Starting phenix.real_space_refine on Sat Feb 17 11:19:26 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sp2_10279/02_2024/6sp2_10279_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sp2_10279/02_2024/6sp2_10279.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.33 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sp2_10279/02_2024/6sp2_10279.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sp2_10279/02_2024/6sp2_10279.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sp2_10279/02_2024/6sp2_10279_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sp2_10279/02_2024/6sp2_10279_updated.pdb" } resolution = 3.33 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.136 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 18 5.49 5 S 156 5.16 5 C 12336 2.51 5 N 2640 2.21 5 O 3348 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 18498 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 2834 Number of conformers: 1 Conformer: "" Number of residues, atoms: 365, 2834 Classifications: {'peptide': 365} Link IDs: {'PTRANS': 12, 'TRANS': 352} Chain breaks: 3 Chain: "B" Number of atoms: 2834 Number of conformers: 1 Conformer: "" Number of residues, atoms: 365, 2834 Classifications: {'peptide': 365} Link IDs: {'PTRANS': 12, 'TRANS': 352} Chain breaks: 3 Chain: "C" Number of atoms: 2834 Number of conformers: 1 Conformer: "" Number of residues, atoms: 365, 2834 Classifications: {'peptide': 365} Link IDs: {'PTRANS': 12, 'TRANS': 352} Chain breaks: 3 Chain: "D" Number of atoms: 2834 Number of conformers: 1 Conformer: "" Number of residues, atoms: 365, 2834 Classifications: {'peptide': 365} Link IDs: {'PTRANS': 12, 'TRANS': 352} Chain breaks: 3 Chain: "E" Number of atoms: 2834 Number of conformers: 1 Conformer: "" Number of residues, atoms: 365, 2834 Classifications: {'peptide': 365} Link IDs: {'PTRANS': 12, 'TRANS': 352} Chain breaks: 3 Chain: "F" Number of atoms: 2834 Number of conformers: 1 Conformer: "" Number of residues, atoms: 365, 2834 Classifications: {'peptide': 365} Link IDs: {'PTRANS': 12, 'TRANS': 352} Chain breaks: 3 Chain: "A" Number of atoms: 249 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 249 Unusual residues: {'CDL': 1, 'LMN': 2} Classifications: {'peptide': 1, 'undetermined': 3} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 57 Unresolved non-hydrogen dihedrals: 72 Unresolved non-hydrogen chiralities: 10 Chain: "B" Number of atoms: 249 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 249 Unusual residues: {'CDL': 1, 'LMN': 2} Classifications: {'peptide': 1, 'undetermined': 3} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 57 Unresolved non-hydrogen dihedrals: 72 Unresolved non-hydrogen chiralities: 10 Chain: "C" Number of atoms: 249 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 249 Unusual residues: {'CDL': 1, 'LMN': 2} Classifications: {'peptide': 1, 'undetermined': 3} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 57 Unresolved non-hydrogen dihedrals: 72 Unresolved non-hydrogen chiralities: 10 Chain: "D" Number of atoms: 249 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 249 Unusual residues: {'CDL': 1, 'LMN': 2} Classifications: {'peptide': 1, 'undetermined': 3} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 57 Unresolved non-hydrogen dihedrals: 72 Unresolved non-hydrogen chiralities: 10 Chain: "E" Number of atoms: 249 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 249 Unusual residues: {'CDL': 1, 'LMN': 2} Classifications: {'peptide': 1, 'undetermined': 3} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 57 Unresolved non-hydrogen dihedrals: 72 Unresolved non-hydrogen chiralities: 10 Chain: "F" Number of atoms: 249 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 249 Unusual residues: {'CDL': 1, 'LMN': 2} Classifications: {'peptide': 1, 'undetermined': 3} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 57 Unresolved non-hydrogen dihedrals: 72 Unresolved non-hydrogen chiralities: 10 Time building chain proxies: 10.33, per 1000 atoms: 0.56 Number of scatterers: 18498 At special positions: 0 Unit cell: (133.86, 144.9, 78.66, 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 156 16.00 P 18 15.00 O 3348 8.00 N 2640 7.00 C 12336 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=12, symmetry=0 Simple disulfide: pdb=" SG CYS A 71 " - pdb=" SG CYS A 95 " distance=2.04 Simple disulfide: pdb=" SG CYS A 238 " - pdb=" SG CYS A 299 " distance=2.03 Simple disulfide: pdb=" SG CYS B 71 " - pdb=" SG CYS B 95 " distance=2.04 Simple disulfide: pdb=" SG CYS B 238 " - pdb=" SG CYS B 299 " distance=2.03 Simple disulfide: pdb=" SG CYS C 71 " - pdb=" SG CYS C 95 " distance=2.04 Simple disulfide: pdb=" SG CYS C 238 " - pdb=" SG CYS C 299 " distance=2.03 Simple disulfide: pdb=" SG CYS D 71 " - pdb=" SG CYS D 95 " distance=2.04 Simple disulfide: pdb=" SG CYS D 238 " - pdb=" SG CYS D 299 " distance=2.03 Simple disulfide: pdb=" SG CYS E 71 " - pdb=" SG CYS E 95 " distance=2.04 Simple disulfide: pdb=" SG CYS E 238 " - pdb=" SG CYS E 299 " distance=2.03 Simple disulfide: pdb=" SG CYS F 71 " - pdb=" SG CYS F 95 " distance=2.04 Simple disulfide: pdb=" SG CYS F 238 " - pdb=" SG CYS F 299 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 7.46 Conformation dependent library (CDL) restraints added in 3.0 seconds 4284 Ramachandran restraints generated. 2142 Oldfield, 0 Emsley, 2142 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4080 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 90 helices and 0 sheets defined 68.5% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.13 Creating SS restraints... Processing helix chain 'A' and resid 31 through 54 removed outlier: 3.568A pdb=" N ALA A 43 " --> pdb=" O ARG A 39 " (cutoff:3.500A) Processing helix chain 'A' and resid 65 through 67 No H-bonds generated for 'chain 'A' and resid 65 through 67' Processing helix chain 'A' and resid 91 through 97 Processing helix chain 'A' and resid 99 through 121 removed outlier: 3.938A pdb=" N GLY A 110 " --> pdb=" O ARG A 106 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N MET A 111 " --> pdb=" O VAL A 107 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 134 Processing helix chain 'A' and resid 140 through 156 removed outlier: 4.092A pdb=" N PHE A 156 " --> pdb=" O ILE A 152 " (cutoff:3.500A) Processing helix chain 'A' and resid 163 through 200 Processing helix chain 'A' and resid 207 through 231 removed outlier: 4.176A pdb=" N THR A 214 " --> pdb=" O LEU A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 240 through 258 removed outlier: 3.583A pdb=" N SER A 246 " --> pdb=" O LYS A 242 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N SER A 256 " --> pdb=" O CYS A 252 " (cutoff:3.500A) Processing helix chain 'A' and resid 262 through 267 removed outlier: 4.290A pdb=" N ARG A 267 " --> pdb=" O ALA A 263 " (cutoff:3.500A) Processing helix chain 'A' and resid 274 through 293 removed outlier: 4.198A pdb=" N ASN A 293 " --> pdb=" O SER A 289 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 347 Processing helix chain 'A' and resid 397 through 415 removed outlier: 4.106A pdb=" N HIS A 401 " --> pdb=" O TRP A 397 " (cutoff:3.500A) Processing helix chain 'A' and resid 433 through 453 removed outlier: 3.896A pdb=" N VAL A 437 " --> pdb=" O ALA A 433 " (cutoff:3.500A) Processing helix chain 'A' and resid 455 through 460 Processing helix chain 'B' and resid 31 through 54 removed outlier: 3.568A pdb=" N ALA B 43 " --> pdb=" O ARG B 39 " (cutoff:3.500A) Processing helix chain 'B' and resid 65 through 67 No H-bonds generated for 'chain 'B' and resid 65 through 67' Processing helix chain 'B' and resid 91 through 97 Processing helix chain 'B' and resid 99 through 121 removed outlier: 3.939A pdb=" N GLY B 110 " --> pdb=" O ARG B 106 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N MET B 111 " --> pdb=" O VAL B 107 " (cutoff:3.500A) Processing helix chain 'B' and resid 131 through 134 Processing helix chain 'B' and resid 140 through 156 removed outlier: 4.092A pdb=" N PHE B 156 " --> pdb=" O ILE B 152 " (cutoff:3.500A) Processing helix chain 'B' and resid 163 through 200 Processing helix chain 'B' and resid 207 through 231 removed outlier: 4.175A pdb=" N THR B 214 " --> pdb=" O LEU B 210 " (cutoff:3.500A) Processing helix chain 'B' and resid 240 through 258 removed outlier: 3.584A pdb=" N SER B 246 " --> pdb=" O LYS B 242 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N SER B 256 " --> pdb=" O CYS B 252 " (cutoff:3.500A) Processing helix chain 'B' and resid 262 through 267 removed outlier: 4.290A pdb=" N ARG B 267 " --> pdb=" O ALA B 263 " (cutoff:3.500A) Processing helix chain 'B' and resid 274 through 293 removed outlier: 4.199A pdb=" N ASN B 293 " --> pdb=" O SER B 289 " (cutoff:3.500A) Processing helix chain 'B' and resid 330 through 347 Processing helix chain 'B' and resid 397 through 415 removed outlier: 4.107A pdb=" N HIS B 401 " --> pdb=" O TRP B 397 " (cutoff:3.500A) Processing helix chain 'B' and resid 433 through 453 removed outlier: 3.897A pdb=" N VAL B 437 " --> pdb=" O ALA B 433 " (cutoff:3.500A) Processing helix chain 'B' and resid 455 through 460 Processing helix chain 'C' and resid 31 through 54 removed outlier: 3.568A pdb=" N ALA C 43 " --> pdb=" O ARG C 39 " (cutoff:3.500A) Processing helix chain 'C' and resid 65 through 67 No H-bonds generated for 'chain 'C' and resid 65 through 67' Processing helix chain 'C' and resid 91 through 97 Processing helix chain 'C' and resid 99 through 121 removed outlier: 3.938A pdb=" N GLY C 110 " --> pdb=" O ARG C 106 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N MET C 111 " --> pdb=" O VAL C 107 " (cutoff:3.500A) Processing helix chain 'C' and resid 131 through 134 Processing helix chain 'C' and resid 140 through 156 removed outlier: 4.092A pdb=" N PHE C 156 " --> pdb=" O ILE C 152 " (cutoff:3.500A) Processing helix chain 'C' and resid 163 through 200 Processing helix chain 'C' and resid 207 through 231 removed outlier: 4.176A pdb=" N THR C 214 " --> pdb=" O LEU C 210 " (cutoff:3.500A) Processing helix chain 'C' and resid 240 through 258 removed outlier: 3.584A pdb=" N SER C 246 " --> pdb=" O LYS C 242 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N SER C 256 " --> pdb=" O CYS C 252 " (cutoff:3.500A) Processing helix chain 'C' and resid 262 through 267 removed outlier: 4.290A pdb=" N ARG C 267 " --> pdb=" O ALA C 263 " (cutoff:3.500A) Processing helix chain 'C' and resid 274 