Starting phenix.real_space_refine on Sat Jun 14 23:41:12 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8drk_27677/06_2025/8drk_27677.cif Found real_map, /net/cci-nas-00/data/ceres_data/8drk_27677/06_2025/8drk_27677.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.95 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8drk_27677/06_2025/8drk_27677.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8drk_27677/06_2025/8drk_27677.map" model { file = "/net/cci-nas-00/data/ceres_data/8drk_27677/06_2025/8drk_27677.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8drk_27677/06_2025/8drk_27677.cif" } resolution = 2.95 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= 0.085 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 9 5.49 5 S 106 5.16 5 C 10903 2.51 5 N 2556 2.21 5 O 2869 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 83 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 16443 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 2671 Number of conformers: 1 Conformer: "" Number of residues, atoms: 319, 2671 Classifications: {'peptide': 319} Link IDs: {'PTRANS': 9, 'TRANS': 309} Chain breaks: 2 Chain: "B" Number of atoms: 2671 Number of conformers: 1 Conformer: "" Number of residues, atoms: 319, 2671 Classifications: {'peptide': 319} Link IDs: {'PTRANS': 9, 'TRANS': 309} Chain breaks: 2 Chain: "C" Number of atoms: 2671 Number of conformers: 1 Conformer: "" Number of residues, atoms: 319, 2671 Classifications: {'peptide': 319} Link IDs: {'PTRANS': 9, 'TRANS': 309} Chain breaks: 2 Chain: "D" Number of atoms: 2646 Number of conformers: 1 Conformer: "" Number of residues, atoms: 316, 2646 Classifications: {'peptide': 316} Link IDs: {'PTRANS': 9, 'TRANS': 306} Chain breaks: 2 Chain: "E" Number of atoms: 2671 Number of conformers: 1 Conformer: "" Number of residues, atoms: 319, 2671 Classifications: {'peptide': 319} Link IDs: {'PTRANS': 9, 'TRANS': 309} Chain breaks: 2 Chain: "F" Number of atoms: 2569 Number of conformers: 1 Conformer: "" Number of residues, atoms: 309, 2569 Classifications: {'peptide': 309} Link IDs: {'PTRANS': 7, 'TRANS': 301} Chain breaks: 2 Chain: "A" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 66 Unusual residues: {'PEE': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 87 Unresolved non-hydrogen angles: 97 Unresolved non-hydrogen dihedrals: 85 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PEE:plan-2': 2} Unresolved non-hydrogen planarities: 8 Chain: "B" Number of atoms: 113 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 113 Unusual residues: {'PEE': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 91 Unresolved non-hydrogen angles: 101 Unresolved non-hydrogen dihedrals: 89 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PEE:plan-2': 2} Unresolved non-hydrogen planarities: 8 Chain: "C" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 66 Unusual residues: {'PEE': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 87 Unresolved non-hydrogen angles: 97 Unresolved non-hydrogen dihedrals: 85 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PEE:plan-2': 2} Unresolved non-hydrogen planarities: 8 Chain: "D" Number of atoms: 115 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 115 Unusual residues: {'PEE': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 89 Unresolved non-hydrogen angles: 99 Unresolved non-hydrogen dihedrals: 87 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PEE:plan-2': 2} Unresolved non-hydrogen planarities: 8 Chain: "E" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 64 Unusual residues: {'PEE': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 89 Unresolved non-hydrogen angles: 99 Unresolved non-hydrogen dihedrals: 87 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PEE:plan-2': 2} Unresolved non-hydrogen planarities: 8 Chain: "F" Number of atoms: 114 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 114 Unusual residues: {'PEE': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 90 Unresolved non-hydrogen angles: 100 Unresolved non-hydrogen dihedrals: 88 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PEE:plan-2': 2} Unresolved non-hydrogen planarities: 8 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 11.26, per 1000 atoms: 0.68 Number of scatterers: 16443 At special positions: 0 Unit cell: (99.56, 105.848, 136.24, 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 106 16.00 P 9 15.00 O 2869 8.00 N 2556 7.00 C 10903 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=17, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 310 " distance=2.03 Simple disulfide: pdb=" SG CYS A 57 " - pdb=" SG CYS A 65 " distance=2.03 Simple disulfide: pdb=" SG CYS A 113 " - pdb=" SG CYS A 295 " distance=2.03 Simple disulfide: pdb=" SG CYS B 54 " - pdb=" SG CYS B 310 " distance=2.03 Simple disulfide: pdb=" SG CYS B 57 " - pdb=" SG CYS B 65 " distance=2.03 Simple disulfide: pdb=" SG CYS B 113 " - pdb=" SG CYS B 295 " distance=2.03 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 310 " distance=2.03 Simple disulfide: pdb=" SG CYS C 57 " - pdb=" SG CYS C 65 " distance=2.03 Simple disulfide: pdb=" SG CYS C 113 " - pdb=" SG CYS C 295 " distance=2.03 Simple disulfide: pdb=" SG CYS D 54 " - pdb=" SG CYS D 310 " distance=2.03 Simple disulfide: pdb=" SG CYS D 57 " - pdb=" SG CYS D 65 " distance=2.03 Simple disulfide: pdb=" SG CYS D 113 " - pdb=" SG CYS D 295 " distance=2.03 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 310 " distance=2.02 Simple disulfide: pdb=" SG CYS E 57 " - pdb=" SG CYS E 65 " distance=2.03 Simple disulfide: pdb=" SG CYS E 113 " - pdb=" SG CYS E 295 " distance=2.03 Simple disulfide: pdb=" SG CYS F 54 " - pdb=" SG CYS F 308 " distance=2.03 Simple disulfide: pdb=" SG CYS F 115 " - pdb=" SG CYS F 293 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 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: 4.60 Conformation dependent library (CDL) restraints added in 2.0 seconds 3730 Ramachandran restraints generated. 1865 Oldfield, 0 Emsley, 1865 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3692 Finding SS restraints... Secondary structure from input PDB file: 85 helices and 9 sheets defined 75.2% alpha, 3.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.46 Creating SS restraints... Processing helix chain 'A' and resid 16 through 21 removed outlier: 4.018A pdb=" N ILE A 19 " --> pdb=" O ALA A 16 " (cutoff:3.500A) Processing helix chain 'A' and resid 22 through 49 Processing helix chain 'A' and resid 102 through 116 Processing helix chain 'A' and resid 119 through 141 Proline residue: A 126 - end of helix Processing helix chain 'A' and resid 146 through 165 removed outlier: 3.668A pdb=" N LYS A 152 " --> pdb=" O ARG A 148 " (cutoff:3.500A) Processing helix chain 'A' and resid 166 through 175 removed outlier: 3.912A pdb=" N THR A 170 " --> pdb=" O SER A 166 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLU A 175 " --> pdb=" O ARG A 171 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 255 Processing helix chain 'A' and resid 258 through 286 removed outlier: 3.840A pdb=" N PHE A 275 " --> pdb=" O LYS A 271 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N TYR A 285 " --> pdb=" O TYR A 281 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 289 No H-bonds generated for 'chain 'A' and resid 287 through 289' Processing helix chain 'A' and resid 315 through 345 Processing helix chain 'A' and resid 353 through 360 Processing helix chain 'A' and resid 370 through 383 removed outlier: 3.527A pdb=" N TYR A 382 " --> pdb=" O LEU A 378 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 392 removed outlier: 4.109A pdb=" N SER A 387 " --> pdb=" O ASP A 383 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N VAL A 392 " --> pdb=" O LYS A 388 " (cutoff:3.500A) Processing helix chain 'A' and resid 395 through 410 Processing helix chain 'B' and resid 16 through 21 removed outlier: 3.595A pdb=" N ILE B 19 " --> pdb=" O ALA B 16 " (cutoff:3.500A) Processing helix chain 'B' and resid 22 through 50 removed outlier: 3.640A pdb=" N ASP B 50 " --> pdb=" O GLN B 46 " (cutoff:3.500A) Processing helix chain 'B' and resid 102 through 117 Processing helix chain 'B' and resid 119 through 141 Proline residue: B 126 - end of helix Processing helix chain 'B' and resid 146 through 165 removed outlier: 3.789A pdb=" N LYS B 152 " --> pdb=" O ARG B 148 " (cutoff:3.500A) Processing helix chain 'B' and resid 166 through 175 removed outlier: 3.606A pdb=" N THR B 170 " --> pdb=" O SER B 166 " (cutoff:3.500A) Processing helix chain 'B' and resid 233 through 255 Processing helix chain 'B' and resid 258 through 285 Processing helix chain 'B' and resid 286 through 289 Processing helix chain 'B' and resid 314 through 343 removed outlier: 3.906A pdb=" N PHE B 324 " --> pdb=" O ILE B 320 " (cutoff:3.500A) Processing helix chain 'B' and resid 353 through 360 Processing helix chain 'B' and resid 370 through 383 Processing helix chain 'B' and resid 383 through 392 removed outlier: 4.208A pdb=" N SER B 387 " --> pdb=" O ASP B 383 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N VAL B 392 " --> pdb=" O LYS B 388 " (cutoff:3.500A) Processing helix chain 'B' and resid 395 through 410 Processing helix chain 'C' and resid 16 through 21 removed outlier: 4.010A pdb=" N ILE C 19 " --> pdb=" O ALA C 16 " (cutoff:3.500A) Processing helix chain 'C' and resid 22 through 49 Processing helix chain 'C' and resid 102 through 117 Processing helix chain 'C' and resid 119 through 141 Proline residue: C 126 - end of helix Processing helix chain 'C' and resid 141 through 146 removed outlier: 3.705A pdb=" N LYS C 145 " --> pdb=" O ASN C 141 " (cutoff:3.500A) Processing helix chain 'C' and resid 146 through 166 removed outlier: 3.690A pdb=" N LYS C 152 " --> pdb=" O ARG C 148 " (cutoff:3.500A) Processing helix chain 'C' and resid 166 through 175 removed outlier: 4.270A pdb=" N THR C 170 " --> pdb=" O SER C 166 " (cutoff:3.500A) Processing helix chain 'C' and resid 233 through 255 Processing helix chain 'C' and resid 258 through 286 Processing helix chain 'C' and resid 287 through 289 No H-bonds generated for 'chain 'C' and resid 287 through 289' Processing helix chain 'C' and resid 315 through 343 Processing helix chain 'C' and resid 353 through 360 Processing helix chain 'C' and resid 369 through 383 removed outlier: 3.537A pdb=" N ALA C 373 " --> pdb=" O LYS C 369 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N TYR C 382 " --> pdb=" O LEU C 378 