-restraints excluded: chain C residue 330 PHE Chi-restraints excluded: chain C residue 334 MET Chi-restraints excluded: chain C residue 379 ASN Chi-restraints excluded: chain C residue 380 LEU Chi-restraints excluded: chain C residue 445 ILE Chi-restraints excluded: chain C residue 489 LEU Chi-restraints excluded: chain C residue 510 LEU Chi-restraints excluded: chain D residue 91 VAL Chi-restraints excluded: chain D residue 115 ASP Chi-restraints excluded: chain D residue 191 ASP Chi-restraints excluded: chain D residue 222 THR Chi-restraints excluded: chain D residue 314 LEU Chi-restraints excluded: chain D residue 324 PHE Chi-restraints excluded: chain D residue 330 PHE Chi-restraints excluded: chain D residue 334 MET Chi-restraints excluded: chain D residue 364 LEU Chi-restraints excluded: chain D residue 379 ASN Chi-restraints excluded: chain D residue 380 LEU Chi-restraints excluded: chain D residue 445 ILE Chi-restraints excluded: chain D residue 489 LEU Chi-restraints excluded: chain D residue 510 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 157 optimal weight: 0.6980 chunk 166 optimal weight: 6.9990 chunk 151 optimal weight: 0.8980 chunk 161 optimal weight: 7.9990 chunk 97 optimal weight: 9.9990 chunk 70 optimal weight: 4.9990 chunk 126 optimal weight: 0.9980 chunk 49 optimal weight: 3.9990 chunk 146 optimal weight: 9.9990 chunk 152 optimal weight: 9.9990 chunk 106 optimal weight: 6.9990 overall best weight: 2.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 483 GLN C 69 GLN C 483 GLN D 483 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7934 moved from start: 0.4851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 15236 Z= 0.199 Angle : 0.606 9.333 20652 Z= 0.299 Chirality : 0.041 0.152 2420 Planarity : 0.003 0.032 2516 Dihedral : 4.929 25.939 2164 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Rotamer: Outliers : 3.65 % Allowed : 18.86 % Favored : 77.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.27 (0.20), residues: 1784 helix: 1.49 (0.16), residues: 1100 sheet: -0.67 (0.35), residues: 200 loop : -2.60 (0.25), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 345 HIS 0.004 0.001 HIS C 234 PHE 0.014 0.001 PHE C 235 TYR 0.025 0.002 TYR D 218 ARG 0.002 0.000 ARG D 403 *********************** 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 246 residues out of total 1644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 186 time to evaluate : 1.869 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 LYS cc_start: 0.8276 (mmpt) cc_final: 0.7205 (ptpt) REVERT: A 225 PHE cc_start: 0.9000 (m-80) cc_final: 0.8388 (m-10) REVERT: A 330 PHE cc_start: 0.8209 (OUTLIER) cc_final: 0.7987 (t80) REVERT: A 349 GLU cc_start: 0.7391 (mt-10) cc_final: 0.7134 (mt-10) REVERT: B 49 PHE cc_start: 0.7597 (OUTLIER) cc_final: 0.6992 (t80) REVERT: B 55 LYS cc_start: 0.8314 (mmpt) cc_final: 0.7257 (ptpt) REVERT: B 330 PHE cc_start: 0.8156 (OUTLIER) cc_final: 0.7953 (t80) REVERT: B 349 GLU cc_start: 0.7418 (mt-10) cc_final: 0.7135 (mt-10) REVERT: C 50 MET cc_start: 0.7490 (tpp) cc_final: 0.6988 (mmm) REVERT: C 55 LYS cc_start: 0.8294 (mmpt) cc_final: 0.7300 (ptpt) REVERT: C 330 PHE cc_start: 0.8059 (OUTLIER) cc_final: 0.7838 (t80) REVERT: C 345 TRP cc_start: 0.7281 (t-100) cc_final: 0.6812 (t-100) REVERT: D 49 PHE cc_start: 0.7510 (OUTLIER) cc_final: 0.6872 (t80) REVERT: D 55 LYS cc_start: 0.8281 (mmpt) cc_final: 0.7182 (ptpt) REVERT: D 67 MET cc_start: 0.6511 (ttp) cc_final: 0.6067 (ttm) REVERT: D 225 PHE cc_start: 0.9010 (m-80) cc_final: 0.8381 (m-10) REVERT: D 349 GLU cc_start: 0.7467 (mt-10) cc_final: 0.7163 (mt-10) outliers start: 60 outliers final: 46 residues processed: 226 average time/residue: 0.2314 time to fit residues: 81.0239 Evaluate side-chains 238 residues out of total 1644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 187 time to evaluate : 1.790 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 115 ASP Chi-restraints excluded: chain A residue 191 ASP Chi-restraints excluded: chain A residue 222 THR Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 324 PHE Chi-restraints excluded: chain A residue 330 PHE Chi-restraints excluded: chain A residue 334 MET Chi-restraints excluded: chain A residue 379 ASN Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 445 