through 293 removed outlier: 4.199A pdb=" N ASN C 293 " --> pdb=" O SER C 289 " (cutoff:3.500A) Processing helix chain 'C' and resid 330 through 347 Processing helix chain 'C' and resid 397 through 415 removed outlier: 4.106A pdb=" N HIS C 401 " --> pdb=" O TRP C 397 " (cutoff:3.500A) Processing helix chain 'C' and resid 433 through 453 removed outlier: 3.897A pdb=" N VAL C 437 " --> pdb=" O ALA C 433 " (cutoff:3.500A) Processing helix chain 'C' and resid 455 through 460 Processing helix chain 'D' and resid 31 through 54 removed outlier: 3.568A pdb=" N ALA D 43 " --> pdb=" O ARG D 39 " (cutoff:3.500A) Processing helix chain 'D' and resid 65 through 67 No H-bonds generated for 'chain 'D' and resid 65 through 67' Processing helix chain 'D' and resid 91 through 97 Processing helix chain 'D' and resid 99 through 121 removed outlier: 3.938A pdb=" N GLY D 110 " --> pdb=" O ARG D 106 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N MET D 111 " --> pdb=" O VAL D 107 " (cutoff:3.500A) Processing helix chain 'D' and resid 131 through 134 Processing helix chain 'D' and resid 140 through 156 removed outlier: 4.092A pdb=" N PHE D 156 " --> pdb=" O ILE D 152 " (cutoff:3.500A) Processing helix chain 'D' and resid 163 through 200 Processing helix chain 'D' and resid 207 through 231 removed outlier: 4.176A pdb=" N THR D 214 " --> pdb=" O LEU D 210 " (cutoff:3.500A) Processing helix chain 'D' and resid 240 through 258 removed outlier: 3.584A pdb=" N SER D 246 " --> pdb=" O LYS D 242 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N SER D 256 " --> pdb=" O CYS D 252 " (cutoff:3.500A) Processing helix chain 'D' and resid 262 through 267 removed outlier: 4.290A pdb=" N ARG D 267 " --> pdb=" O ALA D 263 " (cutoff:3.500A) Processing helix chain 'D' and resid 274 through 293 removed outlier: 4.198A pdb=" N ASN D 293 " --> pdb=" O SER D 289 " (cutoff:3.500A) Processing helix chain 'D' and resid 330 through 347 Processing helix chain 'D' and resid 397 through 415 removed outlier: 4.107A pdb=" N HIS D 401 " --> pdb=" O TRP D 397 " (cutoff:3.500A) Processing helix chain 'D' and resid 433 through 453 removed outlier: 3.897A pdb=" N VAL D 437 " --> pdb=" O ALA D 433 " (cutoff:3.500A) Processing helix chain 'D' and resid 455 through 460 Processing helix chain 'E' and resid 31 through 54 removed outlier: 3.568A pdb=" N ALA E 43 " --> pdb=" O ARG E 39 " (cutoff:3.500A) Processing helix chain 'E' and resid 65 through 67 No H-bonds generated for 'chain 'E' and resid 65 through 67' Processing helix chain 'E' and resid 91 through 97 Processing helix chain 'E' and resid 99 through 121 removed outlier: 3.938A pdb=" N GLY E 110 " --> pdb=" O ARG E 106 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N MET E 111 " --> pdb=" O VAL E 107 " (cutoff:3.500A) Processing helix chain 'E' and resid 131 through 134 Processing helix chain 'E' and resid 140 through 156 removed outlier: 4.093A pdb=" N PHE E 156 " --> pdb=" O ILE E 152 " (cutoff:3.500A) Processing helix chain 'E' and resid 163 through 200 Processing helix chain 'E' and resid 207 through 231 removed outlier: 4.176A pdb=" N THR E 214 " --> pdb=" O LEU E 210 " (cutoff:3.500A) Processing helix chain 'E' and resid 240 through 258 removed outlier: 3.583A pdb=" N SER E 246 " --> pdb=" O LYS E 242 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N SER E 256 " --> pdb=" O CYS E 252 " (cutoff:3.500A) Processing helix chain 'E' and resid 262 through 267 removed outlier: 4.291A pdb=" N ARG E 267 " --> pdb=" O ALA E 263 " (cutoff:3.500A) Processing helix chain 'E' and resid 274 through 293 removed outlier: 4.198A pdb=" N ASN E 293 " --> pdb=" O SER E 289 " (cutoff:3.500A) Processing helix chain 'E' and resid 330 through 347 Processing helix chain 'E' and resid 397 through 415 removed outlier: 4.106A pdb=" N HIS E 401 " --> pdb=" O TRP E 397 " (cutoff:3.500A) Processing helix chain 'E' and resid 433 through 453 removed outlier: 3.896A pdb=" N VAL E 437 " --> pdb=" O ALA E 433 " (cutoff:3.500A) Processing helix chain 'E' and resid 455 through 460 Processing helix chain 'F' and resid 31 through 54 removed outlier: 3.568A pdb=" N ALA F 43 " --> pdb=" O ARG F 39 " (cutoff:3.500A) Processing helix chain 'F' and resid 65 through 67 No H-bonds generated for 'chain 'F' and resid 65 through 67' Processing helix chain 'F' and resid 91 through 97 Processing helix chain 'F' and resid 99 through 121 removed outlier: 3.938A pdb=" N GLY F 110 " --> pdb=" O ARG F 106 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N MET F 111 " --> pdb=" O VAL F 107 " (cutoff:3.500A) Processing helix chain 'F' and resid 131 through 134 Processing helix chain 'F' and resid 140 through 156 removed outlier: 4.091A pdb=" N PHE F 156 " --> pdb=" O ILE F 152 " (cutoff:3.500A) Processing helix chain 'F' and resid 163 through 200 Processing helix chain 'F' and resid 207 through 231 removed outlier: 4.176A pdb=" N THR F 214 " --> pdb=" O LEU F 210 " (cutoff:3.500A) Processing helix chain 'F' and resid 240 through 258 removed outlier: 3.584A pdb=" N SER F 246 " --> pdb=" O LYS F 242 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N SER F 256 " --> pdb=" O CYS F 252 " (cutoff:3.500A) Processing helix chain 'F' and resid 262 through 267 removed outlier: 4.289A pdb=" N ARG F 267 " --> pdb=" O ALA F 263 " (cutoff:3.500A) Processing helix chain 'F' and resid 274 through 293 removed outlier: 4.199A pdb=" N ASN F 293 " --> pdb=" O SER F 289 " (cutoff:3.500A) Processing helix chain 'F' and resid 330 through 347 Processing helix chain 'F' and resid 397 through 415 removed outlier: 4.106A pdb=" N HIS F 401 " --> pdb=" O TRP F 397 " (cutoff:3.500A) Processing helix chain 'F' and resid 433 through 453 removed outlier: 3.897A pdb=" N VAL F 437 " --> pdb=" O ALA F 433 " (cutoff:3.500A) Processing helix chain 'F' and resid 455 through 460 1086 hydrogen bonds defined for protein. 3240 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: 4.51 Time building geometry restraints manager: 8.02 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 2692 1.32 - 1.45: 5412 1.45 - 1.58: 10586 1.58 - 1.70: 36 1.70 - 1.83: 234 Bond restraints: 18960 Sorted by residual: bond pdb=" OB3 CDL B1001 " pdb=" PB2 CDL B1001 " ideal model delta sigma weight residual 1.529 1.479 0.050 1.00e-02 1.00e+04 2.51e+01 bond pdb=" OB3 CDL D1001 " pdb=" PB2 CDL D1001 " ideal model delta sigma weight residual 1.529 1.479 0.050 1.00e-02 1.00e+04 2.51e+01 bond pdb=" OB3 CDL F1001 " pdb=" PB2 CDL F1001 " ideal model delta sigma weight residual 1.529 1.479 0.050 1.00e-02 1.00e+04 2.50e+01 bond pdb=" OB3 CDL E1001 " pdb=" PB2 CDL E1001 " ideal model delta sigma weight residual 1.529 1.479 0.050 1.00e-02 1.00e+04 2.46e+01 bond pdb=" OB3 CDL A 603 " pdb=" PB2 CDL A 603 " ideal model delta sigma weight residual 1.529 1.480 0.049 1.00e-02 1.00e+04 2.44e+01 ... (remaining 18955 not shown) Histogram of bond angle deviations from ideal: 98.92 - 105.94: 390 105.94 - 112.96: 10579 112.96 - 119.98: 7004 119.98 - 127.00: 7422 127.00 - 134.02: 249 Bond angle restraints: 25644 Sorted by residual: angle pdb=" N PRO B 69 " pdb=" CA PRO B 69 " pdb=" C PRO B 69 " ideal model delta sigma weight residual 113.53 119.00 -5.47 1.39e+00 5.18e-01 1.55e+01 angle pdb=" N PRO E 69 " pdb=" CA PRO E 69 " pdb=" C PRO E 69 " ideal model delta sigma weight residual 113.53 118.99 -5.46 1.39e+00 5.18e-01 1.55e+01 angle pdb=" N VAL D 352 " pdb=" CA VAL D 352 " pdb=" C VAL D 352 " ideal model delta sigma weight residual 112.98 108.07 4.91 1.25e+00 6.40e-01 1.54e+01 angle pdb=" N PRO D 69 " pdb=" CA PRO D 69 " pdb=" C PRO D 69 " ideal model delta sigma weight residual 113.53 118.98 -5.45 1.39e+00 5.18e-01 1.54e+01 angle pdb=" N VAL F 352 " pdb=" CA VAL F 352 " pdb=" C VAL F 352 " ideal model delta sigma weight residual 112.98 108.08 4.90 1.25e+00 6.40e-01 1.54e+01 ... (remaining 25639 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.24: 11184 26.24 - 52.48: 444 52.48 - 78.72: 180 78.72 - 104.96: 78 104.96 - 131.21: 78 Dihedral angle restraints: 11964 sinusoidal: 5616 harmonic: 6348 Sorted by residual: dihedral pdb=" CB CYS D 71 " pdb=" SG CYS D 71 " pdb=" SG CYS D 95 " pdb=" CB CYS D 95 " ideal model delta sinusoidal sigma weight residual 93.00 152.59 -59.59 1 1.00e+01 1.00e-02 4.74e+01 dihedral pdb=" CB CYS F 71 " pdb=" SG CYS F 71 " pdb=" SG CYS F 95 " pdb=" CB CYS F 95 " ideal model delta sinusoidal sigma weight residual 93.00 152.58 -59.58 1 1.00e+01 1.00e-02 4.74e+01 dihedral pdb=" CB CYS C 71 " pdb=" SG CYS C 71 " pdb=" SG CYS C 95 " pdb=" CB CYS C 95 " ideal model delta sinusoidal sigma weight residual 93.00 152.56 -59.56 1 1.00e+01 1.00e-02 4.74e+01 ... (remaining 11961 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 2370 0.052 - 0.105: 486 0.105 - 0.157: 118 0.157 - 0.209: 15 0.209 - 0.262: 11 Chirality restraints: 3000 Sorted by residual: chirality pdb=" C2 P5S D1004 " pdb=" C1 P5S D1004 " pdb=" C3 P5S D1004 " pdb=" O37 P5S D1004 " both_signs ideal model delta sigma weight residual False 2.32 2.58 -0.26 2.00e-01 2.50e+01 1.71e+00 chirality pdb=" C2 P5S B1004 " pdb=" C1 P5S B1004 " pdb=" C3 P5S B1004 " pdb=" O37 P5S B1004 " both_signs ideal model delta sigma weight residual False 2.32 2.58 -0.26 2.00e-01 2.50e+01 1.69e+00 chirality pdb=" C2 P5S C1004 " pdb=" C1 P5S C1004 " pdb=" C3 P5S C1004 " pdb=" O37 P5S C1004 " both_signs ideal model delta sigma weight residual False 2.32 2.58 -0.26 2.00e-01 2.50e+01 1.68e+00 ... (remaining 2997 not shown) Planarity restraints: 2904 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU F 268 " 0.027 5.00e-02 4.00e+02 4.06e-02 2.63e+00 pdb=" N PRO F 269 " -0.070 5.00e-02 4.00e+02 pdb=" CA PRO F 269 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO F 269 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU B 268 " 0.027 5.00e-02 4.00e+02 4.05e-02 2.62e+00 pdb=" N PRO B 269 " -0.070 5.00e-02 4.00e+02 pdb=" CA PRO B 269 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO B 269 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 268 " 0.027 5.00e-02 4.00e+02 4.04e-02 2.62e+00 pdb=" N PRO A 269 " -0.070 5.00e-02 4.00e+02 pdb=" CA PRO A 269 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 269 " 0.023 5.00e-02 4.00e+02 ... (remaining 2901 not shown) Histogram of nonbonded interaction distances: 1.59 - 2.25: 6 2.25 - 2.91: 7586 2.91 - 3.58: 26438 3.58 - 4.24: 39017 4.24 - 4.90: 68154 Nonbonded interactions: 141201 Sorted by model distance: nonbonded pdb=" O3 LMN F1002 " pdb=" OAU LMN F1002 " model vdw 1.590 2.440 nonbonded pdb=" O3 LMN A 604 " pdb=" OAU LMN A 604 " model vdw 1.590 2.440 nonbonded pdb=" O3 LMN D1002 " pdb=" OAU LMN D1002 " model vdw 1.590 2.440 nonbonded pdb=" O3 LMN E1002 " pdb=" OAU LMN E1002 " model vdw 1.590 2.440 nonbonded pdb=" O3 LMN B1002 " pdb=" OAU LMN B1002 " model vdw 1.590 2.440 ... (remaining 141196 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 30 through 461) selection = (chain 'B' and resid 30 through 461) selection = (chain 'C' and resid 30 through 461) selection = (chain 'D' and resid 30 through 461) selection = (chain 'E' and resid 30 through 461) selection = (chain 'F' and resid 30 through 461) } 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.070 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: 5.750 Check model and map are aligned: 0.290 Set scattering table: 0.160 Process input model: 48.560 Find NCS groups from input model: 1.320 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: 60.