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 394 removed outlier: 4.068A pdb=" N SER C 387 " --> pdb=" O ASP C 383 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N VAL C 392 " --> pdb=" O LYS C 388 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N PHE C 393 " --> pdb=" O ARG C 389 " (cutoff:3.500A) Processing helix chain 'C' and resid 395 through 410 Processing helix chain 'D' and resid 16 through 21 removed outlier: 4.254A pdb=" N ILE D 19 " --> pdb=" O ALA D 16 " (cutoff:3.500A) Processing helix chain 'D' and resid 22 through 49 Processing helix chain 'D' and resid 102 through 117 Processing helix chain 'D' and resid 119 through 146 removed outlier: 3.565A pdb=" N LYS D 123 " --> pdb=" O HIS D 119 " (cutoff:3.500A) Proline residue: D 126 - end of helix removed outlier: 5.005A pdb=" N TRP D 143 " --> pdb=" O CYS D 139 " (cutoff:3.500A) removed outlier: 5.152A pdb=" N PHE D 144 " --> pdb=" O SER D 140 " (cutoff:3.500A) Processing helix chain 'D' and resid 146 through 165 removed outlier: 3.905A pdb=" N LYS D 152 " --> pdb=" O ARG D 148 " (cutoff:3.500A) Processing helix chain 'D' and resid 166 through 175 removed outlier: 3.653A pdb=" N THR D 170 " --> pdb=" O SER D 166 " (cutoff:3.500A) Processing helix chain 'D' and resid 233 through 255 Processing helix chain 'D' and resid 258 through 286 Processing helix chain 'D' and resid 287 through 289 No H-bonds generated for 'chain 'D' and resid 287 through 289' Processing helix chain 'D' and resid 314 through 346 removed outlier: 3.942A pdb=" N ARG D 346 " --> pdb=" O TRP D 342 " (cutoff:3.500A) Processing helix chain 'D' and resid 353 through 360 Processing helix chain 'D' and resid 370 through 383 Processing helix chain 'D' and resid 383 through 391 removed outlier: 4.006A pdb=" N SER D 387 " --> pdb=" O ASP D 383 " (cutoff:3.500A) Processing helix chain 'D' and resid 392 through 394 No H-bonds generated for 'chain 'D' and resid 392 through 394' Processing helix chain 'D' and resid 395 through 407 Processing helix chain 'E' and resid 22 through 49 Processing helix chain 'E' and resid 102 through 117 Processing helix chain 'E' and resid 119 through 141 Proline residue: E 126 - end of helix Processing helix chain 'E' and resid 146 through 165 removed outlier: 3.766A pdb=" N LYS E 152 " --> pdb=" O ARG E 148 " (cutoff:3.500A) Processing helix chain 'E' and resid 166 through 175 removed outlier: 3.761A pdb=" N THR E 170 " --> pdb=" O SER E 166 " (cutoff:3.500A) Processing helix chain 'E' and resid 233 through 255 Processing helix chain 'E' and resid 258 through 286 Processing helix chain 'E' and resid 287 through 289 No H-bonds generated for 'chain 'E' and resid 287 through 289' Processing helix chain 'E' and resid 315 through 343 Processing helix chain 'E' and resid 353 through 360 Processing helix chain 'E' and resid 370 through 383 Processing helix chain 'E' and resid 383 through 392 removed outlier: 4.005A pdb=" N SER E 387 " --> pdb=" O ASP E 383 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N VAL E 392 " --> pdb=" O LYS E 388 " (cutoff:3.500A) Processing helix chain 'E' and resid 395 through 410 Processing helix chain 'F' and resid 16 through 21 removed outlier: 4.344A pdb=" N VAL F 19 " --> pdb=" O ALA F 16 " (cutoff:3.500A) Processing helix chain 'F' and resid 22 through 48 removed outlier: 3.960A pdb=" N MET F 48 " --> pdb=" O THR F 44 " (cutoff:3.500A) Processing helix chain 'F' and resid 104 through 119 Processing helix chain 'F' and resid 121 through 143 Proline residue: F 128 - end of helix removed outlier: 3.707A pdb=" N ASN F 143 " --> pdb=" O MET F 139 " (cutoff:3.500A) Processing helix chain 'F' and resid 148 through 168 removed outlier: 3.882A pdb=" N SER F 153 " --> pdb=" O PRO F 149 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N LYS F 154 " --> pdb=" O GLY F 150 " (cutoff:3.500A) Processing helix chain 'F' and resid 168 through 179 removed outlier: 4.335A pdb=" N THR F 172 " --> pdb=" O SER F 168 " (cutoff:3.500A) Processing helix chain 'F' and resid 233 through 253 removed outlier: 3.627A pdb=" N GLU F 253 " --> pdb=" O ARG F 249 " (cutoff:3.500A) Processing helix chain 'F' and resid 256 through 284 removed outlier: 3.514A pdb=" N ALA F 260 " --> pdb=" O ASP F 256 " (cutoff:3.500A) Processing helix chain 'F' and resid 285 through 287 No H-bonds generated for 'chain 'F' and resid 285 through 287' Processing helix chain 'F' and resid 312 through 343 Processing helix chain 'F' and resid 351 through 358 Processing helix chain 'F' and resid 368 through 381 Processing helix chain 'F' and resid 382 through 393 removed outlier: 3.718A pdb=" N LYS F 386 " --> pdb=" O PRO F 382 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N VAL F 390 " --> pdb=" O LYS F 386 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N PHE F 391 " --> pdb=" O ARG F 387 " (cutoff:3.500A) Processing helix chain 'F' and resid 394 through 408 Processing sheet with id=AA1, first strand: chain 'A' and resid 53 through 56 Processing sheet with id=AA2, first strand: chain 'A' and resid 59 through 60 removed outlier: 3.720A pdb=" N VAL A 60 " --> pdb=" O VAL F 94 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N VAL F 94 " --> pdb=" O VAL A 60 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 350 through 351 Processing sheet with id=AA4, first strand: chain 'B' and resid 53 through 56 Processing sheet with id=AA5, first strand: chain 'C' and resid 53 through 56 Processing sheet with id=AA6, first strand: chain 'D' and resid 53 through 56 Processing sheet with id=AA7, first strand: chain 'D' and resid 350 through 351 removed outlier: 3.721A pdb=" N VAL D 368 " --> pdb=" O TYR D 351 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 53 through 56 removed outlier: 3.556A pdb=" N LEU E 55 " --> pdb=" O ARG E 309 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'F' and resid 52 through 56 1085 hydrogen bonds defined for protein. 3201 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: 4.73 Time building geometry restraints manager: 5.36 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2761 1.33 - 1.45: 4646 1.45 - 1.57: 9280 1.57 - 1.69: 10 1.69 - 1.81: 161 Bond restraints: 16858 Sorted by residual: bond pdb=" C10 PEE A 902 " pdb=" O4 PEE A 902 " ideal model delta sigma weight residual 1.206 1.358 -0.152 2.00e-02 2.50e+03 5.76e+01 bond pdb=" C10 PEE E 902 " pdb=" O4 PEE E 902 " ideal model delta sigma weight residual 1.206 1.357 -0.151 2.00e-02 2.50e+03 5.72e+01 bond pdb=" C10 PEE D 902 " pdb=" O4 PEE D 902 " ideal model delta sigma weight residual 1.206 1.357 -0.151 2.00e-02 2.50e+03 5.72e+01 bond pdb=" C10 PEE C 902 " pdb=" O4 PEE C 902 " ideal model delta sigma weight residual 1.206 1.357 -0.151 2.00e-02 2.50e+03 5.71e+01 bond pdb=" C10 PEE E 903 " pdb=" O4 PEE E 903 " ideal model delta sigma weight residual 1.206 1.356 -0.150 2.00e-02 2.50e+03 5.64e+01 ... (remaining 16853 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.77: 22345 2.77 - 5.54: 247 5.54 - 8.31: 59 8.31 - 11.08: 11 11.08 - 13.85: 15 Bond angle restraints: 22677 Sorted by residual: angle pdb=" O1P PEE F 904 " pdb=" P PEE F 904 " pdb=" O2P PEE F 904 " ideal model delta sigma weight residual 119.43 133.28 -13.85 3.00e+00 1.11e-01 2.13e+01 angle pdb=" O1P PEE D 901 " pdb=" P PEE D 901 " pdb=" O2P PEE D 901 " ideal model delta sigma weight residual 119.43 133.26 -13.83 3.00e+00 1.11e-01 2.12e+01 angle pdb=" O1P PEE D 904 " pdb=" P PEE D 904 " pdb=" O2P PEE D 904 " ideal model delta sigma weight residual 119.43 133.22 -13.79 3.00e+00 1.11e-01 2.11e+01 angle pdb=" O1P PEE C 901 " pdb=" P PEE C 901 " pdb=" O2P PEE C 901 " ideal model delta sigma weight residual 119.43 133.20 -13.77 3.00e+00 1.11e-01 2.11e+01 angle pdb=" O1P PEE A 901 " pdb=" P PEE A 901 " pdb=" O2P PEE A 901 " ideal model delta sigma weight residual 119.43 133.18 -13.75 3.00e+00 1.11e-01 2.10e+01 ... (remaining 22672 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.96: 9715 35.96 - 71.93: 316 71.93 - 107.89: 24 107.89 - 143.85: 14 143.85 - 179.82: 16 Dihedral angle restraints: 10085 sinusoidal: 4381 harmonic: 5704 Sorted by residual: dihedral pdb=" CB CYS B 113 " pdb=" SG CYS B 113 " pdb=" SG CYS B 295 " pdb=" CB CYS B 295 " ideal model delta sinusoidal sigma weight residual 93.00 50.48 42.52 1 1.00e+01 1.00e-02 2.52e+01 dihedral pdb=" N PEE A 901 " pdb=" C4 PEE A 901 " pdb=" C5 PEE A 901 " pdb=" O4P PEE A 901 " ideal model delta sinusoidal sigma weight residual -56.97 122.85 -179.82 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" N PEE B 901 " pdb=" C4 PEE B 901 " pdb=" C5 PEE B 901 " pdb=" O4P PEE B 901 " ideal model delta sinusoidal sigma weight residual -56.97 119.91 -176.88 1 3.00e+01 1.11e-03 2.13e+01 ... (remaining 10082 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.084: 2293 0.084 - 0.167: 132 0.167 - 0.251: 1 0.251 - 0.335: 0 0.335 - 0.418: 10 Chirality restraints: 2436 Sorted by residual: chirality pdb=" C2 PEE B 904 " pdb=" C1 PEE B 904 " pdb=" C3 PEE B 904 " pdb=" O2 PEE B 904 " both_signs ideal model delta sigma weight residual False -2.33 -2.75 0.42 2.00e-01 2.50e+01 4.37e+00 chirality pdb=" C2 PEE C 901 " pdb=" C1 PEE C 901 " pdb=" C3 PEE C 901 " pdb=" O2 PEE C 901 " both_signs ideal model delta sigma weight residual False -2.33 -2.74 0.41 2.00e-01 2.50e+01 4.22e+00 chirality pdb=" C2 PEE D 901 " pdb=" C1 PEE D 901 " pdb=" C3 PEE D 901 " pdb=" O2 PEE D 901 " both_signs ideal model delta sigma weight residual False -2.33 -2.74 0.41 2.00e-01 2.50e+01 4.22e+00 ... (remaining 2433 not shown) Planarity restraints: 2714 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU D 321 " -0.012 2.00e-02 2.50e+03 2.42e-02 5.84e+00 pdb=" C LEU D 321 " 0.042 2.00e-02 2.50e+03 pdb=" O LEU D 321 " -0.016 2.00e-02 2.50e+03 pdb=" N ALA D 322 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 244 " -0.013 2.00e-02 2.50e+03 1.82e-02 5.81e+00 pdb=" CG PHE A 244 " 0.037 2.00e-02 2.50e+03 pdb=" CD1 PHE A 244 " -0.022 2.00e-02 2.50e+03 pdb=" CD2 PHE A 244 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 PHE A 244 " 0.010 2.00e-02 2.50e+03 pdb=" CE2 PHE A 244 " -0.014 2.00e-02 2.50e+03 pdb=" CZ PHE A 244 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE D 324 " -0.011 2.00e-02 2.50e+03 2.29e-02 5.23e+00 pdb=" C PHE D 324 " 0.040 2.00e-02 2.50e+03 pdb=" O PHE D 324 " -0.015 2.00e-02 2.50e+03 pdb=" N TYR D 325 " -0.013 2.00e-02 2.50e+03 ... (remaining 2711 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1636 2.75 - 3.29: 16335 3.29 - 3.82: 28838 