ILE Chi-restraints excluded: chain A residue 489 LEU Chi-restraints excluded: chain A residue 510 LEU Chi-restraints excluded: chain B residue 49 PHE Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 115 ASP Chi-restraints excluded: chain B residue 191 ASP Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain B residue 314 LEU Chi-restraints excluded: chain B residue 324 PHE Chi-restraints excluded: chain B residue 330 PHE Chi-restraints excluded: chain B residue 334 MET Chi-restraints excluded: chain B residue 364 LEU Chi-restraints excluded: chain B residue 379 ASN Chi-restraints excluded: chain B residue 380 LEU Chi-restraints excluded: chain B residue 445 ILE Chi-restraints excluded: chain C residue 115 ASP Chi-restraints excluded: chain C residue 191 ASP Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 314 LEU Chi-restraints excluded: chain C residue 324 PHE Chi-restraints excluded: chain C residue 330 PHE Chi-restraints excluded: chain C residue 334 MET Chi-restraints excluded: chain C residue 379 ASN Chi-restraints excluded: chain C residue 380 LEU Chi-restraints excluded: chain C residue 445 ILE Chi-restraints excluded: chain C residue 489 LEU Chi-restraints excluded: chain D residue 49 PHE Chi-restraints excluded: chain D residue 91 VAL Chi-restraints excluded: chain D residue 115 ASP Chi-restraints excluded: chain D residue 191 ASP Chi-restraints excluded: chain D residue 222 THR Chi-restraints excluded: chain D residue 314 LEU Chi-restraints excluded: chain D residue 324 PHE Chi-restraints excluded: chain D residue 334 MET Chi-restraints excluded: chain D residue 379 ASN Chi-restraints excluded: chain D residue 380 LEU Chi-restraints excluded: chain D residue 445 ILE Chi-restraints excluded: chain D residue 489 LEU Chi-restraints excluded: chain D residue 510 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 170 optimal weight: 0.7980 chunk 104 optimal weight: 7.9990 chunk 81 optimal weight: 3.9990 chunk 118 optimal weight: 8.9990 chunk 179 optimal weight: 0.8980 chunk 165 optimal weight: 9.9990 chunk 142 optimal weight: 10.0000 chunk 14 optimal weight: 8.9990 chunk 110 optimal weight: 0.5980 chunk 87 optimal weight: 0.9990 chunk 113 optimal weight: 4.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 483 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 moved from start: 0.5003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 15236 Z= 0.160 Angle : 0.591 10.650 20652 Z= 0.289 Chirality : 0.040 0.161 2420 Planarity : 0.003 0.032 2516 Dihedral : 4.679 18.469 2164 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 3.10 % Allowed : 19.53 % Favored : 77.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.60 (0.20), residues: 1784 helix: 1.68 (0.16), residues: 1108 sheet: -0.51 (0.35), residues: 200 loop : -2.36 (0.26), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 345 HIS 0.004 0.001 HIS C 234 PHE 0.016 0.001 PHE A 513 TYR 0.023 0.001 TYR D 218 ARG 0.002 0.000 ARG A 322 ********************** 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 249 residues out of total 1644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 198 time to evaluate : 1.728 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 LYS cc_start: 0.8248 (mmpt) cc_final: 0.7193 (ptpt) REVERT: A 67 MET cc_start: 0.6627 (ttp) cc_final: 0.6030 (ttm) REVERT: A 191 ASP cc_start: 0.7486 (OUTLIER) cc_final: 0.7282 (m-30) REVERT: A 225 PHE cc_start: 0.8994 (m-80) cc_final: 0.8378 (m-10) REVERT: A 227 LYS cc_start: 0.6665 (OUTLIER) cc_final: 0.6131 (ptmt) REVERT: A 349 GLU cc_start: 0.7423 (mt-10) cc_final: 0.7144 (mt-10) REVERT: A 428 PHE cc_start: 0.8458 (t80) cc_final: 0.8207 (t80) REVERT: B 49 PHE cc_start: 0.7606 (OUTLIER) cc_final: 0.7023 (t80) REVERT: B 55 LYS cc_start: 0.8298 (mmpt) cc_final: 0.7242 (ptpt) REVERT: B 191 ASP cc_start: 0.7494 (OUTLIER) cc_final: 0.7289 (m-30) REVERT: B 349 GLU cc_start: 0.7411 (mt-10) cc_final: 0.7138 (mt-10) REVERT: C 50 MET cc_start: 0.7495 (tpp) cc_final: 0.6988 (mmm) REVERT: C 55 LYS cc_start: 0.8220 (mmpt) cc_final: 0.7249 (ptpt) REVERT: C 191 ASP cc_start: 0.7493 (OUTLIER) cc_final: 0.7283 (m-30) REVERT: C 345 TRP cc_start: 0.7222 (t-100) cc_final: 0.6817 (t-100) REVERT: D 49 PHE cc_start: 0.7546 (OUTLIER) cc_final: 0.6866 (t80) REVERT: D 55 LYS cc_start: 0.8270 (mmpt) cc_final: 0.7182 (ptpt) REVERT: D 67 MET cc_start: 0.6621 (ttp) cc_final: 0.6087 (ttm) REVERT: D 191 ASP cc_start: 0.7450 (OUTLIER) cc_final: 0.7233 (m-30) REVERT: D 225 PHE cc_start: 0.8988 (m-80) cc_final: 0.8412 (m-10) REVERT: D 345 TRP cc_start: 0.6605 (t-100) cc_final: 0.5984 (t-100) REVERT: D 349 GLU cc_start: 0.7445 (mt-10) cc_final: 0.6746 (mt-10) outliers start: 51 outliers final: 38 residues processed: 229 average time/residue: 0.2387 time to fit residues: 83.3647 Evaluate side-chains 240 residues out of total 1644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 195 time to evaluate : 1.553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 191 ASP Chi-restraints excluded: chain A residue 222 THR Chi-restraints excluded: chain A residue 227 LYS Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 324 PHE Chi-restraints excluded: chain A residue 334 MET Chi-restraints excluded: chain A residue 379 ASN Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 445 ILE Chi-restraints excluded: chain A residue 489 LEU Chi-restraints excluded: chain A residue 510 LEU Chi-restraints excluded: chain B residue 49 PHE Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 191 ASP Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain B residue 314 LEU Chi-restraints excluded: chain B residue 324 PHE Chi-restraints excluded: chain B residue 334 MET Chi-restraints excluded: chain B residue 379 ASN Chi-restraints excluded: chain B residue 380 LEU Chi-restraints excluded: chain B residue 445 ILE Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain C residue 115 ASP Chi-restraints excluded: chain C residue 191 ASP Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 314 LEU Chi-restraints excluded: chain C residue 324 PHE Chi-restraints excluded: chain C residue 334 MET Chi-restraints excluded: chain C residue 379 ASN Chi-restraints excluded: chain C residue 380 LEU Chi-restraints excluded: chain C residue 445 ILE Chi-restraints excluded: chain C residue 510 LEU Chi-restraints excluded: chain D residue 49 PHE Chi-restraints excluded: chain D residue 91 VAL Chi-restraints excluded: chain D residue 191 ASP Chi-restraints excluded: chain D residue 222 THR Chi-restraints excluded: chain D residue 314 LEU Chi-restraints excluded: chain D residue 324 PHE Chi-restraints excluded: chain D residue 334 MET Chi-restraints excluded: chain D residue 379 ASN Chi-restraints excluded: chain D residue 380 LEU Chi-restraints excluded: chain D residue 445 ILE Chi-restraints excluded: chain D residue 489 LEU Chi-restraints excluded: chain D residue 510 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 152 optimal weight: 10.0000 chunk 43 optimal weight: 2.9990 chunk 131 optimal weight: 0.0000 chunk 21 optimal weight: 6.9990 chunk 39 optimal weight: 0.9980 chunk 143 optimal weight: 5.9990 chunk 59 optimal weight: 8.9990 chunk 146 optimal weight: 4.9990 chunk 18 optimal weight: 6.9990 chunk 26 optimal weight: 0.0170 chunk 125 optimal weight: 0.9980 overall best weight: 1.0024 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.147023 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.119752 restraints weight = 26073.135| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.122473 restraints weight = 15575.074| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.124574 restraints weight = 11080.151| |-----------------------------------------------------------------------------| r_work (final): 0.3486 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7885 moved from start: 0.5148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 15236 Z= 0.142 Angle : 0.582 8.804 20652 Z= 0.281 Chirality : 0.040 0.227 2420 Planarity : 0.003 0.033 2516 Dihedral : 4.484 16.343 2164 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 2.80 % Allowed : 20.01 % Favored : 77.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.91 (0.20), residues: 1784 helix: 1.85 (0.16), residues: 1108 sheet: -0.25 (0.35), residues: 200 loop : -2.10 (0.26), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.000 TRP D 345 HIS 0.003 0.001 HIS B 234 PHE 0.019 0.001 PHE A 428 TYR 0.024 0.001 TYR D 218 ARG 0.002 0.000 ARG D 322 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2869.16 seconds wall clock time: 53 minutes 21.45 seconds (3201.45 seconds total)