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6347 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 18960 Z= 0.345 Angle : 0.849 11.015 25644 Z= 0.430 Chirality : 0.049 0.262 3000 Planarity : 0.005 0.041 2904 Dihedral : 21.512 131.205 7848 Min Nonbonded Distance : 1.590 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % 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: -0.56 (0.17), residues: 2142 helix: 0.38 (0.12), residues: 1434 sheet: None (None), residues: 0 loop : -1.86 (0.24), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.003 TRP E 418 HIS 0.007 0.002 HIS C 190 PHE 0.022 0.002 PHE F 404 TYR 0.019 0.002 TYR E 419 ARG 0.006 0.001 ARG C 106 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4284 Ramachandran restraints generated. 2142 Oldfield, 0 Emsley, 2142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4284 Ramachandran restraints generated. 2142 Oldfield, 0 Emsley, 2142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 1872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 308 time to evaluate : 1.933 Fit side-chains REVERT: A 122 MET cc_start: 0.7416 (mmt) cc_final: 0.6781 (mmt) REVERT: A 166 MET cc_start: 0.7177 (mmm) cc_final: 0.6592 (mmt) REVERT: A 204 ARG cc_start: 0.7555 (mtp180) cc_final: 0.7216 (ttt-90) REVERT: A 271 SER cc_start: 0.8203 (t) cc_final: 0.7910 (t) REVERT: B 102 MET cc_start: 0.7052 (mtm) cc_final: 0.6456 (mtp) REVERT: B 122 MET cc_start: 0.7520 (mmt) cc_final: 0.6984 (mmt) REVERT: B 297 LYS cc_start: 0.9076 (ptmm) cc_final: 0.8721 (tttp) REVERT: B 298 GLU cc_start: 0.8257 (tp30) cc_final: 0.7959 (tp30) REVERT: C 102 MET cc_start: 0.6711 (mtm) cc_final: 0.6242 (mtp) REVERT: C 122 MET cc_start: 0.7250 (mmt) cc_final: 0.6942 (mmt) REVERT: C 271 SER cc_start: 0.8511 (t) cc_final: 0.8282 (t) REVERT: C 297 LYS cc_start: 0.8978 (ptmm) cc_final: 0.8644 (tttp) REVERT: C 298 GLU cc_start: 0.8265 (tp30) cc_final: 0.8056 (tp30) REVERT: D 122 MET cc_start: 0.7347 (mmt) cc_final: 0.6704 (mmt) REVERT: D 166 MET cc_start: 0.7216 (mmm) cc_final: 0.6623 (mmt) REVERT: D 204 ARG cc_start: 0.7674 (mtp180) cc_final: 0.7388 (ttt-90) REVERT: D 271 SER cc_start: 0.8245 (t) cc_final: 0.7947 (t) REVERT: E 102 MET cc_start: 0.7027 (mtm) cc_final: 0.6372 (mtp) REVERT: E 122 MET cc_start: 0.7538 (mmt) cc_final: 0.7021 (mmt) REVERT: E 297 LYS cc_start: 0.9089 (ptmm) cc_final: 0.8697 (tttp) REVERT: F 122 MET cc_start: 0.7240 (mmt) cc_final: 0.6956 (mmt) REVERT: F 271 SER cc_start: 0.8010 (t) cc_final: 0.7740 (t) REVERT: F 297 LYS cc_start: 0.8989 (ptmm) cc_final: 0.8640 (tttp) REVERT: F 298 GLU cc_start: 0.8287 (tp30) cc_final: 0.8077 (tp30) outliers start: 0 outliers final: 0 residues processed: 308 average time/residue: 0.2938 time to fit residues: 138.8003 Evaluate side-chains 218 residues out of total 1872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 218 time to evaluate : 2.512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 182 optimal weight: 0.6980 chunk 163 optimal weight: 0.9990 chunk 90 optimal weight: 1.9990 chunk 55 optimal weight: 0.9990 chunk 110 optimal weight: 0.7980 chunk 87 optimal weight: 5.9990 chunk 169 optimal weight: 2.9990 chunk 65 optimal weight: 0.9990 chunk 102 optimal weight: 0.7980 chunk 126 optimal weight: 1.9990 chunk 196 optimal weight: 1.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 136 GLN A 422 HIS B 136 GLN B 422 HIS C 136 GLN C 422 HIS D 422 HIS E 136 GLN E 422 HIS F 422 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6408 moved from start: 0.1663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 18960 Z= 0.215 Angle : 0.678 12.048 25644 Z= 0.306 Chirality : 0.046 0.297 3000 Planarity : 0.004 0.033 2904 Dihedral : 20.568 154.893 4242 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 1.98 % Allowed : 9.19 % Favored : 88.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.28 (0.19), residues: 2142 helix: 1.88 (0.13), residues: 1428 sheet: None (None), residues: 0 loop : -1.33 (0.26), residues: 714 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP E 288 HIS 0.003 0.001 HIS F 422 PHE 0.013 0.002 PHE E 148 TYR 0.013 0.001 TYR D 419 ARG 0.003 0.000 ARG D 39 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4284 Ramachandran restraints generated. 2142 Oldfield, 0 Emsley, 2142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4284 Ramachandran restraints generated. 2142 Oldfield, 0 Emsley, 2142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 1872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 214 time to evaluate : 2.035 Fit side-chains revert: symmetry clash REVERT: A 166 MET cc_start: 0.7246 (mmm) cc_final: 0.6765 (mmt) REVERT: A 204 ARG cc_start: 0.7703 (mtp180) cc_final: 0.7294 (ttt-90) REVERT: A 271 SER cc_start: 0.8280 (t) cc_final: 0.7987 (t) REVERT: A 413 MET cc_start: 0.7590 (OUTLIER) cc_final: 0.6038 (mpp) REVERT: A 435 MET cc_start: 0.6301 (ptm) cc_final: 0.6084 (ptt) REVERT: B 102 MET cc_start: 0.6860 (mtm) cc_final: 0.6148 (mtp) REVERT: B 122 MET cc_start: 0.7600 (mmt) cc_final: 0.7226 (mmt) REVERT: B 204 ARG cc_start: 0.8089 (mtp180) cc_final: 0.7880 (ttt-90) REVERT: B 297 LYS cc_start: 0.9065 (ptmm) cc_final: 0.8758 (tttp) REVERT: B 303 MET cc_start: 0.6156 (mmm) cc_final: 0.5024 (mmt) REVERT: C 204 ARG cc_start: 0.8008 (tpt170) cc_final: 0.7163 (ttt180) REVERT: C 297 LYS cc_start: 0.8972 (ptmm) cc_final: 0.8700 (tttp) REVERT: C 298 GLU cc_start: 0.8173 (tp30) cc_final: 0.7896 (tp30) REVERT: D 166 MET cc_start: 0.7275 (mmm) cc_final: 0.6783 (mmt) REVERT: D 204 ARG cc_start: 0.7782 (mtp180) cc_final: 0.7454 (ttt-90) REVERT: D 271 SER cc_start: 0.8291 (t) cc_final: 0.7994 (t) REVERT: D 413 MET cc_start: 0.7584 (OUTLIER) cc_final: 0.6047 (mpp) REVERT: D 435 MET cc_start: 0.6299 (ptm) cc_final: 0.6086 (ptt) REVERT: E 102 MET cc_start: 0.6854 (mtm) cc_final: 0.6109 (mtp) REVERT: E 122 MET cc_start: 0.7592 (mmt) cc_final: 0.7213 (mmt) REVERT: E 204 ARG cc_start: 0.8092 (ttt180) cc_final: 0.7829 (ttt180) REVERT: E 297 LYS cc_start: 0.9080 (ptmm) cc_final: 0.8758 (tttp) REVERT: E 303 MET cc_start: 0.6145 (mmm) cc_final: 0.5068 (mmt) REVERT: F 204 ARG cc_start: 0.7935 (tpt170) cc_final: 0.7155 (ttt180) REVERT: F 297 LYS cc_start: 0.8982 (ptmm) cc_final: 0.8692 (tttp) REVERT: F 298 GLU cc_start: 0.8193 (tp30) cc_final: 0.7915 (tp30) outliers start: 37 outliers final: 35 residues processed: 238 average time/residue: 0.3041 time to fit residues: 111.7804 Evaluate side-chains 232 residues out of total 1872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 195 time to evaluate : 1.873 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 55 ILE Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 226 THR Chi-restraints excluded: chain A residue 411 VAL Chi-restraints excluded: chain A residue 413 MET Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 55 ILE Chi-restraints excluded: chain B residue 72 ILE Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 146 ILE Chi-restraints excluded: chain B residue 226 THR Chi-restraints excluded: chain B residue 411 VAL Chi-restraints excluded: chain C residue 39 ARG Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain C residue 55 ILE Chi-restraints excluded: chain C residue 146 ILE Chi-restraints excluded: chain D residue 50 THR Chi-restraints excluded: chain D residue 51 VAL Chi-restraints excluded: chain D residue 55 ILE Chi-restraints excluded: chain D residue 145 LEU Chi-restraints excluded: chain D residue 146 ILE Chi-restraints excluded: chain D residue 226 THR Chi-restraints excluded: chain D residue 411 VAL Chi-restraints excluded: chain D residue 413 MET Chi-restraints excluded: chain E residue 50 THR Chi-restraints excluded: chain E residue 55 ILE Chi-restraints excluded: chain E residue 72 ILE Chi-restraints excluded: chain E residue 145 LEU Chi-restraints excluded: chain E residue 146 ILE Chi-restraints excluded: chain E residue 226 THR Chi-restraints excluded: chain E residue 411 VAL Chi-restraints excluded: chain F residue 50 THR Chi-restraints excluded: chain F residue 55 ILE Chi-restraints excluded: chain F residue 146 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 109 optimal weight: 0.5980 chunk 60 optimal weight: 2.9990 chunk 163 optimal weight: 0.4980 chunk 133 optimal weight: 6.9990 chunk 54 optimal weight: 2.9990 chunk 196 optimal weight: 0.0570 chunk 212 optimal weight: 0.9990 chunk 175 optimal weight: 0.6980 chunk 194 optimal weight: 0.9990 chunk 66 optimal weight: 1.9990 chunk 157 optimal weight: 1.9990 overall best weight: 0.5700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6383 moved from start: 0.2162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 18960 Z= 0.172 Angle : 0.595 11.263 25644 Z= 0.272 Chirality : 0.042 0.247 3000 Planarity : 0.004 0.061 2904 Dihedral : 17.018 147.248 4242 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 2.56 % Allowed : 11.32 % Favored : 86.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.99 (0.19), residues: 2142 helix: 2.48 (0.13), residues: 1434 sheet: None (None), residues: 0 loop : -1.23 (0.26), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 140 HIS 0.002 0.001 HIS F 401 PHE 0.010 0.001 PHE D 177 TYR 0.007 0.001 TYR E 419 ARG 0.002 0.000 ARG A 39 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4284 Ramachandran restraints generated. 2142 Oldfield, 0 Emsley, 2142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4284 Ramachandran restraints generated. 