3.82 - 4.36: 33048 4.36 - 4.90: 57706 Nonbonded interactions: 137563 Sorted by model distance: nonbonded pdb=" O SER E 395 " pdb=" OG SER E 398 " model vdw 2.212 3.040 nonbonded pdb=" OH TYR E 99 " pdb=" O MET F 300 " model vdw 2.213 3.040 nonbonded pdb=" O SER A 166 " pdb=" OG1 THR A 169 " model vdw 2.232 3.040 nonbonded pdb=" O SER D 166 " pdb=" OG1 THR D 169 " model vdw 2.233 3.040 nonbonded pdb=" O SER B 166 " pdb=" OG1 THR B 169 " model vdw 2.233 3.040 ... (remaining 137558 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 15 through 407 or (resid 901 through 903 and (name C10 or \ name C11 or name C12 or name C13 or name C14 or name C15 or name C16 or name O2 \ or name O4 )))) selection = (chain 'B' and (resid 15 through 407 or (resid 901 through 903 and (name C10 or \ name C11 or name C12 or name C13 or name C14 or name C15 or name C16 or name O2 \ or name O4 )))) selection = (chain 'C' and (resid 15 through 407 or (resid 901 through 903 and (name C10 or \ name C11 or name C12 or name C13 or name C14 or name C15 or name C16 or name O2 \ or name O4 )))) selection = (chain 'D' and (resid 15 through 407 or (resid 902 through 904 and (name C10 or \ name C11 or name C12 or name C13 or name C14 or name C15 or name C16 or name O2 \ or name O4 )))) selection = (chain 'E' and (resid 15 through 407 or (resid 901 through 903 and (name C10 or \ name C11 or name C12 or name C13 or name C14 or name C15 or name C16 or name O2 \ or name O4 )))) } 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: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.050 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: 0.020 Extract box with map and model: 0.690 Check model and map are aligned: 0.120 Set scattering table: 0.170 Process input model: 39.010 Find NCS groups from input model: 0.760 Set up NCS constraints: 0.060 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:12.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 58.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7795 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 0.152 16875 Z= 0.318 Angle : 0.839 13.848 22711 Z= 0.403 Chirality : 0.048 0.418 2436 Planarity : 0.005 0.056 2714 Dihedral : 19.554 179.817 6342 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 0.28 % Allowed : 16.62 % Favored : 83.10 % 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: 0.83 (0.19), residues: 1865 helix: 1.11 (0.14), residues: 1276 sheet: 0.24 (0.52), residues: 104 loop : -0.72 (0.28), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP D 168 HIS 0.009 0.001 HIS C 253 PHE 0.037 0.002 PHE A 244 TYR 0.018 0.001 TYR B 281 ARG 0.009 0.001 ARG C 389 Details of bonding type rmsd hydrogen bonds : bond 0.12346 ( 1085) hydrogen bonds : angle 6.01626 ( 3201) SS BOND : bond 0.00289 ( 17) SS BOND : angle 0.75448 ( 34) covalent geometry : bond 0.00641 (16858) covalent geometry : angle 0.83884 (22677) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3730 Ramachandran restraints generated. 1865 Oldfield, 0 Emsley, 1865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3730 Ramachandran restraints generated. 1865 Oldfield, 0 Emsley, 1865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 343 residues out of total 1763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 338 time to evaluate : 1.860 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 115 GLU cc_start: 0.7947 (tp30) cc_final: 0.7364 (tp30) REVERT: A 258 ASP cc_start: 0.8320 (p0) cc_final: 0.7905 (p0) REVERT: B 245 GLU cc_start: 0.7589 (tp30) cc_final: 0.7232 (tp30) REVERT: B 248 LYS cc_start: 0.8311 (mppt) cc_final: 0.8007 (mmtp) REVERT: C 29 ASP cc_start: 0.7859 (t0) cc_final: 0.7526 (t0) REVERT: D 244 PHE cc_start: 0.5627 (m-80) cc_final: 0.5157 (t80) REVERT: D 250 PHE cc_start: 0.7249 (t80) cc_final: 0.7045 (t80) REVERT: E 375 MET cc_start: 0.7691 (mtm) cc_final: 0.7326 (mtp) REVERT: E 393 PHE cc_start: 0.5975 (m-80) cc_final: 0.5181 (m-80) REVERT: F 148 PHE cc_start: 0.6999 (t80) cc_final: 0.6370 (t80) REVERT: F 154 LYS cc_start: 0.7786 (mttt) cc_final: 0.6946 (mmpt) REVERT: F 170 TRP cc_start: 0.6076 (t-100) cc_final: 0.5297 (t-100) REVERT: F 367 LYS cc_start: 0.7639 (ptmt) cc_final: 0.7158 (mttp) REVERT: F 386 LYS cc_start: 0.8400 (mtpp) cc_final: 0.8118 (mmtt) outliers start: 5 outliers final: 0 residues processed: 342 average time/residue: 1.1858 time to fit residues: 455.0018 Evaluate side-chains 221 residues out of total 1763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 221 time to evaluate : 1.882 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 156 optimal weight: 0.6980 chunk 140 optimal weight: 3.9990 chunk 77 optimal weight: 4.9990 chunk 47 optimal weight: 0.0770 chunk 94 optimal weight: 0.6980 chunk 74 optimal weight: 0.8980 chunk 145 optimal weight: 2.9990 chunk 56 optimal weight: 0.8980 chunk 88 optimal weight: 0.6980 chunk 107 optimal weight: 7.9990 chunk 168 optimal weight: 0.4980 overall best weight: 0.5338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 49 GLN C 105 GLN ** D 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 409 ASN F 251 HIS F 305 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4245 r_free = 0.4245 target = 0.175806 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.128445 restraints weight = 19159.814| |-----------------------------------------------------------------------------| r_work (start): 0.3713 rms_B_bonded: 2.22 r_work: 0.3528 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3373 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3373 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7693 moved from start: 0.1820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 16875 Z= 0.126 Angle : 0.486 9.544 22711 Z= 0.256 Chirality : 0.038 0.188 2436 Planarity : 0.003 0.048 2714 Dihedral : 16.333 170.394 2542 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 3.12 % Allowed : 19.57 % Favored : 77.31 % 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: 1.82 (0.19), residues: 1865 helix: 1.92 (0.14), residues: 1311 sheet: 0.72 (0.52), residues: 108 loop : -0.82 (0.29), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP E 168 HIS 0.007 0.001 HIS F 251 PHE 0.016 0.001 PHE D 324 TYR 0.016 0.001 TYR D 338 ARG 0.003 0.000 ARG C 389 Details of bonding type rmsd hydrogen bonds : bond 0.03696 ( 1085) hydrogen bonds : angle 4.09554 ( 3201) SS BOND : bond 0.00447 ( 17) SS BOND : angle 0.81596 ( 34) covalent geometry : bond 0.00277 (16858) covalent geometry : angle 0.48557 (22677) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3730 Ramachandran restraints generated. 1865 Oldfield, 0 Emsley, 1865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3730 Ramachandran restraints generated. 1865 Oldfield, 0 Emsley, 1865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 1763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 255 time to evaluate : 1.750 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 154 GLU cc_start: 0.7747 (tp30) cc_final: 0.7324 (mp0) REVERT: A 258 ASP cc_start: 0.8173 (p0) cc_final: 0.7809 (p0) REVERT: A 275 PHE cc_start: 0.8536 (OUTLIER) cc_final: 0.8311 (t80) REVERT: B 245 GLU cc_start: 0.7887 (tp30) cc_final: 0.7317 (tp30) REVERT: B 385 LEU cc_start: 0.8136 (tt) cc_final: 0.7848 (tm) REVERT: C 29 ASP cc_start: 0.8015 (t0) cc_final: 0.7597 (t0) REVERT: C 168 TRP cc_start: 0.7656 (t-100) cc_final: 0.7342 (t-100) REVERT: C 280 CYS cc_start: 0.8905 (m) cc_final: 0.8618 (m) REVERT: C 352 SER cc_start: 0.8017 (OUTLIER) cc_final: 0.7776 (p) REVERT: D 59 TRP cc_start: 0.7394 (m-10) cc_final: 0.6951 (m100) REVERT: D 244 PHE cc_start: 0.5247 (m-80) cc_final: 0.4758 (t80) REVERT: D 353 PHE cc_start: 0.6401 (m-80) cc_final: 0.6134 (m-80) REVERT: D 396 GLU cc_start: 0.7230 (tp30) cc_final: 0.5936 (pt0) REVERT: E 18 ARG cc_start: 0.8403 (ttp80) cc_final: 0.8067 (ttt-90) REVERT: E 144 PHE cc_start: 0.8667 (m-10) cc_final: 0.8445 (m-10) REVERT: E 164 PHE cc_start: 0.6836 (t80) cc_final: 0.6476 (t80) REVERT: E 243 LEU cc_start: 0.7605 (tt) cc_final: 0.7335 (mt) REVERT: E 306 ARG cc_start: 0.8020 (mtm110) cc_final: 0.7546 (ttp-110) REVERT: E 309 ARG cc_start: 0.8388 (tpt170) cc_final: 0.8070 (ttt180) REVERT: E 375 MET cc_start: 0.7738 (mtm) cc_final: 0.7451 (mtm) REVERT: F 58 ARG cc_start: 0.8487 (OUTLIER) cc_final: 0.7798 (mtm110) REVERT: F 146 PHE cc_start: 0.7663 (m-10) cc_final: 0.7400 (m-80) REVERT: F 170 TRP cc_start: 0.6435 (t-100) cc_final: 0.5793 (t-100) REVERT: F 367 LYS cc_start: 0.7671 (ptmt) cc_final: 0.7316 (ptpp) REVERT: F 386 LYS cc_start: 0.8337 (mtpp) cc_final: 0.8082 (mptt) outliers start: 55 outliers final: 10 residues processed: 291 average time/residue: 1.0540 time to fit residues: 349.9711 Evaluate side-chains 236 residues out of total 1763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 223 time to evaluate : 1.718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 275 PHE Chi-restraints excluded: chain A residue 281 TYR Chi-restraints excluded: chain A residue 343 MET Chi-restraints excluded: chain C residue 243 LEU Chi-restraints excluded: chain C residue 275 PHE Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 352 SER Chi-restraints excluded: chain E residue 169 THR Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 58 ARG Chi-restraints excluded: chain F residue 273 PHE Chi-restraints excluded: chain F residue 341 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 74 optimal weight: 0.8980 chunk 89 optimal weight: 3.9990 chunk 93 optimal weight: 4.9990 chunk 32 optimal weight: 4.9990 chunk 96 optimal weight: 1.9990 chunk 76 optimal weight: 9.9990 chunk 80 optimal weight: 0.6980 chunk 91 optimal weight: 0.8980 chunk 127 optimal weight: 3.9990 chunk 1 optimal weight: 0.8980 chunk 15 optimal weight: 0.9980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 105 GLN D 155 HIS ** D 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 49 GLN F 368 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4236 r_free = 0.4236 target = 0.175227 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.126967 restraints weight = 19380.512| |-----------------------------------------------------------------------------| r_work (start): 0.3708 rms_B_bonded: 2.23 r_work: 0.3527 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3374 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3374 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7733 moved from start: 0.2312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 16875 Z= 0.150 Angle : 0.479 7.690 22711 Z= 0.255 Chirality : 0.038 0.148 2436 Planarity : 0.003 0.045 2714 Dihedral : 14.242 171.607 2542 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 3.69 % Allowed : 20.31 % Favored : 76.01 % 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: 2.04 (0.19), residues: 1865 helix: 2.09 (0.14), residues: 1310 sheet: 0.86 (0.52), residues: 108 loop : -0.78 (0.29), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP E 168 HIS 0.004 0.001 HIS C 253 PHE 0.015 0.001 PHE D 324 TYR 0.016 0.001 TYR E 281 ARG 0.005 0.000 ARG A 18 Details of bonding type rmsd hydrogen bonds : bond 0.03621 ( 1085) hydrogen bonds : angle 3.93115 ( 3201) SS BOND : bond 0.00366 ( 17) SS BOND : angle 1.00368 ( 34) covalent geometry : bond 0.00343 (16858) covalent geometry : angle 0.47781 (22677) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3730 Ramachandran restraints generated. 