2142 Oldfield, 0 Emsley, 2142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 1872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 221 time to evaluate : 1.931 Fit side-chains REVERT: A 95 CYS cc_start: 0.7655 (t) cc_final: 0.7267 (m) REVERT: A 122 MET cc_start: 0.7281 (mmt) cc_final: 0.6968 (mmt) REVERT: A 166 MET cc_start: 0.7188 (mmm) cc_final: 0.6849 (mmt) REVERT: A 204 ARG cc_start: 0.7757 (mtp180) cc_final: 0.7261 (ttt90) REVERT: A 271 SER cc_start: 0.8110 (t) cc_final: 0.7848 (t) REVERT: A 303 MET cc_start: 0.6602 (mmt) cc_final: 0.6283 (mtm) REVERT: B 95 CYS cc_start: 0.7806 (t) cc_final: 0.7589 (m) REVERT: B 102 MET cc_start: 0.6745 (mtm) cc_final: 0.6162 (mtp) REVERT: B 122 MET cc_start: 0.7470 (mmt) cc_final: 0.7125 (mmt) REVERT: B 204 ARG cc_start: 0.8111 (mtp180) cc_final: 0.7654 (tpt170) REVERT: B 297 LYS cc_start: 0.9104 (ptmm) cc_final: 0.8753 (tttp) REVERT: B 399 MET cc_start: 0.6539 (tpp) cc_final: 0.6305 (mmm) REVERT: C 102 MET cc_start: 0.6401 (mtm) cc_final: 0.5994 (mtp) REVERT: C 122 MET cc_start: 0.7422 (mmt) cc_final: 0.7055 (mmm) REVERT: C 129 ARG cc_start: 0.8149 (mmm-85) cc_final: 0.7292 (mtm-85) REVERT: C 204 ARG cc_start: 0.8052 (tpt170) cc_final: 0.7259 (ttt180) REVERT: C 297 LYS cc_start: 0.9026 (ptmm) cc_final: 0.8632 (tttp) REVERT: C 298 GLU cc_start: 0.8212 (tp30) cc_final: 0.7872 (tp30) REVERT: C 303 MET cc_start: 0.7156 (mpp) cc_final: 0.6414 (mtm) REVERT: D 95 CYS cc_start: 0.7735 (t) cc_final: 0.7364 (m) REVERT: D 122 MET cc_start: 0.7282 (mmt) cc_final: 0.6971 (mmt) REVERT: D 166 MET cc_start: 0.7206 (mmm) cc_final: 0.6861 (mmt) REVERT: D 204 ARG cc_start: 0.7732 (mtp180) cc_final: 0.7262 (ttt90) REVERT: D 271 SER cc_start: 0.8263 (t) cc_final: 0.8003 (t) REVERT: E 95 CYS cc_start: 0.7757 (t) cc_final: 0.7173 (m) REVERT: E 102 MET cc_start: 0.6746 (mtm) cc_final: 0.6137 (mtp) REVERT: E 122 MET cc_start: 0.7468 (mmt) cc_final: 0.7125 (mmt) REVERT: E 166 MET cc_start: 0.6500 (mmt) cc_final: 0.6274 (mmt) REVERT: E 204 ARG cc_start: 0.8029 (ttt-90) cc_final: 0.7757 (ttt180) REVERT: E 297 LYS cc_start: 0.9045 (ptmm) cc_final: 0.8722 (tttp) REVERT: E 399 MET cc_start: 0.6526 (tpp) cc_final: 0.6295 (mmm) REVERT: F 102 MET cc_start: 0.6405 (mtm) cc_final: 0.5899 (mtp) REVERT: F 122 MET cc_start: 0.7420 (mmt) cc_final: 0.7074 (mmm) REVERT: F 129 ARG cc_start: 0.8184 (mmm-85) cc_final: 0.7302 (mtm-85) REVERT: F 204 ARG cc_start: 0.7950 (tpt170) cc_final: 0.7171 (ttt180) REVERT: F 297 LYS cc_start: 0.8938 (ptmm) cc_final: 0.8702 (tttp) REVERT: F 298 GLU cc_start: 0.8228 (tp30) cc_final: 0.7895 (tp30) REVERT: F 303 MET cc_start: 0.7448 (mpp) cc_final: 0.6461 (mtm) outliers start: 48 outliers final: 38 residues processed: 248 average time/residue: 0.3012 time to fit residues: 118.1396 Evaluate side-chains 245 residues out of total 1872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 207 time to evaluate : 1.884 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 ILE Chi-restraints excluded: chain A residue 72 ILE Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 226 THR Chi-restraints excluded: chain A residue 326 VAL Chi-restraints excluded: chain A residue 411 VAL Chi-restraints excluded: chain B residue 55 ILE Chi-restraints excluded: chain B residue 72 ILE Chi-restraints excluded: chain B residue 146 ILE Chi-restraints excluded: chain B residue 226 THR Chi-restraints excluded: chain B residue 234 THR Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 411 VAL Chi-restraints excluded: chain B residue 435 MET Chi-restraints excluded: chain C residue 39 ARG Chi-restraints excluded: chain C residue 55 ILE Chi-restraints excluded: chain C residue 146 ILE Chi-restraints excluded: chain C residue 226 THR Chi-restraints excluded: chain D residue 55 ILE Chi-restraints excluded: chain D residue 72 ILE Chi-restraints excluded: chain D residue 145 LEU Chi-restraints excluded: chain D residue 146 ILE Chi-restraints excluded: chain D residue 226 THR Chi-restraints excluded: chain D residue 326 VAL Chi-restraints excluded: chain D residue 411 VAL Chi-restraints excluded: chain E residue 55 ILE Chi-restraints excluded: chain E residue 72 ILE Chi-restraints excluded: chain E residue 126 LYS Chi-restraints excluded: chain E residue 146 ILE Chi-restraints excluded: chain E residue 226 THR Chi-restraints excluded: chain E residue 234 THR Chi-restraints excluded: chain E residue 326 VAL Chi-restraints excluded: chain E residue 411 VAL Chi-restraints excluded: chain E residue 435 MET Chi-restraints excluded: chain F residue 55 ILE Chi-restraints excluded: chain F residue 146 ILE Chi-restraints excluded: chain F residue 226 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 194 optimal weight: 1.9990 chunk 147 optimal weight: 0.9980 chunk 101 optimal weight: 5.9990 chunk 21 optimal weight: 2.9990 chunk 93 optimal weight: 5.9990 chunk 131 optimal weight: 3.9990 chunk 197 optimal weight: 0.7980 chunk 208 optimal weight: 0.0970 chunk 103 optimal weight: 2.9990 chunk 186 optimal weight: 0.9980 chunk 56 optimal weight: 2.9990 overall best weight: 0.9780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 181 GLN B 181 GLN D 181 GLN E 181 GLN F 136 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6437 moved from start: 0.2477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 18960 Z= 0.227 Angle : 0.610 12.063 25644 Z= 0.289 Chirality : 0.043 0.174 3000 Planarity : 0.004 0.064 2904 Dihedral : 15.384 147.092 4242 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 3.53 % Allowed : 11.43 % Favored : 85.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.19 (0.19), residues: 2142 helix: 2.61 (0.13), residues: 1428 sheet: None (None), residues: 0 loop : -1.06 (0.26), residues: 714 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 288 HIS 0.002 0.000 HIS C 401 PHE 0.011 0.001 PHE A 177 TYR 0.015 0.001 TYR D 419 ARG 0.003 0.000 ARG D 39 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4284 Ramachandran restraints generated. 2142 Oldfield, 0 Emsley, 2142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4284 Ramachandran restraints generated. 2142 Oldfield, 0 Emsley, 2142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 1872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 205 time to evaluate : 2.107 Fit side-chains REVERT: A 95 CYS cc_start: 0.7656 (t) cc_final: 0.6939 (m) REVERT: A 122 MET cc_start: 0.7457 (mmt) cc_final: 0.7141 (mmt) REVERT: A 166 MET cc_start: 0.7654 (mmm) cc_final: 0.7058 (mmt) REVERT: A 204 ARG cc_start: 0.7732 (mtp180) cc_final: 0.7244 (ttt90) REVERT: A 303 MET cc_start: 0.6728 (mmt) cc_final: 0.6422 (mtm) REVERT: A 435 MET cc_start: 0.6272 (ptm) cc_final: 0.6044 (ptt) REVERT: B 95 CYS cc_start: 0.7787 (t) cc_final: 0.7275 (m) REVERT: B 102 MET cc_start: 0.6722 (mtm) cc_final: 0.6315 (mtp) REVERT: B 122 MET cc_start: 0.7599 (mmt) cc_final: 0.7324 (mmt) REVERT: B 204 ARG cc_start: 0.8136 (mtp180) cc_final: 0.7607 (tpt170) REVERT: B 297 LYS cc_start: 0.9072 (ptmm) cc_final: 0.8738 (tttp) REVERT: C 129 ARG cc_start: 0.8097 (mmm-85) cc_final: 0.7168 (mtm-85) REVERT: C 204 ARG cc_start: 0.7890 (tpt170) cc_final: 0.7062 (ttt180) REVERT: C 298 GLU cc_start: 0.8239 (tp30) cc_final: 0.7930 (tp30) REVERT: C 303 MET cc_start: 0.7373 (mpp) cc_final: 0.6554 (mtm) REVERT: D 95 CYS cc_start: 0.7648 (t) cc_final: 0.6980 (m) REVERT: D 122 MET cc_start: 0.7449 (mmt) cc_final: 0.7133 (mmt) REVERT: D 166 MET cc_start: 0.7658 (mmm) cc_final: 0.7059 (mmt) REVERT: D 204 ARG cc_start: 0.7771 (mtp180) cc_final: 0.7300 (ttt90) REVERT: D 271 SER cc_start: 0.8180 (t) cc_final: 0.7904 (t) REVERT: D 303 MET cc_start: 0.6755 (mmt) cc_final: 0.6333 (mtm) REVERT: E 95 CYS cc_start: 0.7805 (t) cc_final: 0.6862 (m) REVERT: E 102 MET cc_start: 0.6719 (mtm) cc_final: 0.6284 (mtp) REVERT: E 122 MET cc_start: 0.7617 (mmt) cc_final: 0.7355 (mmt) REVERT: E 166 MET cc_start: 0.7413 (mmt) cc_final: 0.7162 (mmt) REVERT: E 297 LYS cc_start: 0.9079 (ptmm) cc_final: 0.8753 (tttp) REVERT: E 303 MET cc_start: 0.6156 (mmm) cc_final: 0.5212 (mmt) REVERT: F 129 ARG cc_start: 0.8132 (mmm-85) cc_final: 0.7259 (mtm-85) REVERT: F 204 ARG cc_start: 0.7971 (tpt170) cc_final: 0.7169 (ttt180) REVERT: F 297 LYS cc_start: 0.8912 (ptmm) cc_final: 0.8698 (ptmt) REVERT: F 298 GLU cc_start: 0.8253 (tp30) cc_final: 0.7944 (tp30) REVERT: F 303 MET cc_start: 0.7408 (mpp) cc_final: 0.6599 (mtm) outliers start: 66 outliers final: 50 residues processed: 257 average time/residue: 0.3220 time to fit residues: 126.0836 Evaluate side-chains 247 residues out of total 1872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 197 time to evaluate : 1.970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 55 ILE Chi-restraints excluded: chain A residue 72 ILE Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 226 THR Chi-restraints excluded: chain A residue 326 VAL Chi-restraints excluded: chain A residue 411 VAL Chi-restraints excluded: chain A residue 419 TYR Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 55 ILE Chi-restraints excluded: chain B residue 72 ILE Chi-restraints excluded: chain B residue 126 LYS Chi-restraints excluded: chain B residue 146 ILE Chi-restraints excluded: chain B residue 226 THR Chi-restraints excluded: chain B residue 234 THR Chi-restraints excluded: chain B residue 264 VAL Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 411 VAL Chi-restraints excluded: chain C residue 39 ARG Chi-restraints excluded: chain C residue 55 ILE Chi-restraints excluded: chain C residue 146 ILE Chi-restraints excluded: chain C residue 226 THR Chi-restraints excluded: chain C residue 234 THR Chi-restraints excluded: chain D residue 50 THR Chi-restraints excluded: chain D residue 51 VAL Chi-restraints excluded: chain D residue 55 ILE Chi-restraints excluded: chain D residue 72 ILE Chi-restraints excluded: chain D residue 145 LEU Chi-restraints excluded: chain D residue 146 ILE Chi-restraints excluded: chain D residue 226 THR Chi-restraints excluded: chain D residue 326 VAL Chi-restraints excluded: chain D residue 411 VAL Chi-restraints excluded: chain D residue 419 TYR Chi-restraints excluded: chain E residue 50 THR Chi-restraints excluded: chain E residue 55 ILE Chi-restraints excluded: chain E residue 72 ILE Chi-restraints excluded: chain E residue 126 LYS Chi-restraints excluded: chain E residue 146 ILE Chi-restraints excluded: chain E residue 226 THR Chi-restraints excluded: chain E residue 234 THR Chi-restraints excluded: chain E residue 324 THR Chi-restraints excluded: chain E residue 326 VAL Chi-restraints excluded: chain E residue 411 VAL Chi-restraints excluded: chain F residue 55 ILE Chi-restraints excluded: chain F residue 146 ILE Chi-restraints excluded: chain F residue 226 THR Chi-restraints excluded: chain F residue 234 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 173 optimal weight: 5.9990 chunk 118 optimal weight: 0.9990 chunk 3 optimal weight: 0.0970 chunk 155 optimal weight: 0.6980 chunk 86 optimal weight: 0.8980 chunk 178 optimal weight: 1.9990 chunk 144 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 106 optimal weight: 0.7980 chunk 187 optimal weight: 2.9990 chunk 52 optimal weight: 0.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6405 moved from start: 0.2647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 18960 Z= 0.181 Angle : 0.588 11.309 25644 Z= 0.275 Chirality : 0.041 0.158 3000 Planarity : 0.004 0.069 2904 Dihedral : 14.651 147.281 4242 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 3.58 % Allowed : 11.49 % Favored : 84.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.47 (0.19), residues: 2142 helix: 2.90 (0.13), residues: 1422 sheet: None (None), residues: 0 loop : -1.10 (0.26), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 288 HIS 0.002 0.000 HIS C 401 PHE 0.009 0.001 PHE B 177 TYR 0.011 0.001 TYR A 97 ARG 0.002 0.000 ARG A 39 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4284 Ramachandran restraints generated. 2142 Oldfield, 0 Emsley, 2142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4284 Ramachandran restraints generated. 2142 Oldfield, 0 Emsley, 2142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 1872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 208 time to evaluate : 1.982 Fit side-chains REVERT: A 122 MET cc_start: 0.7348 (mmt) cc_final: 0.7017 (mmt) REVERT: A 166 MET cc_start: 0.7561 (mmm) cc_final: 0.7230 (tpp) REVERT: A 204 ARG cc_start: 0.7674 (mtp180) cc_final: 0.7114 (ttt90) REVERT: A 303 MET cc_start: 0.6712 (mmt) cc_final: 0.6333 (mtm) REVERT: A 304 PHE cc_start: 0.6500 (m-10) cc_final: 0.6258 (m-10) REVERT: B 102 MET cc_start: 0.6554 (mtm) cc_final: 0.6222 (mtp) REVERT: B 122 MET cc_start: 0.7503 (mmt) cc_final: 0.7239 (mmt) REVERT: B 204 ARG cc_start: 0.8128 (mtp180) cc_final: 0.7596 (tpt170) REVERT: B 270 HIS cc_start: 0.7017 (p-80) cc_final: 0.6567 (p-80) REVERT: C 129 ARG cc_start: 0.8054 (mmm-85) cc_final: 0.7142 (mtm-85) REVERT: C 204 ARG cc_start: 0.7725 (tpt170) cc_final: 0.6849 (ttt180) REVERT: C 298 GLU cc_start: 0.8243 (tp30) cc_final: 0.7911 (tp30) REVERT: C 303 MET cc_start: 0.7522 (mpp) cc_final: 0.6750 (mtm) REVERT: D 122 MET cc_start: 0.7344 (mmt) cc_final: 0.7008 (mmt) REVERT: D 166 MET cc_start: 0.7576 (mmm) cc_final: 0.7244 (tpp) REVERT: D 190 HIS cc_start: 0.6157 (OUTLIER) cc_final: 0.5061 (m-70) REVERT: D 204 ARG cc_start: 0.7732 (mtp180) cc_final: 0.7197 (ttt90) REVERT: D 303 MET cc_start: 0.6732 (mmt) cc_final: 0.6347 (mtm) REVERT: D 304 PHE cc_start: 0.6480 (m-10) cc_final: 0.6240 (m-10) REVERT: E 102 MET cc_start: 0.6564 (mtm) cc_final: 0.6235 (mtp) REVERT: E 122 MET cc_start: 0.7531 (mmt) cc_final: 0.7249 (mmt) REVERT: E 270 HIS cc_start: 0.6940 (p-80) cc_final: 0.6510 (p-80) REVERT: E 303 MET cc_start: 0.6334 (mmm) cc_final: 0.6109 (mmm) REVERT: F 102 MET cc_start: 0.6240 (mtm) cc_final: 0.5770 (mtp) REVERT: F 129 ARG cc_start: 0.8054 (mmm-85) cc_final: 0.7141 (mtm-85) REVERT: F 204 ARG cc_start: 0.7824 (tpt170) cc_final: 0.6990 (ttt180) REVERT: F 298 GLU cc_start: 0.8284 (tp30) cc_final: 0.7982 (tp30) REVERT: F 303 MET cc_start: 0.7422 (mpp) cc_final: 0.6642 (mtm) outliers start: 67 outliers final: 53 residues processed: 257 average time/residue: 0.2934 time to fit residues: 116.3769 Evaluate side-chains 259 residues out of total 1872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 205 time to evaluate : 1.910 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 ILE Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 226 THR Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 326 VAL Chi-restraints excluded: chain A residue 411 VAL Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 55 ILE Chi-restraints excluded: chain B residue 72 ILE Chi-restraints excluded: chain B residue 126 LYS Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 146 ILE Chi-restraints excluded: chain B residue 226 THR Chi-restraints excluded: chain B residue 229 TYR Chi-restraints excluded: chain B residue 234 THR Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 411 VAL Chi-restraints excluded: chain B residue 435 MET Chi-restraints excluded: chain C residue 39 ARG Chi-restraints excluded: chain C residue 55 ILE Chi-restraints excluded: chain C residue 146 ILE Chi-restraints excluded: chain C residue 226 THR Chi-restraints excluded: chain C residue 234 THR Chi-restraints excluded: chain C residue 273 LEU Chi-restraints excluded: chain C residue 326 VAL Chi-restraints excluded: chain C residue 352 VAL Chi-restraints excluded: chain D residue 55 ILE Chi-restraints excluded: chain D residue 145 LEU Chi-restraints excluded: chain D residue 146 ILE Chi-restraints excluded: chain D residue 190 HIS Chi-restraints excluded: chain D residue 226 THR Chi-restraints excluded: chain D residue 268 LEU Chi-restraints excluded: chain D residue 326 VAL Chi-restraints excluded: chain D residue 411 VAL Chi-restraints excluded: chain E residue 55 ILE Chi-restraints excluded: chain E residue 72 ILE Chi-restraints excluded: chain E residue 126 LYS Chi-restraints excluded: chain E residue 145 LEU Chi-restraints excluded: chain E residue 146 ILE Chi-restraints excluded: chain E residue 226 THR Chi-restraints excluded: chain E residue 229 TYR Chi-restraints excluded: chain E residue 234 THR Chi-restraints excluded: chain E residue 324 THR Chi-restraints excluded: chain E residue 326 VAL Chi-restraints excluded: chain E residue 411 VAL Chi-restraints excluded: chain E residue 435 MET Chi-restraints excluded: chain F residue 55 ILE Chi-restraints excluded: chain F residue 146 ILE Chi-restraints excluded: chain F residue 226 THR Chi-restraints excluded: chain F residue 234 THR Chi-restraints excluded: chain F residue 273 LEU Chi-restraints excluded: chain F residue 352 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 70 optimal weight: 0.9980 chunk 188 optimal weight: 2.9990 chunk 41 optimal weight: 0.8980 chunk 122 optimal weight: 0.6980 chunk 51 optimal weight: 2.9990 chunk 208 optimal weight: 0.8980 chunk 173 optimal weight: 6.9990 chunk 96 optimal weight: 0.0570 chunk 17 optimal weight: 0.6980 chunk 69 optimal weight: 0.9980 chunk 109 optimal weight: 0.5980 overall best weight: 0.5898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6385 moved from start: 0.2865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 18960 Z= 0.163 Angle : 0.565 11.186 25644 Z= 0.263 Chirality : 0.040 0.146 3000 Planarity : 0.004 0.066 2904 Dihedral : 13.743 147.480 4242 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 3.95 % Allowed : 11.22 % Favored : 84.83 % 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: 2.64 (0.19), residues: 2142 helix: 3.08 (0.13), residues: 1422 sheet: None (None), residues: 0 loop : -1.16 (0.26), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E 140 HIS 0.002 0.000 HIS C 401 PHE 0.009 0.001 PHE D 177 TYR 0.009 0.001 TYR A 419 ARG 0.002 0.000 ARG D 39 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4284 Ramachandran restraints generated. 2142 Oldfield, 0 Emsley, 2142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4284 Ramachandran restraints generated. 2142 Oldfield, 0 Emsley, 2142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 1872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 223 time to evaluate : 2.079 Fit side-chains REVERT: A 94 ASP cc_start: 0.7264 (t70) cc_final: 0.7049 (t0) REVERT: A 122 MET cc_start: 0.7307 (mmt) cc_final: 0.6951 (mmt) REVERT: A 166 MET cc_start: 0.7513 (mmm) cc_final: 0.7124 (tpp) REVERT: A 190 HIS cc_start: 0.6135 (OUTLIER) cc_final: 0.5115 (m-70) REVERT: A 204 ARG cc_start: 0.7769 (mtp180) cc_final: 0.7238 (ttt90) REVERT: A 229 TYR cc_start: 0.7613 (OUTLIER) cc_final: 0.6877 (t80) REVERT: A 261 LEU cc_start: 0.6486 (OUTLIER) cc_final: 0.6246 (pp) REVERT: A 303 MET cc_start: 0.6593 (mmt) cc_final: 0.6300 (mtm) REVERT: A 304 PHE cc_start: 0.6530 (m-10) cc_final: 0.6211 (m-10) REVERT: A 451 TRP cc_start: 0.6546 (t-100) cc_final: 0.6024 (t60) REVERT: B 102 MET cc_start: 0.6512 (mtm) cc_final: 0.6269 (mtp) REVERT: B 122 MET cc_start: 0.7402 (mmt) cc_final: 0.7165 (mmt) REVERT: B 204 ARG cc_start: 0.8103 (mtp180) cc_final: 0.7553 (tpt170) REVERT: B 270 HIS cc_start: 0.7066 (p-80) cc_final: 0.6686 (p-80) REVERT: B 297 LYS cc_start: 0.8766 (ptmm) cc_final: 0.8381 (ptmm) REVERT: B 399 MET cc_start: 0.6527 (tpp) cc_final: 0.6091 (mmm) REVERT: C 102 MET cc_start: 0.6208 (mtm) cc_final: 0.5803 (mtp) REVERT: C 129 ARG cc_start: 0.8041 (mmm-85) cc_final: 0.7092 (mtm-85) REVERT: C 204 ARG cc_start: 0.7809 (tpt170) cc_final: 0.6959 (ttt180) REVERT: C 298 GLU cc_start: 0.8277 (tp30) cc_final: 0.7965 (tp30) REVERT: C 303 MET cc_start: 0.7421 (mpp) cc_final: 0.6704 (mtm) REVERT: D 122 MET cc_start: 0.7303 (mmt) cc_final: 0.6941 (mmt) REVERT: D 166 MET cc_start: 0.7532 (mmm) cc_final: 0.7138 (tpp) REVERT: D 190 HIS cc_start: 0.6110 (OUTLIER) cc_final: 0.5080 (m-70) REVERT: D 204 ARG cc_start: 0.7765 (mtp180) cc_final: 0.7240 (ttt180) REVERT: D 229 TYR cc_start: 0.7605 (OUTLIER) cc_final: 0.6916 (t80) REVERT: D 303 MET cc_start: 0.6636 (mmt) cc_final: 0.6296 (mtm) REVERT: D 304 PHE cc_start: 0.6462 (m-10) cc_final: 0.6206 (m-10) REVERT: D 451 TRP cc_start: 0.6621 (t-100) cc_final: 0.6027 (t60) REVERT: E 102 MET cc_start: 0.6516 (mtm) cc_final: 0.6270 (mtp) REVERT: E 122 MET cc_start: 0.7467 (mmt) cc_final: 0.7196 (mmt) REVERT: E 270 HIS cc_start: 0.7016 (p-80) cc_final: 0.6614 (p-80) REVERT: E 399 MET cc_start: 0.6535 (tpp) cc_final: 0.6101 (mmm) REVERT: E 451 TRP cc_start: 0.6849 (t-100) cc_final: 0.6286 (t60) REVERT: F 129 ARG cc_start: 0.8053 (mmm-85) cc_final: 0.7122 (mtm-85) REVERT: F 204 ARG cc_start: 0.7723 (tpt170) cc_final: 0.6802 (ttt180) REVERT: F 298 GLU cc_start: 0.8328 (tp30) cc_final: 0.8065 (tp30) REVERT: F 303 MET cc_start: 0.7475 (mpp) cc_final: 0.6782 (mtm) outliers start: 74 outliers final: 58 residues processed: 278 average time/residue: 0.2949 time to fit residues: 127.5354 Evaluate side-chains 