1865 Oldfield, 0 Emsley, 1865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3730 Ramachandran restraints generated. 1865 Oldfield, 0 Emsley, 1865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 1763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 234 time to evaluate : 1.729 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 154 GLU cc_start: 0.7739 (tp30) cc_final: 0.7314 (mp0) REVERT: A 245 GLU cc_start: 0.8229 (mm-30) cc_final: 0.7926 (mm-30) REVERT: A 258 ASP cc_start: 0.8309 (p0) cc_final: 0.7948 (p0) REVERT: B 162 LYS cc_start: 0.7236 (OUTLIER) cc_final: 0.6680 (mptt) REVERT: B 232 LEU cc_start: 0.6507 (OUTLIER) cc_final: 0.5951 (pt) REVERT: B 245 GLU cc_start: 0.7988 (tp30) cc_final: 0.7437 (tp30) REVERT: C 29 ASP cc_start: 0.8143 (t0) cc_final: 0.7716 (t0) REVERT: C 103 ARG cc_start: 0.8187 (ttt-90) cc_final: 0.7547 (tpp-160) REVERT: C 168 TRP cc_start: 0.7685 (t-100) cc_final: 0.7279 (t-100) REVERT: C 243 LEU cc_start: 0.8093 (OUTLIER) cc_final: 0.7777 (mm) REVERT: C 280 CYS cc_start: 0.8841 (m) cc_final: 0.8506 (m) REVERT: D 244 PHE cc_start: 0.5228 (m-80) cc_final: 0.4765 (t80) REVERT: D 294 ASP cc_start: 0.8632 (OUTLIER) cc_final: 0.8285 (m-30) REVERT: D 353 PHE cc_start: 0.6632 (m-80) cc_final: 0.6329 (OUTLIER) REVERT: D 396 GLU cc_start: 0.7260 (tp30) cc_final: 0.6105 (pt0) REVERT: E 18 ARG cc_start: 0.8381 (ttp80) cc_final: 0.8017 (ttt-90) REVERT: E 164 PHE cc_start: 0.6887 (t80) cc_final: 0.6591 (t80) REVERT: E 306 ARG cc_start: 0.8025 (mtm110) cc_final: 0.7622 (ttp-110) REVERT: E 309 ARG cc_start: 0.8417 (tpt170) cc_final: 0.8095 (ttt180) REVERT: E 343 MET cc_start: 0.8673 (mtp) cc_final: 0.8470 (mtt) REVERT: F 18 ARG cc_start: 0.8339 (ttp-110) cc_final: 0.7886 (ttt-90) REVERT: F 51 LYS cc_start: 0.7495 (OUTLIER) cc_final: 0.7264 (mmtp) REVERT: F 58 ARG cc_start: 0.8495 (OUTLIER) cc_final: 0.7861 (mtm110) REVERT: F 96 MET cc_start: 0.8260 (OUTLIER) cc_final: 0.7864 (mtp) REVERT: F 104 ASP cc_start: 0.8408 (m-30) cc_final: 0.8099 (m-30) REVERT: F 146 PHE cc_start: 0.7686 (m-10) cc_final: 0.7444 (m-80) REVERT: F 170 TRP cc_start: 0.6567 (t-100) cc_final: 0.6023 (t-100) REVERT: F 367 LYS cc_start: 0.7957 (ptmt) cc_final: 0.7332 (ptpp) REVERT: F 386 LYS cc_start: 0.8292 (mtpp) cc_final: 0.7983 (mptt) REVERT: F 388 PHE cc_start: 0.5886 (t80) cc_final: 0.5068 (t80) outliers start: 65 outliers final: 26 residues processed: 276 average time/residue: 1.0249 time to fit residues: 323.0354 Evaluate side-chains 250 residues out of total 1763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 218 time to evaluate : 1.925 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain A residue 281 TYR Chi-restraints excluded: chain A residue 343 MET Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 162 LYS Chi-restraints excluded: chain B residue 232 LEU Chi-restraints excluded: chain B residue 327 SER Chi-restraints excluded: chain C residue 140 SER Chi-restraints excluded: chain C residue 243 LEU Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain C residue 275 PHE Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 314 LEU Chi-restraints excluded: chain D residue 253 HIS Chi-restraints excluded: chain D residue 281 TYR Chi-restraints excluded: chain D residue 294 ASP Chi-restraints excluded: chain E residue 134 LEU Chi-restraints excluded: chain E residue 163 CYS Chi-restraints excluded: chain E residue 169 THR Chi-restraints excluded: chain E residue 253 HIS Chi-restraints excluded: chain E residue 281 TYR Chi-restraints excluded: chain E residue 330 ILE Chi-restraints excluded: chain E residue 379 ILE Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 51 LYS Chi-restraints excluded: chain F residue 58 ARG Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 96 MET Chi-restraints excluded: chain F residue 252 VAL Chi-restraints excluded: chain F residue 273 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 33 optimal weight: 3.9990 chunk 38 optimal weight: 0.9980 chunk 14 optimal weight: 5.9990 chunk 97 optimal weight: 0.6980 chunk 3 optimal weight: 1.9990 chunk 88 optimal weight: 0.5980 chunk 165 optimal weight: 0.9990 chunk 56 optimal weight: 0.0170 chunk 42 optimal weight: 1.9990 chunk 70 optimal weight: 0.3980 chunk 10 optimal weight: 0.3980 overall best weight: 0.4218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 404 GLN B 408 ASN C 105 GLN D 49 GLN ** D 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 49 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4303 r_free = 0.4303 target = 0.182923 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.130142 restraints weight = 19582.926| |-----------------------------------------------------------------------------| r_work (start): 0.3757 rms_B_bonded: 2.43 r_work: 0.3581 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3581 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7587 moved from start: 0.2625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 16875 Z= 0.106 Angle : 0.442 8.913 22711 Z= 0.235 Chirality : 0.037 0.141 2436 Planarity : 0.003 0.042 2714 Dihedral : 12.248 169.120 2542 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 3.01 % Allowed : 21.21 % Favored : 75.78 % 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: 2.30 (0.19), residues: 1865 helix: 2.27 (0.14), residues: 1313 sheet: 1.40 (0.53), residues: 104 loop : -0.78 (0.28), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 168 HIS 0.004 0.001 HIS C 253 PHE 0.024 0.001 PHE D 250 TYR 0.015 0.001 TYR E 281 ARG 0.008 0.000 ARG F 118 Details of bonding type rmsd hydrogen bonds : bond 0.03227 ( 1085) hydrogen bonds : angle 3.73835 ( 3201) SS BOND : bond 0.00191 ( 17) SS BOND : angle 0.86086 ( 34) covalent geometry : bond 0.00229 (16858) covalent geometry : angle 0.44152 (22677) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3730 Ramachandran restraints generated. 1865 Oldfield, 0 Emsley, 1865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3730 Ramachandran restraints generated. 1865 Oldfield, 0 Emsley, 1865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 1763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 244 time to evaluate : 1.912 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 154 GLU cc_start: 0.7573 (tp30) cc_final: 0.7250 (mp0) REVERT: A 245 GLU cc_start: 0.8211 (mm-30) cc_final: 0.7879 (mm-30) REVERT: A 258 ASP cc_start: 0.8172 (p0) cc_final: 0.7814 (p0) REVERT: A 275 PHE cc_start: 0.8414 (OUTLIER) cc_final: 0.8163 (t80) REVERT: B 18 ARG cc_start: 0.8041 (OUTLIER) cc_final: 0.7814 (ptt180) REVERT: B 245 GLU cc_start: 0.7796 (tp30) cc_final: 0.7210 (tp30) REVERT: B 359 GLU cc_start: 0.8241 (tm-30) cc_final: 0.7554 (pt0) REVERT: B 385 LEU cc_start: 0.8123 (tt) cc_final: 0.7910 (tm) REVERT: C 29 ASP cc_start: 0.7833 (t0) cc_final: 0.7255 (t0) REVERT: C 103 ARG cc_start: 0.7882 (ttt-90) cc_final: 0.7452 (tpp-160) REVERT: C 168 TRP cc_start: 0.7599 (t-100) cc_final: 0.7212 (t-100) REVERT: C 243 LEU cc_start: 0.8015 (OUTLIER) cc_final: 0.7687 (mm) REVERT: C 280 CYS cc_start: 0.8703 (m) cc_final: 0.8405 (m) REVERT: D 117 ARG cc_start: 0.8055 (mmt-90) cc_final: 0.7822 (tpp-160) REVERT: D 244 PHE cc_start: 0.5198 (m-80) cc_final: 0.4787 (t80) REVERT: D 396 GLU cc_start: 0.7185 (tp30) cc_final: 0.6340 (mt-10) REVERT: D 405 LEU cc_start: 0.6283 (OUTLIER) cc_final: 0.6018 (pp) REVERT: E 18 ARG cc_start: 0.8370 (ttp80) cc_final: 0.8043 (ttt-90) REVERT: E 164 PHE cc_start: 0.7028 (t80) cc_final: 0.6737 (t80) REVERT: E 275 PHE cc_start: 0.8252 (OUTLIER) cc_final: 0.7052 (t80) REVERT: E 306 ARG cc_start: 0.7840 (mtm110) cc_final: 0.7436 (ttp-110) REVERT: E 343 MET cc_start: 0.8560 (OUTLIER) cc_final: 0.8288 (mtt) REVERT: F 18 ARG cc_start: 0.8320 (ttp-110) cc_final: 0.7893 (ttt-90) REVERT: F 51 LYS cc_start: 0.7175 (mppt) cc_final: 0.6937 (mmtp) REVERT: F 58 ARG cc_start: 0.8394 (OUTLIER) cc_final: 0.7894 (mtm110) REVERT: F 96 MET cc_start: 0.8061 (OUTLIER) cc_final: 0.7656 (mtp) REVERT: F 146 PHE cc_start: 0.7454 (OUTLIER) cc_final: 0.7172 (m-80) REVERT: F 170 TRP cc_start: 0.6520 (t-100) cc_final: 0.6068 (t-100) REVERT: F 367 LYS cc_start: 0.7962 (ptmt) cc_final: 0.7372 (mttp) REVERT: F 386 LYS cc_start: 0.8274 (mtpp) cc_final: 0.7981 (mptt) REVERT: F 388 PHE cc_start: 0.5778 (t80) cc_final: 0.5143 (t80) outliers start: 53 outliers final: 22 residues processed: 278 average time/residue: 1.1685 time to fit residues: 375.8281 Evaluate side-chains 247 residues out of total 1763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 216 time to evaluate : 2.