277 residues out of total 1872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 214 time to evaluate : 1.919 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 ILE Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 155 ILE Chi-restraints excluded: chain A residue 190 HIS Chi-restraints excluded: chain A residue 226 THR Chi-restraints excluded: chain A residue 229 TYR Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 352 VAL Chi-restraints excluded: chain A residue 411 VAL Chi-restraints excluded: chain A residue 419 TYR Chi-restraints excluded: chain B residue 55 ILE Chi-restraints excluded: chain B residue 72 ILE Chi-restraints excluded: chain B residue 126 LYS Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 146 ILE Chi-restraints excluded: chain B residue 190 HIS Chi-restraints excluded: chain B residue 226 THR Chi-restraints excluded: chain B residue 229 TYR Chi-restraints excluded: chain B residue 234 THR Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 352 VAL Chi-restraints excluded: chain B residue 411 VAL Chi-restraints excluded: chain B residue 435 MET Chi-restraints excluded: chain C residue 39 ARG Chi-restraints excluded: chain C residue 55 ILE Chi-restraints excluded: chain C residue 146 ILE Chi-restraints excluded: chain C residue 226 THR Chi-restraints excluded: chain C residue 234 THR Chi-restraints excluded: chain C residue 326 VAL Chi-restraints excluded: chain C residue 352 VAL Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 55 ILE Chi-restraints excluded: chain D residue 145 LEU Chi-restraints excluded: chain D residue 146 ILE Chi-restraints excluded: chain D residue 190 HIS Chi-restraints excluded: chain D residue 226 THR Chi-restraints excluded: chain D residue 229 TYR Chi-restraints excluded: chain D residue 268 LEU Chi-restraints excluded: chain D residue 326 VAL Chi-restraints excluded: chain D residue 352 VAL Chi-restraints excluded: chain D residue 411 VAL Chi-restraints excluded: chain E residue 55 ILE Chi-restraints excluded: chain E residue 72 ILE Chi-restraints excluded: chain E residue 145 LEU Chi-restraints excluded: chain E residue 146 ILE Chi-restraints excluded: chain E residue 190 HIS Chi-restraints excluded: chain E residue 226 THR Chi-restraints excluded: chain E residue 229 TYR Chi-restraints excluded: chain E residue 234 THR Chi-restraints excluded: chain E residue 324 THR Chi-restraints excluded: chain E residue 326 VAL Chi-restraints excluded: chain E residue 352 VAL Chi-restraints excluded: chain E residue 411 VAL Chi-restraints excluded: chain E residue 435 MET Chi-restraints excluded: chain F residue 55 ILE Chi-restraints excluded: chain F residue 146 ILE Chi-restraints excluded: chain F residue 226 THR Chi-restraints excluded: chain F residue 234 THR Chi-restraints excluded: chain F residue 352 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 201 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 chunk 119 optimal weight: 1.9990 chunk 152 optimal weight: 0.7980 chunk 118 optimal weight: 0.8980 chunk 175 optimal weight: 1.9990 chunk 116 optimal weight: 0.8980 chunk 208 optimal weight: 0.0980 chunk 130 optimal weight: 0.0770 chunk 126 optimal weight: 1.9990 chunk 96 optimal weight: 0.8980 overall best weight: 0.5538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6377 moved from start: 0.2993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 18960 Z= 0.160 Angle : 0.567 10.997 25644 Z= 0.262 Chirality : 0.039 0.181 3000 Planarity : 0.004 0.066 2904 Dihedral : 13.413 147.451 4242 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.45 % Favored : 96.50 % Rotamer: Outliers : 3.79 % Allowed : 12.13 % Favored : 84.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.75 (0.19), residues: 2142 helix: 3.20 (0.13), residues: 1422 sheet: None (None), residues: 0 loop : -1.21 (0.26), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 140 HIS 0.003 0.000 HIS D 322 PHE 0.010 0.001 PHE A 177 TYR 0.008 0.001 TYR D 231 ARG 0.002 0.000 ARG D 39 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4284 Ramachandran restraints generated. 2142 Oldfield, 0 Emsley, 2142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4284 Ramachandran restraints generated. 2142 Oldfield, 0 Emsley, 2142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 1872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 227 time to evaluate : 2.079 Fit side-chains REVERT: A 122 MET cc_start: 0.7291 (mmt) cc_final: 0.6919 (mmt) REVERT: A 190 HIS cc_start: 0.6117 (OUTLIER) cc_final: 0.5086 (m-70) REVERT: A 204 ARG cc_start: 0.7732 (mtp180) cc_final: 0.7220 (ttt180) REVERT: A 229 TYR cc_start: 0.7601 (OUTLIER) cc_final: 0.6987 (t80) REVERT: A 304 PHE cc_start: 0.6521 (m-10) cc_final: 0.6168 (m-10) REVERT: A 451 TRP cc_start: 0.6623 (t-100) cc_final: 0.6018 (t60) REVERT: B 102 MET cc_start: 0.6492 (mtm) cc_final: 0.6196 (mtp) REVERT: B 122 MET cc_start: 0.7356 (mmt) cc_final: 0.7141 (mmt) REVERT: B 204 ARG cc_start: 0.8095 (mtp180) cc_final: 0.7526 (tpt170) REVERT: B 270 HIS cc_start: 0.7062 (p-80) cc_final: 0.6687 (p-80) REVERT: B 399 MET cc_start: 0.6531 (tpp) cc_final: 0.6085 (mmm) REVERT: B 451 TRP cc_start: 0.6846 (t-100) cc_final: 0.6303 (t60) REVERT: C 129 ARG cc_start: 0.8037 (mmm-85) cc_final: 0.7089 (mtm-85) REVERT: C 204 ARG cc_start: 0.7825 (tpt170) cc_final: 0.7018 (ttt180) REVERT: C 298 GLU cc_start: 0.8263 (tp30) cc_final: 0.7948 (tp30) REVERT: C 303 MET cc_start: 0.7415 (mpp) cc_final: 0.6769 (mtm) REVERT: D 122 MET cc_start: 0.7286 (mmt) cc_final: 0.6929 (mmt) REVERT: D 190 HIS cc_start: 0.6096 (OUTLIER) cc_final: 0.5128 (m-70) REVERT: D 204 ARG cc_start: 0.7729 (mtp180) cc_final: 0.7227 (ttt180) REVERT: D 229 TYR cc_start: 0.7616 (OUTLIER) cc_final: 0.6997 (t80) REVERT: D 231 TYR cc_start: 0.6790 (m-80) cc_final: 0.6530 (m-80) REVERT: D 304 PHE cc_start: 0.6471 (m-10) cc_final: 0.6207 (m-10) REVERT: D 451 TRP cc_start: 0.6580 (t-100) cc_final: 0.6021 (t60) REVERT: E 102 MET cc_start: 0.6504 (mtm) cc_final: 0.6202 (mtp) REVERT: E 122 MET cc_start: 0.7446 (mmt) cc_final: 0.7172 (mmt) REVERT: E 270 HIS cc_start: 0.6811 (p-80) cc_final: 0.6407 (p-80) REVERT: E 399 MET cc_start: 0.6533 (tpp) cc_final: 0.6089 (mmm) REVERT: E 451 TRP cc_start: 0.6847 (t-100) cc_final: 0.6329 (t60) REVERT: F 129 ARG cc_start: 0.8038 (mmm-85) cc_final: 0.7089 (mtm-85) REVERT: F 159 ASP cc_start: 0.7604 (t70) cc_final: 0.7343 (p0) REVERT: F 204 ARG cc_start: 0.7801 (tpt170) cc_final: 0.7400 (ttt90) REVERT: F 298 GLU cc_start: 0.8282 (tp30) cc_final: 0.7998 (tp30) REVERT: F 303 MET cc_start: 0.7496 (mpp) cc_final: 0.6813 (mtm) outliers start: 71 outliers final: 62 residues processed: 277 average time/residue: 0.2875 time to fit residues: 123.0931 Evaluate side-chains 285 residues out of total 1872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 219 time to evaluate : 1.933 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 ILE Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 155 ILE Chi-restraints excluded: chain A residue 190 HIS Chi-restraints excluded: chain A residue 226 THR Chi-restraints excluded: chain A residue 229 TYR Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 326 VAL Chi-restraints excluded: chain A residue 352 VAL Chi-restraints excluded: chain A residue 411 VAL Chi-restraints excluded: chain B residue 55 ILE Chi-restraints excluded: chain B residue 72 ILE Chi-restraints excluded: chain B residue 126 LYS Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 146 ILE Chi-restraints excluded: chain B residue 190 HIS Chi-restraints excluded: chain B residue 226 THR Chi-restraints excluded: chain B residue 229 TYR Chi-restraints excluded: chain B residue 234 THR Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 352 VAL Chi-restraints excluded: chain B residue 411 VAL Chi-restraints excluded: chain B residue 435 MET Chi-restraints excluded: chain C residue 39 ARG Chi-restraints excluded: chain C residue 55 ILE Chi-restraints excluded: chain C residue 145 LEU Chi-restraints excluded: chain C residue 146 ILE Chi-restraints excluded: chain C residue 226 THR Chi-restraints excluded: chain C residue 234 THR Chi-restraints excluded: chain C residue 326 VAL Chi-restraints excluded: chain C residue 352 VAL Chi-restraints excluded: chain D residue 55 ILE Chi-restraints excluded: chain D residue 145 LEU Chi-restraints excluded: chain D residue 146 ILE Chi-restraints excluded: chain D residue 190 HIS Chi-restraints excluded: chain D residue 226 THR Chi-restraints excluded: chain D residue 229 TYR Chi-restraints excluded: chain D residue 230 ILE Chi-restraints excluded: chain D residue 268 LEU Chi-restraints excluded: chain D residue 326 VAL Chi-restraints excluded: chain D residue 352 VAL Chi-restraints excluded: chain D residue 411 VAL Chi-restraints excluded: chain D residue 419 TYR Chi-restraints excluded: chain E residue 55 ILE Chi-restraints excluded: chain E residue 72 ILE Chi-restraints excluded: chain E residue 126 LYS Chi-restraints excluded: chain E residue 145 LEU Chi-restraints excluded: chain E residue 146 ILE Chi-restraints excluded: chain E residue 190 HIS Chi-restraints excluded: chain E residue 226 THR Chi-restraints excluded: chain E residue 229 TYR Chi-restraints excluded: chain E residue 234 THR Chi-restraints excluded: chain E residue 268 LEU Chi-restraints excluded: chain E residue 324 THR Chi-restraints excluded: chain E residue 326 VAL Chi-restraints excluded: chain E residue 352 VAL Chi-restraints excluded: chain E residue 411 VAL Chi-restraints excluded: chain E residue 435 MET Chi-restraints excluded: chain F residue 55 ILE Chi-restraints excluded: chain F residue 146 ILE Chi-restraints excluded: chain F residue 226 THR Chi-restraints excluded: chain F residue 234 THR Chi-restraints excluded: chain F residue 326 VAL Chi-restraints excluded: chain F residue 352 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 128 optimal weight: 0.9980 chunk 83 optimal weight: 0.9980 chunk 124 optimal weight: 4.9990 chunk 62 optimal weight: 3.9990 chunk 40 optimal weight: 4.9990 chunk 132 optimal weight: 0.7980 chunk 141 optimal weight: 2.9990 chunk 102 optimal weight: 0.9990 chunk 19 optimal weight: 0.8980 chunk 163 optimal weight: 0.7980 chunk 189 optimal weight: 0.9980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 422 HIS F 181 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6422 moved from start: 0.3051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 18960 Z= 0.210 Angle : 0.603 11.632 25644 Z= 0.280 Chirality : 0.041 0.176 3000 Planarity : 0.004 0.067 2904 Dihedral : 13.427 147.302 4242 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 4.06 % Allowed : 12.07 % Favored : 83.87 % 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: 2.71 (0.19), residues: 2142 helix: 3.14 (0.13), residues: 1422 sheet: None (None), residues: 0 loop : -1.15 (0.26), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 288 HIS 0.001 0.000 HIS F 401 PHE 0.010 0.001 PHE C 177 TYR 0.012 0.001 TYR D 419 ARG 0.002 0.000 ARG D 39 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4284 Ramachandran restraints generated. 