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 275 PHE Chi-restraints excluded: chain A residue 281 TYR Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain B residue 18 ARG Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain C residue 140 SER Chi-restraints excluded: chain C residue 243 LEU Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain C residue 275 PHE Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 281 TYR Chi-restraints excluded: chain C residue 314 LEU Chi-restraints excluded: chain C residue 379 ILE Chi-restraints excluded: chain D residue 253 HIS Chi-restraints excluded: chain D residue 281 TYR Chi-restraints excluded: chain D residue 353 PHE Chi-restraints excluded: chain D residue 405 LEU Chi-restraints excluded: chain E residue 134 LEU Chi-restraints excluded: chain E residue 169 THR Chi-restraints excluded: chain E residue 275 PHE Chi-restraints excluded: chain E residue 281 TYR Chi-restraints excluded: chain E residue 343 MET Chi-restraints excluded: chain F residue 58 ARG Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 96 MET Chi-restraints excluded: chain F residue 146 PHE Chi-restraints excluded: chain F residue 252 VAL Chi-restraints excluded: chain F residue 273 PHE Chi-restraints excluded: chain F residue 277 ILE Chi-restraints excluded: chain F residue 279 TYR Chi-restraints excluded: chain F residue 377 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 53 optimal weight: 2.9990 chunk 46 optimal weight: 2.9990 chunk 138 optimal weight: 6.9990 chunk 105 optimal weight: 10.0000 chunk 139 optimal weight: 0.9990 chunk 112 optimal weight: 2.9990 chunk 169 optimal weight: 5.9990 chunk 68 optimal weight: 0.9980 chunk 111 optimal weight: 0.6980 chunk 26 optimal weight: 2.9990 chunk 177 optimal weight: 0.6980 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 408 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 105 GLN D 49 GLN ** D 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 49 GLN F 309 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4249 r_free = 0.4249 target = 0.177200 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.124188 restraints weight = 20174.778| |-----------------------------------------------------------------------------| r_work (start): 0.3693 rms_B_bonded: 2.47 r_work: 0.3510 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3510 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7638 moved from start: 0.2867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 16875 Z= 0.191 Angle : 0.507 9.092 22711 Z= 0.267 Chirality : 0.039 0.153 2436 Planarity : 0.003 0.041 2714 Dihedral : 11.767 153.436 2542 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 4.14 % Allowed : 20.76 % Favored : 75.10 % 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: 2.11 (0.19), residues: 1865 helix: 2.19 (0.14), residues: 1307 sheet: 0.93 (0.53), residues: 108 loop : -0.88 (0.28), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 341 HIS 0.005 0.001 HIS A 104 PHE 0.028 0.002 PHE D 250 TYR 0.017 0.002 TYR C 281 ARG 0.008 0.000 ARG F 118 Details of bonding type rmsd hydrogen bonds : bond 0.03623 ( 1085) hydrogen bonds : angle 3.86237 ( 3201) SS BOND : bond 0.00333 ( 17) SS BOND : angle 0.98220 ( 34) covalent geometry : bond 0.00448 (16858) covalent geometry : angle 0.50579 (22677) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3730 Ramachandran restraints generated. 1865 Oldfield, 0 Emsley, 1865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3730 Ramachandran restraints generated. 1865 Oldfield, 0 Emsley, 1865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 1763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 224 time to evaluate : 2.478 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 154 GLU cc_start: 0.7563 (tp30) cc_final: 0.7227 (mp0) REVERT: A 245 GLU cc_start: 0.8237 (mm-30) cc_final: 0.7907 (mm-30) REVERT: A 258 ASP cc_start: 0.8220 (p0) cc_final: 0.7846 (p0) REVERT: A 275 PHE cc_start: 0.8461 (OUTLIER) cc_final: 0.8234 (t80) REVERT: B 18 ARG cc_start: 0.8055 (OUTLIER) cc_final: 0.7837 (ptt180) REVERT: B 162 LYS cc_start: 0.7337 (OUTLIER) cc_final: 0.6866 (mmpt) REVERT: B 245 GLU cc_start: 0.7876 (tp30) cc_final: 0.7259 (tp30) REVERT: B 359 GLU cc_start: 0.8229 (tm-30) cc_final: 0.7474 (pt0) REVERT: B 365 ILE cc_start: 0.6769 (OUTLIER) cc_final: 0.6545 (mm) REVERT: B 395 SER cc_start: 0.8290 (p) cc_final: 0.8046 (p) REVERT: C 29 ASP cc_start: 0.7827 (t0) cc_final: 0.7165 (t0) REVERT: C 33 ILE cc_start: 0.8377 (OUTLIER) cc_final: 0.8122 (mp) REVERT: C 103 ARG cc_start: 0.8004 (ttt-90) cc_final: 0.7485 (tpp-160) REVERT: C 168 TRP cc_start: 0.7677 (t-100) cc_final: 0.7239 (t-100) REVERT: C 280 CYS cc_start: 0.8777 (m) cc_final: 0.8272 (m) REVERT: D 102 ASP cc_start: 0.8144 (m-30) cc_final: 0.7935 (m-30) REVERT: D 244 PHE cc_start: 0.5319 (OUTLIER) cc_final: 0.4987 (t80) REVERT: D 353 PHE cc_start: 0.6354 (m-80) cc_final: 0.6007 (m-80) REVERT: D 396 GLU cc_start: 0.7010 (tp30) cc_final: 0.6098 (mt-10) REVERT: D 405 LEU cc_start: 0.6250 (OUTLIER) cc_final: 0.5956 (pp) REVERT: E 18 ARG cc_start: 0.8355 (ttp80) cc_final: 0.8005 (ttt-90) REVERT: E 164 PHE cc_start: 0.6979 (t80) cc_final: 0.6688 (t80) REVERT: E 266 ARG cc_start: 0.7532 (mtt180) cc_final: 0.7085 (mtt90) REVERT: E 275 PHE cc_start: 0.8255 (OUTLIER) cc_final: 0.7558 (t80) REVERT: E 306 ARG cc_start: 0.7887 (mtm110) cc_final: 0.7575 (ttp-110) REVERT: F 18 ARG cc_start: 0.8459 (ttp-110) cc_final: 0.8211 (ttt-90) REVERT: F 58 ARG cc_start: 0.8538 (OUTLIER) cc_final: 0.7880 (mtm110) REVERT: F 96 MET cc_start: 0.8147 (OUTLIER) cc_final: 0.7750 (mtp) REVERT: F 146 PHE cc_start: 0.7520 (m-10) cc_final: 0.7232 (m-80) REVERT: F 170 TRP cc_start: 0.6747 (t-100) cc_final: 0.6409 (t-100) REVERT: F 367 LYS cc_start: 0.8045 (ptmt) cc_final: 0.7408 (mttp) REVERT: F 386 LYS cc_start: 0.8278 (mtpp) cc_final: 0.7957 (mptt) outliers start: 73 outliers final: 33 residues processed: 275 average time/residue: 1.0513 time to fit residues: 331.2866 Evaluate side-chains 261 residues out of total 1763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 218 time to evaluate : 1.744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 275 PHE Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain A residue 281 TYR Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 343 MET Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain B residue 18 ARG Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 162 LYS Chi-restraints excluded: chain B residue 327 SER Chi-restraints excluded: chain B residue 365 ILE Chi-restraints excluded: chain C residue 33 ILE Chi-restraints excluded: chain C residue 140 SER Chi-restraints excluded: chain C residue 243 LEU Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain C residue 275 PHE Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 279 ILE Chi-restraints excluded: chain C residue 281 TYR Chi-restraints excluded: chain C residue 352 SER Chi-restraints excluded: chain D residue 244 PHE Chi-restraints excluded: chain D residue 253 HIS Chi-restraints excluded: chain D residue 405 LEU Chi-restraints excluded: chain E residue 163 CYS Chi-restraints excluded: chain E residue 169 THR Chi-restraints excluded: chain E residue 253 HIS Chi-restraints excluded: chain E residue 275 PHE Chi-restraints excluded: chain E residue 279 ILE Chi-restraints excluded: chain E residue 281 TYR Chi-restraints excluded: chain E residue 330 ILE Chi-restraints excluded: chain E residue 379 ILE Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 58 ARG Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 96 MET Chi-restraints excluded: chain F residue 252 VAL Chi-restraints excluded: chain F residue 273 PHE Chi-restraints excluded: chain F residue 277 ILE Chi-restraints excluded: chain F residue 279 TYR Chi-restraints excluded: chain F residue 341 LEU Chi-restraints excluded: chain F residue 377 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 110 optimal weight: 0.3980 chunk 182 optimal weight: 4.9990 chunk 72 optimal weight: 0.0870 chunk 10 optimal weight: 0.6980 chunk 107 optimal weight: 0.0770 chunk 68 optimal weight: 0.9990 chunk 6 optimal weight: 0.5980 chunk 51 optimal weight: 0.9990 chunk 119 optimal weight: 4.9990 chunk 35 optimal weight: 2.9990 chunk 32 optimal weight: 3.9990 overall best weight: 0.3716 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 377 HIS B 408 ASN C 105 GLN D 49 GLN ** D 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 49 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4290 r_free = 0.4290 target = 0.181448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.129495 restraints weight = 19834.879| |-----------------------------------------------------------------------------| r_work (start): 0.3755 rms_B_bonded: 2.42 r_work: 0.3578 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3578 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7591 moved from start: 0.3029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 16875 Z= 0.104 Angle : 0.450 9.883 22711 Z= 0.238 Chirality : 0.037 0.151 2436 Planarity : 0.003 0.040 2714 Dihedral : 10.541 141.425 2542 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 3.74 % Allowed : 21.04 % Favored : 75.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.38 (0.19), residues: 1865 helix: 2.35 (0.14), residues: 1312 sheet: 1.42 (0.53), residues: 104 loop : -0.79 (0.28), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP D 341 HIS 0.005 0.001 HIS C 253 PHE 0.031 0.001 PHE D 250 TYR 0.016 0.001 TYR E 281 ARG 0.008 0.000 ARG F 118 Details of bonding type rmsd hydrogen bonds : bond 0.03154 ( 1085) hydrogen bonds : angle 3.68995 ( 3201) SS BOND : bond 0.00192 ( 17) SS BOND : angle 0.91874 ( 34) covalent geometry : bond 0.00223 (16858) covalent geometry : angle 0.44907 (22677) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3730 Ramachandran restraints generated. 1865 Oldfield, 0 Emsley, 1865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3730 Ramachandran restraints generated. 1865 Oldfield, 0 Emsley, 1865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 1763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 238 time to evaluate : 1.971 Fit side-chains revert: symmetry clash REVERT: A 154 GLU cc_start: 0.7535 (tp30) cc_final: 0.7163 (mp0) REVERT: A 245 GLU cc_start: 0.8255 (mm-30) cc_final: 0.8035 (mm-30) REVERT: A 258 ASP cc_start: 0.8180 (p0) cc_final: 0.7823 (p0) REVERT: A 275 PHE cc_start: 0.8425 (OUTLIER) cc_final: 0.8211 (t80) REVERT: A 319 LYS cc_start: 0.8462 (OUTLIER) cc_final: 0.8191 (ttmt) REVERT: B 18 ARG cc_start: 0.8050 (OUTLIER) cc_final: 0.7829 (ptt180) REVERT: B 162 LYS cc_start: 0.7289 (OUTLIER) cc_final: 0.6838 (mmpt) REVERT: B 245 GLU cc_start: 0.7858 (tp30) cc_final: 0.7219 (tp30) REVERT: B 359 GLU cc_start: 0.8233 (tm-30) cc_final: 0.7572 (pt0) REVERT: B 385 LEU cc_start: 0.8149 (tt) cc_final: 0.7942 (tm) REVERT: C 29 ASP cc_start: 0.7791 (t0) cc_final: 0.7142 (t0) REVERT: C 33 ILE cc_start: 0.8412 (OUTLIER) cc_final: 0.8172 (mp) REVERT: C 103 ARG cc_start: 0.7937 (ttt-90) cc_final: 0.7446 (tpp-160) REVERT: C 168 TRP cc_start: 0.7507 (t-100) cc_final: 0.7192 (t-100) REVERT: C 243 LEU cc_start: 0.8037 (OUTLIER) cc_final: 0.7723 (mm) REVERT: C 280 CYS cc_start: 0.8648 (m) cc_final: 0.8297 (m) REVERT: D 244 PHE cc_start: 0.5340 (OUTLIER) cc_final: 0.5010 (t80) REVERT: D 353 PHE cc_start: 0.6296 (m-80) cc_final: 0.6073 (m-80) REVERT: D 375 MET cc_start: 0.7574 (mtm) cc_final: 0.7306 (mpp) REVERT: D 396 GLU cc_start: 0.6973 (tp30) cc_final: 0.6048 (mt-10) REVERT: D 405 LEU cc_start: 0.6190 (OUTLIER) cc_final: 0.5897 (pp) REVERT: E 18 ARG cc_start: 0.8393 (ttp80) cc_final: 0.8041 (ttt-90) REVERT: E 164 PHE cc_start: 0.6893 (t80) cc_final: 0.6613 (t80) REVERT: E 275 PHE cc_start: 0.8209 (OUTLIER) cc_final: 0.6828 (t80) REVERT: E 306 ARG cc_start: 0.7867 (mtm110) cc_final: 0.7550 (ttp-110) REVERT: E 371 ASP cc_start: 0.7389 (t0) cc_final: 0.7009 (t0) REVERT: E 375 MET cc_start: 0.7635 (mtm) cc_final: 0.6990 (mtm) REVERT: F 18 ARG cc_start: 0.8361 (ttp-110) cc_final: 0.8111 (ttt-90) REVERT: F 51 LYS cc_start: 0.7204 (mppt) cc_final: 0.6958 (mmtm) REVERT: F 58 ARG cc_start: 0.8424 (OUTLIER) cc_final: 0.7887 (mtm110) REVERT: F 96 MET cc_start: 0.8055 (OUTLIER) cc_final: 0.7664 (mtp) REVERT: F 146 PHE cc_start: 0.7437 (OUTLIER) cc_final: 0.7151 (m-80) REVERT: F 170 TRP cc_start: 0.6735 (t-100) cc_final: 0.6480 (t-100) REVERT: F 367 LYS cc_start: 0.8054 (ptmt) cc_final: 0.7593 (ptpp) REVERT: F 370 PHE cc_start: 0.7103 (OUTLIER) cc_final: 0.6840 (t80) REVERT: F 386 LYS cc_start: 0.8271 (mtpp) cc_final: 0.7995 (mmtt) REVERT: F 388 PHE cc_start: 0.6048 (t80) cc_final: 0.5551 (t80) outliers start: 66 outliers final: 30 residues processed: 281 average time/residue: 0.9474 time to fit residues: 306.7105 Evaluate side-chains 257 residues out of total 1763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 214 time to evaluate : 1.