2142 Oldfield, 0 Emsley, 2142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4284 Ramachandran restraints generated. 2142 Oldfield, 0 Emsley, 2142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 1872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 216 time to evaluate : 2.119 Fit side-chains REVERT: A 122 MET cc_start: 0.7400 (mmt) cc_final: 0.7073 (mmt) REVERT: A 190 HIS cc_start: 0.6132 (OUTLIER) cc_final: 0.5105 (m-70) REVERT: A 204 ARG cc_start: 0.7741 (mtp180) cc_final: 0.7222 (ttt180) REVERT: A 229 TYR cc_start: 0.7633 (OUTLIER) cc_final: 0.6956 (t80) REVERT: A 304 PHE cc_start: 0.6676 (m-10) cc_final: 0.6344 (m-10) REVERT: A 451 TRP cc_start: 0.6579 (t-100) cc_final: 0.6026 (t60) REVERT: B 102 MET cc_start: 0.6571 (mtm) cc_final: 0.6152 (mtp) REVERT: B 122 MET cc_start: 0.7468 (mmt) cc_final: 0.7257 (mmt) REVERT: B 204 ARG cc_start: 0.8061 (mtp180) cc_final: 0.7540 (tpt170) REVERT: B 270 HIS cc_start: 0.6917 (p-80) cc_final: 0.6469 (p-80) REVERT: C 129 ARG cc_start: 0.8041 (mmm-85) cc_final: 0.7095 (mtm-85) REVERT: C 204 ARG cc_start: 0.7825 (tpt170) cc_final: 0.7370 (ttt90) REVERT: C 298 GLU cc_start: 0.8247 (tp30) cc_final: 0.7936 (tp30) REVERT: C 303 MET cc_start: 0.7459 (mpp) cc_final: 0.6835 (mtm) REVERT: D 122 MET cc_start: 0.7392 (mmt) cc_final: 0.7056 (mmt) REVERT: D 204 ARG cc_start: 0.7736 (mtp180) cc_final: 0.7228 (ttt180) REVERT: D 229 TYR cc_start: 0.7640 (OUTLIER) cc_final: 0.6968 (t80) REVERT: D 304 PHE cc_start: 0.6604 (m-10) cc_final: 0.6292 (m-10) REVERT: D 451 TRP cc_start: 0.6560 (t-100) cc_final: 0.6002 (t60) REVERT: E 102 MET cc_start: 0.6579 (mtm) cc_final: 0.6153 (mtp) REVERT: E 122 MET cc_start: 0.7597 (mmt) cc_final: 0.7366 (mmt) REVERT: E 270 HIS cc_start: 0.6886 (p-80) cc_final: 0.6419 (p-80) REVERT: E 451 TRP cc_start: 0.6859 (t-100) cc_final: 0.6317 (t60) REVERT: F 129 ARG cc_start: 0.8041 (mmm-85) cc_final: 0.7095 (mtm-85) REVERT: F 159 ASP cc_start: 0.7393 (t70) cc_final: 0.7174 (p0) REVERT: F 204 ARG cc_start: 0.7850 (tpt170) cc_final: 0.7471 (ttt90) REVERT: F 298 GLU cc_start: 0.8313 (tp30) cc_final: 0.8032 (tp30) REVERT: F 303 MET cc_start: 0.7542 (mpp) cc_final: 0.6930 (mtm) outliers start: 76 outliers final: 69 residues processed: 269 average time/residue: 0.2817 time to fit residues: 117.2839 Evaluate side-chains 287 residues out of total 1872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 215 time to evaluate : 1.911 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 ILE Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 155 ILE Chi-restraints excluded: chain A residue 190 HIS Chi-restraints excluded: chain A residue 226 THR Chi-restraints excluded: chain A residue 229 TYR Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 326 VAL Chi-restraints excluded: chain A residue 352 VAL Chi-restraints excluded: chain A residue 411 VAL Chi-restraints excluded: chain A residue 419 TYR Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 55 ILE Chi-restraints excluded: chain B residue 72 ILE Chi-restraints excluded: chain B residue 126 LYS Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 146 ILE Chi-restraints excluded: chain B residue 190 HIS Chi-restraints excluded: chain B residue 226 THR Chi-restraints excluded: chain B residue 229 TYR Chi-restraints excluded: chain B residue 234 THR Chi-restraints excluded: chain B residue 264 VAL Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 411 VAL Chi-restraints excluded: chain B residue 435 MET Chi-restraints excluded: chain C residue 39 ARG Chi-restraints excluded: chain C residue 55 ILE Chi-restraints excluded: chain C residue 122 MET Chi-restraints excluded: chain C residue 145 LEU Chi-restraints excluded: chain C residue 146 ILE Chi-restraints excluded: chain C residue 226 THR Chi-restraints excluded: chain C residue 234 THR Chi-restraints excluded: chain C residue 326 VAL Chi-restraints excluded: chain C residue 352 VAL Chi-restraints excluded: chain D residue 55 ILE Chi-restraints excluded: chain D residue 145 LEU Chi-restraints excluded: chain D residue 146 ILE Chi-restraints excluded: chain D residue 226 THR Chi-restraints excluded: chain D residue 229 TYR Chi-restraints excluded: chain D residue 230 ILE Chi-restraints excluded: chain D residue 268 LEU Chi-restraints excluded: chain D residue 326 VAL Chi-restraints excluded: chain D residue 352 VAL Chi-restraints excluded: chain D residue 411 VAL Chi-restraints excluded: chain D residue 419 TYR Chi-restraints excluded: chain E residue 50 THR Chi-restraints excluded: chain E residue 55 ILE Chi-restraints excluded: chain E residue 72 ILE Chi-restraints excluded: chain E residue 126 LYS Chi-restraints excluded: chain E residue 145 LEU Chi-restraints excluded: chain E residue 146 ILE Chi-restraints excluded: chain E residue 190 HIS Chi-restraints excluded: chain E residue 226 THR Chi-restraints excluded: chain E residue 229 TYR Chi-restraints excluded: chain E residue 234 THR Chi-restraints excluded: chain E residue 264 VAL Chi-restraints excluded: chain E residue 268 LEU Chi-restraints excluded: chain E residue 324 THR Chi-restraints excluded: chain E residue 326 VAL Chi-restraints excluded: chain E residue 411 VAL Chi-restraints excluded: chain E residue 435 MET Chi-restraints excluded: chain F residue 55 ILE Chi-restraints excluded: chain F residue 122 MET Chi-restraints excluded: chain F residue 145 LEU Chi-restraints excluded: chain F residue 146 ILE Chi-restraints excluded: chain F residue 226 THR Chi-restraints excluded: chain F residue 234 THR Chi-restraints excluded: chain F residue 326 VAL Chi-restraints excluded: chain F residue 352 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 199 optimal weight: 0.6980 chunk 181 optimal weight: 0.6980 chunk 194 optimal weight: 0.9980 chunk 116 optimal weight: 2.9990 chunk 84 optimal weight: 0.8980 chunk 152 optimal weight: 0.7980 chunk 59 optimal weight: 3.9990 chunk 175 optimal weight: 0.7980 chunk 183 optimal weight: 0.0370 chunk 193 optimal weight: 0.5980 chunk 127 optimal weight: 0.9990 overall best weight: 0.5658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 136 GLN E 136 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6382 moved from start: 0.3158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 18960 Z= 0.159 Angle : 0.578 10.919 25644 Z= 0.264 Chirality : 0.039 0.168 3000 Planarity : 0.004 0.066 2904 Dihedral : 13.130 147.423 4242 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 3.47 % Allowed : 13.14 % Favored : 83.39 % 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: 2.79 (0.19), residues: 2142 helix: 3.12 (0.13), residues: 1458 sheet: None (None), residues: 0 loop : -1.15 (0.26), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 418 HIS 0.002 0.000 HIS B 422 PHE 0.010 0.001 PHE A 177 TYR 0.007 0.001 TYR D 419 ARG 0.002 0.000 ARG D 39 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4284 Ramachandran restraints generated. 2142 Oldfield, 0 Emsley, 2142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4284 Ramachandran restraints generated. 2142 Oldfield, 0 Emsley, 2142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 1872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 217 time to evaluate : 1.903 Fit side-chains REVERT: A 122 MET cc_start: 0.7265 (mmt) cc_final: 0.6918 (mmt) REVERT: A 190 HIS cc_start: 0.6122 (OUTLIER) cc_final: 0.5100 (m-70) REVERT: A 204 ARG cc_start: 0.7733 (mtp180) cc_final: 0.7222 (ttt180) REVERT: A 229 TYR cc_start: 0.7583 (OUTLIER) cc_final: 0.6959 (t80) REVERT: A 451 TRP cc_start: 0.6538 (t-100) cc_final: 0.6002 (t60) REVERT: B 102 MET cc_start: 0.6473 (mtm) cc_final: 0.6121 (mtp) REVERT: B 122 MET cc_start: 0.7424 (mmt) cc_final: 0.7180 (mmt) REVERT: B 204 ARG cc_start: 0.8008 (mtp180) cc_final: 0.7458 (tpt170) REVERT: B 270 HIS cc_start: 0.7141 (p-80) cc_final: 0.6734 (p-80) REVERT: B 399 MET cc_start: 0.6517 (tpp) cc_final: 0.6102 (mmm) REVERT: B 451 TRP cc_start: 0.6841 (t-100) cc_final: 0.6325 (t60) REVERT: C 129 ARG cc_start: 0.8060 (mmm-85) cc_final: 0.7112 (mtm-85) REVERT: C 204 ARG cc_start: 0.7806 (tpt170) cc_final: 0.7363 (ttt90) REVERT: C 298 GLU cc_start: 0.8277 (tp30) cc_final: 0.7972 (tp30) REVERT: C 303 MET cc_start: 0.7183 (mpp) cc_final: 0.6954 (mtm) REVERT: D 122 MET cc_start: 0.7261 (mmt) cc_final: 0.6902 (mmt) REVERT: D 190 HIS cc_start: 0.6093 (OUTLIER) cc_final: 0.5133 (m-70) REVERT: D 204 ARG cc_start: 0.7727 (mtp180) cc_final: 0.7226 (ttt180) REVERT: D 229 TYR cc_start: 0.7585 (OUTLIER) cc_final: 0.6984 (t80) REVERT: D 231 TYR cc_start: 0.6852 (m-80) cc_final: 0.6434 (m-80) REVERT: D 451 TRP cc_start: 0.6568 (t-100) cc_final: 0.5986 (t60) REVERT: E 102 MET cc_start: 0.6483 (mtm) cc_final: 0.6130 (mtp) REVERT: E 122 MET cc_start: 0.7425 (mmt) cc_final: 0.7156 (mmt) REVERT: E 270 HIS cc_start: 0.7115 (p-80) cc_final: 0.6698 (p-80) REVERT: E 399 MET cc_start: 0.6535 (tpp) cc_final: 0.6121 (mmm) REVERT: E 451 TRP cc_start: 0.6876 (t-100) cc_final: 0.6105 (t60) REVERT: F 129 ARG cc_start: 0.8061 (mmm-85) cc_final: 0.7112 (mtm-85) REVERT: F 204 ARG cc_start: 0.7851 (tpt170) cc_final: 0.7486 (ttt90) REVERT: F 298 GLU cc_start: 0.8290 (tp30) cc_final: 0.7995 (tp30) REVERT: F 303 MET cc_start: 0.7525 (mpp) cc_final: 0.6995 (mtm) outliers start: 65 outliers final: 56 residues processed: 263 average time/residue: 0.2888 time to fit residues: 116.8971 Evaluate side-chains 274 residues out of total 1872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 214 time to evaluate : 1.929 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 ILE Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 155 ILE Chi-restraints excluded: chain A residue 190 HIS Chi-restraints excluded: chain A residue 226 THR Chi-restraints excluded: chain A residue 229 