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 64 SER Chi-restraints excluded: chain A residue 275 PHE Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain A residue 281 TYR Chi-restraints excluded: chain A residue 319 LYS Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain B residue 18 ARG Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 162 LYS Chi-restraints excluded: chain B residue 327 SER Chi-restraints excluded: chain C residue 33 ILE Chi-restraints excluded: chain C residue 49 GLN Chi-restraints excluded: chain C residue 140 SER Chi-restraints excluded: chain C residue 243 LEU Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain C residue 275 PHE Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 281 TYR Chi-restraints excluded: chain C residue 352 SER Chi-restraints excluded: chain C residue 379 ILE Chi-restraints excluded: chain D residue 244 PHE Chi-restraints excluded: chain D residue 253 HIS Chi-restraints excluded: chain D residue 281 TYR Chi-restraints excluded: chain D residue 405 LEU Chi-restraints excluded: chain E residue 134 LEU Chi-restraints excluded: chain E residue 163 CYS Chi-restraints excluded: chain E residue 169 THR Chi-restraints excluded: chain E residue 253 HIS Chi-restraints excluded: chain E residue 275 PHE Chi-restraints excluded: chain E residue 281 TYR Chi-restraints excluded: chain E residue 379 ILE Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 58 ARG Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 96 MET Chi-restraints excluded: chain F residue 146 PHE Chi-restraints excluded: chain F residue 252 VAL Chi-restraints excluded: chain F residue 273 PHE Chi-restraints excluded: chain F residue 277 ILE Chi-restraints excluded: chain F residue 279 TYR Chi-restraints excluded: chain F residue 370 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 81 optimal weight: 1.9990 chunk 135 optimal weight: 0.9990 chunk 155 optimal weight: 2.9990 chunk 147 optimal weight: 3.9990 chunk 14 optimal weight: 0.3980 chunk 8 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 121 optimal weight: 2.9990 chunk 60 optimal weight: 1.9990 chunk 107 optimal weight: 5.9990 chunk 122 optimal weight: 5.9990 overall best weight: 1.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 408 ASN C 105 GLN ** D 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 49 GLN F 305 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4237 r_free = 0.4237 target = 0.176401 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.123858 restraints weight = 19954.859| |-----------------------------------------------------------------------------| r_work (start): 0.3681 rms_B_bonded: 2.44 r_work: 0.3497 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.3340 rms_B_bonded: 5.00 restraints_weight: 0.2500 r_work (final): 0.3340 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7785 moved from start: 0.3175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 16875 Z= 0.217 Angle : 0.537 9.568 22711 Z= 0.283 Chirality : 0.041 0.162 2436 Planarity : 0.003 0.040 2714 Dihedral : 11.075 148.116 2542 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 3.52 % Allowed : 22.06 % Favored : 74.42 % 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: 2.10 (0.19), residues: 1865 helix: 2.19 (0.14), residues: 1307 sheet: 0.84 (0.53), residues: 108 loop : -0.87 (0.28), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP C 143 HIS 0.006 0.001 HIS A 104 PHE 0.033 0.002 PHE D 250 TYR 0.018 0.002 TYR D 285 ARG 0.009 0.000 ARG F 118 Details of bonding type rmsd hydrogen bonds : bond 0.03670 ( 1085) hydrogen bonds : angle 3.88100 ( 3201) SS BOND : bond 0.00387 ( 17) SS BOND : angle 0.99283 ( 34) covalent geometry : bond 0.00513 (16858) covalent geometry : angle 0.53566 (22677) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3730 Ramachandran restraints generated. 1865 Oldfield, 0 Emsley, 1865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3730 Ramachandran restraints generated. 1865 Oldfield, 0 Emsley, 1865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 1763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 219 time to evaluate : 1.939 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 154 GLU cc_start: 0.7696 (tp30) cc_final: 0.7272 (mp0) REVERT: A 245 GLU cc_start: 0.8417 (mm-30) cc_final: 0.8113 (mm-30) REVERT: A 258 ASP cc_start: 0.8381 (p0) cc_final: 0.8033 (p0) REVERT: A 319 LYS cc_start: 0.8720 (OUTLIER) cc_final: 0.8468 (mtmt) REVERT: B 162 LYS cc_start: 0.7345 (OUTLIER) cc_final: 0.6929 (mmpt) REVERT: B 245 GLU cc_start: 0.7974 (tp30) cc_final: 0.7317 (tp30) REVERT: B 359 GLU cc_start: 0.8093 (tm-30) cc_final: 0.7355 (pt0) REVERT: C 29 ASP cc_start: 0.8071 (t0) cc_final: 0.7429 (t0) REVERT: C 33 ILE cc_start: 0.8475 (OUTLIER) cc_final: 0.8212 (mp) REVERT: C 103 ARG cc_start: 0.8309 (ttt-90) cc_final: 0.7633 (tpp-160) REVERT: C 160 LEU cc_start: 0.7141 (OUTLIER) cc_final: 0.6898 (tp) REVERT: C 168 TRP cc_start: 0.7684 (t-100) cc_final: 0.7366 (t-100) REVERT: C 280 CYS cc_start: 0.8990 (m) cc_final: 0.8549 (m) REVERT: D 244 PHE cc_start: 0.5248 (OUTLIER) cc_final: 0.4906 (t80) REVERT: D 396 GLU cc_start: 0.6984 (tp30) cc_final: 0.6036 (mt-10) REVERT: E 164 PHE cc_start: 0.6825 (t80) cc_final: 0.6470 (t80) REVERT: E 250 PHE cc_start: 0.6300 (t80) cc_final: 0.6099 (t80) REVERT: E 266 ARG cc_start: 0.7672 (mtt180) cc_final: 0.7221 (mtt90) REVERT: E 275 PHE cc_start: 0.8362 (OUTLIER) cc_final: 0.7733 (t80) REVERT: E 306 ARG cc_start: 0.8144 (mtm110) cc_final: 0.7723 (ttp-110) REVERT: F 18 ARG cc_start: 0.8528 (ttp-110) cc_final: 0.8255 (ttt-90) REVERT: F 58 ARG cc_start: 0.8530 (OUTLIER) cc_final: 0.7848 (mtm110) REVERT: F 96 MET cc_start: 0.8277 (OUTLIER) cc_final: 0.7939 (mtp) REVERT: F 146 PHE cc_start: 0.7708 (m-10) cc_final: 0.7450 (m-80) REVERT: F 170 TRP cc_start: 0.6966 (t-100) cc_final: 0.6735 (t-100) REVERT: F 357 GLU cc_start: 0.6431 (OUTLIER) cc_final: 0.5834 (mp0) REVERT: F 367 LYS cc_start: 0.8139 (ptmt) cc_final: 0.7650 (ptpp) REVERT: F 386 LYS cc_start: 0.8407 (mtpp) cc_final: 0.8091 (mmtt) outliers start: 62 outliers final: 36 residues processed: 261 average time/residue: 1.1687 time to fit residues: 352.4259 Evaluate side-chains 252 residues out of total 1763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 207 time to evaluate : 1.898 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 64 SER Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain A residue 281 TYR Chi-restraints excluded: chain A residue 319 LYS Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 162 LYS Chi-restraints excluded: chain B residue 327 SER Chi-restraints excluded: chain C residue 33 ILE Chi-restraints excluded: chain C residue 49 GLN Chi-restraints excluded: chain C residue 140 SER Chi-restraints excluded: chain C residue 160 LEU Chi-restraints excluded: chain C residue 243 LEU Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain C residue 275 PHE Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 279 ILE Chi-restraints excluded: chain C residue 281 TYR Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain C residue 352 SER Chi-restraints excluded: chain C residue 379 ILE Chi-restraints excluded: chain D residue 244 PHE Chi-restraints excluded: chain D residue 253 HIS Chi-restraints excluded: chain D residue 254 VAL Chi-restraints excluded: chain D residue 279 ILE Chi-restraints excluded: chain E residue 169 THR Chi-restraints excluded: chain E residue 253 HIS Chi-restraints excluded: chain E residue 275 PHE Chi-restraints excluded: chain E residue 279 ILE Chi-restraints excluded: chain E residue 281 TYR Chi-restraints excluded: chain E residue 330 ILE Chi-restraints excluded: chain E residue 379 ILE Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 58 ARG Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 96 MET Chi-restraints excluded: chain F residue 252 VAL Chi-restraints excluded: chain F residue 265 GLN Chi-restraints excluded: chain F residue 273 PHE Chi-restraints excluded: chain F residue 277 ILE Chi-restraints excluded: chain F residue 357 GLU Chi-restraints excluded: chain F residue 377 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 85 optimal weight: 2.9990 chunk 121 optimal weight: 0.6980 chunk 31 optimal weight: 3.9990 chunk 103 optimal weight: 2.9990 chunk 60 optimal weight: 0.9990 chunk 101 optimal weight: 0.6980 chunk 179 optimal weight: 0.9980 chunk 132 optimal weight: 0.7980 chunk 139 optimal weight: 5.9990 chunk 177 optimal weight: 2.9990 chunk 122 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 408 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 105 GLN D 49 GLN ** D 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 49 GLN F 305 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4198 r_free = 0.4198 target = 0.172430 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.122836 restraints weight = 19532.160| |-----------------------------------------------------------------------------| r_work (start): 0.3657 rms_B_bonded: 2.32 r_work: 0.3478 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3318 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3318 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7741 moved from start: 0.3253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 16875 Z= 0.145 Angle : 0.492 10.470 22711 Z= 0.260 Chirality : 0.038 0.165 2436 Planarity : 0.003 0.040 2714 Dihedral : 10.509 145.272 2542 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 3.46 % Allowed : 22.46 % Favored : 74.08 % 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: 2.19 (0.19), residues: 1865 helix: 2.24 (0.14), residues: 1307 sheet: 0.72 (0.53), residues: 110 loop : -0.79 (0.28), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP D 341 HIS 0.004 0.001 HIS A 104 PHE 0.034 0.001 PHE D 250 TYR 0.015 0.001 TYR E 281 ARG 0.009 0.000 ARG F 118 Details of bonding type rmsd hydrogen bonds : bond 0.03358 ( 1085) hydrogen bonds : angle 3.79473 ( 3201) SS BOND : bond 0.00274 ( 17) SS BOND : angle 0.98257 ( 34) covalent geometry : bond 0.00335 (16858) covalent geometry : angle 0.49130 (22677) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3730 Ramachandran restraints generated. 