TYR Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 326 VAL Chi-restraints excluded: chain A residue 411 VAL Chi-restraints excluded: chain B residue 55 ILE Chi-restraints excluded: chain B residue 72 ILE Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 146 ILE Chi-restraints excluded: chain B residue 190 HIS Chi-restraints excluded: chain B residue 226 THR Chi-restraints excluded: chain B residue 229 TYR Chi-restraints excluded: chain B residue 234 THR Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 411 VAL Chi-restraints excluded: chain B residue 435 MET Chi-restraints excluded: chain C residue 39 ARG Chi-restraints excluded: chain C residue 55 ILE Chi-restraints excluded: chain C residue 145 LEU Chi-restraints excluded: chain C residue 146 ILE Chi-restraints excluded: chain C residue 226 THR Chi-restraints excluded: chain C residue 234 THR Chi-restraints excluded: chain C residue 326 VAL Chi-restraints excluded: chain C residue 352 VAL Chi-restraints excluded: chain D residue 55 ILE Chi-restraints excluded: chain D residue 145 LEU Chi-restraints excluded: chain D residue 146 ILE Chi-restraints excluded: chain D residue 190 HIS Chi-restraints excluded: chain D residue 226 THR Chi-restraints excluded: chain D residue 229 TYR Chi-restraints excluded: chain D residue 268 LEU Chi-restraints excluded: chain D residue 326 VAL Chi-restraints excluded: chain D residue 411 VAL Chi-restraints excluded: chain D residue 419 TYR Chi-restraints excluded: chain E residue 55 ILE Chi-restraints excluded: chain E residue 72 ILE Chi-restraints excluded: chain E residue 145 LEU Chi-restraints excluded: chain E residue 146 ILE Chi-restraints excluded: chain E residue 190 HIS Chi-restraints excluded: chain E residue 226 THR Chi-restraints excluded: chain E residue 229 TYR Chi-restraints excluded: chain E residue 234 THR Chi-restraints excluded: chain E residue 268 LEU Chi-restraints excluded: chain E residue 324 THR Chi-restraints excluded: chain E residue 326 VAL Chi-restraints excluded: chain E residue 411 VAL Chi-restraints excluded: chain E residue 435 MET Chi-restraints excluded: chain F residue 55 ILE Chi-restraints excluded: chain F residue 145 LEU Chi-restraints excluded: chain F residue 146 ILE Chi-restraints excluded: chain F residue 226 THR Chi-restraints excluded: chain F residue 234 THR Chi-restraints excluded: chain F residue 326 VAL Chi-restraints excluded: chain F residue 352 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 205 optimal weight: 7.9990 chunk 125 optimal weight: 3.9990 chunk 97 optimal weight: 5.9990 chunk 142 optimal weight: 0.5980 chunk 215 optimal weight: 3.9990 chunk 198 optimal weight: 1.9990 chunk 171 optimal weight: 0.7980 chunk 17 optimal weight: 3.9990 chunk 132 optimal weight: 0.9990 chunk 105 optimal weight: 0.0020 chunk 136 optimal weight: 0.8980 overall best weight: 0.6590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6399 moved from start: 0.3242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 18960 Z= 0.176 Angle : 0.588 11.345 25644 Z= 0.269 Chirality : 0.040 0.166 3000 Planarity : 0.004 0.065 2904 Dihedral : 12.974 147.660 4242 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 3.21 % Allowed : 13.51 % Favored : 83.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.78 (0.19), residues: 2142 helix: 3.12 (0.13), residues: 1458 sheet: None (None), residues: 0 loop : -1.17 (0.26), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 288 HIS 0.002 0.000 HIS B 422 PHE 0.009 0.001 PHE D 177 TYR 0.009 0.001 TYR D 419 ARG 0.002 0.000 ARG D 39 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4284 Ramachandran restraints generated. 2142 Oldfield, 0 Emsley, 2142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4284 Ramachandran restraints generated. 2142 Oldfield, 0 Emsley, 2142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 1872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 212 time to evaluate : 1.947 Fit side-chains REVERT: A 122 MET cc_start: 0.7337 (mmt) cc_final: 0.7012 (mmt) REVERT: A 190 HIS cc_start: 0.6096 (OUTLIER) cc_final: 0.5133 (m-70) REVERT: A 204 ARG cc_start: 0.7734 (mtp180) cc_final: 0.7221 (ttt180) REVERT: A 229 TYR cc_start: 0.7575 (OUTLIER) cc_final: 0.6975 (t80) REVERT: A 304 PHE cc_start: 0.6813 (m-10) cc_final: 0.6503 (m-10) REVERT: A 451 TRP cc_start: 0.6586 (t-100) cc_final: 0.6056 (t60) REVERT: B 102 MET cc_start: 0.6502 (mtm) cc_final: 0.6144 (mtp) REVERT: B 122 MET cc_start: 0.7409 (mmt) cc_final: 0.7198 (mmt) REVERT: B 204 ARG cc_start: 0.7986 (mtp180) cc_final: 0.7437 (tpt170) REVERT: B 270 HIS cc_start: 0.6793 (p-80) cc_final: 0.6393 (p-80) REVERT: B 399 MET cc_start: 0.6574 (tpp) cc_final: 0.6156 (mmm) REVERT: B 451 TRP cc_start: 0.6990 (t-100) cc_final: 0.6442 (t60) REVERT: C 129 ARG cc_start: 0.8060 (mmm-85) cc_final: 0.7113 (mtm-85) REVERT: C 204 ARG cc_start: 0.7794 (tpt170) cc_final: 0.7371 (ttt90) REVERT: C 298 GLU cc_start: 0.8290 (tp30) cc_final: 0.7977 (tp30) REVERT: D 122 MET cc_start: 0.7335 (mmt) cc_final: 0.6996 (mmt) REVERT: D 204 ARG cc_start: 0.7729 (mtp180) cc_final: 0.7227 (ttt180) REVERT: D 229 TYR cc_start: 0.7580 (OUTLIER) cc_final: 0.7003 (t80) REVERT: D 304 PHE cc_start: 0.6797 (m-10) cc_final: 0.6492 (m-10) REVERT: D 451 TRP cc_start: 0.6476 (t-100) cc_final: 0.5944 (t60) REVERT: E 102 MET cc_start: 0.6516 (mtm) cc_final: 0.6148 (mtp) REVERT: E 122 MET cc_start: 0.7413 (mmt) cc_final: 0.7157 (mmt) REVERT: E 270 HIS cc_start: 0.6768 (p-80) cc_final: 0.6357 (p-80) REVERT: E 399 MET cc_start: 0.6584 (tpp) cc_final: 0.6169 (mmm) REVERT: E 451 TRP cc_start: 0.7011 (t-100) cc_final: 0.6198 (t60) REVERT: F 129 ARG cc_start: 0.8060 (mmm-85) cc_final: 0.7113 (mtm-85) REVERT: F 204 ARG cc_start: 0.7838 (tpt170) cc_final: 0.7491 (ttt90) REVERT: F 298 GLU cc_start: 0.8311 (tp30) cc_final: 0.8015 (tp30) REVERT: F 303 MET cc_start: 0.7336 (mpp) cc_final: 0.6934 (mtm) outliers start: 60 outliers final: 56 residues processed: 258 average time/residue: 0.2976 time to fit residues: 119.4010 Evaluate side-chains 271 residues out of total 1872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 212 time to evaluate : 1.827 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 ILE Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 155 ILE Chi-restraints excluded: chain A residue 190 HIS Chi-restraints excluded: chain A residue 226 THR Chi-restraints excluded: chain A residue 229 TYR Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 326 VAL Chi-restraints excluded: chain A residue 411 VAL Chi-restraints excluded: chain B residue 55 ILE Chi-restraints excluded: chain B residue 72 ILE Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 146 ILE Chi-restraints excluded: chain B residue 190 HIS Chi-restraints excluded: chain B residue 226 THR Chi-restraints excluded: chain B residue 229 TYR Chi-restraints excluded: chain B residue 234 THR Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 411 VAL Chi-restraints excluded: chain B residue 435 MET Chi-restraints excluded: chain C residue 39 ARG Chi-restraints excluded: chain C residue 55 ILE Chi-restraints excluded: chain C residue 145 LEU Chi-restraints excluded: chain C residue 146 ILE Chi-restraints excluded: chain C residue 226 THR Chi-restraints excluded: chain C residue 234 THR Chi-restraints excluded: chain C residue 326 VAL Chi-restraints excluded: chain C residue 352 VAL Chi-restraints excluded: chain D residue 55 ILE Chi-restraints excluded: chain D residue 145 LEU Chi-restraints excluded: chain D residue 146 ILE Chi-restraints excluded: chain D residue 226 THR Chi-restraints excluded: chain D residue 229 TYR Chi-restraints excluded: chain D residue 268 LEU Chi-restraints excluded: chain D residue 326 VAL Chi-restraints excluded: chain D residue 411 VAL Chi-restraints excluded: chain D residue 419 TYR Chi-restraints excluded: chain E residue 55 ILE Chi-restraints excluded: chain E residue 72 ILE Chi-restraints excluded: chain E residue 145 LEU Chi-restraints excluded: chain E residue 146 ILE Chi-restraints excluded: chain E residue 190 HIS Chi-restraints excluded: chain E residue 226 THR Chi-restraints excluded: chain E residue 229 TYR Chi-restraints excluded: chain E residue 234 THR Chi-restraints excluded: chain E residue 268 LEU Chi-restraints excluded: chain E residue 324 THR Chi-restraints excluded: chain E residue 326 VAL Chi-restraints excluded: chain E residue 411 VAL Chi-restraints excluded: chain E residue 435 MET Chi-restraints excluded: chain F residue 55 ILE Chi-restraints excluded: chain F residue 145 LEU Chi-restraints excluded: chain F residue 146 ILE Chi-restraints excluded: chain F residue 226 THR Chi-restraints excluded: chain F residue 234 THR Chi-restraints excluded: chain F residue 326 VAL Chi-restraints excluded: chain F residue 352 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 182 optimal weight: 0.8980 chunk 52 optimal weight: 5.9990 chunk 158 optimal weight: 1.9990 chunk 25 optimal weight: 0.5980 chunk 47 optimal weight: 0.0770 chunk 171 optimal weight: 0.9990 chunk 71 optimal weight: 3.9990 chunk 176 optimal weight: 0.7980 chunk 21 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 150 optimal weight: 0.7980 overall best weight: 0.6338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 322 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.156491 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.114826 restraints weight = 23304.900| |-----------------------------------------------------------------------------| r_work (start): 0.3603 rms_B_bonded: 2.75 r_work: 0.3392 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.3392 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7753 moved from start: 0.3300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 18960 Z= 0.169 Angle : 0.580 11.074 25644 Z= 0.265 Chirality : 0.039 0.165 3000 Planarity : 0.004 0.062 2904 Dihedral : 12.801 147.635 4242 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 3.15 % Allowed : 13.89 % Favored : 82.96 % 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: 2.82 (0.19), residues: 2142 helix: 3.16 (0.13), residues: 1458 sheet: None (None), residues: 0 loop : -1.18 (0.26), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 288 HIS 0.002 0.000 HIS B 422 PHE 0.009 0.001 PHE A 177 TYR 0.008 0.001 TYR A 419 ARG 0.002 0.000 ARG A 39 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3517.17 seconds wall clock time: 65 minutes 26.30 seconds (3926.30 seconds total)