1865 Oldfield, 0 Emsley, 1865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3730 Ramachandran restraints generated. 1865 Oldfield, 0 Emsley, 1865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 1763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 213 time to evaluate : 1.735 Fit side-chains revert: symmetry clash REVERT: A 154 GLU cc_start: 0.7667 (tp30) cc_final: 0.7223 (mp0) REVERT: A 245 GLU cc_start: 0.8426 (mm-30) cc_final: 0.8109 (mm-30) REVERT: A 258 ASP cc_start: 0.8321 (p0) cc_final: 0.7954 (p0) REVERT: A 275 PHE cc_start: 0.8544 (OUTLIER) cc_final: 0.8333 (t80) REVERT: A 319 LYS cc_start: 0.8655 (OUTLIER) cc_final: 0.8381 (ttmt) REVERT: B 162 LYS cc_start: 0.7448 (OUTLIER) cc_final: 0.7013 (mmpt) REVERT: B 245 GLU cc_start: 0.7956 (tp30) cc_final: 0.7287 (tp30) REVERT: B 359 GLU cc_start: 0.8168 (tm-30) cc_final: 0.7564 (pt0) REVERT: B 385 LEU cc_start: 0.8136 (tt) cc_final: 0.7914 (tm) REVERT: C 29 ASP cc_start: 0.8021 (t0) cc_final: 0.7346 (t0) REVERT: C 33 ILE cc_start: 0.8440 (OUTLIER) cc_final: 0.8197 (mp) REVERT: C 103 ARG cc_start: 0.8257 (ttt-90) cc_final: 0.7551 (tpp-160) REVERT: C 160 LEU cc_start: 0.7170 (OUTLIER) cc_final: 0.6912 (tp) REVERT: C 168 TRP cc_start: 0.7619 (t-100) cc_final: 0.7304 (t-100) REVERT: C 243 LEU cc_start: 0.8034 (OUTLIER) cc_final: 0.7718 (mm) REVERT: C 280 CYS cc_start: 0.8818 (m) cc_final: 0.8504 (m) REVERT: D 244 PHE cc_start: 0.5060 (OUTLIER) cc_final: 0.4776 (t80) REVERT: D 396 GLU cc_start: 0.6948 (tp30) cc_final: 0.6013 (mt-10) REVERT: D 405 LEU cc_start: 0.6207 (OUTLIER) cc_final: 0.5926 (pp) REVERT: E 164 PHE cc_start: 0.6788 (t80) cc_final: 0.6489 (t80) REVERT: E 250 PHE cc_start: 0.6395 (t80) cc_final: 0.6159 (t80) REVERT: E 275 PHE cc_start: 0.8276 (OUTLIER) cc_final: 0.7325 (t80) REVERT: E 306 ARG cc_start: 0.8172 (mtm110) cc_final: 0.7743 (ttp-110) REVERT: E 343 MET cc_start: 0.8634 (mtp) cc_final: 0.8404 (mtt) REVERT: E 371 ASP cc_start: 0.7530 (t0) cc_final: 0.7121 (t0) REVERT: E 375 MET cc_start: 0.7980 (mtm) cc_final: 0.7276 (mtm) REVERT: F 18 ARG cc_start: 0.8463 (ttp-110) cc_final: 0.8178 (ttt-90) REVERT: F 51 LYS cc_start: 0.7362 (OUTLIER) cc_final: 0.7123 (mmtm) REVERT: F 58 ARG cc_start: 0.8494 (OUTLIER) cc_final: 0.7845 (mtm110) REVERT: F 96 MET cc_start: 0.8219 (OUTLIER) cc_final: 0.7838 (mtp) REVERT: F 146 PHE cc_start: 0.7684 (m-10) cc_final: 0.7388 (m-80) REVERT: F 357 GLU cc_start: 0.6436 (OUTLIER) cc_final: 0.5853 (mp0) REVERT: F 367 LYS cc_start: 0.8126 (ptmt) cc_final: 0.7653 (ptpp) REVERT: F 386 LYS cc_start: 0.8476 (mtpp) cc_final: 0.8171 (mmtt) REVERT: F 388 PHE cc_start: 0.5955 (t80) cc_final: 0.5077 (t80) outliers start: 61 outliers final: 36 residues processed: 257 average time/residue: 0.9549 time to fit residues: 287.2809 Evaluate side-chains 253 residues out of total 1763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 204 time to evaluate : 1.738 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 64 SER Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 169 THR Chi-restraints excluded: chain A residue 275 PHE Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain A residue 319 LYS Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 162 LYS Chi-restraints excluded: chain B residue 327 SER Chi-restraints excluded: chain B residue 392 VAL Chi-restraints excluded: chain C residue 33 ILE Chi-restraints excluded: chain C residue 49 GLN Chi-restraints excluded: chain C residue 140 SER Chi-restraints excluded: chain C residue 160 LEU Chi-restraints excluded: chain C residue 243 LEU Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain C residue 275 PHE Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 279 ILE Chi-restraints excluded: chain C residue 281 TYR Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain C residue 352 SER Chi-restraints excluded: chain C residue 379 ILE Chi-restraints excluded: chain D residue 244 PHE Chi-restraints excluded: chain D residue 253 HIS Chi-restraints excluded: chain D residue 254 VAL Chi-restraints excluded: chain D residue 279 ILE Chi-restraints excluded: chain D residue 281 TYR Chi-restraints excluded: chain D residue 405 LEU Chi-restraints excluded: chain E residue 169 THR Chi-restraints excluded: chain E residue 253 HIS Chi-restraints excluded: chain E residue 275 PHE Chi-restraints excluded: chain E residue 281 TYR Chi-restraints excluded: chain E residue 330 ILE Chi-restraints excluded: chain E residue 379 ILE Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 51 LYS Chi-restraints excluded: chain F residue 58 ARG Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 96 MET Chi-restraints excluded: chain F residue 252 VAL Chi-restraints excluded: chain F residue 265 GLN Chi-restraints excluded: chain F residue 273 PHE Chi-restraints excluded: chain F residue 277 ILE Chi-restraints excluded: chain F residue 357 GLU Chi-restraints excluded: chain F residue 377 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 36 optimal weight: 3.9990 chunk 149 optimal weight: 0.3980 chunk 146 optimal weight: 0.5980 chunk 157 optimal weight: 0.9980 chunk 111 optimal weight: 0.9980 chunk 23 optimal weight: 0.5980 chunk 102 optimal weight: 0.6980 chunk 123 optimal weight: 0.8980 chunk 81 optimal weight: 1.9990 chunk 92 optimal weight: 0.0980 chunk 83 optimal weight: 1.9990 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 408 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 49 GLN E 381 GLN F 305 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4208 r_free = 0.4208 target = 0.173336 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.126528 restraints weight = 19328.363| |-----------------------------------------------------------------------------| r_work (start): 0.3697 rms_B_bonded: 2.23 r_work: 0.3510 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3357 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3357 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7702 moved from start: 0.3410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 16875 Z= 0.114 Angle : 0.474 10.423 22711 Z= 0.251 Chirality : 0.038 0.166 2436 Planarity : 0.003 0.040 2714 Dihedral : 9.945 141.272 2542 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 3.23 % Allowed : 23.03 % Favored : 73.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.38 (0.19), residues: 1865 helix: 2.33 (0.14), residues: 1312 sheet: 1.14 (0.54), residues: 106 loop : -0.64 (0.29), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP F 170 HIS 0.004 0.001 HIS C 253 PHE 0.035 0.001 PHE D 250 TYR 0.017 0.001 TYR C 284 ARG 0.009 0.000 ARG F 118 Details of bonding type rmsd hydrogen bonds : bond 0.03154 ( 1085) hydrogen bonds : angle 3.70053 ( 3201) SS BOND : bond 0.00211 ( 17) SS BOND : angle 0.98602 ( 34) covalent geometry : bond 0.00250 (16858) covalent geometry : angle 0.47298 (22677) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3730 Ramachandran restraints generated. 1865 Oldfield, 0 Emsley, 1865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3730 Ramachandran restraints generated. 1865 Oldfield, 0 Emsley, 1865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 1763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 224 time to evaluate : 1.923 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 154 GLU cc_start: 0.7629 (tp30) cc_final: 0.7173 (mp0) REVERT: A 245 GLU cc_start: 0.8433 (mm-30) cc_final: 0.8140 (mm-30) REVERT: A 275 PHE cc_start: 0.8499 (OUTLIER) cc_final: 0.8282 (t80) REVERT: A 319 LYS cc_start: 0.8593 (OUTLIER) cc_final: 0.8327 (ttmt) REVERT: B 162 LYS cc_start: 0.7432 (mtpt) cc_final: 0.6963 (mmpt) REVERT: B 245 GLU cc_start: 0.7963 (tp30) cc_final: 0.7183 (tp30) REVERT: B 359 GLU cc_start: 0.8066 (tm-30) cc_final: 0.7513 (pt0) REVERT: C 29 ASP cc_start: 0.7995 (t0) cc_final: 0.7311 (t0) REVERT: C 33 ILE cc_start: 0.8456 (OUTLIER) cc_final: 0.8208 (mp) REVERT: C 103 ARG cc_start: 0.8216 (ttt-90) cc_final: 0.7523 (tpp-160) REVERT: C 168 TRP cc_start: 0.7528 (t-100) cc_final: 0.7276 (t-100) REVERT: C 243 LEU cc_start: 0.8049 (OUTLIER) cc_final: 0.7749 (mm) REVERT: C 280 CYS cc_start: 0.8805 (m) cc_final: 0.8454 (m) REVERT: D 244 PHE cc_start: 0.5128 (OUTLIER) cc_final: 0.4831 (t80) REVERT: D 396 GLU cc_start: 0.6948 (tp30) cc_final: 0.6025 (mt-10) REVERT: D 405 LEU cc_start: 0.6153 (OUTLIER) cc_final: 0.5869 (pp) REVERT: E 164 PHE cc_start: 0.6952 (t80) cc_final: 0.6635 (t80) REVERT: E 275 PHE cc_start: 0.8313 (OUTLIER) cc_final: 0.6996 (t80) REVERT: E 306 ARG cc_start: 0.8172 (mtm110) cc_final: 0.7730 (ttp-110) REVERT: F 18 ARG cc_start: 0.8419 (ttp-110) cc_final: 0.8129 (ttt-90) REVERT: F 51 LYS cc_start: 0.7362 (OUTLIER) cc_final: 0.7108 (mmtm) REVERT: F 58 ARG cc_start: 0.8423 (OUTLIER) cc_final: 0.7868 (mtm110) REVERT: F 96 MET cc_start: 0.8159 (OUTLIER) cc_final: 0.7759 (mtp) REVERT: F 146 PHE cc_start: 0.7589 (OUTLIER) cc_final: 0.7251 (m-80) REVERT: F 357 GLU cc_start: 0.6390 (OUTLIER) cc_final: 0.5816 (mp0) REVERT: F 367 LYS cc_start: 0.8071 (ptmt) cc_final: 0.7200 (pmtt) REVERT: F 386 LYS cc_start: 0.8479 (mtpp) cc_final: 0.8207 (mmtt) REVERT: F 388 PHE cc_start: 0.6033 (t80) cc_final: 0.5605 (t80) outliers start: 57 outliers final: 29 residues processed: 267 average time/residue: 0.9197 time to fit residues: 284.9395 Evaluate side-chains 251 residues out of total 1763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 210 time to evaluate : 1.735 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 64 SER Chi-restraints excluded: chain A residue 275 PHE Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain A residue 281 TYR Chi-restraints excluded: chain A residue 319 LYS Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 327 SER Chi-restraints excluded: chain B residue 392 VAL Chi-restraints excluded: chain C residue 33 ILE Chi-restraints excluded: chain C residue 140 SER Chi-restraints excluded: chain C residue 243 LEU Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain C residue 275 PHE Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 281 TYR Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain C residue 352 SER Chi-restraints excluded: chain D residue 244 PHE Chi-restraints excluded: chain D residue 253 HIS Chi-restraints excluded: chain D residue 254 VAL Chi-restraints excluded: chain D residue 279 ILE Chi-restraints excluded: chain D residue 281 TYR Chi-restraints excluded: chain D residue 405 LEU Chi-restraints excluded: chain E residue 253 HIS Chi-restraints excluded: chain E residue 275 PHE Chi-restraints excluded: chain E residue 279 ILE Chi-restraints excluded: chain E residue 281 TYR Chi-restraints excluded: chain E residue 379 ILE Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 51 LYS Chi-restraints excluded: chain F residue 58 ARG Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 96 MET Chi-restraints excluded: chain F residue 146 PHE Chi-restraints excluded: chain F residue 265 GLN Chi-restraints excluded: chain F residue 273 PHE Chi-restraints excluded: chain F residue 277 ILE Chi-restraints excluded: chain F residue 279 TYR Chi-restraints excluded: chain F residue 357 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 81 optimal weight: 0.7980 chunk 177 optimal weight: 0.6980 chunk 147 optimal weight: 1.9990 chunk 64 optimal weight: 0.8980 chunk 21 optimal weight: 0.7980 chunk 5 optimal weight: 0.5980 chunk 92 optimal weight: 0.5980 chunk 113 optimal weight: 1.9990 chunk 7 optimal weight: 0.5980 chunk 19 optimal weight: 0.9980 chunk 91 optimal weight: 1.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 408 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 105 GLN D 49 GLN ** D 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 49 GLN F 305 ASN ** F 309 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4215 r_free = 0.4215 target = 0.174309 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.125525 restraints weight = 19445.179| |-----------------------------------------------------------------------------| r_work (start): 0.3682 rms_B_bonded: 2.31 r_work: 0.3500 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3345 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3345 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7697 moved from start: 0.3484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 16875 Z= 0.131 Angle : 0.495 10.479 22711 Z= 0.261 Chirality : 0.039 0.169 2436 Planarity : 0.003 0.040 2714 Dihedral : 9.918 139.758 2542 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 2.89 % Allowed : 23.09 % Favored : 74.02 % 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: 2.35 (0.19), residues: 1865 helix: 2.30 (0.14), residues: 1312 sheet: 1.17 (0.54), residues: 106 loop : -0.65 (0.28), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.002 TRP F 170 HIS 0.004 0.001 HIS C 253 PHE 0.035 0.001 PHE D 250 TYR 0.015 0.001 TYR E 281 ARG 0.010 0.000 ARG F 118 Details of bonding type rmsd hydrogen bonds : bond 0.03240 ( 1085) hydrogen bonds : angle 3.73861 ( 3201) SS BOND : bond 0.00232 ( 17) SS BOND : angle 0.98849 ( 34) covalent geometry : bond 0.00297 (16858) covalent geometry : angle 0.49374 (22677) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3730 Ramachandran restraints generated. 1865 Oldfield, 0 Emsley, 1865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3730 Ramachandran restraints generated. 1865 Oldfield, 0 Emsley, 1865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 1763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 213 time to evaluate : 1.901 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 154 GLU cc_start: 0.7609 (tp30) cc_final: 0.7157 (mp0) REVERT: A 245 GLU cc_start: 0.8456 (mm-30) cc_final: 0.8185 (mm-30) REVERT: A 258 ASP cc_start: 0.8171 (p0) cc_final: 0.7842 (p0) REVERT: A 275 PHE cc_start: 0.8501 (OUTLIER) cc_final: 0.8267 (t80) REVERT: A 319 LYS cc_start: 0.8605 (OUTLIER) cc_final: 0.8372 (ttmt) REVERT: B 46 GLN cc_start: 0.8536 (tm-30) cc_final: 0.8191 (tp40) REVERT: B 162 LYS cc_start: 0.7411 (OUTLIER) cc_final: 0.6931 (mmpt) REVERT: B 359 GLU cc_start: 0.8182 (tm-30) cc_final: 0.7579 (pt0) REVERT: C 29 ASP cc_start: 0.8006 (t0) cc_final: 0.7329 (t0) REVERT: C 33 ILE cc_start: 0.8453 (OUTLIER) cc_final: 0.8216 (mp) REVERT: C 103 ARG cc_start: 0.8244 (ttt-90) cc_final: 0.7519 (tpp-160) REVERT: C 243 LEU cc_start: 0.8060 (OUTLIER) cc_final: 0.7759 (mm) REVERT: C 265 MET cc_start: 0.7780 (tpt) cc_final: 0.7560 (tpt) REVERT: C 280 CYS cc_start: 0.8831 (m) cc_final: 0.8464 (m) REVERT: D 244 PHE cc_start: 0.5144 (OUTLIER) cc_final: 0.4840 (t80) REVERT: D 396 GLU cc_start: 0.6955 (tp30) cc_final: 0.6022 (mt-10) REVERT: D 405 LEU cc_start: 0.6127 (OUTLIER) cc_final: 0.5852 (pp) REVERT: E 164 PHE cc_start: 0.6852 (t80) cc_final: 0.6594 (t80) REVERT: E 275 PHE cc_start: 0.8290 (OUTLIER) cc_final: 0.7280 (t80) REVERT: E 306 ARG cc_start: 0.8166 (mtm110) cc_final: 0.7740 (ttp-110) REVERT: E 390 PHE cc_start: 0.8065 (t80) cc_final: 0.7523 (t80) REVERT: F 18 ARG cc_start: 0.8442 (ttp-110) cc_final: 0.8155 (ttt-90) REVERT: F 51 LYS cc_start: 0.7396 (OUTLIER) cc_final: 0.7146 (mmtp) REVERT: F 58 ARG cc_start: 0.8433 (OUTLIER) cc_final: 0.7843 (mtm110) REVERT: F 96 MET cc_start: 0.8202 (OUTLIER) cc_final: 0.7820 (mtp) REVERT: F 146 PHE cc_start: 0.7611 (OUTLIER) cc_final: 0.7269 (m-80) REVERT: F 357 GLU cc_start: 0.6421 (OUTLIER) cc_final: 0.5843 (mp0) REVERT: F 367 LYS cc_start: 0.8030 (ptmt) cc_final: 0.7575 (ptpp) REVERT: F 386 LYS cc_start: 0.8403 (mtpp) cc_final: 0.8086 (mmtt) REVERT: F 388 PHE cc_start: 0.5971 (t80) cc_final: 0.5489 (t80) outliers start: 51 outliers final: 31 residues processed: 247 average time/residue: 0.9783 time to fit residues: 277.8191 Evaluate side-chains 250 residues out of total 1763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 206 time to evaluate : 1.899 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 169 THR Chi-restraints excluded: chain A residue 275 PHE Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain A residue 319 LYS Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 162 LYS Chi-restraints excluded: chain B residue 327 SER Chi-restraints excluded: chain B residue 392 VAL Chi-restraints excluded: chain C residue 33 ILE Chi-restraints excluded: chain C residue 140 SER Chi-restraints excluded: chain C residue 243 LEU Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain C residue 275 PHE Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 279 ILE Chi-restraints excluded: chain C residue 281 TYR Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain C residue 352 SER Chi-restraints excluded: chain D residue 47 VAL Chi-restraints excluded: chain D residue 244 PHE Chi-restraints excluded: chain D residue 253 HIS Chi-restraints excluded: chain D residue 254 VAL Chi-restraints excluded: chain D residue 279 ILE Chi-restraints excluded: chain D residue 281 TYR Chi-restraints excluded: chain D residue 405 LEU Chi-restraints excluded: chain E residue 253 HIS Chi-restraints excluded: chain E residue 275 PHE Chi-restraints excluded: chain E residue 279 ILE Chi-restraints excluded: chain E residue 281 TYR Chi-restraints excluded: chain E residue 330 ILE Chi-restraints excluded: chain E residue 379 ILE Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 51 LYS Chi-restraints excluded: chain F residue 58 ARG Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 96 MET Chi-restraints excluded: chain F residue 146 PHE Chi-restraints excluded: chain F residue 265 GLN Chi-restraints excluded: chain F residue 273 PHE Chi-restraints excluded: chain F residue 277 ILE Chi-restraints excluded: chain F residue 279 TYR Chi-restraints excluded: chain F residue 357 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 124 optimal weight: 0.0770 chunk 171 optimal weight: 1.9990 chunk 71 optimal weight: 0.5980 chunk 123 optimal weight: 2.9990 chunk 14 optimal weight: 3.9990 chunk 6 optimal weight: 0.9980 chunk 101 optimal weight: 0.6980 chunk 162 optimal weight: 2.9990 chunk 107 optimal weight: 8.9990 chunk 11 optimal weight: 0.6980 chunk 184 optimal weight: 0.8980 overall best weight: 0.5938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 116 ASN ** A 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 408 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 105 GLN D 49 GLN ** D 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 49 GLN F 305 ASN ** F 309 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4205 r_free = 0.4205 target = 0.172993 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.126251 restraints weight = 19412.878| |-----------------------------------------------------------------------------| r_work (start): 0.3692 rms_B_bonded: 2.22 r_work: 0.3506 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3351 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3351 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7711 moved from start: 0.3578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 16875 Z= 0.125 Angle : 0.499 10.431 22711 Z= 0.263 Chirality : 0.039 0.177 2436 Planarity : 0.003 0.041 2714 Dihedral : 9.729 136.500 2542 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 2.89 % Allowed : 23.54 % Favored : 73.57 % 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: 2.36 (0.19), residues: 1865 helix: 2.30 (0.14), residues: 1312 sheet: 1.20 (0.54), residues: 106 loop : -0.61 (0.28), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.059 0.002 TRP F 170 HIS 0.004 0.001 HIS B 253 PHE 0.034 0.001 PHE D 250 TYR 0.018 0.001 TYR C 284 ARG 0.010 0.000 ARG F 118 Details of bonding type rmsd hydrogen bonds : bond 0.03209 ( 1085) hydrogen bonds : angle 3.74588 ( 3201) SS BOND : bond 0.00215 ( 17) SS BOND : angle 0.96111 ( 34) covalent geometry : bond 0.00281 (16858) covalent geometry : angle 0.49789 (22677) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11935.70 seconds wall clock time: 208 minutes 26.45 seconds (12506.45 seconds total)